Index (QuPath 0.5.0)

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

above(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification (by name) for objects for which the specified measurement has a value above the threshold.
above(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification for objects for which the specified measurement has a value above the threshold.
aboveEquals(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification (by name) for objects for which the specified measurement has a value above or equal to the threshold.
aboveEquals(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification for objects for which the specified measurement has a value above or equal to the threshold.
abs(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Compute the absolute value of all elements in an array.
AbstractDetectionPlugin<T> - Class in qupath.lib.plugins: Abstract plugin aimed towards cases where new objects will be detected inside existing objects (normally TMA cores or annotations).
AbstractDetectionPlugin() - Constructor for class qupath.lib.plugins.AbstractDetectionPlugin
AbstractDnnModel<T> - Class in qupath.opencv.dnn: Wrapper for a deep learning model in a pipeline using OpenCV.
AbstractDnnModel() - Constructor for class qupath.opencv.dnn.AbstractDnnModel
AbstractImageOverlay - Class in qupath.lib.gui.viewer.overlays: Abstract PathOverlay with additional properties relevant when drawing BufferedImages.
AbstractImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
AbstractImageRenderer - Class in qupath.lib.gui.images.stores: Abstract ImageRenderer, which adds a timestamp variable.
AbstractImageRenderer() - Constructor for class qupath.lib.gui.images.stores.AbstractImageRenderer
AbstractImageServer<T> - Class in qupath.lib.images.servers: Abstract implementation of ImageServer providing some common functionality.
AbstractImageServer(Class<T>) - Constructor for class qupath.lib.images.servers.AbstractImageServer
AbstractInteractivePlugin<T> - Class in qupath.lib.plugins: Abstract class to help with implementing an interactive plugin.
AbstractInteractivePlugin() - Constructor for class qupath.lib.plugins.AbstractInteractivePlugin
AbstractObjectClassifier<T> - Class in qupath.lib.classifiers.object: Abstract class to help with the creation of object classifiers.
AbstractObjectClassifier(PathObjectFilter) - Constructor for class qupath.lib.classifiers.object.AbstractObjectClassifier
AbstractOverlay - Class in qupath.lib.gui.viewer.overlays: Abstract class to help with implementing PathOverlays.
AbstractOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.AbstractOverlay
AbstractOverlay.LocationStringFunction - Interface in qupath.lib.gui.viewer.overlays: Define a function to perform the task of PathOverlay.getLocationString(ImageData, double, double, int, int)
AbstractPlugin<T> - Class in qupath.lib.plugins: General abstract plugin implementation, which defines some methods to facilitate creating plugins that do parallel processing.
AbstractPlugin() - Constructor for class qupath.lib.plugins.AbstractPlugin
AbstractTaskRunner - Class in qupath.lib.plugins: Abstract PluginRunner to help with the creation of plugin runners for specific circumstances, e.g.
AbstractTaskRunner() - Constructor for class qupath.lib.plugins.AbstractTaskRunner: Constructor for a PluginRunner that uses the default number of threads, read from ThreadTools.getParallelism().
AbstractTaskRunner(int) - Constructor for class qupath.lib.plugins.AbstractTaskRunner: Constructor for a PluginRunner that optionally uses a fixed number of threads.
AbstractTileableDetectionPlugin<T> - Class in qupath.lib.plugins: Abstract plugin used for detection tasks that support breaking large regions into smaller ones, and analyzing these in parallel - optionally with overlaps.
AbstractTileableDetectionPlugin() - Constructor for class qupath.lib.plugins.AbstractTileableDetectionPlugin
AbstractTileableImageServer - Class in qupath.lib.images.servers: Abstract ImageServer for BufferedImages that internally breaks up requests into constituent tiles.
AbstractTileableImageServer() - Constructor for class qupath.lib.images.servers.AbstractTileableImageServer
accelerator(ObservableValue<KeyCombination>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Bind the accelerator property of the action to an ObservableValue, bidirectionally if possible.
accelerator(KeyCombination) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Set the accelerator property of the action.
acceleratorTextProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Property corresponding to CommandFinderTools.CommandEntry.getAcceleratorText()
ActionAccelerator - Annotation Interface in qupath.lib.gui.actions.annotations: Annotation used to specify a preferred accelerator for an an action.
actionBuilder() - Static method in class qupath.lib.gui.actions.ActionTools: Create an ActionTools.ActionBuilder with no properties set.
actionBuilder(String, Consumer<ActionEvent>) - Static method in class qupath.lib.gui.actions.ActionTools: Create an ActionTools.ActionBuilder with the specified text and event handler.
actionBuilder(Consumer<ActionEvent>) - Static method in class qupath.lib.gui.actions.ActionTools: Create an ActionTools.ActionBuilder with the specified event handler.
actionCellDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionCellMembraneDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands: Deprecated.
actionChannelTraining - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
actionComposite - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
ActionConfig - Annotation Interface in qupath.lib.gui.actions.annotations: Annotation indicating the a key in the external resources file containing the menu, text and (optional) description.
actionCreateRegions - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
actionDelaunay - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands
actionDensityMap - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands
actionDensityMapLoad - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands
actionDoG - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionExport - Variable in class qupath.lib.extension.svg.SvgExtension.SvgActions
actionExtractRegion - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionFastCellCounts - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands: Deprecated.
ActionIcon - Annotation Interface in qupath.lib.gui.actions.annotations: Default icon for an action.
actionImportROIs - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionIntensity - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
actionLoadObjectClassifier - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
actionLoadPixelClassifier - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
actionMacroRunner - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionMeasurement - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
ActionMenu - Annotation Interface in qupath.lib.gui.actions.annotations: Annotation indicating the menu path where an action should be installed.
ActionMethod - Annotation Interface in qupath.lib.gui.actions.annotations: Annotation indicating that a method should be converted to an Action if possible.
actionObjectClassifier - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
actionPixelClassifier - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
actionPixelCount - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands: Deprecated.
actionPlugins - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionPositiveCellDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
Actions() - Constructor for class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
Actions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
actionSimpleThreshold - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
actionSimpleTissueDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands: Deprecated.
actionSLIC - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionSnapshot - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionSnapshot - Variable in class qupath.lib.extension.svg.SvgExtension.SvgActions
actionSplitProject - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
actionSubcellularDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands: Deprecated.
actionTiles - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
ActionTools - Class in qupath.lib.gui.actions: Helper methods for generating and configuring Actions and UI elements.
ActionTools() - Constructor for class qupath.lib.gui.actions.ActionTools
ActionTools.ActionBuilder - Class in qupath.lib.gui.actions: Builder class for custom Action objects.
actionTrainingImage - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
actionWriter - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.OmeTiffWriterAction
ACTIVE_SERVER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
activeToolProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the activeTool property of this tracker.
activeViewerProperty() - Method in class qupath.lib.gui.viewer.ViewerManager: Get a read-only property representing the currently active viewer.
add(double...) - Static method in class qupath.opencv.ops.ImageOps.Core: Add a constant to all pixels.
add(Padding) - Method in class qupath.lib.regions.Padding: Add this padding to another.
ADD - Enum constant in enum class qupath.lib.roi.RoiTools.CombineOp: Add ROIs (union).
ADD_COLUMN_AFTER - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
ADD_COLUMN_BEFORE - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
ADD_ROW_AFTER - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
ADD_ROW_BEFORE - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
addActions - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
AddActions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
addAllRegions(ImageServer<BufferedImage>, int) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Add all regions for a specific level of an ImageServer.
addBooleanParameter(String, String, boolean) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a boolean parameter.
addBooleanParameter(String, String, boolean, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a boolean parameter, with help text.
addChartExportMenu(XYChart<Number, Number>, ContextMenu) - Static method in class qupath.lib.gui.charts.ChartTools: Add a menu item to a context menu for displaying a chart for export.
addChildObject(PathObject) - Method in class qupath.lib.objects.PathObject: Add an object to the child list of this object.
addChildObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.PathObject: Add a collection of objects to the child list of this object.
addChoiceParameter(String, String, S, List<S>) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a choice parameter, with an list of choices.
addChoiceParameter(String, String, S, List<S>, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a choice parameter, with an list of choices and help text.
addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane: Deprecated.
use PropertyItemBuilder instead
addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String, boolean) - Method in class qupath.lib.gui.panes.PreferencePane: Deprecated.
use PropertyItemBuilder instead
addClusterMeasurements() - Method in class qupath.opencv.features.DelaunayTriangulation: Compute mean measurements from clustering all connected objects.
addColorPropertyPreference(IntegerProperty, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane: Deprecated.
use PropertyItemBuilder instead
addColumn(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
addCompletion(AutoCompletions.Completion) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
addCompletions(Collection<? extends AutoCompletions.Completion>) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
addCompletions(AutoCompletions.Completion...) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
addDensities(String, PathObjectPredicates.PathObjectPredicate) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: Add a filter for computing densities.
addDirectoryPropertyPreference(Property<String>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane: Deprecated.
use PropertyItemBuilder instead
addDoubleParameter(String, String, double) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a double parameter to this list.
addDoubleParameter(String, String, double, String, double, double, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a bounded double parameter to this list.
addDoubleParameter(String, String, double, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a double parameter to this list, optionally including a unit and help text.
addDuplicate(ProjectImageEntry<T>, boolean) - Method in interface qupath.lib.projects.Project: Add an image by duplicating an existing entry.
ADDED - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: An object has been added
addEmptyParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add an 'empty' parameter, that is one that does not take any values.
addEvent(double, boolean) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Insert a new event.
addEvents(Collection<KaplanMeierData.KaplanMeierEvent>) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Add a collection of events.
addFileDropHandler(DragDropImportListener.DropHandler<File>) - Method in class qupath.lib.gui.viewer.DragDropImportListener: Add a new File DropHandler.
addFullResolutionLevel() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder: Add the full-resolution image as a level of the pyramid.
addGridRow(GridPane, int, int, String, Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Add a row of nodes.
addGroup(PathObjectConnectionGroup) - Method in class qupath.lib.objects.PathObjectConnections: Add a new connections group.
addImage(ImageServerBuilder.ServerBuilder<T>) - Method in interface qupath.lib.projects.Project: Add an image for a particular ImageServer.
addIntensityMeasurements(ImageServer<BufferedImage>, PathObject, double, Collection<ObjectMeasurements.Measurements>, Collection<ObjectMeasurements.Compartments>) - Static method in class qupath.lib.analysis.features.ObjectMeasurements: Measure all channels of an image for one individual object or cell.
addIntParameter(String, String, int) - Method in class qupath.lib.plugins.parameters.ParameterList: Add an int parameter.
addIntParameter(String, String, int, String, double, double, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a bounded int parameter, with optional unit and help text.
addIntParameter(String, String, int, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add an int parameter, with optional unit and help text.
addJsonDropHandler(DragDropImportListener.DropHandler<JsonElement>) - Method in class qupath.lib.gui.viewer.DragDropImportListener: Add a new DropHandler specifically for JSON elements.
addLabel(String, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
addLabel(String, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
addLabel(PathClass, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.
addLabel(PathClass, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add a single label by PathClass, where the label represents the integer label used for annotations with the given classification.
addLabels(Map<PathClass, Integer>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add multiple labels by PathClass, where the key represents a PathClass and the value represents the integer label that should be used for annotations of the given class.
addLabelsByName(Map<String, Integer>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add multiple labels by classname, where the key represents a classname and the value represents the integer label that should be used for annotations of the given class.
addLevel(double, int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder: Add a new level by providing a downsample value, width and height.
addLevel(int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder: Add a new level based on level dimensions, estimating the corresponding downsample value as required.
addLevel(ImageServerMetadata.ImageResolutionLevel) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder: Add a new level directly.
addLevelByDownsample(double) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder: Add a new level, calculating dimensions using a downsample factor applied to the full-resolution image.
addListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Add a hierarchy change listener.
addMeasurement(String, double) - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
v0.4.0 use MeasurementList.put(String, double) instead
addMeasurements(Collection<? extends PathObject>, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Add measurements to specified objects
addMeasurements(Collection<? extends PathObject>, PixelClassificationMeasurementManager, String) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Add measurements to specified objects from a PixelClassificationMeasurementManager.
addMeasurementsToSelectedObjects(ImageData<BufferedImage>, PixelClassifier, String) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Add measurements to selected objects based upon the output of a PixelClassifier.
addMenuItems(List<MenuItem>, Object...) - Static method in class qupath.lib.gui.tools.MenuTools: Add menu items to the specified list.
addMenuItems(Menu, Object...) - Static method in class qupath.lib.gui.tools.MenuTools: Add menu items to an existing menu.
addNewScript(String, ScriptLanguage, boolean) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Create a new script in the specified language.
addNodeMeasurements() - Method in class qupath.opencv.features.DelaunayTriangulation: Add Delaunay measurements to each pathObject.
addNoise(Mat, double, double) - Static method in class qupath.opencv.tools.OpenCVTools: Add Gaussian noise with specified mean and standard deviation to all channels of a Mat.
addObject(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Add an object to the hierarchy, firing an event.
addObject(PathObject) - Static method in class qupath.lib.scripting.QP: Add the specified object to the current PathObjectHierarchy.
addObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Add an object to the hierarchy, optionally firing an event.
addObjectBelowParent(PathObject, PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Add path object as descendant of the requested parent.
addObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Add multiple objects to the hierarchy.
addObjects(Collection<PathObject>) - Static method in class qupath.lib.scripting.QP: Add the specified collection of objects to the current PathObjectHierarchy.
addObjects(PathObject[]) - Static method in class qupath.lib.scripting.QP: Add the specified array of objects to the current PathObjectHierarchy.
addParameterChangeListener(ParameterChangeListener) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Add a ParameterChangeListener to be notified as parameters are modified by the user.
addPathObject(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Deprecated.
since v0.4.0; use PathObjectHierarchy.addObject(PathObject) instead (for naming consistency)
addPathObject(PathObject) - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, replaced by PathObject.addChildObject(PathObject)
addPathObjectBelowParent(PathObject, PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Deprecated.
since v0.4.0; use PathObjectHierarchy.addObjectBelowParent(PathObject, PathObject, boolean)
addPathObjectListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Deprecated.
since v0.4.0 (the name was confusing because it wasn't intended primarily to listen to changes within individual PathObjects)
addPathObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Deprecated.
since v0.4.0; use PathObjectHierarchy.addObjects(Collection) instead
addPathObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, replaced by PathObject.addChildObjects(Collection)
addPathObjectSelectionListener(PathObjectSelectionListener) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Add listener for selection changes.
addPathObjectWithoutUpdate(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Deprecated.
since v0.4.0, use PathObjectHierarchy.addObject(PathObject, boolean) instead (for naming consistency)
addPixelClassifierMeasurements(String, String) - Static method in class qupath.lib.scripting.QP: Add measurements from pixel classification to the selected objects.
addPixelClassifierMeasurements(PixelClassifier, String) - Static method in class qupath.lib.scripting.QP: Add measurements from pixel classification to the selected objects.
addPropertyChangeListener(PropertyChangeListener) - Method in class qupath.lib.images.ImageData: Add a new property change listener.
addPropertyPreference(Property<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane: Deprecated.
use PropertyItemBuilder instead
addRow(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.cells.SubcellularDetection
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.gui.ImageJMacroRunner
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.opencv.DetectCytokeratinCV
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.TilerPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.AbstractPlugin: For a specified parent object, generate a task to run.
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin: Intercepts the 'standard' addRunnableTasks to (if necessary) insert ParallelTileObjects along the way, thereby breaking an excessively-large parentObject into more manageable pieces.
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
addShapeMeasurements(String...) - Static method in class qupath.lib.scripting.QP: Add the specified shape measurements to the current selected objects of the current image.
addShapeMeasurements(Collection<? extends PathObject>, PixelCalibration, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.analysis.features.ObjectMeasurements: Add shape measurements for multiple objects.
addShapeMeasurements(ImageData<?>, Collection<? extends PathObject>, String, String...) - Static method in class qupath.lib.scripting.QP: Add shape measurements to the specified objects.
addShapeMeasurements(ImageData<?>, Collection<? extends PathObject>, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.scripting.QP: Add shape measurements to the specified objects.
addShapeMeasurements(PathObject, PixelCalibration, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.analysis.features.ObjectMeasurements: Add shape measurements for one object.
addSingleImageToProject(Project<BufferedImage>, ImageServer<BufferedImage>, ImageData.ImageType) - Static method in class qupath.lib.gui.commands.ProjectCommands: Add a single image to a project.
addSlice(Object, Number) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Add a slice to the pie.
addStep(WorkflowStep) - Method in class qupath.lib.plugins.workflow.Workflow: Append a new step to the end of the workflow, firing an update event.
addSteps(Collection<WorkflowStep>) - Method in class qupath.lib.plugins.workflow.Workflow: Append multiple steps to the end of the workflow, firing a single update event.
addStringParameter(String, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a String parameter.
addStringParameter(String, String, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a String parameter, with help text.
addTextAppendableFX(TextAppendable) - Static method in class qupath.lib.gui.logging.LogManager: Register a TextAppendable that will be accept logging events and be updated on the JavaFX Application thread.
addThreshold(double) - Method in class qupath.lib.gui.charts.ChartThresholdPane: Add a threshold value.
addThreshold(double, Color) - Method in class qupath.lib.gui.charts.ChartThresholdPane: Add a threshold value with its display color.
addThreshold(ObservableNumberValue) - Method in class qupath.lib.gui.charts.ChartThresholdPane: Add a threshold value.
addTileListener(TileListener<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
addTitleParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Add a title parameter.
addTMAGrid(ImageData<?>, String, String, boolean, double) - Static method in class qupath.lib.objects.PathObjectTools: Create a new regular TMAGrid and set it as active on the hierarchy for an image.
addUnclassifiedLabel(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
addUnclassifiedLabel(int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
addValue(double) - Method in class qupath.lib.analysis.stats.RunningStatistics: Add another value; NaN values are counted but do not contribute to the statistics.
addViewerListener(QuPathViewerListener) - Method in class qupath.lib.gui.viewer.QuPathViewer: Add a viewer listener.
addWorkflowListener(WorkflowListener) - Method in class qupath.lib.plugins.workflow.Workflow: Add a listener for changes to the workflow.
addWorkflowStep(ImageData<BufferedImage>, String) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
addWorkflowStep(ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractPlugin: Add a workflow step to the ImageData indicating the argument that this plugin was run with.
AffineTransformImageServer - Class in qupath.lib.images.servers: ImageServer that dynamically applies an AffineTransform to an existing ImageServer.
AffineTransformImageServer(ImageServer<BufferedImage>, AffineTransform) - Constructor for class qupath.lib.images.servers.AffineTransformImageServer
AffineTransforms - Class in qupath.lib.awt.common: Helper class for working with affine transforms.
AffineTransforms() - Constructor for class qupath.lib.awt.common.AffineTransforms
alertType(Alert.AlertType) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Create a dialog styled as a specified alert type.
alignBottomCenter() - Method in class qupath.lib.objects.utils.Tiler.Builder: Start tiles at the bottom center of the ROI bounding box.
alignBottomLeft() - Method in class qupath.lib.objects.utils.Tiler.Builder: Match tiles to the bottom left of the ROI bounding box.
alignBottomRight() - Method in class qupath.lib.objects.utils.Tiler.Builder: Match tiles to the bottom right of the ROI bounding box.
alignCenter() - Method in class qupath.lib.objects.utils.Tiler.Builder: Center tiles within the ROI bounding box.
alignCenterLeft() - Method in class qupath.lib.objects.utils.Tiler.Builder: Match tiles to the center left of the ROI bounding box.
alignCenterRight() - Method in class qupath.lib.objects.utils.Tiler.Builder: Match tiles to the center left of the ROI bounding box.
alignment(Tiler.TileAlignment) - Method in class qupath.lib.objects.utils.Tiler.Builder: Set the tile alignment.
alignTopCenter() - Method in class qupath.lib.objects.utils.Tiler.Builder: Start tiles at the top center of the ROI bounding box.
alignTopLeft() - Method in class qupath.lib.objects.utils.Tiler.Builder: Start tiles at the top left of the ROI bounding box.
alignTopRight() - Method in class qupath.lib.objects.utils.Tiler.Builder: Match tiles to the top right of the ROI bounding box.
ALL - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: All log messages
ALL_WINDOWS - Enum constant in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption: Use the system menubar for all windows.
ALLOW_MEMOIZATION_PROPERTY - Static variable in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: System property controlling whether memoization is allowed or not.
allowMemoization() - Static method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Check whether memoization should be allowed or not.
allowSmoothInterpolation() - Method in class qupath.lib.images.servers.AbstractTileableImageServer: Returns true if this server is permitted to use smooth interpolation when resizing.
allredMinPercentagePositiveProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The minimum positive percentage of cells for Allred proportion score to be non-zero.
allTimePoints() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request that all timepoints of a time series will be written.
allZSlices() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request that all z-slices are exported.
almostTheSame(double, double, double) - Static method in class qupath.lib.common.GeneralTools: Test if two doubles are approximately equal, within a specified tolerance.
alpha(int) - Static method in class qupath.lib.common.ColorTools: Extract the 8-bit alpha value from a packed ARGB value.
ALWAYS - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay: Always display
alwaysPaintSelected - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
alwaysPaintSelectedObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Always paint selected objects in the viewer, even if the opacity setting is 0.
alwaysPromptForObjects() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
alwaysPromptForObjects() - Method in class qupath.lib.plugins.AbstractInteractivePlugin
alwaysPromptForObjects() - Method in interface qupath.lib.plugins.PathInteractivePlugin: If this returns true, then a prompt is requested every time the command is run - even if there are valid parent objects already selected.
AnalyzeMenuActions - Class in qupath.lib.gui.actions.menus
AnalyzeMenuActions.Actions - Class in qupath.lib.gui.actions.menus
and(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Compute the bitwise AND of two arrays.
and(PathObjectPredicates.PathObjectPredicate) - Method in interface qupath.lib.objects.PathObjectPredicates.PathObjectPredicate: Combine with another PathObjectPredicates.PathObjectPredicate through AND.
andThen(OutputHandler<S, T, U>) - Method in interface qupath.lib.experimental.pixels.OutputHandler: Append a second output handler to this one.
annotatedCentroidTilesOnly(boolean) - Method in class qupath.lib.images.writers.TileExporter: Specify whether tiles without any annotations over the tile centroid should be included.
annotatedTilesOnly(boolean) - Method in class qupath.lib.images.writers.TileExporter: Specify whether tiles that do not overlap with any annotations should be included.
ANNOTATION_COPY_TO_PLANE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
ANNOTATION_DUPLICATE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
annotationActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
AnnotationActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
AnnotationPane - Class in qupath.lib.gui.panes: Component for displaying annotations within the active image.
AnnotationPane(QuPathGUI) - Constructor for class qupath.lib.gui.panes.AnnotationPane: Constructor.
AnnotationPane(QuPathGUI, ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.AnnotationPane: Constructor.
ANNOTATIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ANNOTATIONS - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept annotation objects
ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
ANNOTATIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
annotationStrokeThickness - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
annotationStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Preferred stroke thickness to use when drawing annotation ROIs.
ANY_ANNOTATIONS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Regions overlapping the ROIs of any annotations
ANY_ANNOTATIONS_BOUNDS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Regions overlapping the bounding box of any annotations
ANY_CLASS - Static variable in class qupath.process.gui.commands.density.DensityMapUI: Ignore classification (accept all objects).
ANY_OBJECTS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Regions overlapping the ROIs of any objects
ANY_OBJECTS_BOUNDS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Regions overlapping the bounding box of any objects
ANY_POSITIVE_CLASS - Static variable in class qupath.process.gui.commands.density.DensityMapUI: Accept any positive classification, including 1+, 2+, 3+.
AppearancePreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
appendFrame(ViewRecordingFrame) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Append frame to the collection of frames.
appendOps(ImageOp...) - Method in interface qupath.opencv.ops.ImageDataOp: Append one or more additional ImageOps sequentially.
appendText(String) - Method in interface qupath.lib.gui.logging.TextAppendable: Append the specified text to the appendable.
appendText(String) - Method in interface qupath.lib.gui.scripting.EditableText: Append the specified text.
appendText(String) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
appendText(String) - Method in class qupath.lib.gui.scripting.TextAreaControl
apply() - Method in class qupath.lib.objects.classes.Reclassifier: Apply the stored classification.
apply(Mat) - Method in class qupath.opencv.ml.FeaturePreprocessor: Apply preprocessing in-place.
apply(Mat) - Method in interface qupath.opencv.ops.ImageOp: Apply operation to the image.
apply(Mat) - Method in class qupath.opencv.ops.ImageOps.PaddedOp
apply(Mat, boolean) - Method in class qupath.opencv.ml.FeaturePreprocessor: Apply preprocessing in-place.
apply(Mat, DoubleUnaryOperator) - Static method in class qupath.opencv.tools.OpenCVTools: Apply an operation to the pixels of an image.
apply(ImageData<BufferedImage>, RegionRequest) - Method in interface qupath.opencv.ops.ImageDataOp: Apply the operation to the requested region of the image.
applyClassification(ImageData<BufferedImage>, RegionRequest) - Method in interface qupath.lib.classifiers.pixel.PixelClassifier: Apply pixel classifier to a specified region of an image.
applyCompletion(EditableText, AutoCompletions.Completion) - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditor: Insert the text from the completion to the editable text.
applyDisplaySettings(String) - Static method in class qupath.lib.gui.scripting.QPEx: Apply the display settings with the specified name or file path to the current version.
applyDisplaySettings(ImageDisplaySettings) - Static method in class qupath.lib.gui.scripting.QPEx: Apply the display settings to the current viewer.
applyDisplaySettings(QuPathViewer, ImageDisplaySettings) - Static method in class qupath.lib.gui.scripting.QPEx: Apply the display settings to the specified viewer.
applyLastAnnotationToActiveViewer() - Method in class qupath.lib.gui.viewer.ViewerManager
applyReplacements() - Method in class qupath.lib.io.UriUpdater: Apply all current replacements, updating the UriResource objects.
applySettingsToDisplay(ImageDisplay, ImageDisplaySettings) - Static method in class qupath.lib.display.settings.DisplaySettingUtils: Apply the settings to the display, if they are compatible.
applyTiled(Function<Mat, Mat>, Mat, int, int, Padding, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a function to a Mat that strictly requires a specific input size.
applyToChannels(Mat, Consumer<Mat>) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a method that modifies a Mat in-place to all channels of the Mat, merging the result and storing the result in-place.
applyTransforms(BufferedImage, BufferedImage) - Method in class qupath.lib.display.ImageDisplay: Apply the required transforms to a BufferedImage to get the appropriate display.
applyTransforms(BufferedImage, BufferedImage) - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
applyTransforms(BufferedImage, BufferedImage) - Method in interface qupath.lib.gui.images.stores.ImageRenderer: Apply the required transforms to a BufferedImage to get the appropriate display.
applyTransforms(BufferedImage, BufferedImage, List<? extends ChannelDisplayInfo>, boolean) - Static method in class qupath.lib.display.ImageDisplay: Deprecated.
use instead ImageDisplay.applyTransforms(BufferedImage, BufferedImage, List, ChannelDisplayMode)
applyTransforms(BufferedImage, BufferedImage, List<? extends ChannelDisplayInfo>, ChannelDisplayMode) - Static method in class qupath.lib.display.ImageDisplay: Convert an image to RGB by applying the specified ChannelDisplayInfos and ChannelDisplayMode.
AREA - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Area of the shape.
AREA - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode: Show as areas.
AREA - Enum constant in enum class qupath.lib.roi.interfaces.ROI.RoiType: ROI represents a closed area (possibly with holes).
areaContains(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools: Returns true if pathROI is an area that contains x & y somewhere within it.
AreaROI - Class in qupath.lib.roi: Implementation of an arbitrary area ROI - which could contain disjointed or hollow regions.
ARGS - Static variable in class qupath.lib.scripting.ScriptAttributes: Optional string args passed to the script.
arrayAsString(Locale) - Method in class qupath.lib.color.StainVector: Get a String representation of the stain vector array, formatting according to the specified Locale.
arrayToString(Object[], String) - Static method in class qupath.lib.common.GeneralTools: Convert a String array to a single string, with a specified delimiter string.
arrayToString(Locale, double[], int) - Static method in class qupath.lib.common.GeneralTools: Convert a double array to a String using a space as a delimiter.
arrayToString(Locale, double[], String, int) - Static method in class qupath.lib.common.GeneralTools: Convert a double array to string, with a specified number of decimal places.
ArrayWrappers - Class in qupath.lib.analysis.stats: Simple wrappers for primitive arrays that returns values as doubles.
ArrayWrappers() - Constructor for class qupath.lib.analysis.stats.ArrayWrappers
ArrayWrappers.ArrayWrapper - Interface in qupath.lib.analysis.stats: Simple wrapper for an array or list, enabling values to be returned as doubles.
ARROW_DOUBLE - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Arrow drawing tool, with arrowhead at both ends
ARROW_DOUBLE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ARROW_END - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Arrow drawing tool, with arrowhead at the end
ARROW_END_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ARROW_START - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Arrow drawing tool, with arrowhead at the start
ARROW_START_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
asMap() - Method in interface qupath.lib.measurements.MeasurementList: Get a map view of this measurements list.
asType(ImagePlus, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV: Helper method to convert an ImagePlus to a Mat or ImageProcessor using Groovy's 'as' syntax.
asType(ImageProcessor, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV: Helper method to convert an ImageProcessor to a Mat using Groovy's 'as' syntax.
asType(BufferedImage, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV: Helper method to convert a BufferedImage to a Mat, ImageProcessor or ImagePlus using Groovy's 'as' syntax.
asType(Number, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV: Helper function to convert a Number to a Mat or Scalar using Groovy's 'as' syntax.
asType(Mat, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV: Helper method to convert a Mat to a BufferedImage, ImagePlus, ImageProcessor, double or float array using Groovy's 'as' syntax.
ATTACH_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
ATTACH_VIEWER - Variable in class qupath.lib.gui.actions.ViewerActions
attachActiveViewerToGrid() - Method in class qupath.lib.gui.viewer.ViewerManager: Insert the currently active viewer back into the viewer grid.
attachViewerToGrid(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager: Attach the specified viewer to the viewer grid, if possible.
attemptOperation(Geometry, Function<Geometry, Geometry>) - Static method in class qupath.lib.roi.GeometryTools: Attempt to apply a function to a geometry, returning the input unchanged if there was an exception.
AUTO_ESTIMATE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting: Automatically estimate the image type
autoBrightnessContrastSaturationPercentProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Controls percentage of saturated pixels to apply when automatically setting brightness/contrast.
AutoCompletions - Class in qupath.lib.scripting.languages: Class to deal with script auto-completions.
AutoCompletions() - Constructor for class qupath.lib.scripting.languages.AutoCompletions
AutoCompletions.Completion - Interface in qupath.lib.scripting.languages: A single completion.
AutoCompletions.CompletionTokenizer - Interface in qupath.lib.scripting.languages: Functional interface to extract a token from a string needed to determine a completion.
AutomateActions - Class in qupath.lib.gui.actions: Default actions associated with QuPath's 'Automate' (scripting) menu.
AutomateActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.AutomateActions
AutomateMenuActions - Class in qupath.lib.gui.actions.menus
AutomateMenuActions.Actions - Class in qupath.lib.gui.actions.menus
autoSaturationPercent - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
autoSetAnnotationClassProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Classification that should automatically be applied to all new annotations.
autoSetDisplayRange(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay: Automatically set the display range for a channel, using the default saturation defined in PathPrefs.autoBrightnessContrastSaturationPercentProperty().
autoSetDisplayRange(ChannelDisplayInfo, double) - Method in class qupath.lib.display.ImageDisplay: Automatically set the display range for a channel.
autoUnits() - Method in class qupath.lib.common.Timeit
autoUpdate - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
autoUpdate - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
autoUpdateCheckProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Check for updates when launching QuPath, if possible.
availableChannels() - Method in class qupath.lib.display.ImageDisplay: ObservableList containing the channels currently available for display.
availableFontsProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Get a list of available fonts.
availableStylesProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Get the current available styles as an observable list.
averageChannelProject() - Method in class qupath.lib.images.servers.TransformedServerBuilder: Perform an average (mean) projection of the channels.
awaitCompletion() - Method in class qupath.lib.plugins.AbstractTaskRunner: Await the completion of currently-running tasks, notifying any listener if necessary.
AwtTools - Class in qupath.lib.awt.common: A collection of static methods useful when working with AWT shapes and ImageRegions.

B

backend(int) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Specify the backend, e.g.
backgroundColor - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
backgroundColor(int, boolean) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify a base color.
backgroundColor(Color) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify a base color.
backgroundLabel(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Specify the background label (0 by default).
backgroundLabel(int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Specify the background label (0 by default) and color.
badges - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
BAR - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode: Show as bars.
barChart() - Static method in class qupath.lib.gui.charts.Charts: Create a Charts.ScatterChartBuilder for generating a custom scatter plot.
baseClassification(PathClass...) - Static method in class qupath.lib.objects.PathObjectPredicates: Predicate that returns true if an object has any of the specified base classifications, regardless of any subclassification.
BATCH_INDEX - Static variable in class qupath.lib.scripting.ScriptAttributes: Index of the current run when batch processing (starting at 0).
BATCH_LAST - Static variable in class qupath.lib.scripting.ScriptAttributes: Boolean flag to indicate if the current script is the last in a batch.
BATCH_SAVE - Static variable in class qupath.lib.scripting.ScriptAttributes: Boolean flag to indicate whether changes to the image data should automatically be saved.
BATCH_SIZE - Static variable in class qupath.lib.scripting.ScriptAttributes: Size of the current batch processing batch.
batchPredict(List<? extends Mat>) - Method in class qupath.opencv.dnn.AbstractDnnModel: Convenience method to convert one or more image patches to a blob, apply the PredictionFunction, and convert the output to standard Mats.
batchPredict(List<? extends Mat>) - Method in interface qupath.opencv.dnn.DnnModel: Prediction function that can take a batch of inputs and gives a corresponding batch of outputs.
beautify(String) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Beautifies the specified text, according to the syntax.
beautifySourceAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
below(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification (by name) for objects for which the specified measurement has a value below the threshold.
below(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification for objects for which the specified measurement has a value below the threshold.
belowEquals(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification (by name) for objects for which the specified measurement has a value below or equal to the threshold.
belowEquals(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification for objects for which the specified measurement has a value below or equal to the threshold.
bigTiff() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request that the image is written in BigTIFF format.
bigTiff(boolean) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify whether the image should be written in BigTIFF format.
BILINEAR - Enum constant in enum class qupath.lib.gui.viewer.ImageInterpolation: Bilinear interpolation.
binaryReconstruction(ByteProcessor, ByteProcessor, boolean) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Alternative morphological reconstruction (based on ImageJ's FloodFiller) suitable for binary images only.
bindLocale() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
bindObjectClassifierNameInput(TextField, ObjectExpression<Project<BufferedImage>>) - Static method in class qupath.process.gui.commands.ml.ProjectClassifierBindings: Set styling for a text field to use object classifier names for the current project.
bindPixelClassifierNameInput(TextField, ObjectExpression<Project<BufferedImage>>) - Static method in class qupath.process.gui.commands.ml.ProjectClassifierBindings: Set styling for a text field to use pixel classifier names for the current project.
bindUserStylesheetToStyle(WebEngine) - Static method in class qupath.lib.gui.tools.WebViews: Bind the WebEngine.userStyleSheetLocationProperty() to a stylesheet determined based on QuPath's current style (e.g.
bioformatsEnabled() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Returns true if Bio-Formats is enabled and may be used to read images.
BioFormatsImageServer - Class in qupath.lib.images.servers.bioformats: QuPath ImageServer that uses the Bio-Formats library to read image data.
BioFormatsImageServer(URI, String...) - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsImageServer: Create an ImageServer using the Bio-Formats library.
BioFormatsOptionsExtension - Class in qupath.lib.images.servers.bioformats: A QuPath extension that adds options relating to the BioFormatsImageServer to the main QuPath preference pane.
BioFormatsOptionsExtension() - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
BioFormatsOptionsExtension.BioFormatsPreferences - Class in qupath.lib.images.servers.bioformats
BioFormatsOptionsExtension.OmeTiffWriterAction - Class in qupath.lib.images.servers.bioformats
BioFormatsServerBuilder - Class in qupath.lib.images.servers.bioformats: Builder for ImageServers that make use of the Bio-Formats library.
BioFormatsServerBuilder() - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
BioFormatsServerOptions - Class in qupath.lib.images.servers.bioformats: Container for various options that can customize the behavior of the BioFormatsImageServer.
BioimageIoTools - Class in qupath.opencv.ml: Helper class for working with Bioimage Model Zoo model specs, and attempting to replicating the processing within QuPath.
BioimageIoTools() - Constructor for class qupath.opencv.ml.BioimageIoTools
bitwiseNegate(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Compute the bitwise NOT of an array.
Black - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: All pixels black
BLACK - Static variable in class qupath.lib.common.ColorTools: Packed int representing black.
blankString(String, boolean) - Static method in class qupath.lib.common.GeneralTools: Check if a string is blank, i.e.
blobFromImage(Mat) - Static method in class qupath.opencv.dnn.DnnTools: Create an OpenCV blob from a single mat.
blobFromImages(Collection<Mat>, double, Size, Scalar, boolean, boolean) - Static method in class qupath.opencv.dnn.DnnTools: Create an OpenCV blob from a batch of Mats with optional scaling, resizing and cropping.
blobFromImages(Mat...) - Static method in class qupath.opencv.dnn.DnnTools: Create an OpenCV blob from one or more mats.
blobFromImages(Mat, double, Size, Scalar, boolean, boolean) - Static method in class qupath.opencv.dnn.DnnTools: Create an OpenCV blob from a Mat with optional scaling, resizing and cropping.
BlobFunction<T> - Interface in qupath.opencv.dnn: Convert OpenCV Mats into blobs (tensors) for use with a deep learning framework.
blue(int) - Static method in class qupath.lib.common.ColorTools: Extract the 8-bit blue value from a packed RGB value.
Blue - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Blue channel only
BLUE - Static variable in class qupath.lib.common.ColorTools: Packed int representing blue.
BLUE - Static variable in class qupath.lib.images.servers.ImageChannel: Default blue channel for RGB images.
Blue_chromaticity - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Blue chromaticity value, blue / max(1, red + green + blue)
Blue_OD - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Blue channel optical densities
blueChromaticity(int) - Static method in class qupath.lib.color.ColorTransformer: Extract blue chromaticity value from a packed RGB pixel, blue / max(1, red + green + blue)
BooleanParameter - Class in qupath.lib.plugins.parameters: Parameter that can take on true of false value - or null.
BOTTOM_CENTER - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
BOTTOM_LEFT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
BOTTOM_RIGHT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
BOUNDARIES_ONLY - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode: Show only cell boundaries.
boundaryDistancePredicate(double, boolean) - Static method in class qupath.lib.analysis.DelaunayTools: BiPredicate that returns true for objects with ROI boundaries within a specified distance.
BoundaryStrategy - Class in qupath.process.gui.commands.ml: Helper class for handling the boundaries of training annotations when creating a pixel classifier.
BRIGHTFIELD_H_DAB - Enum constant in enum class qupath.lib.images.ImageData.ImageType: Brightfield image with hematoxylin and DAB stains.
BRIGHTFIELD_H_DAB - Static variable in class qupath.lib.scripting.QP: Brightfield image type with hematoxylin and DAB staining
BRIGHTFIELD_H_E - Enum constant in enum class qupath.lib.images.ImageData.ImageType: Brightfield image with hematoxylin and eosin stains.
BRIGHTFIELD_H_E - Static variable in class qupath.lib.scripting.QP: Brightfield image type with hematoxylin and eosin staining
BRIGHTFIELD_OTHER - Enum constant in enum class qupath.lib.images.ImageData.ImageType: Brightfield image with any stains.
BRIGHTFIELD_OTHER - Static variable in class qupath.lib.scripting.QP: Brightfield image type
brightness(int) - Static method in class qupath.lib.color.ColorTransformer: Extract brightness value from RGB-to-HSB transform.
Brightness - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Brightness value (from RGB-HSB transform)
BRIGHTNESS_CONTRAST - Variable in class qupath.lib.gui.actions.CommonActions
BRIGHTNESS_CONTRAST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
BrightnessContrastChannelPane - Class in qupath.lib.gui.commands.display: A pane responsible for the display and selection of channels from an image display.
BrightnessContrastChannelPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
BrightnessContrastCommand - Class in qupath.lib.gui.commands: Command to show a Brightness/Contrast dialog to adjust the image display.
BrightnessContrastCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.BrightnessContrastCommand: Constructor.
BrightnessContrastHistogramPane - Class in qupath.lib.gui.commands.display: A pane to display a histogram for brightness/contrast adjustment, allowing the user to select min/max values.
BrightnessContrastHistogramPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
BrightnessContrastSettingsPane - Class in qupath.lib.gui.commands.display: A pane to save and load display settings, using a ResourceManager.
BrightnessContrastSettingsPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane
BrightnessContrastSliderPane - Class in qupath.lib.gui.commands.display: A pane containing sliders for adjusting the min/max display range and gamma value associated with an ImageDisplay.
BrightnessContrastSliderPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
brown(int) - Static method in class qupath.lib.color.ColorTransformer: Extract brown value, (blue - (red + green)*0.3f)
Brown - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Brown value, (blue - (red + green)*0.3f)
browseDirectory(File) - Static method in class qupath.lib.gui.tools.GuiTools: Open the directory containing a file for browsing.
browseURI(URI) - Static method in class qupath.lib.gui.tools.GuiTools: Try to open a URI in a web browser.
BRUSH - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Brush drawing tool
BRUSH_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
BRUSH_TOOL - Variable in class qupath.lib.gui.ToolManager
brushCreateNewObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Create new objects by default when drawing with the Brush tool.
brushDiameter - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
brushDiameterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Default brush tool diameter, in pixels.
brushScaleByMag - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
brushScaleByMagProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Optionally scale the default brush tool diameter by the viewer magnification (downsample value).
BrushToolEventHandler - Class in qupath.lib.gui.viewer.tools.handlers: Tool for drawing (and subtract from) freehand regions, optionally adapting brush size to magnification.
BrushToolEventHandler() - Constructor for class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
buffer(ROI, double) - Static method in class qupath.lib.roi.RoiTools: Buffer the specified ROI, dilating (or eroding) by the specified distance.
BufferedImageOverlay - Class in qupath.lib.gui.viewer.overlays: An overlay used to display one or more BufferedImage objects on top of a primary image shown in a viewer.
BufferedImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Create an empty overlay without any images to display.
BufferedImageOverlay(OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Create an overlay to display multiple image regions.
BufferedImageOverlay(OverlayOptions, ImageRegion, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Create an overlay to display one specified image region.
BufferedImageOverlay(QuPathViewer, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
BufferedImageOverlay(QuPathViewer, Map<ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
BufferedImageOverlay(QuPathViewer, OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Create an overlay to display multiple image regions.
bufferedImageProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get a read-only property representing the buffered image.
BufferedImageTools - Class in qupath.lib.awt.common: Static methods for working with BufferedImages and QuPath objects.
BUGS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
build() - Method in class qupath.lib.analysis.DelaunayTools.Builder: Build the DelaunayTools.Subdivision with the current parameters.
build() - Method in interface qupath.lib.analysis.heatmaps.ColorModels.ColorModelBuilder: Build a ColorModel.
build() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Build the classifier defined by the parameters of this builder.
build() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Build a new PixelClassifierMetadata object.
build() - Method in interface qupath.lib.color.ColorModels.ColorModelBuilder: Build a ColorModel.
build() - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Build the parameters.
build() - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Build a PixelProcessor from the current state of the builder.
build() - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Create an Action with this builder.
build() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Build a chart according to the specified parameters.
build() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Build a chart according to the specified parameters.
build() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Build a chart according to the specified parameters.
build() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Build the dialog.
build() - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Create the rendered image server.
build() - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder: Creates a new OMEPixelParser instance.
build() - Method in class qupath.lib.images.servers.ImageServerBuilder.AbstractServerBuilder
build() - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder: Build a new ImageServer instance.
build() - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Build an ImageServerMetadata.
build() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder: Build a list of ImageResolutionLevels, which can be used with an ImageServerMetadata object.
build() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Build the ImageServer with the requested parameters.
build() - Method in class qupath.lib.images.servers.PixelCalibration.Builder: Build PixelCalibration object.
build() - Method in class qupath.lib.images.servers.SparseImageServer.Builder: Build a new SparseImageServer.
build() - Method in class qupath.lib.images.servers.TransformedServerBuilder: Get the ImageServer that applies all the requested transforms.
build() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Create an OMEPyramidWriter.OMEPyramidSeries to write the OME-TIFF.
build() - Method in class qupath.lib.objects.utils.Tiler.Builder: Build a tiler object with the current settings.
build() - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder: Build a new converter with the specified parameters.
build() - Method in class qupath.lib.scripting.ScriptParameters.Builder: Build the ScriptParameters with the current options.
build() - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Build the params.
build() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Build a new OpenCVDnn.
build() - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Build the patch classifier parameters.
build() - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Build the pane
build(List<Mat>) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate results as a list of maps connecting features and Mats for all slices of a z-stack.
build(List<Mat>, int) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate results for a map of features and Mats for one slice of a z-stack.
build(Mat) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate results for a single Mat.
build(Mat, boolean) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder: Build a FeaturePreprocessor.
buildClassifier(ImageData<BufferedImage>) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: Build a PixelClassifier for a density map using the current parameters and the specified ImageData.
buildDnnModel(BioimageIoSpec.BioimageIoModel) - Static method in class qupath.opencv.ml.BioimageIoTools: Attempt to build a DnnModel that follows this spec as closely as possible.
builder() - Static method in class qupath.lib.experimental.pixels.Parameters: Create a new builder for parameters.
builder() - Static method in class qupath.lib.experimental.pixels.PixelProcessor: Create a new builder to construct a PixelProcessor.
builder() - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Create a new builder to generate a custom dialog.
builder() - Static method in class qupath.lib.scripting.ScriptParameters: Create a new builder for ScriptParameters.
builder() - Static method in class qupath.opencv.dnn.DnnModelParams: Create a new params builder, with default values.
builder() - Static method in class qupath.opencv.ml.FeaturePreprocessor: Create a FeaturePreprocessor.Builder to build a custom FeaturePreprocessor.
builder() - Static method in class qupath.opencv.ml.PatchClassifierParams: Create a builder to generate new patch classifier params.
builder(int) - Static method in class qupath.lib.objects.utils.Tiler: Create a new builder to generate square tiles.
builder(int, int) - Static method in class qupath.lib.objects.utils.Tiler: Create a new builder to generate rectangular tiles.
builder(String) - Static method in class qupath.opencv.dnn.DnnTools: Initiative building and configuring an OpenCVDnn.
builder(String) - Static method in class qupath.opencv.dnn.OpenCVDnn: Create a new builder.
builder(Collection<? extends MeasurementProcessor.CustomMeasurement<BufferedImage, BufferedImage>>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor: Create a new builder for a PixelProcessor that can make custom measurements for an image object.
builder(DensityMaps.DensityMapBuilder) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps: Create a new DensityMaps.DensityMapBuilder initialized with the same properties as an existing builder.
builder(Processor<ImagePlus, ImagePlus, Object>) - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create a PixelProcessor.Builder for an ImageJ ImagePlus.
builder(Processor<Mat, Mat, Mat>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create a PixelProcessor.Builder for an OpenCV Mat.
builder(PathObjectPredicates.PathObjectPredicate) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps: Create a new DensityMaps.DensityMapBuilder to generate a customized density map.
builder(Tiler) - Static method in class qupath.lib.objects.utils.Tiler: Create a new builder initialized with the settings from an existing Tiler.
builder(DnnModelParams) - Static method in class qupath.opencv.dnn.DnnModelParams: Create a new params builder, initialized with the values from existing params.
builder(PatchClassifierParams) - Static method in class qupath.opencv.ml.PatchClassifierParams: Create a builder to generate new patch classifier params, initialized with the values from an existing parameter object.
Builder() - Constructor for class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
Builder() - Constructor for class qupath.lib.experimental.pixels.Parameters.Builder
Builder() - Constructor for class qupath.lib.experimental.pixels.PixelProcessor.Builder
Builder() - Constructor for class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.
Builder() - Constructor for class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
Builder() - Constructor for class qupath.lib.images.servers.ImageServerMetadata.Builder: Minimal builder for a new ImageServerMetadata; further properties must be set.
Builder() - Constructor for class qupath.lib.images.servers.PixelCalibration.Builder: Create a new builder with default (uncalibrated) values.
Builder() - Constructor for class qupath.lib.images.servers.SparseImageServer.Builder
Builder() - Constructor for class qupath.lib.roi.GeometryTools.GeometryConverter.Builder: Default constructor for a builder with flatness 0.5 and pixel width/height of 1.0.
Builder(int, int) - Constructor for class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder: Constructor to help build a list of ImageServerMetadata.ImageResolutionLevel objects to represent pyramidal resolutions.
Builder(Class<? extends ImageServer<?>>, String, int, int) - Constructor for class qupath.lib.images.servers.ImageServerMetadata.Builder: Builder for a new ImageServerMetadata; further properties must be set.
Builder(QuPathViewer) - Constructor for class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Create a rendered image server build using viewer defaults.
Builder(ImageData<BufferedImage>) - Constructor for class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Create a rendered image server for the specified ImageData;
Builder(ImageData<BufferedImage>) - Constructor for class qupath.lib.images.servers.LabeledImageServer.Builder: Create a Builder for a LabeledImageServer for the specified ImageData.
Builder(ImageServer<BufferedImage>) - Constructor for class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Constructor.
Builder(ImageServerMetadata) - Constructor for class qupath.lib.images.servers.ImageServerMetadata.Builder: Builder for a new ImageServerMetadata object that takes an existing metadata object as a starting point, but allows individual properties to be overridden.
Builder(PixelCalibration) - Constructor for class qupath.lib.images.servers.PixelCalibration.Builder: Create a new builder, initialized values of an existing PixelCalibration.
buildFilePath(String, String...) - Static method in class qupath.lib.scripting.QP: Build a file path from multiple components.
buildImageDataOp(Collection<? extends ColorTransforms.ColorTransform>) - Static method in class qupath.opencv.ops.ImageOps: Create an ImageDataOp, optionally using a specified collection of input channels.
buildImageDataOp(ColorTransforms.ColorTransform...) - Static method in class qupath.opencv.ops.ImageOps: Create an ImageDataOp, optionally using a specified array of input channels.
BuildInfo - Class in qupath.lib.gui: Basic version information about the current QuPath build.
buildModel() - Method in class qupath.opencv.dnn.OpenCVDnn: Build a model.
buildModel(DnnModelParams) - Method in interface qupath.opencv.dnn.DnnModelBuilder: Build a DnnModel if possible, or return null otherwise.
buildModel(DnnModelParams) - Static method in class qupath.opencv.dnn.DnnModels: Build a DnnModel from the given parameters.
buildModel(DnnModelParams) - Method in class qupath.opencv.dnn.OpenCVDnnModelBuilder
buildModel(OpenCVDnn.ModelType) - Method in class qupath.opencv.dnn.OpenCVDnn: Build a model, specifying the OpenCVDnn.ModelType.
buildNet() - Method in class qupath.opencv.dnn.OpenCVDnn: Build the OpenCV Net.
buildOriginal() - Method in class qupath.lib.images.servers.ImageServerBuilder.AbstractServerBuilder
buildOriginal() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
buildParameters() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: Build a DensityMaps.DensityMapParameters object containing the main density map parameters.
buildPatchClassifierParams(BioimageIoSpec.BioimageIoModel, int, int, ImageOp...) - Static method in class qupath.opencv.ml.BioimageIoTools: Create an instance of PatchClassifierParams from a model spec.
buildPatchClassifierParams(BioimageIoSpec.BioimageIoModel, ImageOp...) - Static method in class qupath.opencv.ml.BioimageIoTools: Create an instance of PatchClassifierParams from a model spec.
buildPathInProject(String...) - Static method in class qupath.lib.scripting.QP: Build a file or directory path relative to the current project, but do not make any changes on the file system.
buildPixelClassifier(PatchClassifierParams) - Static method in class qupath.opencv.ml.PatchClassifierParams: Build a pixel classifier using these parameters
buildServer(String, Class<T>, String...) - Static method in class qupath.lib.images.servers.ImageServerProvider: Attempt to create ImageServer<T> from the specified path and arguments.
buildServer(String, Class<T>, String...) - Static method in class qupath.lib.scripting.QP: Deprecated.
In the usual case where BufferedImage is the class, use QP.buildServer(String, String...) instead because it handles default args.
buildServer(String, String...) - Static method in class qupath.lib.images.servers.ImageServers: Build a ImageServer for the specified URI path and optional args.
buildServer(String, String...) - Static method in class qupath.lib.scripting.QP: Build an ImageServer with the class BufferedImage.
buildServer(URI, String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
buildServer(URI, String...) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
buildServer(URI, String...) - Method in interface qupath.lib.images.servers.ImageServerBuilder: Attempt to create ImageServer<T> from the specified path.
buildServer(URI, String...) - Static method in class qupath.lib.images.servers.ImageServers: Build a ImageServer for the specified URI and optional args.
buildServer(URI, String...) - Method in class qupath.lib.images.servers.JsonImageServerBuilder
buildServer(URI, String...) - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
buildServer(URI, String...) - Static method in class qupath.lib.scripting.QP: Build an ImageServer with the class BufferedImage.
buildServer(ImageData<BufferedImage>) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: Build an ImageServer representing this density map.
buildServer(ImageData<BufferedImage>, ImageDataOp, PixelCalibration) - Static method in class qupath.opencv.ops.ImageOps: Build an ImageServer that generates pixels on demand from an ImageData by applying an ImageDataOp.
buildServer(ImageData<BufferedImage>, ImageDataOp, PixelCalibration, int, int) - Static method in class qupath.opencv.ops.ImageOps: Build an ImageServer that generates pixels on demand from an ImageData by applying an ImageDataOp.
bundle() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
buttons(String...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the buttons to display in the dialog.
buttons(ButtonType...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the buttons to display in the dialog.
byteOrder(ByteOrder) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder

C

cache - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
calculatePadding() - Method in class qupath.opencv.ops.ImageOps.PaddedOp: Calculate the required padding.
calculatePreferredParallelism() - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Make a semi-educated guess as to an appropriate number of threads to use.
calibratedLocationString - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
calibrateImagePlus(ImagePlus, RegionRequest, ImageServer<BufferedImage>) - Static method in class qupath.imagej.tools.IJTools: Set an ImagePlus's Calibration and FileInfo properties based on a RegionRequest and PathImageServer.
calibrateObject(PathObject, Roi) - Static method in class qupath.imagej.tools.IJTools: Set the properties of a PathObject based upon an ImageJ Roi.
calibration(PixelCalibration) - Method in class qupath.lib.analysis.DelaunayTools.Builder: Specify pixel calibration, which is used to calibrate the x and y coordinates.
canBeautify() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Returns true if ScriptSyntax.beautify(String) is capable of beautifying the text, false otherwise.
CANCEL - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton: Deprecated.

"Cancel" option
cancelDirection(boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover: Cancel either the x- or y-axis direction of the movement.
cancelled() - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
cancelled() - Method in interface qupath.lib.plugins.SimpleProgressMonitor: Returns true if cancel has been requested, for example by the user pressing a 'cancel' button.
canCompress() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Returns true if ScriptSyntax.compress(String) is capable of compressing the text, false otherwise.
canRedo() - Method in class qupath.lib.gui.UndoRedoManager: True if it's possible to call redoOnce for the currently-active viewer in QuPath, false otherwise.
canUndo() - Method in class qupath.lib.gui.UndoRedoManager: True if it's possible to call undoOnce for the currently-active viewer in QuPath, false otherwise.
caretPositionProperty() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
caretPositionProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Property for the current caret position.
caretPositionProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
ceil() - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that ceils floating point values.
ceil(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Ceil values in a floating point Mat.
CELL - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments: Full cell region
CELL_NUCLEI_BOTH - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
CELL_ONLY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
CellCountsCV - Class in qupath.opencv: Simple plugin to attempt a very fast cell counting based upon (smoothed) peak detection.
CellCountsCV() - Constructor for class qupath.opencv.CellCountsCV
cellDisplayActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
CellDisplayActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
CellIntensityClassificationCommand - Class in qupath.process.gui.commands: Command to (sub)classify cells as Negative/Positive or Negative/1+/2+/3+ based on a single (usually intensity-based) measurement.
CellIntensityClassificationCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.CellIntensityClassificationCommand: Constructor.
cells() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the filter to accept cell objects only.
CELLS - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept cells
CellTools - Class in qupath.lib.objects: Helper class for working with PathObjects that represent cells.
CellTools() - Constructor for class qupath.lib.objects.CellTools
CENTER - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
CENTER_LEFT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
CENTER_RIGHT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
centerImage() - Method in class qupath.lib.gui.viewer.QuPathViewer: Center the current image in the viewer, while keeping the same downsample factor.
centerROI(ROI) - Method in class qupath.lib.gui.viewer.QuPathViewer: Center the specified ROI in the viewer
centroidDistancePredicate(double, boolean) - Static method in class qupath.lib.analysis.DelaunayTools: BiPredicate that returns true for objects with ROI centroids within a specified distance.
centroids() - Method in class qupath.lib.analysis.DelaunayTools.Builder: Specify that the triangulation should be based on ROI centroids.
centroids(Collection<? extends PathObject>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Plot centroids for the specified objects in pixel units.
centroids(Collection<? extends PathObject>, PixelCalibration) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Plot centroids for the specified objects using a fixed pixel calibration.
CENTROIDS - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode: Show only detection centroids, not boundaries.
CENTROIDS_ONLY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
centroidToBoundsDistance2D(Collection<PathObject>, Collection<PathObject>, double, double, String) - Static method in class qupath.lib.analysis.DistanceTools: Calculate the distance between source object centroids and the boundary of specified target objects, adding the result to the measurement list of the source objects.
centroidToBoundsDistance2D(Collection<PathObject>, Collection<PathObject>, double, double, String, boolean) - Static method in class qupath.lib.analysis.DistanceTools: Calculate the (optionally signed) distance between source object centroids and the boundary of specified target objects, adding the result to the measurement list of the source objects.
centroidToCentroidDistance2D(Collection<PathObject>, Collection<PathObject>, double, double, String) - Static method in class qupath.lib.analysis.DistanceTools: Calculate the distance between source object centroids and the centroid of specified target objects, adding the result to the measurement list of the source objects.
CHANGE_CLASSIFICATION - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: A change was made to one or more object classifications
CHANGE_MEASUREMENTS - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: A change was made to one or more object measurements
CHANGE_OTHER - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: A change was made to one or more objects that is more complex than the other changes allow for
changed(ObservableValue<? extends QuPathViewer>, QuPathViewer, QuPathViewer) - Method in class qupath.lib.gui.UndoRedoManager
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.CountingDialogCommand
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.PathObjectGridView
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.AnnotationPane
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.ImageDetailsPane
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.ProjectBrowser
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.SlideLabelView
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
changeMaxValues(double, double, double) - Method in class qupath.lib.color.ColorDeconvolutionStains: Create a new stains object with the same StainVectors but new max (background) values.
changeName(String) - Method in class qupath.lib.color.ColorDeconvolutionStains: Create a new stains object with the same StainVectors but a new name.
changeStain(StainVector, int) - Method in class qupath.lib.color.ColorDeconvolutionStains: Create a new stains object, identical to this one but for one StainVector having been changed.
changeTimestampProperty() - Method in class qupath.lib.display.ImageDisplay: Timestamp for the most recent change.
CHANNEL_ALL_OBJECTS - Static variable in class qupath.lib.analysis.heatmaps.DensityMaps: Channel name for the channel with all object counts (not always present).
CHANNEL_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
ChannelColor - Class in qupath.lib.display.settings: A simple class to store the color of an image channel.
ChannelColor() - Constructor for class qupath.lib.display.settings.ChannelColor
ChannelDisplayInfo - Interface in qupath.lib.display: Interface used to control the display of single channels of image data, where 'single channel' means one value per pixel (in Java's parlance, one band for the SampleModel).
ChannelDisplayInfo.ModifiableChannelDisplayInfo - Interface in qupath.lib.display: Helper interface to indicate that the display ranges can be modified.
ChannelDisplayMode - Enum Class in qupath.lib.display: Display mode for an image channel, used in combination with ImageDisplay and ChannelDisplayInfo.
ChannelDisplayTransformServer - Class in qupath.lib.gui.images.servers: ImageServer that applies a color transform to an image.
channelMaximum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the minimum of an image channel, ignoring NaNs.
channelMean(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the mean of an image channel, ignoring NaNs.
channelMinimum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the minimum of an image channel, ignoring NaNs.
channels(int...) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Override default of writing all channels in their original order to be able to specify which channels are output, and in which order.
channels(int...) - Method in class qupath.lib.images.writers.TileExporter: Export only specified channels.
channels(String...) - Method in class qupath.lib.images.writers.TileExporter: Export only specified channels, identified by name.
channels(Collection<ImageChannel>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the image channels.
Channels() - Constructor for class qupath.opencv.ops.ImageOps.Channels
ChannelSettings - Class in qupath.lib.display.settings: A simple class to store the main information needed by QuPath to display an image channel with a requested color and brightness/contrast setting.
ChannelSettings() - Constructor for class qupath.lib.display.settings.ChannelSettings
channelsImages() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request that channels are written as separate images.
channelsInterleaved() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request that channels are written interleaved within a single image plane.
channelSoftmax(double) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Apply softmax, with the specified output maxValue.
channelsPlanar() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request that channels are written as separate image planes.
channelStdDev(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the standard deviation of image channels, ignoring NaNs.
channelSum(double) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Normalize channels so that they sum to the specified value.
channelSum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the sum of image channels, ignoring NaNs.
ChannelTransformFeatureServer - Class in qupath.lib.images.servers: A TransformingImageServer that applies color transforms to generate channels.
channelType(ImageServerMetadata.ChannelType) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the interpretation of channels.
Charts - Class in qupath.lib.gui.charts: Helper class for generating interactive charts.
Charts() - Constructor for class qupath.lib.gui.charts.Charts
Charts.BarChartBuilder - Class in qupath.lib.gui.charts: Builder for creating scatter charts.
Charts.PieChartBuilder - Class in qupath.lib.gui.charts: Builder for creating pie charts.
Charts.ScatterChartBuilder - Class in qupath.lib.gui.charts: Builder for creating scatter charts.
ChartThresholdPane - Class in qupath.lib.gui.charts: Pane that can be used to contain an XYChart, adding adjustable thresholds to be displayed.
ChartThresholdPane(XYChart<Number, Number>) - Constructor for class qupath.lib.gui.charts.ChartThresholdPane: Note: xAxis and yAxis must be instances of NumberAxis.
ChartTools - Class in qupath.lib.gui.charts: Collection of static methods to help when working with JavaFX charts, and adapting these for QuPath's purposes.
ChartTools() - Constructor for class qupath.lib.gui.charts.ChartTools
CHECK_URIS - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
checkExtensions(String, String...) - Static method in class qupath.lib.common.GeneralTools: Check whether a path ends with one of a number of specified extensions (case insensitive).
checkForUpdate() - Static method in class qupath.lib.gui.extensions.UpdateChecker: Query the most recent QuPath release on GitHub.
checkForUpdate(GitHubProject.GitHubRepo) - Static method in class qupath.lib.gui.extensions.UpdateChecker: Query the latest release from a GitHub repo.
checkImageSupport(URI, String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
checkImageSupport(URI, String...) - Method in interface qupath.lib.images.servers.ImageServerBuilder: Check whether a URI is supported by this builder.
checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.JsonImageServerBuilder
checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
checkMinVersion(String) - Static method in class qupath.lib.scripting.QP: Check whether the current QuPath version is ≥ the specified version.
checkpoint() - Method in class qupath.lib.common.Timeit: Create a new checkpoint with a default name.
checkpoint(String) - Method in class qupath.lib.common.Timeit: Create a new checkpoint with the specified name.
checkpointAndRun(Runnable) - Method in class qupath.lib.common.Timeit: Create a checkpoint with the default name and immediately run the provided runnable.
checkpointAndRun(String, Runnable) - Method in class qupath.lib.common.Timeit: Create a checkpoint and immediately run the provided Runnable.
checkpointAndRun(String, Runnable, int) - Method in class qupath.lib.common.Timeit: Create a checkpoint and immediately run the provided Runnable nIterations times.
checkType(URI) - Static method in class qupath.lib.images.servers.FileFormatInfo: Check the type of an image for a specified URI.
checkVersionRange(String, String) - Static method in class qupath.lib.scripting.QP: Check whether the current QuPath version is ≥ the specified minimum version, and < the specified maximum.
ChoiceParameter<S> - Class in qupath.lib.plugins.parameters: Parameter that supports a list of choices.
choices - Variable in class qupath.lib.plugins.parameters.ChoiceParameter
CIRCULARITY - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Circularity.
CITE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
classification() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Set the model type to be OpenCVDnn.ModelType.CLASSIFICATION.
CLASSIFICATION - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Each channel represents a classification, such as in a labelled image.
CLASSIFICATION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Refers to ClassificationModel.
classificationLabels(Map<Integer, PathClass>) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Specify classification labels.
classificationLabels(Map<Integer, PathClass>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the interpretation of classification labels.
classificationLabelsToChannels(Map<Integer, PathClass>, boolean) - Static method in class qupath.lib.images.servers.ServerTools: Create a list of channels from classification labels.
ClassificationResolution - Class in qupath.process.gui.commands.ml: Wrapper for a PixelCalibration to be used to define classifier resolution.
classifications(Collection<? extends PathObject>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Plot two measurements against one another for the specified objects.
classify(ClassificationModel, PathObject, Mat, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools: Apply a classification model to an existing image patch to classify an object.
classify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, int, int, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools: Apply a classification model to an image patch to classify an object.
classify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools: Apply a classification model to an image patch to classify an object.
ClassifyByMeasurementBuilder(String) - Constructor for class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Constructor.
classifyCellsByCentroid(ImageData<BufferedImage>, PixelClassifier, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Classify cells according to the prediction of the pixel corresponding to the cell centroid using a PixelClassifier.
classifyDetectionsByCentroid(String) - Static method in class qupath.lib.scripting.QP: Classify detections according to the prediction of the pixel corresponding to the detection centroid using a PixelClassifier.
classifyDetectionsByCentroid(PixelClassifier) - Static method in class qupath.lib.scripting.QP: Classify detections according to the prediction of the pixel corresponding to the detection centroid using a PixelClassifier.
classifyDetectionsByCentroid(ImageData<BufferedImage>, PixelClassifier) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Classify detections according to the prediction of the pixel corresponding to the detection centroid using a PixelClassifier.
ClassifyMenuActions - Class in qupath.lib.gui.actions.menus
ClassifyMenuActions.Actions - Class in qupath.lib.gui.actions.menus
classifyObjects(ImageData<BufferedImage>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.dnn.DnnObjectClassifier
classifyObjects(ImageData<BufferedImage>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
classifyObjects(ImageData<T>, boolean) - Method in class qupath.lib.classifiers.object.AbstractObjectClassifier
classifyObjects(ImageData<T>, boolean) - Method in interface qupath.lib.classifiers.object.ObjectClassifier: Classify all compatible objects from an ImageData.
classifyObjects(ImageData<T>, Collection<? extends PathObject>, boolean) - Method in interface qupath.lib.classifiers.object.ObjectClassifier: Classify the objects in the specified collection.
classifyObjects(ImageData<T>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
classifyObjectsByCentroid(ImageData<BufferedImage>, PixelClassifier, Collection<PathObject>, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Classify objects according to the prediction of the pixel corresponding to the object's ROI centroid using a PixelClassifier.
classifyObjectsByCentroid(ImageServer<BufferedImage>, Collection<PathObject>, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Apply classification from a server to a collection of objects.
classifyObjectsByCluster(Collection<Collection<? extends PathObject>>) - Static method in class qupath.lib.analysis.DelaunayTools: Assign object classifications based upon pre-computed clusters.
classifyObjectsByCluster(Collection<Collection<? extends PathObject>>, Function<Integer, PathClass>) - Static method in class qupath.lib.analysis.DelaunayTools: Assign object classifications based upon pre-computed clusters.
classifySelected(String) - Static method in class qupath.lib.scripting.QP: Set the classification of the selected objects in the current hierarchy.
classifySelected(PathObjectHierarchy, String) - Static method in class qupath.lib.scripting.QP: Set the classification of the selected objects.
clear() - Method in interface qupath.lib.gui.scripting.EditableText: Request clear the contents of the control.
clear() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
clear() - Method in class qupath.lib.gui.scripting.TextAreaControl
clear() - Method in class qupath.lib.gui.UndoRedoManager: Clear all undo/redo stacks (useful when memory is low).
clear() - Method in interface qupath.lib.measurements.MeasurementList: Remove all the measurements from the list.
clear() - Method in class qupath.lib.objects.PathObjectConnections: Clear all existing connections.
clear() - Method in class qupath.lib.plugins.workflow.Workflow: Remove all steps, firing an update event if the workflow was not previously empty.
CLEAR_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
CLEAR_CORES - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
CLEAR_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
CLEAR_HIERARCHY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
clearAll() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Remove all objects from the hierarchy.
clearAllObjects() - Static method in class qupath.lib.scripting.QP: Remove all the objects in the current PathObjectHierarchy, and clear the selection.
clearAllObjects(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Remove all the objects of a specified Java class.
clearAnnotationMeasurements() - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all annotations in the current hierarchy.
clearAnnotationMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all annotations in a hierarchy.
clearAnnotations() - Static method in class qupath.lib.scripting.QP: Remove all the annotation objects from the current PathObjectHierarchy.
clearBoundary(ByteProcessor, Roi, double) - Static method in class qupath.imagej.processing.RoiLabeling: Starting from all white pixels (value = 255) on a ROI's boundary, fill the pixels with black
clearCache() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Clear the cache, including thumbnails, and cancel any pending requests.
clearCache() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Clear any cached tiles.
clearCache(boolean, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Clear the cache, optionally including thumbnails and stopping any pending requests.
clearCachedOverlay() - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay: Clear previously-cached tiles for this overlay.
clearCachedOverlayForRegion(ImageRegion) - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay: Clear previously-cached tiles for a specified region of this overlay.
clearCacheForRequestOverlap(RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
clearCacheForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
clearCellMeasurements() - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all cells in the current hierarchy.
clearCellMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all cells in a hierarchy.
clearChildObjects() - Method in class qupath.lib.objects.PathObject: Remove all child objects.
clearDetectionMeasurements() - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all detections in the current hierarchy.
clearDetectionMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all detections in a hierarchy (including sub-classes of detections).
clearDetections() - Static method in class qupath.lib.scripting.QP: Remove all the detection objects from the current PathObjectHierarchy.
clearMeasurements() - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all detections in the current hierarchy.
clearMeasurements(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for objects of a specific class in the current hierarchy (subclasses are not included!).
clearMeasurements(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for objects of a specific class in a hierarchy (subclasses are not included!).
clearMeasurements(PathObjectHierarchy, Collection<PathObject>) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for specified objects within a hierarchy.
clearMeasurements(PathObjectHierarchy, PathObject...) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for specified objects within a hierarchy.
clearMetadata() - Method in class qupath.lib.objects.TMACoreObject: Clear all associated metadata.
clearMetadata() - Method in interface qupath.lib.projects.ProjectImageEntry: Remove all metadata.
clearMetadataMap() - Method in class qupath.lib.objects.PathObject: Remove all stored metadata values.
clearOutside(ImageProcessor, Roi) - Static method in class qupath.imagej.processing.RoiLabeling: Clear (i.e.
clearPathObjects() - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, replaced by PathObject.clearChildObjects()
clearReaderOptions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Clear all reader options, returning these to their defaults.
clearRootMeasurements() - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for the root object.
clearRootMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for the root object.
clearSelectedObjects() - Static method in class qupath.lib.scripting.QP: Clear selected objects, but keep child (descendant) objects.
clearSelectedObjects(boolean) - Static method in class qupath.lib.scripting.QP: Delete the selected objects from the current hierarchy, optionally keeping their child (descendant) objects.
clearSelection() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Clear selection so that no objects are selected.
clearThresholds() - Method in class qupath.lib.gui.charts.ChartThresholdPane: Clear all thresholds.
clearTileMeasurements() - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all tiles in the current hierarchy.
clearTileMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all tiles in a hierarchy.
clearTMACoreMeasurements() - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all TMA core objects in the current hierarchy.
clearTMACoreMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Clear the measurement lists for all TMA core objects in a hierarchy.
clearTMAGrid() - Static method in class qupath.lib.scripting.QP: Remove the TMA grid from the current PathObjectHierarchy.
clip(double, double) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that clips Mat values to the specified minimum and maximum.
clip(Mat, double, double) - Static method in class qupath.opencv.tools.GroovyCV: Clip values of a Mat to be within a specified minimum and maximum.
clip255(double) - Static method in class qupath.lib.common.ColorTools: Convert a double value to an int, flooring and clipping to the range 0-255.
clipROIsForHierarchy - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
clipROIsForHierarchyProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request ROIs to be clipped and inserted as the right place in the hierarchy when drawing (to prevent overlapping ROIs being created accidentally).
clipToAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
clipToROI(ROI, Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools: Intersect a collection of ROIs with a single parent ROI, returning all results that are valid.
clipValue(double, double, double) - Static method in class qupath.lib.common.GeneralTools: Clip a value to be within a specific range.
clipValue(int, int, int) - Static method in class qupath.lib.common.GeneralTools: Clip a value to be within a specific range.
close() - Method in class qupath.imagej.images.servers.ImageJServer
close() - Method in class qupath.lib.gui.ExtensionClassLoader
close() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
close() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
close() - Method in class qupath.lib.gui.SharedThreadPoolManager: Shutdown any threadpools created by this manager.
close() - Method in class qupath.lib.images.servers.AbstractImageServer
close() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
close() - Method in class qupath.lib.images.servers.LabeledImageServer
close() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Close; this is important for cleanup.
close() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
close() - Method in class qupath.lib.images.servers.SparseImageServer
close() - Method in class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager
close() - Method in interface qupath.lib.measurements.MeasurementList: Close the list.
close() - Method in interface qupath.opencv.dnn.DnnModel: Close this model if it will not be needed again.
close() - Method in class qupath.opencv.dnn.OpenCVDnn
close() - Method in class qupath.opencv.ml.objects.features.Preprocessing.PCAProjector
close() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
close() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
closeProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Close the current project open in the QuPathGUI.
closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewer: Request that this viewer is closed.
closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
closeViewer(QuPathViewer) - Method in class qupath.lib.gui.QuPathGUI: Close the image within a viewer, prompting to save changes if necessary.
closing(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D morphological closing filter.
closingByReconstruction(ImageProcessor, double) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Apply a morphological closing by reconstruction.
closingFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D closing filter (dilation followed by erosion) to all channels of an image.
CM_GRAYSCALE - Static variable in class qupath.lib.display.DirectServerChannelInfo
CM_GRAYSCALE_INVERTED - Static variable in class qupath.lib.display.DirectServerChannelInfo
CodeAreaControl - Class in qupath.lib.gui.scripting.richtextfx: Code area control using RichTextFX.
COG - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
CoherenceFeaturePlugin - Class in qupath.lib.algorithms: Plugin to calculate coherence features for image tiles.
CoherenceFeaturePlugin() - Constructor for class qupath.lib.algorithms.CoherenceFeaturePlugin: Default constructor.
COLOR - Enum constant in enum class qupath.lib.display.ChannelDisplayMode: Show using default color LUT (may be composite)
COLOR_DECONVOLUTION_REFINE - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
ColorDeconvMatrix3x3 - Class in qupath.lib.color: Simple class for representing - and inverting a 3x3 matrix.
ColorDeconvMatrix3x3(double[][]) - Constructor for class qupath.lib.color.ColorDeconvMatrix3x3: Constructor for a 3x3 matrix.
ColorDeconvolutionHelper - Class in qupath.lib.color: Static methods to assist with color deconvolution.
ColorDeconvolutionHelper() - Constructor for class qupath.lib.color.ColorDeconvolutionHelper
ColorDeconvolutionStains - Class in qupath.lib.color: Helper class for storing stain vectors and maximum channel values to be used for color deconvolution.
ColorDeconvolutionStains() - Constructor for class qupath.lib.color.ColorDeconvolutionStains: Default constructor, for Externalizable.
ColorDeconvolutionStains(String, StainVector, StainVector, double, double, double) - Constructor for class qupath.lib.color.ColorDeconvolutionStains: Constructor for ColorDeconvolutionStains with two stain vectors.
ColorDeconvolutionStains(String, StainVector, StainVector, StainVector, double, double, double) - Constructor for class qupath.lib.color.ColorDeconvolutionStains: Constructor for ColorDeconvolutionStains with three stain vectors.
ColorDeconvolutionStains.DefaultColorDeconvolutionStains - Enum Class in qupath.lib.color: Enum for common stain defaults.
colorDeconvolve(ColorProcessor, ColorDeconvolutionStains) - Static method in class qupath.imagej.tools.IJTools: Apply color deconvolution, outputting 3 'stain' images in the same order as the stain vectors.
colorDeconvolveReconvolveRGBArray(int[], ColorDeconvolutionStains, ColorDeconvolutionStains, boolean, int[]) - Static method in class qupath.lib.color.ColorTransformer: Deconvolve RGB array with one set of stain vectors, and reconvolve with another.
colorDeconvolveReconvolveRGBArray(int[], ColorDeconvolutionStains, ColorDeconvolutionStains, boolean, int[], float, float) - Static method in class qupath.lib.color.ColorTransformer: Deconvolve RGB array with one set of stain vectors, and reconvolve with another - with optional scaling.
colorDeconvolveRGBPixel(int, ColorDeconvolutionStains, int) - Static method in class qupath.lib.color.ColorTransformer: Calculate the color deconvolved value for a single pixel, stored as a packed (A)RGB int.
colorDefaultObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The default color used to display objects of any type, where a default has not otherwise been specified.
ColorMapCanvas - Class in qupath.lib.gui: Canvas to show the range of a ColorMap (i.e.
ColorMapCanvas(double, ColorMaps.ColorMap) - Constructor for class qupath.lib.gui.ColorMapCanvas
ColorMapCanvas(double, ColorMaps.ColorMap, Function<Double, String>) - Constructor for class qupath.lib.gui.ColorMapCanvas: Create a canvas that displays the range of the specified ColorMaps.ColorMap with key tooltips.
colorMapProperty() - Method in class qupath.lib.gui.ColorMapCanvas: Return the ColorMap property of this canvas.
ColorMaps - Class in qupath.lib.color: Helper class to manage colormaps, which are rather like lookup tables but easily support interpolation.
ColorMaps() - Constructor for class qupath.lib.color.ColorMaps
ColorMaps.ColorMap - Interface in qupath.lib.color: colormap, which acts as an interpolating lookup table with an arbitrary range.
colormapsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager: Read only property representing the custom colormaps directory.
colorModel(ColorModels.ColorModelBuilder) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: Set a ColorModels.ColorModelBuilder that can be used in conjunction with DensityMaps.DensityMapBuilder.buildServer(ImageData).
ColorModelFactory - Class in qupath.lib.color: Factory methods to help create ColorModels for use with BufferedImages.
ColorModelRenderer - Class in qupath.lib.gui.images.stores: An ImageRenderer that uses a ColorModel.
ColorModelRenderer(ColorModel) - Constructor for class qupath.lib.gui.images.stores.ColorModelRenderer: Constructor.
ColorModels - Class in qupath.lib.analysis.heatmaps: Helper class for creating a JSON-serializable way to generate a ColorModel.
ColorModels - Class in qupath.lib.color: Helper class for creating a JSON-serializable way to generate a ColorModel.
ColorModels() - Constructor for class qupath.lib.analysis.heatmaps.ColorModels
ColorModels() - Constructor for class qupath.lib.color.ColorModels
ColorModels.ColorModelBuilder - Interface in qupath.lib.analysis.heatmaps: Simple builder to create a ColorModel.
ColorModels.ColorModelBuilder - Interface in qupath.lib.color: Simple builder to create a ColorModel.
ColorModels.DisplayBand - Class in qupath.lib.analysis.heatmaps: Helper class to the display of a single channel (band) in a ColorModel.
ColorModels.DisplayBand - Class in qupath.lib.color: Helper class to the display of a single channel (band) in a ColorModel.
colorSelectedObjectProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The default color used to display selected objects.
colorTileProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The default color used to display tile objects.
colorTMAMissingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The default color used to display missing TMA core objects.
colorTMAProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The default color used to display TMA core objects.
ColorTools - Class in qupath.lib.common: Static functions to help work with RGB(A) colors using packed ints.
ColorToolsAwt - Class in qupath.lib.color: Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
ColorToolsAwt() - Constructor for class qupath.lib.color.ColorToolsAwt
ColorToolsFX - Class in qupath.lib.gui.tools: Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
ColorToolsFX() - Constructor for class qupath.lib.gui.tools.ColorToolsFX
ColorTransformer - Class in qupath.lib.color: Static methods for computing a range of color transforms for packed RGB values.
ColorTransformer() - Constructor for class qupath.lib.color.ColorTransformer
ColorTransformer.ColorTransformMethod - Enum Class in qupath.lib.color: Enum consisting of color transforms that may be applied to RGB images.
ColorTransforms - Class in qupath.lib.images.servers: Color transforms that may be used to extract single-channel images from BufferedImages.
ColorTransforms() - Constructor for class qupath.lib.images.servers.ColorTransforms
ColorTransforms.ColorTransform - Interface in qupath.lib.images.servers: Interface defining a color transform that can extract a float values from a BufferedImage.
ColorTransforms.ColorTransformTypeAdapter - Class in qupath.lib.images.servers: TypeAdapter to support serializing a ColorTransforms.ColorTransform.
ColorTransformTypeAdapter() - Constructor for class qupath.lib.images.servers.ColorTransforms.ColorTransformTypeAdapter
combineROIs(ROI, ROI, RoiTools.CombineOp) - Static method in class qupath.lib.roi.RoiTools: Combine two shape ROIs together.
combineSelectedAnnotations(ImageData<?>, RoiTools.CombineOp) - Static method in class qupath.lib.gui.commands.Commands: Combine the selected annotations for the specified hierarchy.
comboPasteEscape - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
COMMAND_LIST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
commandBarDisplay - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
commandBarDisplayProperty() - Static method in class qupath.lib.gui.tools.CommandFinderTools: Property specifying where the command bar should be displayed relative to the main viewer window.
CommandFinderTools - Class in qupath.lib.gui.tools: Helper tools for creating components that enable fast access to menu commands via a filtered list.
CommandFinderTools() - Constructor for class qupath.lib.gui.tools.CommandFinderTools
CommandFinderTools.CommandBarDisplay - Enum Class in qupath.lib.gui.tools: Available modes for displaying the command bar.
CommandFinderTools.CommandEntry - Class in qupath.lib.gui.tools: Helper class to wrap summary data for a command to display in the list.
CommandLineProgressMonitor() - Constructor for class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
CommandLineTaskRunner - Class in qupath.lib.plugins: A PluginRunner that simply logs progress and output.
CommandLineTaskRunner() - Constructor for class qupath.lib.plugins.CommandLineTaskRunner: Constructor for a PluginRunner that send progress to a log, and runs tasks using the default number of threads
CommandLineTaskRunner(int) - Constructor for class qupath.lib.plugins.CommandLineTaskRunner: Constructor for a PluginRunner that send progress to a log.
CommandLineTaskRunner.CommandLineProgressMonitor - Class in qupath.lib.plugins: A SimpleProgressMonitor that sends progress to a log.
Commands - Class in qupath.lib.gui.commands: Helper class implementing simple 'single-method' commands for easy inclusion in the GUI.
Commands() - Constructor for class qupath.lib.gui.commands.Commands
CommonActions - Class in qupath.lib.gui.actions: Default actions associated with a specific QuPath instance.
CommonActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.CommonActions
COMPARATOR_FULL - Static variable in class qupath.lib.common.Version: Compare full version, including any suffixes.
COMPARATOR_MAJOR - Static variable in class qupath.lib.common.Version: Compare major versions only.
COMPARATOR_MAJOR_MINOR - Static variable in class qupath.lib.common.Version: Compare major then minor versions.
COMPARATOR_MAJOR_MINOR_PATCH - Static variable in class qupath.lib.common.Version: Compare major then minor then patch versions (ignoring suffixes).
compare(PathObject, PathObject) - Method in class qupath.lib.objects.DefaultPathObjectComparator
compare(ROI, ROI) - Method in class qupath.lib.roi.DefaultROIComparator
compareTo(KaplanMeierData.KaplanMeierEvent) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent
compareTo(Version) - Method in class qupath.lib.common.Version
compareTo(PathClass) - Method in class qupath.lib.objects.classes.PathClass: This is now equivalent to this.toString().compareTo(o.toString()).
compareTo(ImagePlane) - Method in class qupath.lib.regions.ImagePlane: Compare with another ImagePlane, in the order t, z, c.
completionCodeCombination - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
componentContains(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
componentPointToImagePoint(double, double, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Convert x and y coordinates from the component space to the image space.
componentPointToImagePoint(Point2D, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Convert a coordinate from the viewer into the corresponding pixel coordinate in the full-resolution image - optionally constraining it to any server bounds.
compress(String) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Compresses the specified text by removing extra space, according to the syntax.
compression(OMEPyramidWriter.CompressionType) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request the output compression type.
compressSourceAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
computeAboveThresholdCounts(WritableRaster, int, double, WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools: Count the number of above-threshold pixels in a specified band of a raster, with optional mask.
computeAboveThresholdCounts(WritableRaster, int, double, WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools: Count the number of above-threshold pixels in a specified band of a raster, with optional mask and/or bounding rectangle.
computeAngle(StainVector, StainVector) - Static method in class qupath.lib.color.StainVector: Calculate the angle between two stain vectors, in degrees.
computeArgMaxHistogram(WritableRaster, long[], WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a histogram that identifies the channels (bands) of an image with the maximum values according to the argmax criterion.
computeArgMaxHistogram(WritableRaster, long[], WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a histogram that identifies the channels (bands) of an image with the maximum values according to the argmax criterion, with an optional bounding rectangle.
computeConsoleStyles(String, boolean) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.GroovyStyler
computeConsoleStyles(String, boolean) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PropertiesStyler
computeConsoleStyles(String, boolean) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PythonStyler
computeConsoleStyles(String, boolean) - Method in interface qupath.lib.gui.scripting.richtextfx.stylers.ScriptStyler: Compute styling for the specified text, considering it will be used in the console.
computeCoordinateDistance(Coordinate, Collection<Coordinate>) - Static method in class qupath.lib.analysis.DistanceTools: Compute the shortest distance from a coordinate to one of a collection of target coordinates.
computeCoordinateDistance(Coordinate, STRtree) - Static method in class qupath.lib.analysis.DistanceTools: Compute the distance to the nearest coordinate stored within an STRtree.
computeDistance(Coordinate, Geometry, PointOnGeometryLocator) - Static method in class qupath.lib.analysis.DistanceTools: Compute the (unsigned) shortest distance from a coordinate to a target geometry, or zero if the coordinate occurs within
computeDistance(Coordinate, Geometry, PointOnGeometryLocator, boolean) - Static method in class qupath.lib.analysis.DistanceTools: Compute the shortest distance from a coordinate to a target geometry.
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.GroovyStyler
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.JsonStyler
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.MarkdownStyler
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PlainStyler
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PropertiesStyler
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PythonStyler
computeEditorStyles(String) - Method in interface qupath.lib.gui.scripting.richtextfx.stylers.ScriptStyler: Compute styling for the specified text, considering it will be used in the main editor.
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.XmlStyler
computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.YamlStyler
computeFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Compute features.
computeLocalBinaryPatterns16(SimpleImage, double) - Static method in class qupath.lib.analysis.features.LocalBinaryPatterns: Compute local binary pattern descriptor for a SimpleImage.
computeLogRankTest(KaplanMeierData, KaplanMeierData) - Static method in class qupath.lib.analysis.stats.survival.LogRankTest: Compare KaplanMeier objects using log-rank test.
computeRunningStatistics(double[]) - Static method in class qupath.lib.analysis.stats.StatisticsHelper: Create a RunningStatistics object using all the values from a specified array.
computeRunningStatistics(SimpleImage) - Static method in class qupath.lib.analysis.stats.StatisticsHelper: Compute running statistics using all pixels from a SimpleImage.
computeRunningStatistics(SimpleImage, SimpleImage, List<RunningStatistics>) - Static method in class qupath.lib.analysis.stats.StatisticsHelper: Calculate RunningStatistics for each label > 0 in an image, up to a maximum of statsList.size().
computeTiledROIs(ROI, ImmutableDimension, ImmutableDimension, boolean, int) - Static method in class qupath.lib.roi.RoiTools: Create a collection of tiled ROIs corresponding to a specified parentROI if it is larger than sizeMax, with optional overlaps.
computeUnsignedIntHistogram(WritableRaster, long[], WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools: Compute the full histogram for a raster containing 8-bit or 16-bit unsigned integer values.
computeUnsignedIntHistogram(WritableRaster, long[], WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools: Compute the full histogram for a raster containing 8-bit or 16-bit unsigned integer values, optionally restricted to a bounding rectangle.
concatChannels(Collection<ImageServer<BufferedImage>>) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Concatenate a collection of additional servers along the 'channels' dimension (iteration order is used).
concatChannels(ImageServer<BufferedImage>...) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Concatenate additional servers along the 'channels' dimension.
config(String) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Path to config file (if required).
config(URI) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Path to config file (if required).
confirmation() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Create an confirmation alert dialog.
constrainCellByNucleusDistance(PathCellObject, double, boolean) - Static method in class qupath.lib.objects.CellTools: Constrain a cell boundary to fall within a maximum region, determined by buffering the convex hull of the nucleus ROI by a fixed distance.
constrainCellByScaledNucleus(PathCellObject, double, boolean) - Static method in class qupath.lib.objects.CellTools: Constrain a cell boundary to fall within a maximum region, determined by scaling the nucleus ROI by a fixed scale factor about its centroid.
constrainCellOverlaps(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.CellTools: Adjust cell boundary ROIs to be non-overlapping, by assigning overlaps to the cell with the closest nucleus.
constrainToBounds(Geometry, double, double, double, double) - Static method in class qupath.lib.roi.GeometryTools: Compute the intersection of a Geometry and a specified bounding box.
consumeOutput() - Static method in interface qupath.lib.experimental.pixels.OutputHandler: Create a basic do-nothing output handler that consumes the output with no changes.
contains(double, double) - Method in class qupath.lib.roi.AreaROI
contains(double, double) - Method in class qupath.lib.roi.EllipseROI
contains(double, double) - Method in class qupath.lib.roi.GeometryROI
contains(double, double) - Method in interface qupath.lib.roi.interfaces.ROI: Test is the ROI contains specified x, y coordinates.
contains(double, double) - Method in class qupath.lib.roi.LineROI
contains(double, double) - Method in class qupath.lib.roi.PointsROI
contains(double, double) - Method in class qupath.lib.roi.PolygonROI
contains(double, double) - Method in class qupath.lib.roi.PolylineROI
contains(double, double) - Method in class qupath.lib.roi.RectangleROI
contains(int, int, int, int) - Method in class qupath.lib.regions.ImageRegion: Check if this region contains a specified coordinate.
contains(String) - Method in interface qupath.lib.projects.ResourceManager.Manager: Returns true if the manager knows a resource with the specified name exists.
containsCentroid(ROI, PathObject) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils: Check whether a child object's centroid is contained within a ROI.
containsClassification(String...) - Static method in class qupath.lib.objects.PathObjectPredicates: Predicate that returns true if any component of its classification has any of the specified names.
containsImageJRois(File) - Static method in class qupath.imagej.tools.IJTools: Check whether a file is likely to contain an ImageJ ROI, based upon its extension or .zip file contents.
containsKey(Object) - Method in class qupath.lib.plugins.parameters.ParameterList: Returns true if a parameter exists in this list with a specified key.
containsKey(String) - Method in interface qupath.lib.measurements.MeasurementList: Returns true if this list contains a measurement with the specified name.
containsMetadata(String) - Method in interface qupath.lib.projects.ProjectImageEntry: Check if a metadata value is present for a specified key.
containsName(PathClass, String) - Static method in class qupath.lib.objects.classes.PathClassTools: Query whether a PathClass or any of its ancestor classes contains a specified name.
containsNamedMeasurement(String) - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
since v0.4.0; replaced by MeasurementList.containsKey(String)
containsObject(PathObject) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
containsObject(PathObject) - Method in interface qupath.lib.objects.PathObjectConnectionGroup: Returns true if the specified PathObject is contained within this group.
containsObject(PathObject) - Method in class qupath.opencv.features.DelaunayTriangulation
containsObject(PathObject, PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Deprecated.
containsROI(ROI, ROI) - Static method in class qupath.lib.objects.PathObjectTools: Deprecated.
content(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify a Node to display within the dialog.
contentText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the dialog content text.
ContextHelpViewer - Class in qupath.lib.gui.commands: Help window providing context-dependent help.
ContourTracing - Class in qupath.lib.analysis.images: Class to convert labelled images to Geometry objects, ROIs and PathObjects.
ContourTracing() - Constructor for class qupath.lib.analysis.images.ContourTracing
ContourTracing.ChannelThreshold - Class in qupath.lib.analysis.images: Helper class defining global thresholds to apply to a single image channel.
CONTRAST - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ConvertCommand - Class in qupath.lib.images.writers.ome: Allows command line option to convert an input image to OME-TIFF
ConvertCommand() - Constructor for class qupath.lib.images.writers.ome.ConvertCommand
convertDetectionsToPoints(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands: Convert detection objects to point annotations based upon their ROI centroids.
convertLabelsToCells(ImageProcessor, ImageProcessor, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Convert integer labeled images into cell objects.
convertLabelsToCells(ImageProcessor, ImageProcessor, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Convert integer labeled images into cell objects.
convertPixelsToOpticalDensities(float[], double, boolean) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: For originally-8-bit images, optical densities can usually be computed faster by preallocating a LUT with the 0-255 required values.
convertToAnnotation(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Create an annotation object for a specific ImageJ Roi, using an ImagePlus to help set properties.
convertToAnnotation(Roi, double, ImagePlus) - Static method in class qupath.imagej.tools.IJTools: Create an annotation object for a specific ImageJ Roi.
convertToAnnotation(ImagePlus, ImageServer<?>, Roi, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Deprecated.
use instead IJTools.convertToAnnotation(Roi, double, double, double, ImagePlane)
convertToBufferedImage(ImagePlus, int, int, ColorModel) - Static method in class qupath.imagej.images.servers.ImageJServer: Convert an ImagePlus to a BufferedImage, for a specific z-slice and timepoint.
convertToDetection(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Create a detection object for a specific ImageJ Roi, using an ImagePlus to help set properties.
convertToDetection(Roi, double, ImagePlus) - Static method in class qupath.imagej.tools.IJTools: Create a detection object for a specific ImageJ Roi.
convertToDetection(ImagePlus, ImageServer<?>, Roi, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Deprecated.
use instead IJTools.convertToDetection(Roi, double, double, double, ImagePlane)
convertToFloatProcessor(SimpleImage) - Static method in class qupath.imagej.tools.IJTools: Convert a SimpleImage to an ImageProcessor.
convertToIJRoi(ROI, double, double, double) - Static method in class qupath.imagej.tools.IJTools: Convert a QuPath ROI to an ImageJ Roi.
convertToIJRoi(ROI, Calibration, double) - Static method in class qupath.imagej.tools.IJTools: Convert a QuPath ROI to an ImageJ Roi for an image with the specified calibration.
convertToIJRoi(ROI, T) - Static method in class qupath.imagej.tools.IJTools: Create an ImageJ Roi from a ROI, suitable for displaying on the ImagePlus of an PathImage<ImagePlus>.
convertToImagePlus(String, ImageServer<BufferedImage>, BufferedImage, RegionRequest) - Static method in class qupath.imagej.tools.IJTools: Convert a BufferedImage into a PathImage<ImagePlus>.
convertToImagePlus(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.imagej.tools.IJTools: Read a region from an ImageServer<BufferedImage as a PathImage<ImagePlus>.
convertToImageProcessor(BufferedImage, int) - Static method in class qupath.imagej.tools.IJTools: Extract pixels as an an ImageProcessor from a single band of a BufferedImage.
convertToJson(Map<String, ?>) - Static method in class qupath.lib.plugins.parameters.ParameterList: Convert a Map to a one-line JSON representation, omitting hidden parameters.
convertToJson(ParameterList) - Static method in class qupath.lib.plugins.parameters.ParameterList: Convert a ParameterList a one-line JSON representation, omitting hidden parameters.
convertToObjects(Parameters<S, T>, U) - Method in interface qupath.lib.experimental.pixels.OutputHandler.OutputToObjectConverter: Convert the output of a pixel processor to a list of PathObjects.
convertToOpticalDensitySum(ColorProcessor, double, double, double) - Static method in class qupath.imagej.tools.IJTools: Calculate optical density values for the red, green and blue channels, then add these all together.
convertToPathObject(Roi, double, double, double, Function<ROI, PathObject>, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Create a PathObject for a specific ImageJ Roi.
convertToPathObject(Roi, double, Function<ROI, PathObject>, ImagePlus) - Static method in class qupath.imagej.tools.IJTools: Create a PathObject for a specific ImageJ Roi, using an ImagePlus to help set properties.
convertToPathObject(ImagePlus, ImageServer<?>, Roi, double, Function<ROI, PathObject>, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Deprecated.
use instead IJTools.convertToPathObject(Roi, double, double, double, Function, ImagePlane)
convertToPercentages(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Request that pie chart values are converted to percentages for tooltips.
convertToPoints(Collection<PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Convert a collection of PathObjects to Point annotations, based on ROI centroids.
convertToPoints(PathObjectHierarchy, Collection<PathObject>, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Convert a collection of PathObjects to Point annotations, based on ROI centroids, and add the points to the hierarchy.
convertToPolygonROI(PolygonRoi, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Convert an ImageJ PolygonRoi to a QuPath PolygonROI.
convertToROI(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Create a ROI from an ImageJ Roi.
convertToROI(Roi, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools: Create a ROI from an ImageJ Roi, using the Calibration object of an ImagePlus.
convertToROI(Roi, T) - Static method in class qupath.imagej.tools.IJTools: Create a ROI from an ImageJ Roi.
convertToUncalibratedImagePlus(String, BufferedImage) - Static method in class qupath.imagej.tools.IJTools: Convert a BufferedImage to an ImagePlus, without pixel size information or other calibration.
convertTransform(AffineTransform) - Static method in class qupath.lib.roi.GeometryTools: Convert an AffineTransform to an AffineTransformation.
convertTransform(AffineTransformation) - Static method in class qupath.lib.roi.GeometryTools: Convert an AffineTransformation to an AffineTransform.
CONVEX_HULL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
CONVEX_POINTS - Variable in class qupath.lib.gui.actions.CommonActions
ConvexHull - Class in qupath.lib.roi: Helper method for calculating the convex hull from a list of points.
ConvexHull() - Constructor for class qupath.lib.roi.ConvexHull
CoocurranceMatrices - Class in qupath.lib.analysis.features: Data structure to hold cooccurrence matrices for computation of Haralick features.
CoocurranceMatrices(int) - Constructor for class qupath.lib.analysis.features.CoocurranceMatrices: Initialize coocurrence matrices.
coordinateExtractor(Function<PathObject, Collection<Coordinate>>) - Method in class qupath.lib.analysis.DelaunayTools.Builder: Specify a default method of extracting coordinates for triangulation from an object, rather than centroids or the ROI boundary.
copy() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
copy() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request copy the current selection.
copy() - Method in class qupath.lib.gui.scripting.TextAreaControl
COPY_ANNOTATION_OBJECTS - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
COPY_FULL_SCREENSHOT - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
COPY_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
COPY_VIEW - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
COPY_WINDOW - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
COPY_WINDOW_SCREENSHOT - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
copyAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
copyActions - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
CopyActions() - Constructor for class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
copyAnnotationsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Attempt to annotation objects to the system clipboard, if available
copySelectedAnnotationsToCurrentPlane(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands: Copy the selected objects and add them to the plane currently active in the viewer.
copySelectedAnnotationsToPlane(int, int) - Static method in class qupath.lib.scripting.QP: Copy the selected annotations in the current hierarchy to the specified z-slice and timepoint.
copySelectedAnnotationsToPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP: Copy the selected annotations in the specified hierarchy to the specified image plane.
copySelectedAnnotationsToPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP: Copy the selected annotations in the current hierarchy to the specified image plane.
copySelectedObjectsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Attempt to copy selected objects to the system clipboard, if available
copySelectedObjectsToPlane(int, int) - Static method in class qupath.lib.scripting.QP: Copy the selected objects in the current hierarchy to the specified z-slice and timepoint.
copySelectedObjectsToPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP: Copy the selected objects in the specified hierarchy to the specified image plane.
copySelectedObjectsToPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP: Copy the selected objects in the current hierarchy to the specified image plane.
copyTableContentsToClipboard(PathTableData<?>, Collection<String>) - Static method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand: Get a single String representing the data in a table and copy it to the clipboard.
copyToClipboard(Object) - Static method in class qupath.lib.gui.scripting.QPEx: Try to copy an object to the clipboard.
Core() - Constructor for class qupath.opencv.ops.ImageOps.Core
countDescendants(PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Count the descendants of a PathObject recursively.
CountingDialogCommand - Class in qupath.lib.gui.commands: Command to open up a counting panel to aid with creating Point annotations.
CountingDialogCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.CountingDialogCommand: Constructor.
countMissing() - Method in class qupath.lib.io.UriUpdater: Get a count of the items flagged as missing.
countObjectsWithClass(Collection<? extends PathObject>, PathClass, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Count the number of PathObjects in a collection with a specified class or base class.
countProperty() - Method in class qupath.lib.gui.actions.InfoMessage: Read only property containing any count associated with the text (may be null).
countReplacements() - Method in class qupath.lib.io.UriUpdater: Get a count of the number of replacements for missing items.
countsTransformProperty() - Method in class qupath.lib.gui.charts.HistogramChart: Property to control how counts should be transformed before being shown in the histogram
cpu() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Request CPU backend and target, if available.
create() - Static method in class qupath.lib.gui.SharedThreadPoolManager: Create a new instance
create() - Static method in class qupath.lib.gui.ToolManager: Create a new instance
create(boolean) - Static method in class qupath.lib.gui.tools.WebViews: Create a new WebView.
create(int) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Create a simple channel threshold.
create(int, double, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Create a threshold to select values between a minimum and maximum (inclusive).
create(Gson, TypeToken<R>) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory
create(Gson, TypeToken<T>) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ObjectClassifierTypeAdapterFactory
create(Gson, TypeToken<T>) - Method in class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdaptorFactory
create(String, double, boolean, List<ChannelSettings>) - Static method in class qupath.lib.display.settings.ImageDisplaySettings: Create a new image display settings object.
create(String, float, float, ChannelColor, boolean) - Static method in class qupath.lib.display.settings.ChannelSettings: Create a new channel settings object.
create(String, String, String) - Static method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo: Create a new GitHubProject.
create(String, Version, URI) - Static method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion: Create a new UpdateChecker.ReleaseVersion.
create(Collection<? extends ImageServer<BufferedImage>>) - Static method in class qupath.lib.gui.panes.ServerSelector
create(Collection<T>) - Static method in class qupath.lib.io.UriUpdater: Create a new UriUpdater to support updating URIs for one or more UriResource objects.
create(Collection<T>, Collection<UriUpdater.SingleUriItem>, Map<UriUpdater.SingleUriItem, UriUpdater.SingleUriItem>) - Static method in class qupath.lib.io.UriUpdater: Create a new UriUpdater using the specified collections.
create(List<TMACoreObject>, int) - Static method in class qupath.lib.objects.hierarchy.DefaultTMAGrid: Create a new TMAGrid based on a list of cores and grid width.
create(QuPathGUI) - Static method in class qupath.lib.gui.viewer.ViewerManager: Create a new instance
create(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Create an overlay to display a live image that can be created from an existing ImageData.
create(OverlayOptions, Map<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Create an overlay to display a live image that can be created from an existing ImageData.
create(OverlayOptions, PixelClassifier) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Create an overlay to display the live application of a PixelClassifier to an image, using the default number of parallel threads for classification.
create(OverlayOptions, PixelClassifier, int) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Create an overlay to display the live application of a PixelClassifier to an image.
create(ImageData<BufferedImage>) - Static method in class qupath.lib.display.ImageDisplay: Create a new image display, and set the specified image data.
create(OpenCVClassifiers.OpenCVStatModel, PathObjectFilter, FeatureExtractor<T>, List<PathClass>) - Static method in class qupath.opencv.ml.objects.OpenCVMLClassifier: Create a new ObjectClassifier that uses an OpenCVClassifiers.OpenCVStatModel for classification.
create(T) - Static method in class qupath.lib.io.UriUpdater: Create a new UriUpdater to support updating URIs for a single UriResource.
CREATE_MANUAL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
CREATE_TILES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
createAbove(int, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Create a threshold to select values greater than or equal to a specified threshold.
createAction(Runnable) - Static method in class qupath.lib.gui.actions.ActionTools: Create an action whose event handler calls a runnable.
createAction(Runnable, String) - Static method in class qupath.lib.gui.actions.ActionTools: Create an action whose event handler calls a runnable, with a specified name.
createAllFullImageAnnotations(boolean) - Static method in class qupath.lib.scripting.QP: Create annotation around the full image for the current image, on all z-slices and timepoints.
createAllFullImageAnnotations(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP: Create annotation around the full image for the specified image, on all z-slices and timepoints.
createAllMenuActions(QuPathGUI) - Static method in class qupath.lib.gui.actions.menus.Menus: Create a collection of all the actions that should be installed in QuPath's main menubar.
createAllRequests(ImageServer<?>, double) - Static method in class qupath.lib.regions.RegionRequest: Create requests for the full width and height of an ImageServer, for all planes (z-slices and time points).
createAnnotationConverter() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.
createAnnotationConverter() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.
createAnnotationConverter(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into annotation objects.
createAnnotationObject(ROI) - Static method in class qupath.lib.objects.PathObjects: Create an unclassified annotation object.
createAnnotationObject(ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects: Create a classified annotation object.
createAnnotationObject(ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects: Create a classified annotation object with a specified measurement list.
createAnnotationOutputHandler() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create an OutputHandler that attempts to convert the output into annotation objects.
createAnnotationOutputHandler() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler that attempts to convert the output into annotation objects.
createAnnotationOutputHandler(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler that attempts to convert the output into annotation objects.
createAnnotations(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Create annotation objects by tracing contours in a labelled image.
createAnnotations(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Create annotation objects from a labelled image.
createAnnotations(ROI) - Method in class qupath.lib.objects.utils.Tiler: Create a list of PathAnnotationObject tiles from the input.
createAnnotationsFromDensityMap(String, Map<Integer, ? extends Number>, String, String...) - Static method in class qupath.lib.scripting.QP: Create annotations from a density map for the current image.
createAnnotationsFromDensityMap(ImageData<BufferedImage>, String, Map<Integer, ? extends Number>, String, String...) - Static method in class qupath.lib.scripting.QP: Create annotations from a density map for the specified image.
createAnnotationsFromDensityMap(ImageData<BufferedImage>, DensityMaps.DensityMapBuilder, Map<Integer, ? extends Number>, String, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.lib.scripting.QP: Create annotations from a density map for the specified image.
createAnnotationsFromPixelClassifier(String, double, double, String...) - Static method in class qupath.lib.scripting.QP: Create annotation objects based upon the output of a pixel classifier, applied to selected objects.
createAnnotationsFromPixelClassifier(PixelClassifier, double, double, String...) - Static method in class qupath.lib.scripting.QP: Create annotation objects based upon the output of a pixel classifier, applied to selected objects.
createAnnotationsFromPixelClassifier(ImageData<BufferedImage>, PixelClassifier, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create annotation objects based upon the output of a pixel classifier, applied to selected objects.
createAnnotationsFromPixelClassifier(PathObjectHierarchy, ImageServer<BufferedImage>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create annotation objects based upon an ImageServer that provides classification or probability output, applied to selected objects.
createAnnotationsFromSubdivision(DelaunayTools.Subdivision, ROI) - Static method in class qupath.lib.analysis.DelaunayTools: Create annotations surrounding objects within a specified subdivision based on Voronoi faces.
createAnnotationView(QuPathGUI) - Static method in class qupath.lib.gui.commands.PathObjectGridView: Create a grid view for annotations.
createAreaROI(Shape, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create an area ROI representing a 2D shape.
createArrowEndEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createArrowStartEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createBand(String, int, double, double) - Static method in class qupath.lib.analysis.heatmaps.ColorModels: Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBand(String, int, double, double) - Static method in class qupath.lib.color.ColorModels: Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBand(String, int, double, double, double) - Static method in class qupath.lib.analysis.heatmaps.ColorModels: Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBand(String, int, double, double, double) - Static method in class qupath.lib.color.ColorModels: Create a ColorModels.DisplayBand to define the colormap associated with an image band (channel).
createBelow(int, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Create a threshold to select values less than or equal to a specified threshold.
createBinaryMask(Mat, DoublePredicate) - Static method in class qupath.opencv.tools.OpenCVTools: Create a binary mask (0, 255 values) by applying a predicate to pixel values.
createBrushEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createBufferedImageMaskSupplier() - Static method in interface qupath.lib.experimental.pixels.MaskSupplier: Create a image supplier that returns a buffered image.
createBufferedImageSupplier() - Static method in interface qupath.lib.experimental.pixels.ImageSupplier: Create a image supplier that returns a buffered image.
createButton(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Create a button from an action, showing both the text and graphic if available.
createButtonPane(QuPathGUI, ObjectExpression<ImageData<BufferedImage>>, ObjectExpression<DensityMaps.DensityMapBuilder>, StringExpression, ObjectExpression<PixelClassificationOverlay>, boolean) - Static method in class qupath.process.gui.commands.density.DensityMapUI: Create a pane containing standardized buttons associated with processing a density map (find hotspots, threshold, export map).
createButtonWithGraphicOnly(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Create a button from an action, showing only the graphic and not any text.
createCellObject(ROI, ROI) - Static method in class qupath.lib.objects.PathObjects: Create a cell object.
createCellObject(ROI, ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects: Create a cell object with an optional classification.
createCellObject(ROI, ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects: Create a cell object with an optional classification and measurements list.
createCells(Raster, int, int, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Create cell objects from two bands of a raster representing a labelled image.
createCells(Mat, Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Create cell objects by tracing contours in a labelled image.
createCells(SimpleImage, SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Create cell objects from a pair of labelled images.
createChannelClassifier(PathObjectFilter, ImageChannel, String, double) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers: Create a classifier that thresholds a single measurement, assigning a class based on an ImageChannel if the value is ≥ threshold.
createChannelExtractor(int) - Static method in class qupath.lib.images.servers.ColorTransforms: Create ColorTransform to extract a channel based on its number (0-based index, although result of ColorTransforms.ColorTransform.getName() is 1-based).
createChannelExtractor(String) - Static method in class qupath.lib.images.servers.ColorTransforms: Create ColorTransform to extract a channel based on its name.
CreateChannelTrainingImagesCommand - Class in qupath.process.gui.commands: Command to create training images based upon channel names, and add these to a project.
CreateChannelTrainingImagesCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.CreateChannelTrainingImagesCommand: Constructor.
createCheckBox(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Create a checkbox from an action.
createCheckMenuItem(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Create a menu item from an action that makes use of a selected property.
createCheckMenuItem(Action, ToggleGroup) - Static method in class qupath.lib.gui.actions.ActionTools: Create a menu item from an action that makes use of a selected property.
createClassificationMap(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Create a mapping between PathObjects and their current PathClasses.
createClassifier(OpenCVClassifiers.OpenCVStatModel, ImageDataOp, PixelClassifierMetadata, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Create a PixelClassifier based on an OpenCV StatModel and feature calculator.
createClassifier(ImageDataOp, PixelClassifierMetadata) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Convert an ImageDataOp into a simple classifier.
createClassifier(ImageDataOp, PixelCalibration, Map<Integer, PathClass>) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Convert an ImageDataOp into a simple classifier by adding an interpretation to the output labels.
createColorDeconvolvedChannel(ColorDeconvolutionStains, int) - Static method in class qupath.lib.images.servers.ColorTransforms: Create a ColorTransform that applies color deconvolution.
createColorMap(String, double[], double[], double[]) - Static method in class qupath.lib.color.ColorMaps: Create a colormap using floating point values for red, green and blue.
createColorMap(String, int[], int[], int[]) - Static method in class qupath.lib.color.ColorMaps: Create a colormap using integer values for red, green and blue.
createColorMap(String, int, int, int) - Static method in class qupath.lib.color.ColorMaps: Create a colormap using int values for red, green and blue corresponding to the maximum value; the minimum color will be black.
createColorModel(PixelType, int, boolean, int...) - Static method in class qupath.lib.color.ColorModelFactory: Create a new ColorModel that can be used to display an image where pixels per channel reflect probabilities, either as float or byte.
createColorModel(PixelType, List<ImageChannel>) - Static method in class qupath.lib.color.ColorModelFactory: Create a ColorModel for displaying an image with the specified channel colors.
createColorModel(PixelType, ColorMaps.ColorMap, int) - Static method in class qupath.lib.color.ColorModelFactory: Create a color model from a ColorMaps.ColorMap.
createColorModel(PixelType, ColorMaps.ColorMap, int, double, double, int, DoubleToIntFunction) - Static method in class qupath.lib.color.ColorModelFactory: Create a color model from a ColorMaps.ColorMap, scaled within a defined range and with an optional additional alpha channel used to determine opacity.
createColorModelBuilder(ColorModels.DisplayBand, ColorModels.DisplayBand) - Static method in class qupath.lib.analysis.heatmaps.ColorModels: Create a ColorModels.ColorModelBuilder with a main channel and an optional alpha channel.
createColorModelBuilder(ColorModels.DisplayBand, ColorModels.DisplayBand) - Static method in class qupath.lib.color.ColorModels: Create a ColorModels.ColorModelBuilder with a main channel and an optional alpha channel.
createColorTransformServer(ImageServer<BufferedImage>, List<ChannelDisplayInfo>) - Static method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer: Create an ImageServer for which the channels are created dynamically from a list of ChannelDisplayInfos.
createColumnGrid(int) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Create a GridPane containing columns that resize similarly to Swing's GridLayout().
createColumnGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Create a GridPane containing columns that resize similarly to Swing's GridLayout().
createColumnGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Create a GridPane containing columns that resize similarly to Swing's GridLayout(), where controls have their widths bound to their parent.
createCommandFinderDialog(QuPathGUI) - Static method in class qupath.lib.gui.tools.CommandFinderTools: Create a dialog showing a filtered list of menu commands, for fast selection.
createCommandFinderPane(QuPathGUI, Node, ObjectProperty<CommandFinderTools.CommandBarDisplay>) - Static method in class qupath.lib.gui.tools.CommandFinderTools: Create a component that contains a TextField for entering menu commands to run quickly.
createCompositeClassifier(Collection<ObjectClassifier<T>>) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers: Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers.
createCompositeClassifier(ObjectClassifier<T>...) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers: Create a composite ObjectClassifier, which sequentially applies multiple (usually single-class) classifiers.
CreateCompositeClassifierCommand - Class in qupath.process.gui.commands: Command to create a composite classifier by merging together two or more other classifiers.
CreateCompositeClassifierCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.CreateCompositeClassifierCommand: Constructor.
createContext(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Create a ScriptContext containing information from the ScriptParameters.
createCoordinateCache(Collection<Coordinate>) - Static method in class qupath.lib.analysis.DistanceTools: Create an STRtree to enable nearest neighbor searching for a collection of coordinates.
createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.RenderedImageServer
createDefaultRGBImage(int, int) - Method in class qupath.lib.images.servers.AbstractTileableImageServer: Create the default (blank) RGB image for this server.
createDefaultRGBImage(int, int) - Method in class qupath.lib.images.servers.LabeledImageServer
createDetectionConverter() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.
createDetectionConverter() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.
createDetectionConverter(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler.OutputToObjectConverter that attempts to convert the output into detection objects.
createDetectionObject(ROI) - Static method in class qupath.lib.objects.PathObjects: Create an unclassified detection object.
createDetectionObject(ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects: Create a classified detection object.
createDetectionObject(ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects: Create a classified detection object with a specified measurement list.
createDetectionOutputHandler() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create an OutputHandler that attempts to convert the output into detection objects.
createDetectionOutputHandler() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler that attempts to convert the output into detection objects.
createDetectionOutputHandler(Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler that attempts to convert the output into detection objects.
createDetections(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Create detection objects by tracing contours in a labelled image.
createDetections(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Create detection objects from a labelled image.
createDetectionsFromPixelClassifier(String, double, double, String...) - Static method in class qupath.lib.scripting.QP: Create detection objects based upon the output of a pixel classifier, applied to selected objects.
createDetectionsFromPixelClassifier(PixelClassifier, double, double, String...) - Static method in class qupath.lib.scripting.QP: Create detection objects based upon the output of a pixel classifier, applied to selected objects.
createDetectionsFromPixelClassifier(ImageData<BufferedImage>, PixelClassifier, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create detection objects based upon the output of a pixel classifier, applied to selected objects.
createDetectionsFromPixelClassifier(PathObjectHierarchy, ImageServer<BufferedImage>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create detection objects based upon an ImageServer that provides classification or probability output, applied to selected objects.
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.PositiveCellDetection: Wrap the detector to apply any required classification.
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.CellCountsCV
createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.WatershedNucleiCV
createDetector(ImageData<T>, ParameterList) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin: Create a new ObjectDetector, compatible with the specified ImageData and ParameterList.
createDisk(int, boolean) - Static method in class qupath.opencv.tools.OpenCVTools: Create a disk filter.
createDocument() - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Create a String representation of the SVG document.
createDoubleArrowEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createEllipseEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createEllipseROI(double, double, double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create an ellipse ROI defined by its bounding box.
createEmptyMeasurementList() - Method in class qupath.lib.objects.PathDetectionObject: Default to a simple, float measurement list.
createEmptyMeasurementList() - Method in class qupath.lib.objects.PathObject: Create a new MeasurementList of the preferred type for this object.
createEmptyROI() - Static method in class qupath.lib.roi.ROIs: Create an 'empty' ROI with no length or area.
createExactly(int, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Create a threshold to select values that are exactly equal to a specified threshold.
createExtendedTool(PathTool...) - Static method in class qupath.lib.gui.viewer.tools.PathTools
createFeatureDisplayOverlay(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Deprecated.
Use PixelClassificationOverlay.create(OverlayOptions, Function, ImageRenderer) instead.
createFloatImage(float[], int, int) - Static method in class qupath.lib.analysis.images.SimpleImages: Create a SimpleImage backed by an existing float array of pixels.
createFloatImage(int, int) - Static method in class qupath.lib.analysis.images.SimpleImages: Create a SimpleImage backed by a float array of pixels.
createFormatter(int) - Static method in class qupath.lib.common.GeneralTools: Create a new DecimalFormat that may be used to convert a number to have a maximum of nDecimalPlaces (trailing zeros are not shown).
createForObservableViewer(ObservableValue<? extends QuPathViewer>) - Static method in class qupath.lib.gui.UndoRedoManager
createFromBuilders(Collection<? extends ImageServerBuilder.ServerBuilder<BufferedImage>>) - Static method in class qupath.lib.gui.panes.ServerSelector
createFromCentroids(Collection<PathObject>, boolean) - Static method in class qupath.lib.analysis.DelaunayTools: Create a DelaunayTools.Subdivision using the centroid coordinates of ROIs.
createFromGeometryCoordinates(Collection<PathObject>, boolean, double) - Static method in class qupath.lib.analysis.DelaunayTools: Create a DelaunayTools.Subdivision using the boundary coordinates of ROIs.
createFullImageAnnotation(boolean) - Static method in class qupath.lib.scripting.QP: Create an annotation around the full image for the current image, on the default (first) z-slice and timepoint.
createFullImageAnnotation(boolean, int, int) - Static method in class qupath.lib.scripting.QP: Create an annotation around the full image for the current image, on the specified z-slice and timepoint.
createFullImageAnnotation(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands: Create a full image annotation for the image in the specified viewer.
createFullImageAnnotation(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP: Create an annotation around the full image for the specified image, on the default (first) z-slice and timepoint.
createFullImageAnnotation(ImageData<?>, boolean, int, int) - Static method in class qupath.lib.scripting.QP: Create an annotation around the full image for the specified image, on the specified z-slice and timepoint.
createGammaFunction(double, double, double) - Static method in class qupath.lib.color.ColorModelFactory: Create a gamma function between a given range, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createGammaFunction(double, PixelType) - Static method in class qupath.lib.color.ColorModelFactory: Create a gamma function for a specific pixel type, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createGeometries(Geometry) - Method in class qupath.lib.objects.utils.Tiler: Create a list of Geometry tiles from the input.
createGridView(QuPathGUI, Function<PathObjectHierarchy, Collection<? extends PathObject>>) - Static method in class qupath.lib.gui.commands.PathObjectGridView: Create a grid view for a custom object extractor.
createHeadlessTaskRunner() - Method in class qupath.lib.plugins.TaskRunnerUtils: Create a new headless TaskRunner instance, using the default number of threads from ThreadTools.getParallelism().
createHeadlessTaskRunner(int) - Method in class qupath.lib.plugins.TaskRunnerUtils: Create a new headless TaskRunner instance with the specified number of threads.
createHiddenInstance() - Static method in class qupath.lib.gui.QuPathGUI: Create a new QuPath instance that is not visible (i.e.
createHistogramData(Histogram, Integer) - Static method in class qupath.lib.gui.charts.HistogramChart: Create a HistogramData object to wrap a histogram & some info about its display.
createHistogramData(Histogram, Color) - Static method in class qupath.lib.gui.charts.HistogramChart: Create a HistogramData object to wrap a histogram & some info about its display.
createIconImage(IconFactory.PathIcons, int) - Static method in class qupath.lib.gui.tools.IconFactory: Create an image from a default icon glyph.
createID() - Method in class qupath.imagej.images.servers.ImageJServer
createID() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Returns a random UUID.
createID() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
createID() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer: Returns a UUID.
createID() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
createID() - Method in class qupath.lib.images.servers.AbstractImageServer: Create a unique ID for the server, which can be returned as the default value of AbstractImageServer.getPath().
createID() - Method in class qupath.lib.images.servers.AffineTransformImageServer
createID() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
createID() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer: Returns a UUID.
createID() - Method in class qupath.lib.images.servers.CroppedImageServer
createID() - Method in class qupath.lib.images.servers.LabeledImageServer: Returns a UUID.
createID() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
createID() - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
createID() - Method in class qupath.lib.images.servers.RotatedImageServer
createID() - Method in class qupath.lib.images.servers.SparseImageServer: Returns a UUID.
createID() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer: Returns a UUID.
createImageChoicePane(QuPathGUI, List<ProjectImageEntry<BufferedImage>>, List<ProjectImageEntry<BufferedImage>>, String) - Static method in class qupath.lib.gui.dialogs.ProjectDialogs: Populates a given ListSelectionView with all the project entries.
createImageDataAction(Consumer<ImageData<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI: Create an Action that depends upon an ImageData.
createImageDataAction(Consumer<ImageData<BufferedImage>>, String) - Method in class qupath.lib.gui.QuPathGUI: Create an Action that depends upon an ImageData.
createImagePlusImageSupplier() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create an ImageSupplier that returns an ImageJ ImagePlus.
createImagePlusMaskSupplier() - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create a MaskSupplier that returns an ImageJ ByteProcessor.
createImageRegionPredicate(ImageRegion) - Static method in class qupath.lib.objects.PathObjectTools: Create a predicate that only accepts PathObjects if they have ROIs that fall within a specified ImageRegion.
createImageRegionStore() - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreFactory: Create an ImageRegionStore using a default tile cache size, based upon the available memory and user preferences.
createImageRegionStore(long) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreFactory: Create an ImageRegionStore with a specified tile cache size, in bytes.
createImageStack(ImageProcessor...) - Static method in class qupath.imagej.tools.IJTools: Create an ImageStack containing the specified ImageProcessors.
createIndexColorModel(int, int, int, boolean) - Static method in class qupath.lib.color.ColorToolsAwt: Get an IndexColorModel representing a linear LUT based on a RGB color.
createIndexedColorModel(Map<Integer, Integer>, boolean) - Static method in class qupath.lib.color.ColorModelFactory: Create an indexed colormap for a labelled (indexed color) image.
createIndexedColorModel8bit(ColorMaps.ColorMap) - Static method in class qupath.lib.color.ColorModelFactory: Create an 8-bit IndexColorModel from a ColorMaps.ColorMap.
createIndexedColorModel8bit(ColorMaps.ColorMap, int) - Static method in class qupath.lib.color.ColorModelFactory: Create an 8-bit IndexColorModel from a ColorMaps.ColorMap, allowing for a transparent pixel to be set (e.g.
createInstance() - Static method in class qupath.lib.gui.ExtensionControlPane: Create an instance of the ExtensionControlPane UI pane.
createInstance() - Static method in class qupath.lib.roi.RoiEditor: Create a new RoiEditor.
createInstance(int, int, int, int, int, int) - Static method in class qupath.lib.regions.ImageRegion: Create a region based on its bounding box coordinates, z-slice index and time point index.
createInstance(Class<? extends ImageServerBuilder<T>>, float, Collection<ImageServerBuilder.ServerBuilder<T>>) - Static method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport: Create a ImageServerBuilder.UriImageSupport for (possibly multiple) images that can be read from a single URI.
createInstance(Class<? extends ImageServerBuilder<T>>, float, ImageServerBuilder.ServerBuilder<T>) - Static method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport: Create a ImageServerBuilder.UriImageSupport for a single image that can be read from a single URI.
createInstance(Class<? extends ImageServerBuilder<T>>, URI, String...) - Static method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder: Create a ImageServerBuilder.ServerBuilder that reads an image from a URI and args, using the default server metadata.
createInstance(Class<? extends ImageServerBuilder<T>>, ImageServerMetadata, URI, String...) - Static method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder: Create a ImageServerBuilder.ServerBuilder that reads an image from a URI and args, and uses the specified metadata (possibly replacing the default metadata).
createInstance(String, double, int, int, int, int) - Static method in class qupath.lib.regions.RegionRequest: Create a request for a region specified in terms of its bounding box, using the first z-slice and time point.
createInstance(String, double, int, int, int, int, int, int) - Static method in class qupath.lib.regions.RegionRequest: Create a request for a region specified in terms of its bounding box, z-slice and time point.
createInstance(String, double, int, int, int, int, ImagePlane) - Static method in class qupath.lib.regions.RegionRequest: Create a request for a region specified in terms of its bounding box and ImagePlane.
createInstance(String, double, Collection<? extends ROI>) - Static method in class qupath.lib.regions.RegionRequest: Create a request that contains the pixels of the specified ROIs.
createInstance(String, double, ImageRegion) - Static method in class qupath.lib.regions.RegionRequest: Create a request corresponding to a specified ImageRegion.
createInstance(String, double, ROI) - Static method in class qupath.lib.regions.RegionRequest: Create a request that contains the pixels of the specified ROI.
createInstance(String, int, double, ImageRegion) - Static method in class qupath.lib.images.servers.TileRequest: Create a new tile request for a specified region, downsample and resolution level.
createInstance(String, RegionRequest) - Static method in class qupath.lib.regions.RegionRequest: Create a request that matches another request but with a different path.
createInstance(Collection<? extends ROI>) - Static method in class qupath.lib.regions.ImageRegion: Create the smallest region that completely contains the specified ROIs.
createInstance(Stage) - Static method in class qupath.lib.gui.QuPathGUI: Static method to launch QuPath on the JavaFX Application thread.
createInstance(Stage, HostServices) - Static method in class qupath.lib.gui.QuPathGUI: Static method to launch QuPath from a JavaFX application.
createInstance(ImageServer<?>) - Static method in class qupath.lib.regions.RegionRequest: Create a request for the full width and height of an ImageServer, for the default plane (first z-slice, time point) and first resolution level downsample (usually 1, but not always).
createInstance(ImageServer<?>, double) - Static method in class qupath.lib.regions.RegionRequest: Create a request for the full width and height of an ImageServer, for the default plane (first z-slice, time point).
createInstance(ImageServer<?>, int, ImageRegion) - Static method in class qupath.lib.images.servers.TileRequest: Create a new tile request for a specified region and resolution level of an image.
createInstance(ROI) - Static method in class qupath.lib.regions.ImageRegion: Create the smallest region that completely contains a specified ROI.
createJavaCompletion(Class<?>) - Static method in class qupath.lib.scripting.languages.AutoCompletions: Create a new completion for a class.
createJavaCompletion(Class<?>, Field) - Static method in class qupath.lib.scripting.languages.AutoCompletions: Create a new completion for a field.
createJavaCompletion(Class<?>, Method) - Static method in class qupath.lib.scripting.languages.AutoCompletions: Create a new completion for a method.
createJavaCompletion(Class<?>, String, String) - Static method in class qupath.lib.scripting.languages.AutoCompletions: Create a new completion with fixed display and completion text.
createJsonTreeBrowser(String, Object) - Static method in class qupath.lib.gui.panes.ObjectTreeBrowser: Create a TreeTableView showing the names and values of fields within a JsonElement.
createLicensesWindow(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a window summarizing license information for QuPath and its third party dependencies.
createLike(PathObject, ROI) - Static method in class qupath.lib.objects.PathObjectTools: Create a new object with the same type and classification as the input object, but a new ROI and ID.
createLike(PathObject, ROI, ROI) - Static method in class qupath.lib.objects.PathObjectTools: Create a new object with the same type and classification as the input object, but a new ROI and ID.
createLinearFunction(double, double) - Static method in class qupath.lib.color.ColorModelFactory: Create a linear function between a given range, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createLinearFunction(PixelType) - Static method in class qupath.lib.color.ColorModelFactory: Create a linear function for a specific pixel type, which can be used to determine a suitable alpha value for an image that should have opacity based upon pixel values.
createLineEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createLineROI(double, double, double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a line ROI with start and end coordinates.
createLineROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a ROI representing a line with zero length.
createListCell() - Static method in class qupath.lib.gui.tools.PathObjectLabels: Create a ListCell for displaying a PathObject using the default PathObject.toString() method.
createListCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels: Create a ListCell for displaying a PathObject using a custom method to create a string representation of the object.
createListSelectionView() - Static method in class qupath.lib.gui.tools.GuiTools: Create a new ListSelectionView.
createLoadDensityMapCommand(QuPathGUI) - Static method in class qupath.process.gui.commands.ui.LoadResourceCommand: Create a Runnable to interactively load a density map and display it in all viewers.
createLoadPixelClassifierCommand(QuPathGUI) - Static method in class qupath.process.gui.commands.ui.LoadResourceCommand: Create a Runnable to interactively load a pixel classifier and display it in all viewers.
createLogFiles - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
createLogWriter(Logger, Level) - Static method in class qupath.lib.scripting.LoggingTools: Create a Writer that passes messages to the log at a specified level.
createManager(QuPathViewer) - Static method in class qupath.lib.gui.commands.MiniViewers: Create a MiniViewers.MiniViewerManager associated with a specified viewer.
createManager(QuPathViewer, Collection<? extends ChannelDisplayInfo>) - Static method in class qupath.lib.gui.commands.MiniViewers: Create a MiniViewers.MiniViewerManager displaying multiple channels and associated with a specified viewer.
createMask(Mat, DoublePredicate, double, double) - Static method in class qupath.opencv.tools.OpenCVTools: Create a mask by applying a predicate to pixel values.
createMaskAndSplitObjectOutputHandler(OutputHandler.OutputToObjectConverter<S, T, U>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler: Create an output handler that can be used to add objects to the parent object, applying the ROI mask and splitting objects with discontinuous ROIs.
createMatImageSupplier() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an ImageSupplier that returns an OpenCV Mat.
createMatMaskSupplier() - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create a MaskSupplier that returns an OpenCV Mat.
createMaximumChannelTransform() - Static method in class qupath.lib.images.servers.ColorTransforms: Create a ColorTransform that calculates the maximum of all channels.
createMeanChannelTransform() - Static method in class qupath.lib.images.servers.ColorTransforms: Create a ColorTransform that calculates the mean of all channels.
createMeasurement(String, double) - Static method in class qupath.lib.measurements.MeasurementFactory: Deprecated.

Create a measurement with a double value.
createMeasurement(String, float) - Static method in class qupath.lib.measurements.MeasurementFactory: Deprecated.

Create a measurement with a float value.
createMeasurementList(int, MeasurementList.MeasurementListType) - Static method in class qupath.lib.measurements.MeasurementListFactory: Create a measurement list.
createMeasurementListFeatureExtractor(List<String>) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors: Create a FeatureExtractor that determines features for the MeasurementList of the PathObject.
createMeasurementManager(ImageData<BufferedImage>, PixelClassifier) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create a PixelClassificationMeasurementManager that can be used to generate measurements from applying a pixel classifier to an image.
createMeasurementManager(ImageServer<BufferedImage>) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create a PixelClassificationMeasurementManager that can be used to generate measurements from an ImageServer where pixels provide classification or probability information.
createMeasurementMapDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a dialog for displaying measurement maps.
createMemoryMonitorDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a dialog to monitor memory usage.
createMenu(String, Object...) - Static method in class qupath.lib.gui.tools.MenuTools: Create a menu, optionally add new menu items with MenuTools.addMenuItems(List, Object...).
createMenuItem(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Create a menu item from an action.
createMinimumChannelTransform() - Static method in class qupath.lib.images.servers.ColorTransforms: Create a ColorTransform that calculates the minimum of all channels.
createMoreButton(ContextMenu, Side) - Static method in class qupath.lib.gui.tools.GuiTools: Create a Button with a standardized icon and tooltip text to indicate 'More', which triggers a ContextMenu when clicked.
createMoveEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createNewAnnotation(MouseEvent, double, double) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Create a new annotation and set it in the current viewer.
createNewAnnotation(MouseEvent, double, double) - Method in class qupath.process.gui.WandToolEventHandler: Create a new annotation and set it in the current viewer.
createNewChart() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
createNewChart() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
createNewChart() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
createNewChart(Axis<Number>, Axis<Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
createNewChart(Axis<String>, Axis<Number>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
createNode(int, int, IconFactory.PathIcons) - Static method in class qupath.lib.gui.tools.IconFactory: Create a node from a default icon glyph.
createNormalizer(double[], double[], double) - Static method in class qupath.opencv.ml.objects.features.Normalizer: Create a Normalizer with the specified parameters.
createNormalizer(Normalization, Mat, double) - Static method in class qupath.opencv.ml.objects.features.Preprocessing: Create a simple normalizer to rescale input data.
createNormalizingFeatureExtractor(FeatureExtractor<T>, Normalizer) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors: Wrap an existing FeatureExtractor to apply normalization prior to returning the values.
createNumberedObjectFunction(Function<ROI, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing: Create a (bi)function to generate an object from a ROI and a number, setting the name of the object to match the number.
createNumericMeasurement(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Deprecated.
createObjectAddedEvent(Object, PathObjectHierarchy, PathObject, PathObject) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Create a hierarchy event indicated objects were added.
createObjectConverter(Class<U>, Function<ROI, PathObject>) - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create an OutputHandler.OutputToObjectConverter for one specify type.
createObjectConverter(BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler.OutputToObjectConverter to convert Mat binary or labeled images to path objects, optionally using the label number.
createObjectConverter(Function<ROI, PathObject>) - Static method in class qupath.lib.experimental.pixels.ImageJProcessor: Create an OutputHandler.OutputToObjectConverter that attempts to convert a range of output types into objects.
createObjectConverter(Function<ROI, PathObject>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler.OutputToObjectConverter to convert Mat binary or labeled images to path objects.
createObjectConverter(Function<ROI, PathObject>, Map<? extends Number, String>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Create an OutputHandler.OutputToObjectConverter to convert Mat labeled images to path objects, optionally setting the classification.
createObjectDescriptionsDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a stage to display object descriptions.
createObjectFunction(Function<ROI, PathObject>, BiConsumer<PathObject, Number>) - Static method in class qupath.lib.analysis.images.ContourTracing: Create a (bi)function to generate an object from a ROI and a number.
createObjectInputStream(InputStream) - Static method in class qupath.lib.io.PathIO: Create a new ObjectInputStream, setting the default ObjectInputFilter for core QuPath-related and Java classes only.
createObjectOutputHandler(OutputHandler.OutputToObjectConverter<S, T, U>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler: Create an output handler that can be used to add objects to the parent object, applying the ROI mask.
createObjectRemovedEvent(Object, PathObjectHierarchy, PathObject, PathObject) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Create a hierarchy event indicating objects were removed.
createObjects(Raster, int, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing: Create objects from one band of a raster containing integer labels.
createObjects(Mat, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.opencv.tools.OpenCVTools: Create objects by tracing contours in a labelled image.
createObjects(SimpleImage, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing: Create objects from a labelled image.
createObjects(ROI, Function<ROI, PathObject>) - Method in class qupath.lib.objects.utils.Tiler: Create a list of PathObject tiles from the input.
createObjectsChangedEvent(Object, PathObjectHierarchy, PathObjectHierarchyEvent.HierarchyEventType, Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Create a hierarchy event indicating objects have changed in a way consistent with the specified event type.
createObjectsFromPixelClassifier(ImageServer<BufferedImage>, Map<Integer, PathClass>, ROI, Function<ROI, ? extends PathObject>, double, double, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create objects based upon an ImageServer that provides classification or probability output.
createObjectsFromPredictions(ImageServer<BufferedImage>, PathObjectHierarchy, Collection<PathObject>, Function<ROI, ? extends PathObject>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create objects from an image (usually created with a pixel classifier) where values represent classifications or predictions.
createObjectsFromROIs(ImagePlus, Collection<? extends Roi>, double, boolean, boolean, ImagePlane) - Static method in class qupathj.QuPath_Send_Overlay_to_QuPath: Turn an array of ImageJ ROIs into a list of QuPath PathObjects, optionally adding measurements as well.
createObjectTreeBrowser(String, Object) - Static method in class qupath.lib.gui.panes.ObjectTreeBrowser: Create a TreeTableView showing the names and values of object fields, accessed via reflection.
createPane() - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
createPane() - Static method in class qupath.lib.gui.tools.PathObjectLabels: Create a PathObjectLabels.PathObjectMiniPane using the default PathObject.toString() method.
createPane(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels: Create a PathObjectLabels.PathObjectMiniPane using a custom method to create a string representation of the object.
createPane(ObservableValue<ImageData<T>>) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
createPane(ObservableValue<ImageData<T>>, boolean) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
createPathImage(ImageServer<BufferedImage>, ImagePlus, RegionRequest) - Static method in class qupath.imagej.tools.IJTools: Create a PathImage from an ImagePlus and region.
createPathObjectIcon(PathObject, int, int) - Static method in class qupath.lib.gui.tools.IconFactory: Create an icon depicting a PathObject.
createPathObjectsFromROIs(ImagePlus, Roi[], ImageServer<?>, double, boolean, boolean, ImagePlane) - Static method in class qupathj.QuPath_Send_Overlay_to_QuPath: Deprecated.
use instead QuPath_Send_Overlay_to_QuPath.createObjectsFromROIs(ImagePlus, Collection, double, boolean, boolean, ImagePlane)
createPCAProjectFeatureExtractor(FeatureExtractor<T>, Preprocessing.PCAProjector) - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors: Wrap an existing FeatureExtractor to apply PCA projection prior to returning the values.
createPCAProjector(Mat, double, boolean) - Static method in class qupath.opencv.ml.objects.features.Preprocessing: Create a principle components analysis projection to reduce features.
createPersistentPreference(String, boolean) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, double) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, int) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, long) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, String) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, T, Class<T>) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, T, Function<T, String>, Function<String, T>) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property representing any object serializable as a String, which will be saved to/reloaded from the user preferences.
createPixelClassificationServer(ImageData<BufferedImage>, PixelClassifier) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create an ImageServer that displays the results of applying a PixelClassifier to an image.
createPixelClassificationServer(ImageData<BufferedImage>, PixelClassifier, String, ColorModel, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create an ImageServer that displays the results of applying a PixelClassifier to an image.
createPixelClassifierButtons(ObjectExpression<ImageData<BufferedImage>>, ObjectExpression<PixelClassifier>, StringExpression) - Static method in class qupath.process.gui.commands.ml.PixelClassifierUI: Create a standard button pane for pixel classifiers, to create, measure and classify objects.
createPlugin(Class<? extends PathPlugin>) - Method in class qupath.lib.gui.QuPathGUI: Create a plugin from a specified class.
createPluginAction(String, Class<? extends PathPlugin>, String) - Method in class qupath.lib.gui.QuPathGUI: Create an action for a plugin to be run through this QuPath instance.
createPluginAction(String, PathPlugin<BufferedImage>, String) - Method in class qupath.lib.gui.QuPathGUI: Create an Action to call the specified plugin for the current image.
createPointsEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createPointsROI(double[], double[], ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a points ROI from an array of x and y coordinates.
createPointsROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a points ROI containing a single point.
createPointsROI(List<? extends Point2>, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a points ROI from a list of points.
createPointsROI(ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create an empty points ROI.
createPolygonEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createPolygonROI(double[], double[], ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a polygon ROI from an array of x and y coordinates.
createPolygonROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create an empty, closed polygon ROI consisting of a single point.
createPolygonROI(List<Point2>, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a closed polygon ROI from a list of points.
createPolylineEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createPolylineROI(double[], double[], ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a polygon ROI from an array of x and y coordinates.
createPolylineROI(double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create an empty polyline ROI consisting of a single point.
createPolylineROI(List<Point2>, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a polyline ROI from a list of points.
createPreferencesDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Show a dialog to adjust QuPath preferences.
createProcessor(Collection<? extends MeasurementProcessor.CustomMeasurement<S, T>>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor: Create a processor that can make custom measurements for an image object.
createProcessor(MeasurementProcessor.CustomMeasurement<S, T>...) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor: Create a processor that can make custom measurements for an image object.
createProject(File, Class<T>) - Static method in class qupath.lib.projects.Projects: Create a new project using the local file system.
createProjectAction(Consumer<Project<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI: Create an Action that depends upon a Project.
createPropertySheetItem(Property<T>, Class<? extends T>) - Static method in class qupath.lib.gui.panes.PreferencePane: Deprecated.
use PropertyItemBuilder instead
createRandomRectangle(ImageRegion, double, double) - Static method in class qupath.lib.roi.RoiTools: Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask region.
createRandomRectangle(ImageRegion, double, double, Random) - Static method in class qupath.lib.roi.RoiTools: Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask region.
createRandomRectangle(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools: Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask ROI.
createRandomRectangle(ROI, double, double, int, boolean, Random) - Static method in class qupath.lib.roi.RoiTools: Create a randomly-located rectangle ROI with the specified width and height, constrained to fall within the provided mask ROI, using a specified maximum number of attempts.
createRecentCommandsDialog(QuPathGUI) - Static method in class qupath.lib.gui.tools.CommandFinderTools: Create a dialog showing a filtered list of recently-used commands, for fast selection.
createRecentItemsMenu(String, ObservableList<URI>, Consumer<URI>) - Static method in class qupath.lib.gui.tools.GuiTools: Create a menu that displays recent items, stored in the form of URIs, using default text to show for the menu item.
createRecentItemsMenu(String, ObservableList<URI>, Consumer<URI>, Function<URI, String>) - Static method in class qupath.lib.gui.tools.GuiTools: Create a menu that displays recent items, stored in the form of URIs, customizing the text displayed for the menu items.
createRectangle(double, double, double, double) - Static method in class qupath.lib.roi.GeometryTools: Create a rectangular Geometry for the specified bounding box.
createRectangleEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
createRectangleROI(double, double, double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs: Create a rectangle ROI defined by its bounding box.
createRectangleROI(ImageRegion) - Static method in class qupath.lib.roi.ROIs: Create a rectangle ROI that matches an ImageRegion.
CreateRegionAnnotationsCommand - Class in qupath.process.gui.commands: Command to help create annotations defining regions that will be further annotated for algorithm training.
CreateRegionAnnotationsCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.CreateRegionAnnotationsCommand: Constructor.
createRegionFilterCombo(OverlayOptions) - Static method in class qupath.process.gui.commands.ml.PixelClassifierUI: Create a ComboBox that can be used to select the pixel classification region filter.
createRelativePathProperty(String) - Method in class qupath.lib.gui.UserDirectoryManager: Create a read only property for a relative path of the user subdirectory.
createRenderedServer(QuPathViewer) - Static method in class qupath.lib.gui.images.servers.RenderedImageServer: Create an ImageServer that returns tiles based on how approximately they would appear within the viewer.
createRenderedServer(ImageServer<BufferedImage>, ImageRenderer) - Static method in class qupath.lib.gui.images.servers.RenderedImageServer: Create an ImageServer that converts the image to RGB using the specified ImageRenderer.
createROIIcon(ROI, int, int, Color) - Static method in class qupath.lib.gui.tools.IconFactory: Create an icon depicting a ROI.
createROIMask(int, int, ROI, double, double, double) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a grayscale BufferedImage representing a mask for a specified ROI.
createROIMask(int, int, ROI, RegionRequest) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a grayscale BufferedImage representing a mask for a specified ROI.
createROIMask(Shape, double) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a Shape mask using the minimal bounding box for the Shape.
createROIMask(ROI, double) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a ROI mask using the minimal bounding box for the ROI.
createROIs(Raster, int, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Create ROIs from one band of a raster containing integer label values.
createROIs(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Convert integer labels into ROIs.
createROIs(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Create ROIs from a labelled image containing integer labels.
createROIs(ROI) - Method in class qupath.lib.objects.utils.Tiler: Create a list of ROI tiles from the input.
createRotateImageDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a dialog for rotating the image in the current viewer (for display only).
createRowGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Create a GridPane containing rows that resize similarly to Swing's GridLayout().
createRowGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Create a GridPane containing columns that resize similarly to Swing's GridLayout(), while also resizing contained objects to have the corresponding widths.
createRunnableTask(ObjectDetector<T>, ParameterList, ImageData<T>, PathObject) - Static method in class qupath.lib.plugins.DetectionPluginTools: Create a task that applies an object detector to a parent object.
createRunningStatisticsList(int) - Static method in class qupath.lib.analysis.stats.StatisticsHelper: Create a list of n (empty) RunningStatistics objects.
createSaveDensityMapPane(ObjectExpression<Project<BufferedImage>>, ObjectExpression<DensityMaps.DensityMapBuilder>, StringProperty) - Static method in class qupath.process.gui.commands.density.DensityMapUI: Create a pane that can be used to save a DensityMaps.DensityMapBuilder, with standardized display and prompts.
createSavePixelClassifierPane(ObjectExpression<Project<BufferedImage>>, ObjectExpression<PixelClassifier>, StringProperty) - Static method in class qupath.process.gui.commands.ml.PixelClassifierUI: Create a pane that contains a text field and save button to allow a pixel classifier to be saved in a project.
createScaledInstance(double, double) - Method in class qupath.lib.images.servers.PixelCalibration: Get a scaled instance of this PixelCalibration, multiplying pixel sizes for x and y by the specified scale values.
createScaledInstance(double, double, double) - Method in class qupath.lib.images.servers.PixelCalibration: Get a scaled instance of this PixelCalibration, multiplying pixel sizes for x, y and z by the specified scale values.
createScript() - Method in class qupath.lib.plugins.workflow.Workflow: Generate a script from the current workflow steps.
createSelectableAction(ObservableValue<Boolean>) - Static method in class qupath.lib.gui.actions.ActionTools: Create an unnamed action with its Action.selectedProperty() bound to a specified property.
createSelectableAction(ObservableValue<Boolean>, String) - Static method in class qupath.lib.gui.actions.ActionTools: Create an action with its Action.selectedProperty() bound to a specified property.
createSelectableAction(ObservableValue<Boolean>, String, Node, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools: Create an action with its Action.selectedProperty() bound to a specified property, with optional graphic and accelerator.
createSelectableCommandAction(ObservableBooleanValue) - Static method in class qupath.lib.gui.actions.ActionTools
createSelectableCommandAction(SelectableItem<T>) - Static method in class qupath.lib.gui.actions.ActionTools
createSelectableCommandAction(SelectableItem<T>, String) - Static method in class qupath.lib.gui.actions.ActionTools: Create an action from a selectable icon.
createSelectableCommandAction(SelectableItem<T>, String, Node, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
createSelectableCommandAction(SelectableItem<T>, ObservableValue<String>, ObservableValue<Node>, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
createSelectAllObject(boolean) - Static method in class qupath.lib.scripting.QP: Deprecated.
v0.4.0 use QP.createFullImageAnnotation(boolean) instead
createSelectAllObject(boolean, int, int) - Static method in class qupath.lib.scripting.QP: Deprecated.
v0.4.0 use QP.createFullImageAnnotation(boolean, int, int) instead
createSeparator() - Static method in class qupath.lib.gui.actions.ActionTools: Create an action indicating that a separator should be added (e.g.
createServerBuilder() - Method in class qupath.imagej.images.servers.ImageJServer
createServerBuilder() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer: Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer: Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
createServerBuilder() - Method in class qupath.lib.images.servers.AbstractImageServer: Create a ServerBuilder, which can be used to construct an identical ImageServer.
createServerBuilder() - Method in class qupath.lib.images.servers.AffineTransformImageServer
createServerBuilder() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer: Returns a builder capable of creating a server like this one.
createServerBuilder() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer: Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.images.servers.CroppedImageServer
createServerBuilder() - Method in class qupath.lib.images.servers.LabeledImageServer: Returns null (does not support ServerBuilders).
createServerBuilder() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
createServerBuilder() - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
createServerBuilder() - Method in class qupath.lib.images.servers.RotatedImageServer
createServerBuilder() - Method in class qupath.lib.images.servers.SparseImageServer
createServerBuilder() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer: Returns null (does not support ServerBuilders).
createShape(MouseEvent, double, double, boolean, Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Create a new Geometry using the specified tool, assuming a user click/drag at the provided x & y coordinates.
createShape(MouseEvent, double, double, boolean, Geometry) - Method in class qupath.process.gui.WandToolEventHandler
createShapeMask(int, int, Shape, double, double, double) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a grayscale BufferedImage representing a mask for a specified ROI.
createSharedClassificationMerger() - Static method in class qupath.lib.objects.utils.ObjectMerger: Create an object merger that can merge together any objects with similar ROIs (e.g.
createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.QuPathGUI: Deprecated.
since v0.5.0; use QuPathGUI.getThreadPoolManager()
createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.SharedThreadPoolManager: Create a completion service that uses a shared threadpool for the application.
createSharedTileBoundaryMerger(double) - Static method in class qupath.lib.objects.utils.ObjectMerger: Create an object merger that uses a shared boundary IoU criterion and default overlap tolerance.
createSharedTileBoundaryMerger(double, double) - Static method in class qupath.lib.objects.utils.ObjectMerger: Create an object merger that uses a shared boundary IoU criterion and overlap tolerance.
createShowSystemInfoDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a window summarizing key system information relevant for QuPath.
createSingleStageAction(Supplier<Stage>) - Static method in class qupath.lib.gui.commands.Commands: Create a command that generates a persistent single dialog on demand.
createSingleStageAction(Supplier<Stage>, String) - Static method in class qupath.lib.gui.commands.Commands: Create a named command that generates a persistent single dialog on demand.
createSingleThreadExecutor(Object) - Method in class qupath.lib.gui.QuPathGUI: Deprecated.
since v0.5.0; use QuPathGUI.getThreadPoolManager()
createSpecifyAnnotationDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a stage to prompt the user to specify an annotation to add.
createStainVector(String, double, double, double) - Static method in class qupath.lib.color.StainVector: Create a stain vector.
createStatModel(Class<? extends StatModel>) - Static method in class qupath.opencv.ml.OpenCVClassifiers: Create an OpenCVClassifiers.OpenCVStatModel for a specific class of StatModel.
createStringMeasurement(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Deprecated.
createStructureChangeEvent(Object, PathObjectHierarchy, PathObject) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Create a hierarchy event indicating that the hierarchy structure has been changed.
createSubProject(String, Collection<ProjectImageEntry<T>>) - Method in interface qupath.lib.projects.Project: Create a sub-project that provides a view on the specified entries.
createSubTypeAdapterFactory(Class<T>, String) - Static method in class qupath.lib.io.GsonTools: Create a TypeAdapterFactory that is suitable for handling class hierarchies.
createTaskRunner() - Static method in class qupath.lib.gui.scripting.QPEx: Create a task runner with the default number of threads defined by ThreadTools.getParallelism().
createTaskRunner() - Method in class qupath.lib.plugins.TaskRunnerUtils: Create a new TaskRunner instance, using the default number of threads from ThreadTools.getParallelism().
createTaskRunner(int) - Static method in class qupath.lib.gui.scripting.QPEx: Create a task runner with the specified number of threads.
createTaskRunner(int) - Method in class qupath.lib.plugins.TaskRunnerUtils: Create a new TaskRunner instance with the specified number of threads.
createThreadFactory(String, boolean) - Static method in class qupath.lib.common.ThreadTools: Create a named thread factory with Thread.NORM_PRIORITY.
createThreadFactory(String, boolean, int) - Static method in class qupath.lib.common.ThreadTools: Create a named thread factory with a specified priority.
createThresholdClassifier(PixelCalibration, int, double, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Create a new PixelClassifier that applies a threshold to one channel of an image.
createThresholdClassifier(PixelCalibration, Map<Integer, ? extends Number>, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Create a new PixelClassifier that applies a threshold to one or more channels of an image.
createThresholdServer(ImageServer<BufferedImage>, int, double, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create a new ImageServer by applying a threshold to one channel of another server.
createThresholdServer(ImageServer<BufferedImage>, Map<Integer, ? extends Number>, PathClass, PathClass) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Create a new ImageServer by applying a threshold to one or more channels of another server.
createTileObject(ROI) - Static method in class qupath.lib.objects.PathObjects: Create an unclassified tile object.
createTileObject(ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects: Create a tile object.
createTileObject(ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects: Create a tile object, with a classification and measurements list.
createTiles(ROI) - Method in class qupath.lib.objects.utils.Tiler: Create a list of PathTileObject tiles from the input.
createTileWorker(ImageServer<BufferedImage>, RegionRequest, Map<RegionRequest, BufferedImage>, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
createTMACoreObject(double, double, double, boolean) - Static method in class qupath.lib.objects.PathObjects: Create a TMA core object with an circular ROI.
createTMACoreObject(double, double, double, boolean, ImagePlane) - Static method in class qupath.lib.objects.PathObjects: Create a TMA core object with an circular ROI.
createTMACoreObject(double, double, double, double, boolean) - Static method in class qupath.lib.objects.PathObjects: Create a TMA core object with an ellipse ROI.
createTMACoreObject(double, double, double, double, boolean, ImagePlane) - Static method in class qupath.lib.objects.PathObjects: Create a TMA core object with an ellipse ROI.
createTmaCoreView(QuPathGUI) - Static method in class qupath.lib.gui.commands.PathObjectGridView: Create a grid view for TMA core objects.
createTMAGrid(String, String, boolean, double) - Static method in class qupath.lib.scripting.QP: Create a new regular TMAGrid and set it as active on the hierarchy for the current image.
createTMAGrid(String, String, boolean, double, ImageRegion) - Static method in class qupath.lib.objects.PathObjectTools: Create a new regular TMAGrid, fit within a specified region.
createTMAGrid(ImageData<?>, String, String, boolean, double) - Static method in class qupath.lib.scripting.QP: Create a new regular TMAGrid and set it as active on the hierarchy for an image.
createToggleButton(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Create a toggle button from an action, showing both the text and graphic if available.
createToggleButtonWithGraphicOnly(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Create a toggle button from an action, showing only the graphic and not any text.
createTool(EventHandler<MouseEvent>, String, Node) - Static method in class qupath.lib.gui.viewer.tools.PathTools: Create a tool from the specified MouseEvent handler.
createTool(EventType<T>, EventHandler<T>, String, Node) - Static method in class qupath.lib.gui.viewer.tools.PathTools: Create a tool from the specified event handler.
createTouchingMerger() - Static method in class qupath.lib.objects.utils.ObjectMerger: Create an object merger that can merge together any objects with similar ROIs (e.g.
createTracedGeometry(Raster, double, double, int, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing: Create a traced geometry from a raster.
createTracedGeometry(SimpleImage, double, double, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing: Create a traced geometry from a SimpleImage.
createTracedROI(Raster, double, double, int, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing: Create a traced ROI from a raster.
createTracedROI(SimpleImage, double, double, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing: Create a traced ROI from a SimpleImage.
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
createTrainData(Mat, Mat, Mat, boolean) - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Create training data in the format required by this classifier.
createTrainingData(Collection<ImageData<BufferedImage>>) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Create training data, using a label map automatically generated from the available classifications.
createTrainingData(ImageData<BufferedImage>) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Create training data, using a label map automatically generated from the available classifications.
createTrainingDataForLabelMap(Collection<ImageData<BufferedImage>>, Map<PathClass, Integer>) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Get a classifier training map, using a predefined label map (which determines which classifications to use).
CreateTrainingImageCommand - Class in qupath.process.gui.commands: Command to generate a SparseImageServer from multiple image regions across a project.
CreateTrainingImageCommand() - Constructor for class qupath.process.gui.commands.CreateTrainingImageCommand
createTreeCell() - Static method in class qupath.lib.gui.tools.PathObjectLabels: Create a TreeCell for displaying a PathObject using the default PathObject.toString() method.
createTreeCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels: Create a TreeCell for displaying a PathObject using a custom method to create a string representation of the object.
createUnmaskedObjectOutputHandler(OutputHandler.OutputToObjectConverter<S, T, U>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler: Create an output handler that can be used to add objects to the parent object.
createViewer() - Method in class qupath.lib.gui.viewer.ViewerManager: Create a viewer, adding it to the stored array but not adding it to any component (which is left up to the calling code to handle)
createViewerAction(Consumer<QuPathViewer>) - Method in class qupath.lib.gui.QuPathGUI: Create an Action that depends upon an QuPathViewer.
createWindow(QuPathGUI) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
createWorkflowDisplayDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Create a dialog to show the workflow history for the current image data.
createWriter(Collection<OMEPyramidWriter.OMEPyramidSeries>) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter: Create a writer capable of writing an image with a collection of series.
createWriter(OMEPyramidWriter.OMEPyramidSeries...) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter: Create a writer capable of writing an image with one or more series.
createZoomCommand(QuPathGUI, int) - Static method in class qupath.lib.gui.commands.Commands: Create a zoom in/out command action.
crop(BufferedImage, int, int, int, int) - Static method in class qupath.lib.awt.common.BufferedImageTools: Create a crop of the image using the specified bounding box.
crop(Mat, int, int, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Crop a region from a Mat based on its bounding box, returning a new image (not a subregion).
crop(Mat, Padding) - Static method in class qupath.opencv.tools.OpenCVTools: Crop a region from a Mat by stripping off padding, returning a new image (not a subregion).
crop(ImageRegion) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Crop an specified region based on a bounding box.
CroppedImageServer - Class in qupath.lib.images.servers: ImageServer that treats a particular sub-region of another ImageServer as a full image, i.e.
CroppedImageServer(ImageServer<BufferedImage>, ImageRegion) - Constructor for class qupath.lib.images.servers.CroppedImageServer: Create an ImageServer that represents a cropped region of another (larger) server.
cropTiles(boolean) - Method in class qupath.lib.objects.utils.Tiler.Builder: Set whether the tiler is set to crop the output to the input parent.
cross3(double[], double[]) - Static method in class qupath.lib.color.StainVector: Compute the cross product of two vectors.
cssDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager: Read only property representing the css directory.
CssLanguage - Class in qupath.lib.gui.scripting.languages: Class for representing CSS in QuPath.
CssLanguage() - Constructor for class qupath.lib.gui.scripting.languages.CssLanguage: Constructor for JSON language.
cuda() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Request CUDA backend and target, if available.
cuda16() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Request CUDA backend and target, if available, with 16-bit floating point.
currentChannelProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Get the currently-selected channel.
currentChannelVisible() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Read-only property indicating whether the currently-selected channel is visible, i.e.
currentLanguageProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
currentSyntaxProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
cursorTrackingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the cursorTracking property of this tracker.
cut() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
cut() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request cut the current selection.
cut() - Method in class qupath.lib.gui.scripting.TextAreaControl
cutAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
CYAN - Static variable in class qupath.lib.common.ColorTools: Packed int representing cyan.
CYTOPLASM - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments: Full cell region, with nucleus removed

D

DAB - Enum constant in enum class qupath.lib.color.StainVector.DefaultStains: DAB
DAB - Static variable in class qupath.lib.color.ColorDeconvolutionStains: Default name for DAB stain
DAB_H_DAB - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: DAB after color deconvolution with default H-DAB stains
DAB_H_DAB_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: DAB after color deconvolution with default H-DAB stains and conversion to 8-bit
darkenColor(Color) - Static method in class qupath.lib.color.ColorToolsAwt: Get a (slightly) darker version of the specified color.
data(Map<?, ? extends Number>) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify data for the pie chart as a map.
DEBUG - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: Debug logging (a lot of messages)
decelerate() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover: Stop moving, by smoothly decelerating.
deconvolve(ColorDeconvolutionStains) - Static method in class qupath.opencv.ops.ImageOps.Channels: Apply the (fixed) color deconvolution stains to an image.
deconvolveStains(ColorDeconvolutionStains, int...) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Apply color deconvolution to the brightfield image, so that deconvolved stains behave as separate channels/
DEFAULT - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts: JavaFX default.
DEFAULT - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Default channel interpretation.
DEFAULT - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType: Leave it up to the writer to choose the appropriate method.
DEFAULT - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Default (QuPath will select compression option based on image size and type, may be lossless or lossy).
DEFAULT - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Default Model class.
DEFAULT_CLASSIFICATION_LABELS_CHANNEL - Static variable in class qupath.lib.images.servers.ImageServerMetadata: Default channel to use with images where the channel type is ImageServerMetadata.ChannelType.CLASSIFICATION.
DEFAULT_INPUT_NAME - Static variable in interface qupath.opencv.dnn.DnnModel: Default input layer name.
DEFAULT_INPUT_NAME - Static variable in interface qupath.opencv.dnn.PredictionFunction: Default name to use for single input.
DEFAULT_OUTPUT_NAME - Static variable in interface qupath.opencv.dnn.DnnModel: Default output layer name.
DEFAULT_OUTPUT_NAME - Static variable in interface qupath.opencv.dnn.PredictionFunction: Default name to use for single output.
DEFAULT_PREFIX - Static variable in class qupath.lib.gui.images.servers.PathHierarchyImageServer: Prefix used for the path of all instances of this class.
DEFAULT_PROJECT_EXTENSION - Static variable in class qupath.lib.projects.ProjectIO: Default file extension for a QuPath project.
DEFAULT_PROJECT_NAME - Static variable in class qupath.lib.projects.ProjectIO: Default file name for a QuPath project.
DefaultAutoCompletor - Class in qupath.lib.gui.scripting.completors: Default auto-completor for JVM-based languages, optionally including QuPath default imports.
DefaultAutoCompletor(boolean) - Constructor for class qupath.lib.gui.scripting.completors.DefaultAutoCompletor: Constructor.
defaultColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
DefaultImageRegionStore - Class in qupath.lib.gui.images.stores: An ImageRegionStore suitable for either Swing or JavaFX applications.
defaultLocaleDisplayProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get a property for setting the default Locale for Locale.Category.DISPLAY.
defaultLocaleFormatProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get a property for setting the default Locale for Locale.Category.FORMAT.
defaultLocaleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get a property for setting the default Locale.
DefaultPathObjectComparator - Class in qupath.lib.objects: Default comparator to enable objects to be sorted in a more predictable manner.
DefaultPathObjectComparator() - Constructor for class qupath.lib.objects.DefaultPathObjectComparator
DefaultPathObjectConnectionGroup - Class in qupath.lib.objects: Simple, default implementation of PathObjectConnectionGroup.
DefaultPathObjectConnectionGroup() - Constructor for class qupath.lib.objects.DefaultPathObjectConnectionGroup: Default constructor.
DefaultPathObjectConnectionGroup(PathObjectConnectionGroup) - Constructor for class qupath.lib.objects.DefaultPathObjectConnectionGroup: Create a connections group, copying the connections from an existing group.
DefaultROIComparator - Class in qupath.lib.roi: Default comparator to enable ROIs to be sorted in a more predictable manner.
DefaultROIComparator() - Constructor for class qupath.lib.roi.DefaultROIComparator
DefaultScriptableWorkflowStep - Class in qupath.lib.plugins.workflow: A scriptable workflow step where the script is provided directly as an argument.
DefaultScriptableWorkflowStep(String, String) - Constructor for class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep: Create a workflow step using a provided script string that will be called as-is.
DefaultScriptableWorkflowStep(String, Map<String, ?>, String) - Constructor for class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep: Constructor that takes a parameter map for display.
DefaultScriptEditor - Class in qupath.lib.gui.scripting: Default multilingual script editor.
DefaultScriptEditor(QuPathGUI) - Constructor for class qupath.lib.gui.scripting.DefaultScriptEditor: Constructor.
DefaultScriptLanguage - Class in qupath.lib.gui.scripting.languages: Default implementation for a ScriptLanguage, based on a ScriptEngine.
DefaultScriptLanguage(String, Collection<String>, ScriptAutoCompletor) - Constructor for class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Constructor for a ExecutableLanguage.
DefaultScriptLanguage(ScriptEngineFactory) - Constructor for class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Constructor for a ExecutableLanguage based on a ScriptEngineFactory.
DefaultScriptLanguage.ImportStatementGenerator - Interface in qupath.lib.gui.scripting.languages: Interface defining how the import statements should be generated for the language.
DefaultTMAGrid - Class in qupath.lib.objects.hierarchy: Default implementation of a TMAGrid.
DelaunayClusteringPlugin<T> - Class in qupath.opencv.features: Plugin for calculating Delaunay clustering, and associated features.
DelaunayClusteringPlugin() - Constructor for class qupath.opencv.features.DelaunayClusteringPlugin: Constructor.
DelaunayTools - Class in qupath.lib.analysis: Tools for creating and querying Delaunay triangulations and Voronoi diagrams.
DelaunayTools() - Constructor for class qupath.lib.analysis.DelaunayTools
DelaunayTools.Builder - Class in qupath.lib.analysis: Builder class to create a DelaunayTools.Subdivision based on Delaunay triangulation.
DelaunayTools.Subdivision - Class in qupath.lib.analysis: Helper class for extracting information from a Delaunay triangulation computed from PathObjects.
DelaunayTriangulation - Class in qupath.opencv.features: Compute Delaunay triangulation using OpenCV.
DelaunayTriangulation(List<PathObject>, double, double, double, boolean) - Constructor for class qupath.opencv.features.DelaunayTriangulation: Compute Delaunay triangulation - optionally omitting links above a fixed distance.
DELETE_EXISTING - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions: Delete existing child objects
DELETE_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
deleteActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
DeleteActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
deleteFile(File, boolean) - Static method in class qupath.lib.common.GeneralTools: Delete a file, optionally requesting that it be moved to the trash rather than permanently deleted.
deleteText(int, int) - Method in interface qupath.lib.gui.scripting.EditableText: Request deleting the text within the specified range.
deleteText(int, int) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
deleteText(int, int) - Method in class qupath.lib.gui.scripting.TextAreaControl
DELIMITER - Static variable in class qupath.lib.objects.classes.PathClass: Get the delimiter to use between names of the PathClass when converting to a string.
DEMOS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
DENSITY - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Each channel represents a density value, such as in a density map (e.g.
DensityMapCommand - Class in qupath.process.gui.commands: Command for generating density maps from detections on an image.
DensityMapCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.DensityMapCommand: Constructor.
DensityMapDialog - Class in qupath.process.gui.commands.density: Dialog for interactively generating a custom density map.
DensityMapDialog(QuPathGUI) - Constructor for class qupath.process.gui.commands.density.DensityMapDialog: Constructor.
DensityMaps - Class in qupath.lib.analysis.heatmaps: Class for constructing and using density maps.
DensityMaps() - Constructor for class qupath.lib.analysis.heatmaps.DensityMaps
DensityMaps.DensityMapBuilder - Class in qupath.lib.analysis.heatmaps: Builder for an ImageServer representing a density map or for DensityMaps.DensityMapParameters.
DensityMaps.DensityMapParameters - Class in qupath.lib.analysis.heatmaps: Class for storing parameters to build a ImageServer representing a density map.
DensityMaps.DensityMapType - Enum Class in qupath.lib.analysis.heatmaps: Density map types.
DensityMapUI - Class in qupath.process.gui.commands.density: UI elements associated with density maps.
DensityMapUI() - Constructor for class qupath.process.gui.commands.density.DensityMapUI
deregister() - Method in class qupath.process.gui.commands.density.DensityMapDialog: Deregister listeners.
deregisterTool(QuPathViewer) - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
deregisterTool(QuPathViewer) - Method in interface qupath.lib.gui.viewer.tools.PathTool: Deregister the tool from the viewer.
describe(Class<?>) - Static method in class qupath.lib.scripting.QP: List the fields and methods of a specified class.
describe(Object) - Static method in class qupath.lib.scripting.QP: List the fields and methods of a specified object.
deselect() - Method in interface qupath.lib.gui.scripting.EditableText: Deselect any currently-selected text.
deselect() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
deselect() - Method in class qupath.lib.gui.scripting.TextAreaControl
deselectAll() - Static method in class qupath.lib.scripting.QP: Clear the selection for the current hierarchy, so that no objects of any kind are selected.
deselectAll(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Clear the selection, so that no objects of any kind are selected.
deselectObject(PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Ensure that the specified object is removed from the selection.
deselectObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Ensure the specified objects are deselected.
DETACH_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
DETACH_VIEWER - Variable in class qupath.lib.gui.actions.ViewerActions
detachActiveViewerFromGrid() - Method in class qupath.lib.gui.viewer.ViewerManager: Detach the currently active viewer from the viewer grid, if possible.
detachViewerFromGrid(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager: Detach the specified viewer from the viewer grid, if possible.
detect(DetectionModel, Mat, RegionRequest, IntFunction<PathClass>, Function<ROI, PathObject>) - Static method in class qupath.opencv.dnn.DnnTools: Apply a detection model to generate rectangles surrounding distinct structures.
detect(DetectionModel, ImageServer<BufferedImage>, RegionRequest, IntFunction<PathClass>, Function<ROI, PathObject>) - Static method in class qupath.opencv.dnn.DnnTools: Apply a detection model to generate rectangles surrounding distinct structures.
DetectCytokeratinCV - Class in qupath.opencv: Simple command to detect tumor regions stained with cytokeratin.
DetectCytokeratinCV() - Constructor for class qupath.opencv.DetectCytokeratinCV
detection() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Set the model type to be OpenCVDnn.ModelType.DETECTION.
DETECTION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Refers to DetectionModel.
detectionCentroidDistances() - Static method in class qupath.lib.scripting.QP: Deprecated.
retained only for compatibility of v0.2.0 milestone releases; use instead #detectionCentroidDistances(boolean)
detectionCentroidDistances(boolean) - Static method in class qupath.lib.scripting.QP: Compute the distance for all detection object centroids to the closest detection with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
detectionCentroidDistances(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools: Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionCentroidDistances(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP: Compute the distance for all detection object centroids to the closest detection with each valid, not-ignored classification and add the result to the detection measurement list.
detectionCentroidDistances2D(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Compute the distance between the centroids of all detections, for all available classifications.
detectionDisplayModeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions: Property representing the current OverlayOptions.DetectionDisplayMode.
DetectionPluginTools - Class in qupath.lib.plugins: Helper methods to convert ObjectDetectors into runnable tasks, which take care of resolving overlaps when using ParallelTileObjects after the detection is complete and firing notification events in a PathObjectHierarchy.
DetectionPluginTools() - Constructor for class qupath.lib.plugins.DetectionPluginTools
detections() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the filter to accept all detection objects only.
DETECTIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
DETECTIONS - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept detection objects (no subtypes, e.g.
DETECTIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
DETECTIONS_ALL - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept detection objects (all subtypes)
DETECTIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
detectionsToCells(Collection<? extends PathObject>, double, double) - Static method in class qupath.lib.objects.CellTools: Create cell objects by expanding the (nucleus) ROIs from existing detections to approximate the full cell boundary.
detectionStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Preferred stroke thickness to use when drawing detections ROIs.
detectionToAnnotationDistances() - Static method in class qupath.lib.scripting.QP: Deprecated.
retained only for compatibility of v0.2.0 milestone releases; use instead #detectionToAnnotationDistances(boolean)
detectionToAnnotationDistances(boolean) - Static method in class qupath.lib.scripting.QP: Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
detectionToAnnotationDistances(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools: Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistances(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP: Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistances(ImageData<?>, boolean, boolean) - Static method in class qupath.lib.analysis.DistanceTools: Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistancesSigned(boolean) - Static method in class qupath.lib.scripting.QP: Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
detectionToAnnotationDistancesSigned(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools: Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionToAnnotationDistancesSigned(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP: Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
detectionTreeDisplayModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Define how detections should be displayed in lists and tree views.
detectonStrokeThickness - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
detectTMACoresFromBinary(ByteProcessor, double, int, int, Roi) - Static method in class qupath.imagej.detect.dearray.TMADearrayer: Detect TMA cores from a (low-resolution) whole slide image that has been thresholded to give a binary image.
detectVendor(String) - Static method in class qupath.lib.images.servers.openslide.jna.OpenSlideLoader: Try to detect the vendor of the image at the specified path.
determinant() - Method in class qupath.lib.color.ColorDeconvMatrix3x3: Calculate the determinant of the matrix.
df - Static variable in class qupath.lib.display.DirectServerChannelInfo
df - Static variable in class qupath.lib.gui.viewer.recording.ViewTracker
Dialogs - Class in qupath.lib.gui.dialogs: Deprecated.
since v0.5.0.
Dialogs() - Constructor for class qupath.lib.gui.dialogs.Dialogs: Deprecated.
Dialogs.Builder - Class in qupath.lib.gui.dialogs: Deprecated.
Dialogs.DialogButton - Enum Class in qupath.lib.gui.dialogs: Deprecated.

Possible buttons pressed in a yes/no/cancel dialog.
difference(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools: Compute the difference between two ROIs.
DilateAnnotationPlugin<T> - Class in qupath.lib.plugins.objects: Plugin to create new annotations by expanding the size of existing annotations.
DilateAnnotationPlugin() - Constructor for class qupath.lib.plugins.objects.DilateAnnotationPlugin
DilateAnnotationPlugin.LineCap - Enum Class in qupath.lib.plugins.objects: Line cap to use for annotation expansion.
dim() - Method in interface qupath.lib.geom.Point: Number of values used to represent this point.
dim() - Method in class qupath.lib.geom.Point2
DIR_COLORMAPS - Static variable in class qupath.lib.gui.UserDirectoryManager: Name of subdirectory containing colormaps.
DIR_CSS - Static variable in class qupath.lib.gui.UserDirectoryManager: Name of subdirectory containing css files for styling.
DIR_EXTENSIONS - Static variable in class qupath.lib.gui.UserDirectoryManager: Name of subdirectory containing extensions.
DIR_LOCALIZATION - Static variable in class qupath.lib.gui.UserDirectoryManager: Name of subdirectory containing properties files for localization.
DIR_LOGS - Static variable in class qupath.lib.gui.UserDirectoryManager: Name of subdirectory containing log files.
DIR_SCRIPTS - Static variable in class qupath.lib.gui.UserDirectoryManager: Name of subdirectory containing shared scripts.
DirectServerChannelInfo - Class in qupath.lib.display: ChannelInfo intended for use with a single or multichannel image (possibly fluorescence) where the pixel's value is used to scale a single color according to a specified display range according to the following rules: If the pixel's value is >= maxDisplay, the pure color is used. If the pixel's value is <= minDisplay, the black is used. Otherwise, a scaled version of the color is used The end result is like having a lookup table (LUT) that stretches from black to the 'pure' color specified, but without actually generating the LUT.
DirectServerChannelInfo(ImageData<BufferedImage>, int) - Constructor for class qupath.lib.display.DirectServerChannelInfo: Constructor.
disabled(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Set the disabled property of the action.
disabled(ObservableValue<Boolean>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Bind the disabled property of the action to an ObservableValue, bidirectionally if possible.
disableGammaAdjustmentProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: Prevent gamma from being adjusted.
disableMinMaxAdjustmentProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: Prevent the min and max sliders from being adjusted.
disableToggleMenuItemsProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Property to disable options to toggle the visibility of channels.
disableUpdatesProperty() - Method in class qupath.lib.gui.panes.AnnotationPane: Property that may be used to prevent updates on every hierarchy or selection change event.
disableUpdatesProperty() - Method in class qupath.lib.gui.panes.PathObjectHierarchyView: Property that may be used to prevent updates on every hierarchy or selection change event.
display(ImageDisplay) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Deprecated.
use RenderedImageServer.Builder.renderer(ImageRenderer) instead (since an ImageDisplay is also an ImageRenderer.
displayMode() - Method in class qupath.lib.display.ImageDisplay: Get the value of ImageDisplay.useInvertedBackgroundProperty()
displayModeProperty() - Method in class qupath.lib.gui.charts.HistogramChart: Property to control how the histogram is displayed, either using areas or bars.
DisplaySettingUtils - Class in qupath.lib.display.settings: Utility class for working with image display and image display settings objects.
DisplaySettingUtils() - Constructor for class qupath.lib.display.settings.DisplaySettingUtils
displayToSettings(ImageDisplay, String) - Static method in class qupath.lib.display.settings.DisplaySettingUtils: Create a new image display settings object from the image display.
dispose() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Dispose the OpenSlide object; this is equivalent to OpenSlide.close().
distance(double, double) - Method in class qupath.lib.geom.Point2: Calculate the distance between this point and a specified x and y location.
distance(Point) - Method in class qupath.lib.geom.Point2
distance(Point) - Method in interface qupath.lib.geom.Point: Calculate the distance to another point, with the same Point.dim().
distance(Point2) - Method in class qupath.lib.geom.Point2: Calculate the distance between this point and another point.
DISTANCE_CENTROIDS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
DISTANCE_TO_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
distanceSq(double, double) - Method in class qupath.lib.geom.Point2: Calculate the squared distance between this point and a specified x and y location.
distanceSq(Point) - Method in class qupath.lib.geom.Point2
distanceSq(Point) - Method in interface qupath.lib.geom.Point: Calculate the squared distance to another point, with the same Point.dim().
distanceSq(OpenCVTools.IndexedPixel) - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel: Get the euclidean distance to another pixel, based upon the inds array and assuming unit spacing for all dimensions.
distanceToAnnotations2D(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands: Compute the distance between all detections and the closest annotation, for all annotation classifications.
DistanceTools - Class in qupath.lib.analysis: Static methods for calculating distances between objects.
DistanceTools() - Constructor for class qupath.lib.analysis.DistanceTools
div(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Divide array elements by a constant.
div(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Per-element division of two arrays.
divide(double...) - Static method in class qupath.opencv.ops.ImageOps.Core: Divide all pixels by a constant.
dnn(DnnModel, int, int, Padding, String...) - Static method in class qupath.opencv.ops.ImageOps.ML: Apply a DnnModel to pixels to generate a prediction.
DnnModel - Interface in qupath.opencv.dnn: General interface for implementing a deep learning model in a pipeline using OpenCV.
DnnModelBuilder - Interface in qupath.opencv.dnn: Builder to create a DnnModel from DnnModelParams.
DnnModelParams - Class in qupath.opencv.dnn: Parameters to build a DnnModel.
DnnModelParams.Builder - Class in qupath.opencv.dnn: Builder for DnnModelParams.
DnnModels - Class in qupath.opencv.dnn: Helper class for building new DnnModels.
DnnModels() - Constructor for class qupath.opencv.dnn.DnnModels
DnnObjectClassifier - Class in qupath.opencv.dnn: Initial implementation of a patch-based ObjectClassifier using an OpenCV-compatible DNN.
DnnObjectClassifier(PathObjectFilter, DnnModel, List<PathClass>, int, int, double) - Constructor for class qupath.opencv.dnn.DnnObjectClassifier: Constructor.
DnnShape - Class in qupath.opencv.dnn: Helper class to represent input and output shapes associated with PredictionFunction.
DnnTools - Class in qupath.opencv.dnn: Tools for working with OpenCV's DNN module.
DnnTools() - Constructor for class qupath.opencv.dnn.DnnTools
DnnTools.DNNLayer - Class in qupath.opencv.dnn: Helper class to summarize a DNN layer.
do8BitRangeCheck(double) - Static method in class qupath.lib.common.ColorTools: Clip an input value to be an integer in the range 0-255 (with rounding down).
do8BitRangeCheck(float) - Static method in class qupath.lib.common.ColorTools: Clip an input value to be an integer in the range 0-255 (with rounding down).
do8BitRangeCheck(int) - Static method in class qupath.lib.common.ColorTools: Clip an input value to be an integer in the range 0-255.
DocGenerator - Class in qupath.lib.gui.tools: Command line tool to export icons and markdown documentation for QuPath commands.
DocGenerator() - Constructor for class qupath.lib.gui.tools.DocGenerator
doCopy() - Method in class qupath.lib.gui.FileCopier: Perform the copying.
doCreateLogFilesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request a log file to be generated.
DOCS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
doesFeatureTransform() - Method in class qupath.opencv.ml.FeaturePreprocessor: Returns true if this preprocessor transforms the features beyond a simple normalization.
doesSomething() - Method in interface qupath.lib.display.ChannelDisplayInfo: Returns true if this does something - anything - and false otherwise.
doesSomething() - Method in class qupath.lib.display.DirectServerChannelInfo
doesSomething() - Method in class qupath.opencv.ml.FeaturePreprocessor: Returns true if this preprocessor has any effect.
DoGSuperpixelsPlugin - Class in qupath.imagej.superpixels: A simple superpixel-generating command based upon applying ImageJ's watershed transform to the absolute values of a Difference-of-Gaussians filtered image.
DoGSuperpixelsPlugin() - Constructor for class qupath.imagej.superpixels.DoGSuperpixelsPlugin
doLogCountsProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane: Property to control whether the histogram shows pixel counts, or the natural logarithm of the counts.
DONE - Enum constant in enum class qupath.lib.plugins.ParallelTileObject.Status: Tile processing complete
DOUBLE - Enum constant in enum class qupath.lib.measurements.MeasurementList.MeasurementListType: A list backed by an array of doubles.
doubleClickToZoom - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
doubleClickToZoomProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request that double-clicking the viewer can be used to zoom in.
DoubleParameter - Class in qupath.lib.plugins.parameters: Parameter to represent a floating point numeric value.
doUpdateHierarchy() - Method in class qupath.lib.scripting.ScriptParameters: Request whether to fire an update event for the object hierarchy, if an image data object is available.
doUpdateHierarchy(boolean) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Optionally request a hierarchy update event after running a script (default is true for scripts that operate on image data).
doWatershed(ImageProcessor, ImageProcessor, boolean) - Static method in class qupath.imagej.processing.Watershed: Apply a watershed transform.
doWatershed(ImageProcessor, ImageProcessor, double, boolean) - Static method in class qupath.imagej.processing.Watershed: Apply an intensity-constrained watershed transform, preventing regions from expanding to pixels below a specified minimum threshold
doWatershed(Mat, Mat, boolean) - Static method in class qupath.opencv.tools.ProcessingCV: Apply a watershed transform.
doWatershed(Mat, Mat, double, boolean) - Static method in class qupath.opencv.tools.ProcessingCV: Apply an intensity-constrained watershed transform, preventing regions from expanding to pixels below a specified minimum threshold
doWatershed(SimpleImage, SimpleModifiableImage, boolean) - Static method in class qupath.lib.analysis.algorithms.Watershed: Apply a 2D watershed transform.
doWatershed(SimpleImage, SimpleModifiableImage, double, boolean) - Static method in class qupath.lib.analysis.algorithms.Watershed: Apply a 2D watershed transform, constraining region growing using an intensity threshold.
DOWNLOAD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
downsample(double) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the downsample factor to use with requesting image regions.
downsample(double) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify downsample factor (defined in terms of the full resolution image space).
downsample(double) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Specify downsample factor.
downsample(double) - Method in class qupath.lib.images.writers.TileExporter: Define resolution as a downsample value.
downsamples(double...) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify downsamples; this is especially important for 'thick' objects (annotations, TMA cores) because the downsamples define the resolutions at which these will be rendered.
downsamples(double...) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify downsample factors to use in the final pyramid.
DragDropImportListener - Class in qupath.lib.gui.viewer: Drag and drop support for main QuPath application, which can support a range of different object types (Files, URLs, Strings,..)
DragDropImportListener(QuPathGUI) - Constructor for class qupath.lib.gui.viewer.DragDropImportListener: Constructor.
DragDropImportListener.DropHandler<T> - Interface in qupath.lib.gui.viewer: Interface to define a new drop handler.
DrawingPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
dumpMetadata() - Method in class qupath.imagej.images.servers.ImageJServer: Get a String representing the image metadata.
dumpMetadata() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer: Retrieve a string representation of the metadata OME-XML.
dumpMetadata() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer: Retrieve a JSON string representation of the properties, as stored as key-value pairs by OpenSlide.
duplicate() - Method in class qupath.lib.images.servers.ImageServerMetadata: Duplicate this metatadata.
duplicate() - Method in class qupath.lib.plugins.parameters.BooleanParameter
duplicate() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
duplicate() - Method in class qupath.lib.plugins.parameters.DoubleParameter
duplicate() - Method in class qupath.lib.plugins.parameters.EmptyParameter
duplicate() - Method in class qupath.lib.plugins.parameters.IntParameter
duplicate() - Method in interface qupath.lib.plugins.parameters.Parameter: Create a new Parameter with the same text and value.
duplicate() - Method in class qupath.lib.plugins.parameters.ParameterList: Create a deep copy of this parameter list.
duplicate() - Method in class qupath.lib.plugins.parameters.StringParameter
duplicate() - Method in class qupath.lib.roi.AreaROI: Deprecated.
duplicate() - Method in class qupath.lib.roi.EllipseROI: Deprecated.
duplicate() - Method in class qupath.lib.roi.GeometryROI
duplicate() - Method in interface qupath.lib.roi.interfaces.ROI: Deprecated.
duplicate() - Method in class qupath.lib.roi.LineROI: Deprecated.
duplicate() - Method in class qupath.lib.roi.PointsROI: Deprecated.
duplicate() - Method in class qupath.lib.roi.PolygonROI: Deprecated.
duplicate() - Method in class qupath.lib.roi.PolylineROI: Deprecated.
duplicate() - Method in class qupath.lib.roi.RectangleROI: Deprecated.
duplicate(BufferedImage) - Static method in class qupath.lib.awt.common.BufferedImageTools: Duplicate a BufferedImage.
duplicateAllSelectedObjects(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools: Duplicate all the selected objects in a hierarchy.
duplicateObjects(PathObjectHierarchy, Collection<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Duplicate the specified objects, assigning new IDs for each object.
duplicateObjects(PathObjectHierarchy, Collection<PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Duplicate the specified objects, optionally creating new IDs.
duplicateSelectedAnnotations() - Static method in class qupath.lib.scripting.QP: Duplicate the selected annotations in the current hierarchy.
duplicateSelectedAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Duplicate the selected annotations.
duplicateSelectedAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools: Duplicate the selected annotation objects.
duplicateSelectedAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Duplicate the selected annotations in the specified hierarchy.
duplicateSelectedObjects(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Duplicate the selected objects
dyadicDownsampling() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Downsample by factors of 2.

E

EditableText - Interface in qupath.lib.gui.scripting: Interface for objects that manage editable text, including a caret position and selection.
EditMenuActions - Class in qupath.lib.gui.actions.menus
EditMenuActions.Actions - Class in qupath.lib.gui.actions.menus
EditMenuActions.CopyActions - Class in qupath.lib.gui.actions.menus
editSelectedAnnotation(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Prompt to edit the selected annotation by translation and rotation.
effectiveNChannels(int) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
ELLIPSE - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Ellipse drawing tool
ELLIPSE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ELLIPSE_TOOL - Variable in class qupath.lib.gui.ToolManager
EllipseROI - Class in qupath.lib.roi: ROI implementing a circle, or (unrotated) ellipse.
EMBED - Enum constant in enum class qupath.lib.extension.svg.SvgTools.SvgBuilder.ImageIncludeType: Embed the image (as Base64-encoded PNG).
embedImages() - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify whether the underlying (raster) image should be embedded in any export.
empty() - Static method in class qupath.lib.regions.Padding: Get an empty padding object (0 on all sides).
EmptyParameter - Class in qupath.lib.plugins.parameters: Parameter that doesn't actually store any value, but might contain some useful text (or a title) that may need to be displayed.
enableBioformats - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
enableFreehand - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
enableFreehandToolsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Enable polygon/polyline tools to support 'freehand' mode; this means that if the ROI is started by dragging, then it will end by lifting the mouse (rather than requiring a double-click).
ensureBufferedImage(Image) - Static method in class qupath.lib.awt.common.BufferedImageTools: Convert an Image to a BufferedImage if necessary, or return the original image unchanged if it is already a BufferedImage.
ensureBufferedImageType(BufferedImage, int) - Static method in class qupath.lib.awt.common.BufferedImageTools: Convert a BufferedImage to have a specified type.
ensureContinuous(Mat, boolean) - Static method in class qupath.opencv.tools.OpenCVTools: Ensure a Mat is continuous, creating a copy of the data if necessary.
ensureCursorType(Cursor) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Ensure that the specified cursor is set in the current viewer.
ensureCursorType(Cursor) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler: Ensure that the specified cursor is set in the current viewer.
ensureCursorType(Cursor) - Method in class qupath.process.gui.WandToolEventHandler: Ensure that the specified cursor is set in the current viewer.
ensureDuplicatableGlyph(Glyph) - Static method in class qupath.lib.gui.tools.GuiTools: Ensure that a Glyph is 'duplicatable', without losing its key properties.
ensureDuplicatableGlyph(Glyph, boolean) - Static method in class qupath.lib.gui.tools.GuiTools: Ensure that a Glyph is 'duplicatable', optionally retaining any fill.
ensureHandlesUpdated() - Method in class qupath.lib.roi.RoiEditor: In the event that the current ROI has been modified elsewhere (which generally it shouldn't be) request the handles to be recomputed to avoid inconsistency.
ensurePolygonal(Geometry) - Static method in class qupath.lib.roi.GeometryTools: Strip non-polygonal parts from a GeometryCollection (non-recursive).
ensureType(PixelType) - Static method in class qupath.opencv.ops.ImageOps.Core: Convert the Mat to match a specified pixel type.
entrySet() - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder.FeatureMap
envelopToRegion(Envelope, int, int) - Static method in class qupath.lib.roi.GeometryTools: Convert an Envelope to an ImageRegion.
EOSIN - Enum constant in enum class qupath.lib.color.StainVector.DefaultStains: Eosin
EOSIN - Static variable in class qupath.lib.color.ColorDeconvolutionStains: Default name for eosin stain
Eosin_H_E - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Eosin after color deconvolution with default H&E stains
Eosin_H_E_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Eosin after color deconvolution with default H&E stains and conversion to 8-bit
eq(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Create a binary image showing where an array has a specific value.
eq(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Create a binary image showing where two arrays have matching values.
equalParameters(ParameterList, ParameterList) - Static method in class qupath.lib.plugins.parameters.ParameterList: Check whether two parameter lists contain the same parameters with the same values (or defaults, if no values are set).
equals(Object) - Method in class qupath.lib.common.Version
equals(Object) - Method in class qupath.lib.geom.Point2
equals(Object) - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
equals(Object) - Method in class qupath.lib.images.servers.ImageChannel
equals(Object) - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
equals(Object) - Method in class qupath.lib.images.servers.ImageServerMetadata
equals(Object) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
equals(Object) - Method in class qupath.lib.images.servers.PixelCalibration
equals(Object) - Method in class qupath.lib.images.servers.TileRequest
equals(Object) - Method in class qupath.lib.io.UriUpdater.SingleUriItem
equals(Object) - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
equals(Object) - Method in class qupath.lib.regions.ImagePlane
equals(Object) - Method in class qupath.lib.regions.ImageRegion
equals(Object) - Method in class qupath.lib.regions.RegionRequest
equals(Object) - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
equals(Object) - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
equals(Object) - Method in class qupath.process.gui.commands.ml.ClassificationResolution
equalTo(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification (by name) for objects for which the specified measurement has a value exactly equal to the threshold.
equalTo(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the classification for objects for which the specified measurement has a value exactly equal to the threshold.
error() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Create an error alert dialog.
error(String) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an error message with static text.
error(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an error message with static text and a count.
error(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage: Create a error message to show a count of errors.
error(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an error message.
error(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an error message with a count.
ERROR - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType: Error or exception.
ERROR - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: Error logging (only if something goes recognizably wrong)
escapeFilePath(String) - Static method in class qupath.lib.common.GeneralTools: Escape backslashes in an absolute file path - useful when scripting.
estimateAvailableMemory() - Static method in class qupath.lib.common.GeneralTools: Estimate the current available memory in bytes, based upon the JVM max and the memory currently used.
estimateCellBoundary(Geometry, double, double) - Static method in class qupath.lib.objects.CellTools: Estimate a cell boundary using Geometry objects.
estimateDownsampleFactor(ImagePlus, ImageServer<?>) - Static method in class qupath.imagej.tools.IJTools: Estimate the downsample factor for an image region extracted from an image server, based upon the ratio of pixel sizes if possible or ratio of dimensions if necessary.
estimateImageType(ImageServer<BufferedImage>, BufferedImage) - Static method in class qupath.lib.gui.tools.GuiTools: Make a semi-educated guess at the image type of a PathImageServer.
estimateStains(int[], float[], float[], float[], ColorDeconvolutionStains, double, double, double, boolean) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors: Check colors only currently applies to H&E.
estimateStains(BufferedImage, ColorDeconvolutionStains, boolean) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors: Estimate two stains from a BufferedImage, with default parameter settings.
estimateStains(BufferedImage, ColorDeconvolutionStains, double, double, double, boolean) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors: Estimate two stains from a BufferedImage.
EstimateStainVectors - Class in qupath.lib.analysis.algorithms: Code for estimating stain vectors automatically from an image, or to launch an editor for visually/interactively modifying stain vectors.
EstimateStainVectors() - Constructor for class qupath.lib.analysis.algorithms.EstimateStainVectors
estimateUsedMemory() - Static method in class qupath.lib.common.GeneralTools: Estimate the current used memory.
estimateWhiteValues(int[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Estimate white (background) values for a brightfield image.
EVERYWHERE - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Accept all requests
exactClassification(PathClass...) - Static method in class qupath.lib.objects.PathObjectPredicates: Predicate that returns true if a PathObject has at least one of the specified PathClasses.
EXCLUDE_MEASUREMENTS - Enum constant in enum class qupath.lib.io.PathIO.GeoJsonExportOptions: Optionally exclude measurements from objects.
excludeColumns(String...) - Method in class qupath.lib.gui.tools.MeasurementExporter: Specify the columns that will be excluded during the export.
ExecutableLanguage - Interface in qupath.lib.scripting.languages: Functional interface for scripting languages that are runnable (e.g.
execute(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
execute(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.MarkdownLanguage
execute(ScriptParameters) - Method in interface qupath.lib.scripting.languages.ExecutableLanguage: Execute the given script String.
EXISTS - Enum constant in enum class qupath.lib.io.UriUpdater.UriStatus: URI refers to a file that is known to exist.
exp() - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that returns Euler's number e raise to the power of the Mat values.
EXPAND_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
expandableContent(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify a Node to display within the dialog as expandable content, not initially visible.
expandChartClip(Chart, double) - Static method in class qupath.lib.gui.charts.ChartTools: Expand the clip region for a chart.
expandToWindowProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the property indicating whether the image should grow to fill the window (while maintaining its aspect ratio).
EXPORT - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
EXPORT_GEOJSON - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
EXPORT_IMAGE_LIST - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
EXPORT_ORIGINAL - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
EXPORT_RENDERED - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
exportAllObjectsToGeoJson(String, String, String...) - Static method in class qupath.lib.scripting.QP: Export all objects (excluding root object) to an output file as GeoJSON.
exportAllObjectsToGeoJson(String, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.scripting.QP: Export all objects (excluding root object) to an output file as GeoJSON.
exportImageActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
ExportImageActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
exportJson(boolean) - Method in class qupath.lib.images.writers.TileExporter: Optionally export a JSON file that includes label information and image/label pairs, where available.
exportMeasurements(File) - Method in class qupath.lib.gui.tools.MeasurementExporter: Exports the measurements of one or more entries in the project.
exportMeasurements(OutputStream) - Method in class qupath.lib.gui.tools.MeasurementExporter: Exports the measurements of one or more entries in the project.
exportObjectsAsGeoJSON(File, Collection<? extends PathObject>, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.io.PathIO: Export a collection of objects as a GeoJSON "FeatureCollection" to a file.
exportObjectsAsGeoJSON(OutputStream, Collection<? extends PathObject>, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.io.PathIO: Export a collection of objects as a GeoJSON "FeatureCollection" to an output stream.
exportObjectsAsGeoJSON(Path, Collection<? extends PathObject>, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.io.PathIO: Export a collection of objects as a GeoJSON "FeatureCollection" to a file specified by its path.
ExportObjectsCommand - Class in qupath.lib.gui.commands: Command to export object(s) in GeoJSON format to an output file.
exportObjectsToGeoJson(Collection<? extends PathObject>, String, String, String...) - Static method in class qupath.lib.scripting.QP: Export specified objects to an output file as GeoJSON.
exportObjectsToGeoJson(Collection<? extends PathObject>, String, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.scripting.QP: Export specified objects to an output file as GeoJSON.
exportPreferences(OutputStream) - Static method in class qupath.lib.gui.prefs.PathPrefs: Export preferences to a stream.
exportSelectedObjectsToGeoJson(String, String, String...) - Static method in class qupath.lib.scripting.QP: Export the selected objects to an output file as GeoJSON.
exportSelectedObjectsToGeoJson(String, PathIO.GeoJsonExportOptions...) - Static method in class qupath.lib.scripting.QP: Export the selected objects to an output file as GeoJSON.
exportSnapshotActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
ExportSnapshotActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
exportTMAData(String, double) - Static method in class qupath.lib.gui.scripting.QPEx: Export TMA summary data for the current image.
exportTMAData(ImageData<BufferedImage>, String, double) - Static method in class qupath.lib.gui.scripting.QPEx: Export TMA summary data for the specified image.
ExportTrainingRegionsCommand - Class in qupath.process.gui.commands: Command to help export training regions as labelled images to train AI algorithms elsewhere.
ExportTrainingRegionsCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.ExportTrainingRegionsCommand: Constructor.
exportType(Class<? extends PathObject>) - Method in class qupath.lib.gui.tools.MeasurementExporter: Specify what type of object should be exported.
ExtendedPathTool - Class in qupath.lib.gui.viewer.tools
ExtensionClassLoader - Class in qupath.lib.gui: ClassLoader for loading QuPath extensions and other jars from the user directory.
ExtensionControlPane - Class in qupath.lib.gui: Borderpane that displays extensions, with options to remove, open containing folder, update, where possible.
ExtensionManager - Class in qupath.lib.gui: Manage loading extensions for a QuPathGUI instance.
ExtensionPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ExtensionPreferences
EXTENSIONS - Variable in class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
EXTENSIONS_ONLY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType: Check for extensions on GitHub only (not new QuPath releases)
extensionsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager: Read only property representing the extensions directory.
ExtensionsMenuActions - Class in qupath.lib.gui.actions.menus
ExtensionsMenuActions.Actions - Class in qupath.lib.gui.actions.menus
extract(int...) - Static method in class qupath.opencv.ops.ImageOps.Channels: Extract or rearrange channels by index.
EXTRACT_REGION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
extractBand(Raster, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Extract a band from a a raster as a SimpleImage.
extractChannel(ImageServer<BufferedImage>, BufferedImage, float[]) - Method in interface qupath.lib.images.servers.ColorTransforms.ColorTransform: Extract a (row-wise) array containing the pixels extracted from a BufferedImage.
extractChannels(int...) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Extract specified channels for an image.
extractChannels(String...) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Extract specified channels for an image.
extractDoubles(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Extract pixels as a double array.
extractFeatures(ImageData<T>, Collection<? extends PathObject>, FloatBuffer) - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor: Extract features from a collection of objects, adding the corresponding values to a FloatBuffer.
extractFloats(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Extract pixels as a float array.
extractHyperstack(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.imagej.tools.IJTools: Extract a full ImageJ hyperstack for a specific region, using all z-slices and time points.
extractHyperstack(ImageServer<BufferedImage>, RegionRequest, int, int, int, int) - Static method in class qupath.imagej.tools.IJTools: Extract a full ImageJ hyperstack for a specific region, for specified ranges of z-slices and time points.
extractMaskedDoubles(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Extract pixels from an image using a mask, limited to the specified channel index.
extractMaskedFloats(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Extract pixels from an image using a mask, limited to the specified channel index.
extractMaskedPixels(Parameters<BufferedImage, BufferedImage>, int, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils: Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.
extractMaskedPixels(Parameters<BufferedImage, BufferedImage>, String, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils: Extract the pixels from one channel of an image using the specified transform, and applying any ROI mask.
extractMaskedPixels(Parameters<BufferedImage, BufferedImage>, ColorTransforms.ColorTransform, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils: Extract the pixels from the image using the specified transform, and applying any ROI mask.
extractOverlay(PathObjectHierarchy, RegionRequest, OverlayOptions, Predicate<PathObject>) - Static method in class qupath.imagej.gui.IJExtension: Extract an ImageJ overlay for the specified region.
extractPixels(Mat, double[]) - Static method in class qupath.opencv.tools.OpenCVTools: Extract pixels as a double array.
extractPixels(Mat, float[]) - Static method in class qupath.opencv.tools.OpenCVTools: Extract pixels as a float[] array.
extractROI(ImageServer<BufferedImage>, PathObject, RegionRequest, boolean) - Static method in class qupath.imagej.gui.IJExtension: Similar to IJExtension.extractROI(ImageServer, ROI, RegionRequest, boolean), except that the title of the ImagePlus is set according to the parent object type (which is used to get the ROI).
extractROI(ImageServer<BufferedImage>, ROI, RegionRequest, boolean) - Static method in class qupath.imagej.gui.IJExtension: Extract a region of interest from an image as an ImageJ ImagePlus.
extractROIWithOverlay(ImageServer<BufferedImage>, PathObject, PathObjectHierarchy, RegionRequest, boolean, OverlayOptions) - Static method in class qupath.imagej.gui.IJExtension: Extract an image region as an ImagePlus, optionally setting ImageJ Rois corresponding to QuPath objects.
extractServerBuilder(Path) - Static method in class qupath.lib.io.PathIO: Extract a ImageServerBuilder.ServerBuilder from a serialized .qpdata file.
extractZStack(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.opencv.tools.OpenCVTools: Extract a list of Mats, where each Mat corresponds to a z-slice, for all available z-slices of a region.
extractZStack(ImageServer<BufferedImage>, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Extract a list of Mats, where each Mat corresponds to a z-slice.
eyeTrackingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the eyeTracking property of this tracker.

F

factory(GeometryFactory) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder: Specify the GeometryFactory, which can define a precision model in JTS.
FEATURE - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Each channel represents a feature for a pixel classifier.
FEATURE_COLLECTION - Enum constant in enum class qupath.lib.io.PathIO.GeoJsonExportOptions: Request that objects are export as a FeatureCollection.
FeatureCollection - Class in qupath.lib.io: Class to wrap a collection of objects to indicate they should be export as a GeoJSON "FeatureCollection".
FeatureExtractor<T> - Interface in qupath.opencv.ml.objects.features: Interface for extracting features from PathObjects for the purpose of object classification.
FeatureExtractors - Class in qupath.opencv.ml.objects.features: Helper class for extracting features from objects, used along with ObjectClassifiers.
FeatureExtractors() - Constructor for class qupath.opencv.ml.objects.features.FeatureExtractors
FeaturePreprocessor - Class in qupath.opencv.ml: Create a preprocessor for an image or training matrix.
FeaturePreprocessor() - Constructor for class qupath.opencv.ml.FeaturePreprocessor
FeaturePreprocessor.Builder - Class in qupath.opencv.ml: Builder to create a custom FeaturePreprocessor.
features(Collection<MultiscaleFeatures.MultiscaleFeature>, double, double) - Static method in class qupath.opencv.ops.ImageOps.Filters: Compute one or more MultiscaleFeatures.MultiscaleFeatures for the specified smoothing values (must be > 0).
FILE_PATH - Static variable in class qupath.lib.scripting.ScriptAttributes: File path of the running script file.
FileCopier - Class in qupath.lib.gui: Copy files to an output directory, prompting the user if necessary.
FileCopier() - Constructor for class qupath.lib.gui.FileCopier
fileExists(String) - Static method in class qupath.lib.scripting.QP: Query if a file exists.
FileFormatInfo - Class in qupath.lib.images.servers: Helper class that, given a path, determines some basic file format information without enlisting the help of an external library or performing extensive parsing of the data.
FileFormatInfo() - Constructor for class qupath.lib.images.servers.FileFormatInfo
FileFormatInfo.ImageCheckType - Interface in qupath.lib.images.servers: Interface defining some basic image metadata that may be extracted from an image file to help ascertain whether an ImageServerBuilder can handle it.
FileMenuActions - Class in qupath.lib.gui.actions.menus
FileMenuActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions
FileMenuActions.Actions - Class in qupath.lib.gui.actions.menus
FileMenuActions.ExportImageActions - Class in qupath.lib.gui.actions.menus
FileMenuActions.ExportSnapshotActions - Class in qupath.lib.gui.actions.menus
FileMenuActions.ProjectActions - Class in qupath.lib.gui.actions.menus
FileMenuActions.TmaActions - Class in qupath.lib.gui.actions.menus
files(File...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the URIs as files.
filesOnly - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
fill(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools: Fill the pixels of an image with a specific value.
fill(Mat, Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools: Fill the pixels of an image with a specific value, corresponding to a mask.
FILL_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
FILL_ANNOTATIONS - Variable in class qupath.lib.gui.actions.OverlayActions
FILL_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
FILL_DETECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
FILL_HOLES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
FillAnnotationHolesPlugin<T> - Class in qupath.lib.plugins.objects: Plugin to create new annotations by expanding the size of existing annotations.
FillAnnotationHolesPlugin() - Constructor for class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
fillAnnotations(boolean) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Request whether annotations are drawn as 'filled' shapes.
fillAnnotationsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
fillDetections(boolean) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Request whether detections are drawn as 'filled' shapes.
fillDetectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
fillHoles(ByteProcessor) - Static method in class qupath.imagej.processing.RoiLabeling: Fill holes in a binary image.
fillHoles(Geometry) - Static method in class qupath.lib.roi.GeometryTools: Fill all interior rings for the specified geometry.
fillHoles(ROI) - Static method in class qupath.lib.roi.RoiTools: Fill the holes of an Area ROI, or return the ROI unchanged if it contains no holes.
fillOutside(ImageProcessor, Roi, double) - Static method in class qupath.imagej.processing.RoiLabeling: Fill in a region outside a specified ROI
fillSmallHoles(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools: Fill holes in a binary image (1-channel, 8-bit unsigned) with an area <= maxArea.
filter(Predicate<PathObject>) - Method in class qupath.lib.gui.tools.MeasurementExporter: Filter the PathObjects before export (objects returning true for the predicate will be exported).
filter(PathObjectFilter) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Define the filter used to identify objects compatible with this classifier.
filter(PathObjectFilter) - Static method in class qupath.lib.objects.PathObjectPredicates: Wrap a PathObjectFilter as a PathObjectPredicates.PathObjectPredicate so that it can remain JSON-serializable when used in combination with other predicates.
filter2D(Mat) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D filter.
filter2D(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D filter to all channels of an image, with symmetric boundary padding.
filter2D(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D filter to all channels of an image.
filterByCentroid(boolean) - Method in class qupath.lib.objects.utils.Tiler.Builder: Set if the tiler will filter the output based on whether the centroid of tiles lies within the parent
Filters() - Constructor for class qupath.opencv.ops.ImageOps.Filters
filterSingleZ(List<Mat>, double[], int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a filter along the 'list' dimension for a list of Mats, computing the value for a single entry.
filterZ(List<Mat>, Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Filter filter along entries in the input list.
finalize() - Method in class qupath.lib.images.servers.AbstractImageServer: Attempt to close the server.
findAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
findByStringID(Collection<String>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Find objects based on a String representation of their IDs.
findByUUID(Collection<UUID>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Find objects based on their IDs.
FindConvexHullDetectionsPlugin<T> - Class in qupath.lib.plugins.objects: Plugin to identify/remove detections from the convex hull of all detections.
FindConvexHullDetectionsPlugin() - Constructor for class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
findDensityMapHotspots(String, int, int, double, boolean, boolean) - Static method in class qupath.lib.scripting.QP: Find hotspots in a density map for the current image.
findDensityMapHotspots(ImageData<BufferedImage>, String, int, int, double, boolean, boolean) - Static method in class qupath.lib.scripting.QP: Find hotspots in a density map.
findDensityMapHotspots(ImageData<BufferedImage>, DensityMaps.DensityMapBuilder, int, int, double, boolean, boolean) - Static method in class qupath.lib.scripting.QP: Find hotspots in a density map.
findDirectionalMaxima(ImageProcessor) - Static method in class qupath.imagej.processing.RoiLabeling: Create a binary image for pixels that have a higher value than their neighbors.
findDirectionalMinima(ImageProcessor) - Static method in class qupath.imagej.processing.RoiLabeling: Create a binary image for pixels that have a lower value than their neighbors.
findHotspots(PathObjectHierarchy, ImageServer<BufferedImage>, int, int, double, double, PathClass, boolean, boolean) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps: Find hotspots in a density map.
findMaxima(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Find maxima within an image.
findObjectsOutsideImage(Collection<? extends PathObject>, ImageServer<?>, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Get all the objects with ROIs that are outside the bounds of an image.
findObjectsOutsideRegion(Collection<? extends PathObject>, ImageRegion, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Get all the objects in a collection that are outside a defined region.
findObjectsOutsideRegion(Collection<? extends PathObject>, ImageRegion, int, int, int, int, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Get all the objects in a collection that are outside a defined region, expanded for multiple z-slices and timepoints.
findRegionalMaxima(ImageProcessor, float, boolean) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Find regional maxima using morphological reconstruction.
findRegionalMaxima(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the regional maxima within a Mat, providing the output as a labeled image.
finishTranslation() - Method in class qupath.lib.roi.RoiEditor: Notify the editor that translation should end.
fireHierarchyChangedEvent(Object) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Fire a hierarchy update indicating the hierarchy structure has changed.
fireHierarchyChangedEvent(Object, PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Fire a hierarchy update indicating the hierarchy structure has changed, impacting descendants of a specified object.
fireHierarchyUpdate() - Static method in class qupath.lib.scripting.QP: Trigger an update for the current hierarchy.
fireHierarchyUpdate(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Trigger an update for the specified hierarchy.
fireImageDataChanged(ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
fireObjectClassificationsChangedEvent(Object, Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Fire a hierarchy update indicating object classifications have changed.
fireObjectMeasurementsChangedEvent(Object, Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Fire a hierarchy update indicating object measurements have changed.
fireObjectMeasurementsChangedEvent(Object, Collection<? extends PathObject>, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Fire a hierarchy update indicating object measurements have changed.
fireObjectsChangedEvent(Object, Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Fire a hierarchy update indicating objects have changed.
fireObjectsChangedEvent(Object, Collection<? extends PathObject>, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Fire a hierarchy update indicating objects have changed, and may still be changing.
fireVisibleRegionChangedEvent(Shape) - Method in class qupath.lib.gui.viewer.QuPathViewer
fireWorkflowUpdatedEvent() - Method in class qupath.lib.plugins.workflow.Workflow
fitCorePolygonToGrid(Polygon, double, int, int) - Static method in class qupath.imagej.detect.dearray.TMADearrayer: Given a polygon representing TMA core centroids in any order, fit this to a coordinate grid.
fixUris(UriResource, Project<?>) - Static method in class qupath.lib.io.UriUpdater: Attempt to fix any broken paths by updating URIs based upon the current project.
FLAT - Enum constant in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap: Flat cap
flatness(double) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder: Specify the flatness for any operation where a PathIterator is required.
flatten(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Flatten a Mat to give a single column.
FLOAT - Enum constant in enum class qupath.lib.measurements.MeasurementList.MeasurementListType: A list backed by an array of floats.
FLOAT32 - Enum constant in enum class qupath.lib.images.servers.PixelType: 32-bit floating point
FLOAT64 - Enum constant in enum class qupath.lib.images.servers.PixelType: 64-bit floating point
floor() - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that floors floating point values.
floor(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Floor values in a floating point Mat.
FLUORESCENCE - Enum constant in enum class qupath.lib.images.ImageData.ImageType: Fluorescence image.
FLUORESCENCE - Static variable in class qupath.lib.scripting.QP: Fluorescence image type
fontProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Get the current selected font.
fontSizeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
forceOverlayUpdate() - Method in class qupath.lib.gui.viewer.QuPathViewer: Force the overlay displaying detections and annotations to be repainted.
formatNumber(double, int) - Static method in class qupath.lib.common.GeneralTools: Format a value with a maximum number of decimal places, using the default Locale.
formatNumber(Locale, double, int) - Static method in class qupath.lib.common.GeneralTools: Format a value with a maximum number of decimal places, using a specified Locale.
FORUM - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
framework(String) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the deep learning framework that can use the model.
framework(String) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Specify the framework (used to identify the appropriate loader for the model).
FRAMEWORK_MXNET - Static variable in class qupath.opencv.dnn.DnnModelParams: Default name to identify MXNet.
FRAMEWORK_ONNX_RUNTIME - Static variable in class qupath.opencv.dnn.DnnModelParams: Default name to identify ONNX Runtime.
FRAMEWORK_OPENCV_DNN - Static variable in class qupath.opencv.dnn.DnnModelParams: Default name to identify OpenCV DNN.
FRAMEWORK_PYTORCH - Static variable in class qupath.opencv.dnn.DnnModelParams: Default name to identify PyTorch.
FRAMEWORK_TENSORFLOW - Static variable in class qupath.opencv.dnn.DnnModelParams: Default name to identify TensorFlow.
FRAMEWORK_TF_LITE - Static variable in class qupath.opencv.dnn.DnnModelParams: Default name to identify TensorFlow Lite.
from2D(double[][]) - Static method in class qupath.lib.awt.common.AffineTransforms: Create an affine transform from a 2x3 double array, or 3x3 if the last row has the values [0, 0, 1] only.
fromArray(String...) - Static method in class qupath.lib.objects.classes.PathClass: Get a PathClass from an array of individual names.
fromBlob(T) - Method in interface qupath.opencv.dnn.BlobFunction: Convert a blob (generally the result of a prediction) to a list of mats.
fromCollection(Collection<String>) - Static method in class qupath.lib.objects.classes.PathClass: Get a PathClass using all the name elements specified in the collection, without providing a default color.
fromCollection(Collection<String>, Integer) - Static method in class qupath.lib.objects.classes.PathClass: Get a PathClass instance using all the name elements specified in the collection, with optional default color if a new instance is created.
fromColumns(double...) - Static method in class qupath.lib.awt.common.AffineTransforms: Create an affine transform from a flat matrix with 6 elements, assumed to be in the order [[0, 2, 4], [1, 3, 5]].
fromFriendlyString(String) - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Get the CompressionType corresponding to the given input
fromJTS(AffineTransformation) - Static method in class qupath.lib.awt.common.AffineTransforms: Create a Java affine transform from a Java Topology Suite representation.
fromPackedARGB(int) - Static method in class qupath.lib.display.settings.ChannelColor: Create a channel color from a packed ARGB value.
fromRGB(int, int, int) - Static method in class qupath.lib.display.settings.ChannelColor: Create a channel color from 8-bit RGB values.
fromRows(double...) - Static method in class qupath.lib.awt.common.AffineTransforms: Create an affine transform from a flat matrix with 6 elements, assumed to be in the order [[0, 1, 2], [3, 4, 5]].
fromScale(double) - Static method in class qupath.lib.awt.common.AffineTransforms: Create an affine transform representing scaling, using the same scale for x and y.
fromScale(double, double) - Static method in class qupath.lib.awt.common.AffineTransforms: Create an affine transform representing scaling, optionally using a different scale for x and y.
fromString(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider: Get the ScriptLanguage object corresponding to the specified String.
fromString(String) - Static method in class qupath.lib.objects.classes.PathClass: Get a PathClass instance from a string representation, without specifying a default color.
fromString(String, Integer) - Static method in class qupath.lib.objects.classes.PathClass: Get a PathClass instance from a string representation, optionally providing a default color if a new instance needs to be created.
FULL_SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType: Full screenshot, including items outside of QuPath.
fullImageTile() - Method in class qupath.lib.images.writers.TileExporter: Specify that a single tile should be generated corresponding to the full image.
Functions() - Constructor for class qupath.lib.experimental.pixels.MeasurementProcessor.Functions

G

gammaColorMap(ColorMaps.ColorMap, double) - Static method in class qupath.lib.color.ColorMaps: Apply gamma to a colormap.
gammaProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the gamma property for this viewer.
gammaValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: Value of the gamma slider.
GAUSSIAN - Enum constant in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType: Gaussian-weighted area normalization; maps provide weighted averaged object counts in a defined radius.
GAUSSIAN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Gaussian filter
GAUSSIAN_MEAN_ONLY - Enum constant in enum class qupath.opencv.tools.LocalNormalization.NormalizationType: Subtract Gaussian-filtered image
GAUSSIAN_MEAN_VARIANCE - Enum constant in enum class qupath.opencv.tools.LocalNormalization.NormalizationType: Subtract Gaussian-filtered image, then divide by a weighted estimate of the local standard deviation
gaussianBlur(double) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D Gaussian filter.
gaussianBlur(double, double) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a (possibly anisotropic) 2D Gaussian filter.
gaussianFilter(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D Gaussian filter to all channels of an image, with symmetric boundary padding.
gaussianFilter(Mat, double, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D Gaussian filter to all channels of an image.
gaussianNormalize(List<Mat>, LocalNormalization.LocalNormalizationType, PixelCalibration, int) - Static method in class qupath.opencv.tools.LocalNormalization: Apply local normalization to a stack of Mats representing a z-stack.
gaussianNormalize2D(Mat, double, double, int) - Static method in class qupath.opencv.tools.LocalNormalization: Apply local normalization to a 2D Mat.
gaussianNormalize3D(List<Mat>, double, double, double, double, double, double, int) - Static method in class qupath.opencv.tools.LocalNormalization: Apply 3D normalization.
gaussianSmoothed(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate the Gaussian-smoothed image.
GENERAL - Enum constant in enum class qupath.lib.measurements.MeasurementList.MeasurementListType: A general list, which can contain any kind of measurement - at the expense of being rather memory-hungry.
GeneralPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
GeneralTools - Class in qupath.lib.common: Collection of generally useful static methods.
generateDistinctName(String, Collection<String>) - Static method in class qupath.lib.common.GeneralTools: Generate a name that is distinct from the names in an existing collection, while being based on a provided name.
generateMedianStainVectorFromPixels(String, int[], double, double, double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Determine median RGB optical densities for an array of pixels (packed RGB), and combine these into a StainVector with the specified name.
GeneratingImageServer<T> - Interface in qupath.lib.images.servers: Marker interface to indicate that this ImageServer generates tiles on request.
GeometryROI - Class in qupath.lib.roi: ROI based on Java Topology Suite Geometry objects.
GeometryTools - Class in qupath.lib.roi: Convert between QuPath ROI objects and Java Topology Suite Geometry objects.
GeometryTools() - Constructor for class qupath.lib.roi.GeometryTools
GeometryTools.GeometryConverter - Class in qupath.lib.roi: Converter to help switch from a ROI to a Geometry.
GeometryTools.GeometryConverter.Builder - Class in qupath.lib.roi: Builder to help define how ROIs and Geometry objects should be converted.
geometryToROI(Geometry, ImagePlane) - Static method in class qupath.lib.roi.GeometryTools: Convert a JTS Geometry to a QuPath ROI.
geometryToShape(Geometry) - Static method in class qupath.lib.roi.GeometryTools: Convert a JTS Geometry to a java.awt.Shape.
geq(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Apply a greater than or equal to threshold.
geq(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Apply a greater than or equal to threshold between two arrays.
GESTURES_ALL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
GESTURES_NONE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
GESTURES_ROTATE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
GESTURES_SCROLL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
GESTURES_ZOOM - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
get(int) - Method in interface qupath.lib.geom.Point: Get the value of the ordinate for the specified dimension.
get(int) - Method in class qupath.lib.geom.Point2
get(int) - Method in class qupath.opencv.dnn.DnnShape: Get the length of the specified dimension.
get(String) - Method in interface qupath.lib.measurements.MeasurementList: Get value for the measurement with the specified name.
get(String) - Method in interface qupath.lib.projects.ResourceManager.Manager: Retrieve a resource by name.
get2D(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale: Get a 2D Gaussian scale.
get3DAnisotropic(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale: Get a 3D anisotropic Gaussian scale.
get3DIsotropic(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale: Get a 3D isotropic Gaussian scale.
getAcceleratorText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Get a String representation of any accelerator for the command
getActionProperty(MenuItem) - Static method in class qupath.lib.gui.actions.ActionTools: Retrieve an Action stored within the properties of a menu item, or null if no action is found.
getActionProperty(Node) - Static method in class qupath.lib.gui.actions.ActionTools: Retrieve an Action stored within the properties of a node, or null if no action is found.
getActions() - Method in class qupath.lib.gui.actions.menus.AnalyzeMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.AutomateMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.ClassifyMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.EditMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.ExtensionsMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.FileMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.HelpMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.MeasureMenuActions
getActions() - Method in interface qupath.lib.gui.actions.menus.MenuActions: Get all the actions to include in the menu, in order.
getActions() - Method in class qupath.lib.gui.actions.menus.ObjectsMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.TMAMenuActions
getActions() - Method in class qupath.lib.gui.actions.menus.ViewMenuActions
getActiveTool() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the active PathTool for this viewer.
getActiveToolIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
getActiveViewer() - Method in class qupath.lib.gui.viewer.ViewerManager: Get the value of ViewerManager.activeViewerProperty().
getAlignment() - Method in class qupath.lib.objects.utils.Tiler: Get the tiling alignment.
getAllFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the collection of recorded frames.
getAllImageSupports(URI, String...) - Static method in class qupath.lib.images.servers.ImageServers: Get all ImageServerBuilder.UriImageSupport that claim to be able to open the specified URI with optional args.
getAllNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
getAllNames() - Method in interface qupath.lib.gui.measure.PathTableData: Return an ordered list of all names, including both numeric measurements and String values.
getAllNeighbors() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get a list of neighbors for all objects.
getAllObjects() - Static method in class qupath.lib.scripting.QP: Get all objects in the current hierarchy, including the root object.
getAllObjects(boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get all the objects in the hierarchy, optionally including the root object.
getAllObjects(boolean) - Static method in class qupath.lib.scripting.QP: Get all objects in the current hierarchy.
getAllPathClassesVisible() - Method in class qupath.lib.gui.viewer.OverlayOptions
getAllPoints() - Method in class qupath.lib.roi.AreaROI: Beware this method! This will return all polygon points (useful e.g.
getAllPoints() - Method in class qupath.lib.roi.EllipseROI: Since ellipses aren't represented internally with simple polygon points, this currently returns only 4 points (rather more diamond-like that would be ideal).
getAllPoints() - Method in class qupath.lib.roi.GeometryROI
getAllPoints() - Method in interface qupath.lib.roi.interfaces.ROI: Get a list of points representing the vertices of the ROI.
getAllPoints() - Method in class qupath.lib.roi.LineROI
getAllPoints() - Method in class qupath.lib.roi.PointsROI
getAllPoints() - Method in class qupath.lib.roi.PolygonROI
getAllPoints() - Method in class qupath.lib.roi.PolylineROI
getAllPoints() - Method in class qupath.lib.roi.RectangleROI
getAllSelectedObjects() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get all currently-selected objects from the hierarchy.
getAllThumbnails() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get thumbnails for all z-slices & time points
getAllTileRequests() - Method in interface qupath.lib.images.servers.TileRequestManager: Get TileRequest objects for all tiles that this server supports.
getAllTimes() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Retrieve a sorted array containing all times where 'something happened' (observed or censored).
getAllViewers() - Method in class qupath.lib.gui.QuPathGUI: Get an unmodifiable observable list of all viewers.
getAllViewers() - Method in class qupath.lib.gui.viewer.ViewerManager: Get an observable list of viewers.
getAlphaComposite() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
getAnalysisTabPane() - Method in class qupath.lib.gui.QuPathGUI: Access the main tab pane shown in the QuPath window.
getAncestorList(PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Return a list of object ancestors, starting from the root object and ending with PathObject (assuming that the object is part of a hierarchy with a root).
getAncestorTMACore(PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Get the TMA core object that contains a specified PathObject, or null if the object is not contained within a TMA core.
getAnnotatedActions(Object) - Static method in class qupath.lib.gui.actions.ActionTools: Actions can be parsed from the accessible (usually public) fields of any object, as well as methods annotated with ActionMethod.
getAnnotationObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get all annotation objects in the hierarchy.
getAnnotationObjects() - Static method in class qupath.lib.scripting.QP: Get a list of the current annotation objects.
getArea() - Method in class qupath.lib.roi.EllipseROI
getArea() - Method in class qupath.lib.roi.RectangleROI
getArea() - Method in class qupath.lib.roi.AreaROI
getArea() - Method in class qupath.lib.roi.GeometryROI
getArea() - Method in interface qupath.lib.roi.interfaces.ROI: Get the area of this ROI.
getArea() - Method in class qupath.lib.roi.LineROI
getArea() - Method in class qupath.lib.roi.PointsROI
getArea() - Method in class qupath.lib.roi.PolygonROI
getArea() - Method in class qupath.lib.roi.PolylineROI
getArea(ROI) - Static method in class qupath.lib.roi.RoiTools: Get an Area object representing a ROI.
getAreaObjects(Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools: Get a list of objects with area ROIs from a collection of objects.
getARGB(Color) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get a packed int (ARGB) representation of a Color object.
getArgs() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder: Get the args array.
getArgs() - Method in class qupath.lib.scripting.ScriptParameters: Get an optional array of string arguments passed to the script.
getArray() - Method in class qupath.lib.color.StainVector: Get the stain vector as a 3 element array (red, green, blue).
getArray(boolean) - Method in class qupath.imagej.tools.PixelImageIJ
getArray(boolean) - Method in interface qupath.lib.analysis.images.SimpleModifiableImage: Request the pixel array representing all the pixels in this image, returned row-wise.
getAssociatedImage(String) - Method in class qupath.lib.images.servers.AbstractImageServer
getAssociatedImage(String) - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
getAssociatedImage(String) - Method in interface qupath.lib.images.servers.ImageServer: Get the image for a given associated image name.
getAssociatedImage(String) - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get a named associated image.
getAssociatedImage(String) - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
getAssociatedImageList() - Method in class qupath.lib.images.servers.AbstractImageServer
getAssociatedImageList() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
getAssociatedImageList() - Method in interface qupath.lib.images.servers.ImageServer: Get a list of 'associated images', e.g.
getAssociatedImageList() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
getAssociatedImages() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get a list of all associated image names.
getAtRisk(double) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get the number at risk at a specified time.
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.CssLanguage
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.JsonLanguage
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.MarkdownLanguage
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.PlainLanguage
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.PropertiesLanguage
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.XmlLanguage
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.YamlLanguage
getAutoCompletor() - Method in class qupath.lib.scripting.languages.ScriptLanguage: Get the ScriptAutoCompletor object that takes care of this language's auto-completion.
getAutomateActions() - Method in class qupath.lib.gui.QuPathGUI: Get the automated actions associated with this QuPath instance.
getAvailableFeatures(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Get a set containing the names of all measurements found in the measurement lists of a specified object collection.
getAvailableLanguages() - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider: Get the available script languages.
getAvailablePathClasses() - Method in class qupath.lib.gui.QuPathGUI: Get an observable list of available PathClasses.
getAvailableSyntaxes() - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider: Get the available script syntaxes.
getAvailableTools() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
getAveragedPixelSize() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the averaged pixel size in microns, if available - or Double.NaN otherwise.
getAveragedPixelSize() - Method in class qupath.lib.images.servers.PixelCalibration: Get an average of PixelCalibration.getPixelWidth() and PixelCalibration.getPixelHeight().
getAveragedPixelSizeMicrons() - Method in class qupath.lib.images.servers.PixelCalibration: Get the average of the pixel width and height in microns if possible, or Double.NaN if the pixel size is not available.
getBackingListEntries() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Access the underlying entries, for which getEntries provides a filtered view.
getBaseClass() - Method in class qupath.lib.objects.classes.PathClass: Get the 'base' class, i.e.
getBaseDirectory(Project<?>) - Static method in class qupath.lib.projects.Projects: Get the base directory of a project stored on the local file system.
getBasePathClass(PathObject) - Static method in class qupath.lib.scripting.QP: Get a base class - which is either a valid PathClass which is *not* an intensity class, or else null.
getBaseStyle() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.MarkdownStyler: Returns "-fx-font-family: sans-serif" to indicate the text should not be formatted as code by default.
getBaseStyle() - Method in interface qupath.lib.gui.scripting.richtextfx.stylers.ScriptStyler: Optionally return a base style for the code area.
getBatchIndex() - Method in class qupath.lib.scripting.ScriptParameters: Get the index of the current image for batch processing, where 0 is the first and getBatchSize() - 1 is the last.
getBatchSaveResult() - Method in class qupath.lib.scripting.ScriptParameters: Get whether changes to the image data should be saved.
getBatchSize() - Method in class qupath.lib.scripting.ScriptParameters: Get the number of images being batch processed, or 1 if just a single image is being processed.
getBinIndexForValue(double, double) - Method in class qupath.lib.analysis.stats.Histogram: Get the index of the bin that should contain the specified value.
getBinLeftEdge(int) - Method in class qupath.lib.analysis.stats.Histogram: Get the lower edge for a specified bin.
getBinRightEdge(int) - Method in class qupath.lib.analysis.stats.Histogram: Get the upper edge for a specified bin.
getBinWidth(int) - Method in class qupath.lib.analysis.stats.Histogram: Get the width of a bin, which is the difference between its upper and lower edges.
getBitsPerPixel() - Method in enum class qupath.lib.images.servers.PixelType: Number of bits per pixel.
getBlobFunction() - Method in class qupath.opencv.dnn.AbstractDnnModel: Get the function that can convert one or more OpenCV Mats into a blob supported by the prediction function for the first (or only) input.
getBlobFunction() - Method in class qupath.opencv.dnn.OpenCVDnn
getBlobFunction(String) - Method in class qupath.opencv.dnn.AbstractDnnModel: Get the function that can convert one or more OpenCV Mats into a blob supported by the prediction function for a specified input layer.
getBlobFunction(String) - Method in class qupath.opencv.dnn.OpenCVDnn
getBlue() - Method in class qupath.lib.color.StainVector: Get the blue component of the (normalized) stain vector.
getBlue() - Method in class qupath.lib.display.settings.ChannelColor: Get the blue value.
getBlueOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
getBooleanParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Get a boolean parameter value (or its default) for the specified key.
getBorderColor() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the border color set for this viewer.
getBoundaryClass(PathClass) - Method in class qupath.process.gui.commands.ml.BoundaryStrategy: Get the classification to be used for the annotation boundary, given the classification of the annotated region.
getBoundaryDistance(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools: Get the Euclidean distance between the boundaries of two ROIs.
getBoundaryDistance(ROI, ROI, double, double) - Static method in class qupath.lib.roi.RoiTools: Get the calibrated Euclidean distance between the boundaries of two ROIs using specified pixel sizes.
getBoundaryLabels() - Method in class qupath.lib.images.servers.LabeledImageServer: Get an unmodifiable map of classifications and their corresponding boundary labels, if available.
getBoundaryStrategy() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Get the strategy for handling the boundaries of area annotations.
getBoundaryThickness() - Method in class qupath.process.gui.commands.ml.BoundaryStrategy: Get the boundary thickness, in pixels.
getBounds(ImageRegion) - Static method in class qupath.lib.awt.common.AwtTools: Create a Rectangle corresponding to the x,y,width,height of an ImageRegion.
getBounds(ImageRegion, Rectangle) - Static method in class qupath.lib.awt.common.AwtTools: Set the bounds of an existing Rectangle to the x,y,width,height of an ImageRegion.
getBounds(ROI) - Static method in class qupath.lib.awt.common.AwtTools: Create a Rectangle corresponding to bounding box of a ROI.
getBounds2D(ROI) - Static method in class qupath.lib.awt.common.AwtTools: Create a Rectangle2D corresponding to bounding box of a ROI.
getBounds2D(ROI, Rectangle2D) - Static method in class qupath.lib.awt.common.AwtTools: Set the bounds of an existing Rectangle2D to the x,y,width,height of a ROI.
getBoundsHeight() - Method in class qupath.lib.roi.EllipseROI
getBoundsHeight() - Method in class qupath.lib.roi.RectangleROI
getBoundsHeight() - Method in class qupath.lib.roi.AreaROI
getBoundsHeight() - Method in class qupath.lib.roi.GeometryROI
getBoundsHeight() - Method in interface qupath.lib.roi.interfaces.ROI: Returns the height of the ROI bounding box.
getBoundsHeight() - Method in class qupath.lib.roi.LineROI
getBoundsHeight() - Method in class qupath.lib.roi.PointsROI
getBoundsHeight() - Method in class qupath.lib.roi.PolygonROI
getBoundsHeight() - Method in class qupath.lib.roi.PolylineROI
getBoundsWidth() - Method in class qupath.lib.roi.EllipseROI
getBoundsWidth() - Method in class qupath.lib.roi.RectangleROI
getBoundsWidth() - Method in class qupath.lib.roi.AreaROI
getBoundsWidth() - Method in class qupath.lib.roi.GeometryROI
getBoundsWidth() - Method in interface qupath.lib.roi.interfaces.ROI: Returns the width of the ROI bounding box.
getBoundsWidth() - Method in class qupath.lib.roi.LineROI
getBoundsWidth() - Method in class qupath.lib.roi.PointsROI
getBoundsWidth() - Method in class qupath.lib.roi.PolygonROI
getBoundsWidth() - Method in class qupath.lib.roi.PolylineROI
getBoundsX() - Method in class qupath.lib.roi.EllipseROI
getBoundsX() - Method in class qupath.lib.roi.RectangleROI
getBoundsX() - Method in class qupath.lib.roi.AreaROI
getBoundsX() - Method in class qupath.lib.roi.GeometryROI
getBoundsX() - Method in interface qupath.lib.roi.interfaces.ROI: Returns the x coordinate for the top left of the ROI bounding box.
getBoundsX() - Method in class qupath.lib.roi.LineROI
getBoundsX() - Method in class qupath.lib.roi.PointsROI
getBoundsX() - Method in class qupath.lib.roi.PolygonROI
getBoundsX() - Method in class qupath.lib.roi.PolylineROI
getBoundsY() - Method in class qupath.lib.roi.EllipseROI
getBoundsY() - Method in class qupath.lib.roi.RectangleROI
getBoundsY() - Method in class qupath.lib.roi.AreaROI
getBoundsY() - Method in class qupath.lib.roi.GeometryROI
getBoundsY() - Method in interface qupath.lib.roi.interfaces.ROI: Returns the y coordinate for the top left of the ROI bounding box.
getBoundsY() - Method in class qupath.lib.roi.LineROI
getBoundsY() - Method in class qupath.lib.roi.PointsROI
getBoundsY() - Method in class qupath.lib.roi.PolygonROI
getBoundsY() - Method in class qupath.lib.roi.PolylineROI
getBrushDiameter() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
getBrushDiameter() - Method in class qupath.process.gui.WandToolEventHandler: Don't actually need the diameter for calculations here, but it's helpful for setting the cursor
getBufferedImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the buffered image.
getBuilder() - Method in class qupath.lib.images.servers.AbstractImageServer
getBuilder() - Method in interface qupath.lib.images.servers.ImageServer: Get a ServerBuilder capable of building a server the same as this one.
getBuilders() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport: Get a list of ServerBuilders, one for each image that can be read based on the specified URI.
getBuildString() - Method in class qupath.lib.gui.BuildInfo: Get the build String, or null if no build String is available.
getBuildString() - Static method in class qupath.lib.gui.QuPathGUI: Get a String representing the QuPath version & build time.
getBytesPerPixel() - Method in enum class qupath.lib.images.servers.PixelType: Number of bytes per pixel.
getC() - Method in class qupath.lib.regions.ImagePlane: Get the channel index.
getC() - Method in class qupath.lib.roi.AreaROI
getC() - Method in class qupath.lib.roi.EllipseROI
getC() - Method in class qupath.lib.roi.GeometryROI
getC() - Method in class qupath.lib.roi.LineROI
getC() - Method in class qupath.lib.roi.PointsROI
getC() - Method in class qupath.lib.roi.PolygonROI
getC() - Method in class qupath.lib.roi.PolylineROI
getC() - Method in class qupath.lib.roi.RectangleROI
getC() - Method in interface qupath.lib.roi.interfaces.ROI: Get channel index, or -1 if the ROI relates to all available channels.
getC() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel: Get channel index.
getCache() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
getCache() - Method in class qupath.lib.images.servers.AbstractImageServer: Get the internal cache.
getCache(Class<T>) - Static method in class qupath.lib.images.servers.ImageServerProvider: Get the cache in use for image tiles of a specific type.
getCachedColor(int, int, int) - Static method in class qupath.lib.color.ColorToolsAwt: Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
getCachedColor(int, int, int) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
getCachedColor(int, int, int, int) - Static method in class qupath.lib.color.ColorToolsAwt: Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
getCachedColor(int, int, int, int) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
getCachedColor(Integer) - Static method in class qupath.lib.color.ColorToolsAwt: Get cached color.
getCachedColor(Integer) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get cached color.
getCachedColor(Integer, boolean) - Static method in class qupath.lib.color.ColorToolsAwt: Get cached color, explicitly stating whether alpha should be included or not.
getCachedColor(Integer, boolean) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get cached color, explicitly stating whether alpha should be included or not.
getCachedMeasurementValue(PathObject, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Get the value of a single measurement for a specified PathObject if all tiles are cached, otherwise return null.
getCachedMeasurementValue(ROI, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Get the value of a single measurement for a specified ROI if all tiles are cached, otherwise return null.
getCachedRegion(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
getCachedStroke(double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Get a BasicStroke with the specified thickness.
getCachedThumbnail(ImageServer<BufferedImage>, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
getCachedTile(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
getCachedTile(TileRequest) - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
getCachedTile(TileRequest) - Method in class qupath.lib.images.servers.AbstractImageServer: Get a cached tile, or null if the tile has not been cached.
getCachedTile(TileRequest) - Method in interface qupath.lib.images.servers.ImageServer: Get a cached tile, or null if the tile has not been cached.
getCachedTilesForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Get a map of all cached tiles pertaining to a specific ImageServer.
getCaretPosition() - Method in interface qupath.lib.gui.scripting.EditableText: Get the current caret position.
getCaretPosition() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl: Gets the value of the caretPosition property.
getCaretPosition() - Method in class qupath.lib.gui.scripting.TextAreaControl: Gets the value of the caretPosition property.
getCaseID() - Method in class qupath.lib.objects.TMACoreObject: Get the case ID metadata value.
getCellObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get all cell objects in the hierarchy.
getCellObjects() - Static method in class qupath.lib.scripting.QP: Get a list of the current cell objects.
getCenterPixelX() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the x-coordinate of the pixel currently centered in the viewer, in the full size image space.
getCenterPixelY() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the y-coordinate of the pixel currently centered in the viewer, in the full size image space.
getCentroidDistance(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools: Get the Euclidean distance between the centroids of two ROIs.
getCentroidDistance(ROI, ROI, double, double) - Static method in class qupath.lib.roi.RoiTools: Get the calibrated Euclidean distance between the centroids of two ROIs using specified pixel sizes.
getCentroidX() - Method in class qupath.lib.roi.EllipseROI
getCentroidX() - Method in class qupath.lib.roi.RectangleROI
getCentroidX() - Method in class qupath.lib.roi.AreaROI: Get the x coordinate of the ROI centroid;
getCentroidX() - Method in class qupath.lib.roi.GeometryROI
getCentroidX() - Method in interface qupath.lib.roi.interfaces.ROI: Returns the x coordinate for the ROI centroid.
getCentroidX() - Method in class qupath.lib.roi.LineROI
getCentroidX() - Method in class qupath.lib.roi.PointsROI
getCentroidX() - Method in class qupath.lib.roi.PolygonROI
getCentroidX() - Method in class qupath.lib.roi.PolylineROI: The centroid for a Polyline here is represented by the centroid of its bounding box.
getCentroidY() - Method in class qupath.lib.roi.EllipseROI
getCentroidY() - Method in class qupath.lib.roi.RectangleROI
getCentroidY() - Method in class qupath.lib.roi.AreaROI: Get the y coordinate of the ROI centroid;
getCentroidY() - Method in class qupath.lib.roi.GeometryROI
getCentroidY() - Method in interface qupath.lib.roi.interfaces.ROI: Returns the y coordinate for the ROI centroid.
getCentroidY() - Method in class qupath.lib.roi.LineROI
getCentroidY() - Method in class qupath.lib.roi.PointsROI
getCentroidY() - Method in class qupath.lib.roi.PolygonROI
getCentroidY() - Method in class qupath.lib.roi.PolylineROI: The centroid for a Polyline here is represented by the centroid of its bounding box.
getChangedObjects() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: The objects that were affected by whichever changes were made.
getChannel() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Get the channel to threshold.
getChannel() - Method in class qupath.lib.display.DirectServerChannelInfo: Get the channel number.
getChannel(int) - Method in class qupath.lib.images.servers.AbstractImageServer
getChannel(int) - Method in interface qupath.lib.images.servers.ImageServer: Request information for one channel (0-based index).
getChannel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the specified channel.
getChannelIndex(ImageServer<?>, String) - Static method in class qupath.lib.images.servers.ServerTools: Get the index of the first channel of a server with a specified channel name.
getChannelList(String...) - Static method in class qupath.lib.images.servers.ImageChannel: Convert an array of channel names into a list of ImageChannel using default colors.
getChannels() - Method in class qupath.lib.display.settings.ImageDisplaySettings: Get all the available channels.
getChannels() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get an unmodifiable list of all channels.
getChannels(List<ImageChannel>) - Method in interface qupath.opencv.ops.ImageOp: Get appropriate channels to reflect the output of this transform.
getChannels(ImageData<BufferedImage>) - Method in interface qupath.opencv.ops.ImageDataOp: Get appropriate channels to reflect the output of this transform, given the input.
getChannelType() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the channel type, which can be used to interpret the channels.
getChartDataAsString(XYChart<Number, Number>) - Static method in class qupath.lib.gui.charts.ChartTools: Get a string representation of chart data, in such a way that it could be pasted into a spreadsheet.
getCheckpoints() - Method in class qupath.lib.common.Timeit: Get an list of all the checkpoints.
getChildObjects() - Method in class qupath.lib.objects.PathObject: Get a collection of child objects.
getChildObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject: Get a collection containing all child objects.
getChildObjectsAsArray() - Method in class qupath.lib.objects.PathObject: Get a defensive copy of child objects as an array.
getChoiceParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Get a choice parameter value (or its default) for the specified key.
getChoices() - Method in class qupath.lib.plugins.parameters.ChoiceParameter: Get a list of available choices.
getChooser(Window) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Get a QuPathChooser instance linked to a specific window.
getCircularity(ROI) - Static method in class qupath.lib.roi.RoiTools: Get circularity measurement for Area ROIs, calculated as 4 * PI * (area / perimeter^2).
getCircularity(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools: Get circularity measurement for area ROIs, with optional pixel calibration, calculated as 4 * PI * (area / perimeter^2).
getCircularStructuringElement(int) - Static method in class qupath.opencv.tools.OpenCVTools: Deprecated.
OpenCVTools.createDisk(int, boolean) gives more reliable shapes.
getCitationUrl() - Static method in class qupath.lib.gui.Urls: Get a URL pointing to a page that explains how to cite this version of QuPath in a publication.
getClassification(ImageServer<BufferedImage>, int, int, int, int) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools: Request the classification for a specific pixel.
getClassificationLabels() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Map between integer labels and classifications.
getClassificationLabels() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get map between labels and classification names.
getClassifications() - Method in class qupath.lib.objects.PathObject: Get the components of the PathClass as an unmodifiable set.
getClassifier() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Get the PixelClassifier performing the classification.
getClassifyBoundaryStrategy(PathClass, double) - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy: Create a boundary strategy that trains a classifier for a specific PathClass for annotation boundaries.
getClassProbability() - Method in class qupath.lib.objects.PathObject: Request the classification probability, or Double.NaN if no probability is available.
getClassProbability() - Method in class qupath.lib.objects.PathROIObject
getClassProbability() - Method in class qupath.lib.objects.PathRootObject
getClipboardText(boolean) - Static method in class qupath.lib.gui.scripting.DefaultScriptEditor
getClusters(BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get clusters of connected objects, where connections are made between neighboring objects that meet the specified predicate.
getColor() - Method in class qupath.lib.color.StainVector: Get a Color that (roughly) corresponds to color represented by this stain vector.
getColor() - Method in interface qupath.lib.display.ChannelDisplayInfo: Predominate color used when this ChannelDisplayInfo uses a Color LUT (e.g.
getColor() - Method in class qupath.lib.display.DirectServerChannelInfo
getColor() - Method in class qupath.lib.display.settings.ChannelSettings: Get the color used to display the channel, or null if a color is not relevant.
getColor() - Method in class qupath.lib.images.servers.ImageChannel: Color used to display the output channel
getColor() - Method in class qupath.lib.objects.classes.PathClass: Get the color that should be used to display objects with this classification.
getColor() - Method in class qupath.lib.objects.PathObject: Return any stored color as a packed RGB value.
getColor(double, double, double) - Method in interface qupath.lib.color.ColorMaps.ColorMap: Get a packed ARGB representation of the (interpolated) color at the specified value,.
getColorDeconvolutionStains() - Method in class qupath.lib.images.ImageData: Get the stains defined for this image, or null if this is not a brightfield image suitable for color deconvolution.
getColorDeconvolutionStainsAsString(ColorDeconvolutionStains, int) - Static method in class qupath.lib.color.ColorDeconvolutionStains: Get a String representation of the stains and background.
getColorForObject(PathObject) - Method in class qupath.lib.gui.tools.MeasurementMapper: Get the display color for a specified object, according to the settings of this mapper.
getColorMap() - Method in class qupath.lib.gui.ColorMapCanvas: Return the currently displayed ColorMaps.ColorMap.
getColorMapper() - Method in class qupath.lib.gui.tools.MeasurementMapper: Get the color mapper, which is effectively a lookup table.
getColorMaps() - Static method in class qupath.lib.color.ColorMaps: Get an unmodifiable map representing all the currently-available colormaps.
getColormapsDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager: Get the path to where colormaps should be written.
getColorModel() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer: Get the ColorModel for this renderer (may be null).
getColorModel() - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
getColorModel() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
getColorModel(ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
getColorRGB() - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, use PathObject.getColor() instead.
getColorRGB(int...) - Static method in class qupath.lib.scripting.QP: Deprecated.
Use instead QP.makeRGB(int, int, int) or QP.makeARGB(int, int, int, int)
getColors(ColorMaps.ColorMap, int, boolean) - Static method in class qupath.lib.color.ColorMaps: Get an array of packed RGB values for a specific colormap.
getColorWithOpacity(Color, double) - Static method in class qupath.lib.color.ColorToolsAwt: Get a color with a specified opacity, setting the alpha channel accordingly.
getColorWithOpacity(Integer, double) - Static method in class qupath.lib.color.ColorToolsAwt: Get a color with a specified opacity, based on the packed RGB values in an Integer.
getColorWithOpacity(Color, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Derived a Color from an existing one, setting the alpha component to match the desired opacity.
getColorWithOpacityFX(Integer, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get a Color from a packed RGB value, setting the alpha component to match the desired opacity.
getCommandPath() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Get a string representation of the menu path for this command, including the menu path and the text.
getCommonActions() - Method in class qupath.lib.gui.QuPathGUI: Get the common actions associated with this QuPath instance.
getComparator() - Static method in class qupath.lib.scripting.languages.AutoCompletions: Get a comparator to order completions.
getCompatibleObjects(ImageData<T>) - Method in class qupath.lib.classifiers.object.AbstractObjectClassifier
getCompatibleObjects(ImageData<T>) - Method in interface qupath.lib.classifiers.object.ObjectClassifier: Get the objects from an ImageData that are compatible with this classifier.
getCompatibleWriters(Class<T>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools: Get a list of compatible ImageWriters for a specific image class.
getCompatibleWriters(ImageServer<T>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools: Get a list of compatible ImageWriters compatible with a specific server.
getCompletions(String, int) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
getCompletions(String, int) - Method in interface qupath.lib.scripting.languages.ScriptAutoCompletor: Get a list of possible auto-completions for the given text with the caret at the specified position.
getCompletionText() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion: Get the text that should be inserted for the full completion.
getConfigPath() - Static method in class qupath.lib.gui.prefs.PathPrefs: Try to get the path to the config file.
getConfigUri() - Method in class qupath.opencv.dnn.OpenCVDnn: Get the path to the model configuration, if required.
getConnectedClusters() - Method in class qupath.opencv.features.DelaunayTriangulation: Get a list of PathObjects that are connected to each other in this triangulation.
getConnectedNodes(Collection<PathObject>, Collection<double[]>) - Method in class qupath.opencv.features.DelaunayTriangulation: Deprecated.
getConnectedNodes(PathObject, Collection<PathObject>) - Method in class qupath.opencv.features.DelaunayTriangulation: Get all the PathObjects immediately connected to the specified object, adding the points into a collection (or creating a new one).
getConnectedObjects(PathObject) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
getConnectedObjects(PathObject) - Method in interface qupath.lib.objects.PathObjectConnectionGroup: Get all the connections to a specified PathObject stored in this group.
getConnectedObjects(PathObject) - Method in class qupath.opencv.features.DelaunayTriangulation
getConnectionGroups() - Method in class qupath.lib.objects.PathObjectConnections: Get an unmodifiable list containing all connections groups.
getConnections(PathObject) - Method in class qupath.lib.objects.PathObjectConnections: Get all the connections to a specified PathObject.
getContents(Parent, Collection<Node>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Get the nodes that are included within a Parent, optionally adding other nodes recursively.
getContentsOfType(Parent, Class<T>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Get the nodes of type T that are contained within a Parent, optionally adding other nodes recursively.
getContextMenu() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
getContextMenu() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Get the context menu for the control.
getContextMenu() - Method in class qupath.lib.gui.scripting.TextAreaControl
getConvexHull() - Method in class qupath.lib.roi.AreaROI: Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.GeometryROI: Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.PolygonROI: Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.PolylineROI: Default implementation using JTS.
getConvexHull() - Method in class qupath.lib.roi.EllipseROI
getConvexHull() - Method in interface qupath.lib.roi.interfaces.ROI: Get a ROI representing the convex hull of this ROI.
getConvexHull() - Method in class qupath.lib.roi.LineROI
getConvexHull() - Method in class qupath.lib.roi.PointsROI
getConvexHull() - Method in class qupath.lib.roi.RectangleROI
getConvexHull(List<Point2>) - Static method in class qupath.lib.roi.ConvexHull: TODO: Consider a more efficient convex hull calculation.
getCoreClasses() - Static method in class qupath.lib.gui.scripting.QPEx: Get a list of core classes that are likely to be useful for scripting.
getCoreClasses() - Static method in class qupath.lib.scripting.QP: Get a list of core classes that are likely to be useful for scripting.
getCount() - Method in class qupath.lib.gui.actions.InfoMessage: Counts associated with the message, or -1 if the count is null.
getCountsForBin(int) - Method in class qupath.lib.analysis.stats.Histogram: Get the histogram counts for the specified bin.
getCountsTransform() - Method in class qupath.lib.gui.charts.HistogramChart: Get the current counts transform.
getCountSum() - Method in class qupath.lib.analysis.stats.Histogram: Sum of all histogram counts.
getCreationTimestamp() - Method in interface qupath.lib.projects.Project: Request a timestamp from when the project was created.
getCropRegion() - Method in class qupath.lib.images.servers.CroppedImageServer: Get the region being cropped, in terms of the bounding box within the base ImageServer.
getCropToParent() - Method in class qupath.lib.objects.utils.Tiler: Check if the tiler is set to crop the output to the input parent.
getCssStylesPath() - Method in class qupath.lib.gui.UserDirectoryManager: Get the path to where user directory for storing CSS styles.
getCurrentConsoleControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
getCurrentDataFileVersion() - Static method in class qupath.lib.io.PathIO: Get the current preferred data file version.
getCurrentEditorControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
getCurrentHierarchy() - Static method in class qupath.lib.scripting.QP: Get the PathObjectHierarchy of the current ImageData.
getCurrentImageData() - Static method in class qupath.lib.scripting.QP: Get the path to the current ImageData.
getCurrentImageName() - Static method in class qupath.lib.scripting.QP: Get the name of the current image.
getCurrentImageNameWithoutExtension() - Static method in class qupath.lib.scripting.QP: Get the name of the current image, removing any file extension.
getCurrentImages(QuPathGUI) - Static method in class qupath.lib.gui.dialogs.ProjectDialogs: Get the ProjectImageEntry for each of the current images open in QuPath, if available.
getCurrentLanguage() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Gets the value of the currentLanguage property.
getCurrentParent() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
getCurrentParent() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
getCurrentParent() - Method in class qupath.process.gui.WandToolEventHandler
getCurrentROI() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the current ROI, i.e.
getCurrentScriptTab() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
getCurrentServer() - Static method in class qupath.lib.scripting.QP: Get the ImageServer of the current ImageData.
getCurrentServerPath() - Static method in class qupath.lib.scripting.QP: Get the path to the ImageServer of the current ImageData.
getCurrentSyntax() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Gets the value of the currentSyntax property.
getCurrentText() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
getCurrentViewer() - Static method in class qupath.lib.gui.scripting.QPEx: Get the active viewer in the current QuPath instance.
getCursor() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the current cursor for this viewer
getCustomOverlayLayers() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get direct access to the custom overlay list.
getCustomPixelLayerOverlay() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the custom pixel layer overlay, or null if it has not be set.
getDataMaxValue() - Method in class qupath.lib.gui.tools.MeasurementMapper: Get the maximum measurement value from the objects passed to the constructor of this mapper.
getDataMinValue() - Method in class qupath.lib.gui.tools.MeasurementMapper: Get the minimum measurement value from the objects passed to the constructor of this mapper.
getDebugMode() - Static method in class qupath.imagej.detect.cells.WatershedCellDetection: Get whether debug mode is on or off.
getDefaultAutoCompletor(String) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Default method to get a suitable auto completor for the given language name.
getDefaultBuilder() - Static method in class qupath.lib.io.GsonTools: Access the builder used with GsonTools.getInstance().
getDefaultChannelColor(int) - Static method in class qupath.lib.images.servers.ImageChannel: Get the default color for a specified channel, for use when no channel colors are already known.
getDefaultChannelList(int) - Static method in class qupath.lib.images.servers.ImageChannel: Get default channel list for an image with a specified number of channels.
getDefaultColorMap() - Static method in class qupath.lib.color.ColorMaps: Get a default, general-purpose ColorMaps.ColorMap.
getDefaultColorModel() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
getDefaultColorModel() - Method in class qupath.lib.images.servers.AbstractTileableImageServer: Get an appropriate colormodel that may be used.
getDefaultColorModel() - Method in class qupath.lib.images.servers.SparseImageServer
getDefaultColorModel(ColorTransformer.ColorTransformMethod) - Static method in class qupath.lib.color.ColorTransformer: This does not guarantee a ColorModel will be returned! If it is not, then a default grayscale LUT should be used.
getDefaultCreateFunction() - Static method in class qupath.lib.plugins.TaskRunnerUtils: Get the default function used to create TaskRunner instances.
getDefaultDragDropListener() - Method in class qupath.lib.gui.QuPathGUI: Get a reference to the default drag & drop listener, so this may be added to additional windows if needed.
getDefaultExtension() - Method in interface qupath.lib.images.writers.ImageWriter: Get the default extension.
getDefaultFactory() - Static method in class qupath.lib.roi.GeometryTools: Get the default GeometryFactory to construct Geometries within QuPath.
getDefaultImports() - Method in class qupath.lib.scripting.ScriptParameters: Get default imports that should be included with the script, where possible.
getDefaultInstance() - Static method in class qupath.lib.images.servers.PixelCalibration: Get the default PixelCalibration.
getDefaultInstance() - Static method in class qupath.lib.plugins.TaskRunnerUtils: Get the default instance.
getDefaultLocationString(ImageServer<BufferedImage>, double, double, int, int) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Default method for getting a location string from an ImageServer using cached tiles.
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.PositiveCellDetection
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.SubcellularDetection
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.opencv.CellCountsCV
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.opencv.DetectCytokeratinCV
getDefaultParameterList(ImageData<BufferedImage>) - Method in class qupath.opencv.WatershedNucleiCV
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.algorithms.TilerPlugin
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.AbstractInteractivePlugin: This should return a default ParameterList containing any information that is needed to repeat the task exactly.
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin: Returns an empty ParameterList.
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin: Returns an empty ParameterList.
getDefaultParameterList(ImageData<T>) - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
getDefaultParameterList(ImageData<T>) - Method in interface qupath.lib.plugins.PathInteractivePlugin: This should return a default ParameterList.
getDefaultParameterList(ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
getDefaultPlane() - Static method in class qupath.lib.regions.ImagePlane: Returns an ImagePlane with channel -1, z of 0 and t of 0.
getDefaultPyramidCompression() - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand: Query the default compression type when writing OME-TIFF images.
getDefaultQuPathUserDirectory() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get the default location for extensions.
getDefaultResolutions(ImageData<?>, ClassificationResolution) - Static method in class qupath.process.gui.commands.ml.ClassificationResolution: Get a list of default resolutions to show, derived from PixelCalibration objects.
getDefaultRGBChannels() - Static method in class qupath.lib.images.servers.ImageChannel: Get default channel list for RGB images.
getDefaultScriptName() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
getDefaultShortServerName(URI) - Static method in class qupath.lib.images.servers.ServerTools: Get the default shortened server name given the server's path.
getDefaultStaticImports() - Method in class qupath.lib.scripting.ScriptParameters: Get default static imports that should be included with the script, where possible.
getDefaultThumbnail(int, int) - Method in class qupath.lib.images.servers.AbstractImageServer
getDefaultThumbnail(int, int) - Method in interface qupath.lib.images.servers.ImageServer: Get the default thumbnail for a specified z-slice and timepoint.
getDefaultTileSize() - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand: Query the default tile size when writing OME-TIFF images.
getDefaultTransformedMax(ColorTransformer.ColorTransformMethod) - Static method in class qupath.lib.color.ColorTransformer: Get default maximum value to use with a specific transform method.
getDefaultValue() - Method in class qupath.lib.plugins.parameters.BooleanParameter
getDefaultValue() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
getDefaultValue() - Method in class qupath.lib.plugins.parameters.DoubleParameter
getDefaultValue() - Method in class qupath.lib.plugins.parameters.EmptyParameter
getDefaultValue() - Method in class qupath.lib.plugins.parameters.IntParameter
getDefaultValue() - Method in class qupath.lib.plugins.parameters.NumericParameter
getDefaultValue() - Method in class qupath.lib.plugins.parameters.StringParameter
getDefaultValue() - Method in interface qupath.lib.plugins.parameters.Parameter: Get a default value to use if the Parameter has not been otherwise set.
getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
getDefaultZoomFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer: The amount by which the downsample factor is scaled for one increment of QuPathViewer.zoomIn() or QuPathViewer.zoomOut().
getDensityType() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters: Get the normalization type of the density map.
getDerivedBoundaryStrategy(double) - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy: Create a boundary strategy that trains a classifier for a PathClass derived from the original classification for annotation boundaries.
getDerivedPathClass(PathClass, String) - Static method in class qupath.lib.scripting.QP: Get a PathClass with the specified name, derived from another PathClass.
getDerivedPathClass(PathClass, String, Integer) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use PathClass.getInstance(PathClass, String, Integer)
getDerivedPathClass(PathClass, String, Integer) - Static method in class qupath.lib.scripting.QP: Get a PathClass with the specified name, derived from another PathClass.
getDescendantObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject: Get a collection containing all descendant objects.
getDescendantObjects(PathObject, Collection<PathObject>, Class<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Get all descendant objects with a specified type.
getDescription() - Method in class qupath.ext.openslide.OpenSlideExtension
getDescription() - Method in class qupath.imagej.detect.cells.SubcellularDetection
getDescription() - Method in class qupath.imagej.detect.cells.WatershedCellDetection
getDescription() - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
getDescription() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
getDescription() - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
getDescription() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
getDescription() - Method in class qupath.imagej.gui.IJExtension
getDescription() - Method in class qupath.imagej.gui.ImageJMacroRunner
getDescription() - Method in class qupath.imagej.images.servers.ImageJServerBuilder
getDescription() - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
getDescription() - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
getDescription() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
getDescription() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
getDescription() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
getDescription() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
getDescription() - Method in class qupath.lib.algorithms.TilerPlugin
getDescription() - Method in class qupath.lib.extension.svg.SvgExtension
getDescription() - Method in interface qupath.lib.gui.extensions.QuPathExtension: A short description of the extension for displaying in the main GUI.
getDescription() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption: Get a user-friendly description of the style.
getDescription() - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditorExtension
getDescription() - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
getDescription() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
getDescription() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Get the image description, as stored in a TIFF, or null if no description is available.
getDescription() - Method in interface qupath.lib.images.servers.ImageServerBuilder: Get a short, human-readable description for display in a GUI.
getDescription() - Method in class qupath.lib.images.servers.JsonImageServerBuilder
getDescription() - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
getDescription() - Method in class qupath.lib.objects.PathAnnotationObject: Get a free text description previously set for this annotation.
getDescription() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
getDescription() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
getDescription() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
getDescription() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
getDescription() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
getDescription() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
getDescription() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
getDescription() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
getDescription() - Method in interface qupath.lib.plugins.PathPlugin: Get a brief description of the plugin's purpose & operation.
getDescription() - Method in interface qupath.lib.projects.ProjectImageEntry: Get a description; this is free text describing the image.
getDescription() - Method in class qupath.opencv.CellCountsCV
getDescription() - Method in class qupath.opencv.DetectCytokeratinCV
getDescription() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
getDescription() - Method in class qupath.opencv.WatershedNucleiCV
getDescription() - Method in class qupath.process.gui.ProcessingExtension
getDetails() - Method in class qupath.imagej.images.writers.TiffWriterIJ
getDetails() - Method in class qupath.imagej.images.writers.ZipWriterIJ
getDetails() - Method in interface qupath.lib.images.writers.ImageWriter: Get further details of the writer, which may be displayed to a user.
getDetails() - Method in class qupath.lib.images.writers.JpegWriter
getDetails() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
getDetails() - Method in class qupath.lib.images.writers.PngWriter
getDetectionDisplayMode() - Method in class qupath.lib.gui.viewer.OverlayOptions: Get the current OverlayOptions.DetectionDisplayMode.
getDetectionObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get all detection objects in the hierarchy (including sub-classes of detections).
getDetectionObjects() - Static method in class qupath.lib.scripting.QP: Get a list of the current detection objects.
getDeterminant() - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian: Get the determinant for each pixel.
getDeterminant() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
getDeterminant() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
getDisplayableImageName(ImageServer<?>) - Static method in class qupath.lib.images.servers.ServerTools: Get an ImageServer name suitable for displaying.
getDisplayedClipShape(Shape) - Method in class qupath.lib.gui.viewer.QuPathViewer: Transform a clip shape into image coordinates for this viewer.
getDisplayedColor(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get a Color appropriate for displaying an object.
getDisplayedColorARGB(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get the color with which an object should be displayed, as a packaged ARGB integer.
getDisplayedImageName(ImageData<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI: Get the image name to display for a specified image.
getDisplayedName() - Method in class qupath.lib.objects.PathObject: Request an object name in a form suitable for displaying.
getDisplayedRegionShape() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get a shape corresponding to the region of the image currently visible in this viewer.
getDisplayMaxValue() - Method in class qupath.lib.gui.tools.MeasurementMapper: Get the measurement value that maps to the last color in the color mapper.
getDisplayMinValue() - Method in class qupath.lib.gui.tools.MeasurementMapper: Get the measurement value that maps to the first color in the color mapper.
getDisplayMode() - Method in class qupath.lib.gui.charts.HistogramChart: Get the histogram display mode.
getDisplayText() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion: Get the text that should be displayed for this completion.
getDocsUrl() - Static method in class qupath.lib.gui.Urls: Get the base URL for the QuPath documentation (independent of version).
getDouble(int) - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper: Extract one entry from the array, converting to double as necessary.
getDoubleParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Get a double parameter value (or its default) for the specified key.
getDoubleValues(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
getDoubleValues(String) - Method in interface qupath.lib.gui.measure.PathTableData: Get all double values for all items.
getDownsample() - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager: Get the downsample used within the mini viewers.
getDownsample() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel: Get the downsample factor for this level.
getDownsample() - Method in class qupath.lib.images.servers.TileRequest: Get the downsample value for this tile.
getDownsample() - Method in class qupath.lib.regions.RegionRequest: Get the requested downsample factor, defining the resolution at which pixels should be returned.
getDownsampleFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the current downsample factor.
getDownsampleFactor() - Method in interface qupath.lib.images.PathImage: Get the downsample factor originally used when obtaining the image from an ImageServer; will be 1 if the image is full-resolution.
getDownsampleFactor(ImageServer<?>, double) - Static method in class qupath.lib.images.servers.ServerTools: Calculate a downsample factor for a server given a preferred pixel size.
getDownsampleForLevel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the downsample factor for a specific resolution level.
getDownsampleForResolution(int) - Method in class qupath.lib.images.servers.AbstractImageServer
getDownsampleForResolution(int) - Method in interface qupath.lib.images.servers.ImageServer: Get the downsample factor for a specified resolution level, where level 0 is the full resolution image and nResolutions() - 1 is the lowest resolution available.
getDummyColorModel(int) - Static method in class qupath.lib.color.ColorModelFactory: Get a dummy ColorModel instance.
getEdgeMax() - Method in class qupath.lib.analysis.stats.Histogram: Get the maximum edge of the histogram.
getEdgeMin() - Method in class qupath.lib.analysis.stats.Histogram: Get the minimum edge of the histogram.
getEdgeRange() - Method in class qupath.lib.analysis.stats.Histogram: Get the histogram edge range, defined as the maximum edge - the minimum edge.
getEigenvalues(boolean) - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian: Get the eigenvalues, ranked from highest to lowest.
getEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
getEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
getEigenvectors(boolean) - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian: Get the eigenvectors, returned in the same order as the eigenvalues.
getEigenvectors(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
getEigenvectors(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
getEmptyTile(int, int) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
getEmptyTile(int, int, boolean) - Method in class qupath.lib.images.servers.AbstractTileableImageServer: Create an empty tile for this server, using the default color model.
getEngineByName(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider: Get the ScriptEngine based on its name.
getEntry(ImageData<T>) - Method in interface qupath.lib.projects.Project: Request a ProjectImageEntry associated with an ImageData
getEntryPath() - Method in interface qupath.lib.projects.ProjectImageEntry: Get a path to the data for this image entry, or null if this entry is not stored on the local file system.
getErrorWriter() - Method in class qupath.lib.scripting.ScriptParameters: Get the error writer for script output.
getEvents() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get an unmodifiable list of all events.
getEventsAtTime(double) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get the number of events at a specified time (exactly).
getEventType() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Get the hierarchy event type.
getExcludeColumns() - Method in class qupath.lib.gui.tools.MeasurementExporter: Returns the list of columns to exclude from export.
getExcludeOutsideRange() - Method in class qupath.lib.gui.tools.MeasurementMapper: Returns true if objects with values outside the specified min/max range have the min/max colors returned, false if null should be returned instead.
getExpandToWindow() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Query whether the image is allowed to expand beyond its preferred width and height to fill the window.
getExtension(File) - Static method in class qupath.lib.common.GeneralTools: Get filename extension.
getExtension(String) - Static method in class qupath.lib.common.GeneralTools: Get extension from a filename.
getExtensionManager() - Method in class qupath.lib.gui.QuPathGUI: Get an ExtensionManager to facilitating working with extensions.
getExtensions() - Method in class qupath.imagej.images.writers.TiffWriterIJ
getExtensions() - Method in class qupath.imagej.images.writers.ZipWriterIJ
getExtensions() - Method in interface qupath.lib.images.writers.ImageWriter: Get the file extensions used by the image writer.
getExtensions() - Method in class qupath.lib.images.writers.JpegWriter
getExtensions() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
getExtensions() - Method in class qupath.lib.images.writers.PngWriter
getExtensions() - Method in class qupath.lib.scripting.languages.ScriptLanguage: Get an unmodifiable set containing the possible extensions for this language.
getExtensionsDirectory() - Method in class qupath.lib.gui.ExtensionClassLoader: Directory containing extensions.
getExtensionsPath() - Method in class qupath.lib.gui.UserDirectoryManager: Get the path to where extensions should be stored.
getEyeFixatedIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
getEyePointIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
getFailedExtensions() - Method in class qupath.lib.gui.ExtensionManager
getFeature(int) - Method in class qupath.lib.analysis.features.HaralickFeatures: Get the value of the specified feature.
getFeatureImportance() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier: Request the variable importance values from the last trained RTrees classifier, if available.
getFeatureName(int) - Method in class qupath.lib.analysis.features.HaralickFeatures: Get the name of the specified feature.
getFeatureNames() - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor
getFeatureOp() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Get an ImageDataOp used for feature calculation.
getFile() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the file associated with this ViewTracker.
getFile() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer: Get the underlying file.
getFile() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Get a File object representing the local image file - or null if no file could be found.
getFile() - Method in class qupath.lib.scripting.ScriptParameters: Get the file where the script is located.
getFilesOnly() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Returns true if Bio-Formats is restricted to support only local files, not other URLs.
getFill() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData: Get the histogram fill color.
getFillAnnotations() - Method in class qupath.lib.gui.viewer.OverlayOptions
getFillDetections() - Method in class qupath.lib.gui.viewer.OverlayOptions
getFilledPolygonROIs(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling: Get filled PolygonRois for connected pixels with the same value in an image.
getFilledPolygonROIsExperimental(ImageProcessor) - Static method in class qupath.imagej.processing.RoiLabeling: Experimental 8-connected ROI creation; non-zero pixels considered within objects
getFilledPolygonROIsFromLabels(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling: Get filled Polygon ROIs using distinct labels, creating a map between labels and ROIs.
getFilterByCentroid() - Method in class qupath.lib.objects.utils.Tiler: Check if the tiler will filter the output based on whether the centroid of tiles lies within the parent
getFilteredNeighbors(BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get a list of neighbors for all objects, filtering out objects that do not meet specified criteria.
getFilteredNeighbors(PathObject, BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get a list of neighbors for a specified object, filtering out objects that do not meet specified criteria.
getFlattenedMenuItems(boolean, MenuItem...) - Static method in class qupath.lib.gui.tools.MenuTools: Get a flattened list of all menu items recursively.
getFlattenedMenuItems(List<? extends MenuItem>, boolean) - Static method in class qupath.lib.gui.tools.MenuTools: Get a flattened list of all menu items recursively.
getFlattenedObjectList(List<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get a flattened list containing all PathObjects in the hierarchy (including from the root object).
getFlattenedObjectList(PathObject, List<PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Get all descendant objects as a flattened list.
getFontSize() - Method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize: Get the font size as a CSS-compatible string.
getFontSize() - Method in class qupath.lib.gui.viewer.OverlayOptions
getFormat() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer: Get the format String, as returned by Bio-Formats IFormatReader.getFormat().
getFrame(int) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the frame at the specified index.
getFrameForTime(long) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the frame visible at the specified timestamp (in ms).
getFrameIndexForTime(long) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the index of the frame visible at the specified timestamp (in ms).
getFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return an unmodifiable list of all the frames stored by this view tracker.
getFramework() - Method in class qupath.opencv.dnn.DnnModelParams: Get the name of the deep learning framework that may be used.
getFramework() - Method in class qupath.opencv.dnn.OpenCVDnn: Get the framework used to create the model.
getFullLocationString(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Get a string to summarize the pixel found below the most recent known mouse location, or "" if the mouse is outside this viewer.
getFullMagnification() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the full magnification for the image.
getGamma() - Method in class qupath.lib.display.settings.ImageDisplaySettings: Get the requested vamma value for the viewer.
getGamma() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the gamma value used for this viewer.
getGammaOp() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get a LookupOp that can perform any requested gamma correction in this viewer.
getGaussianDeriv(double, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Get filter coefficients for a 1D Gaussian (derivative) kernel.
getGaussianDerivKernel(double, int, boolean) - Static method in class qupath.opencv.tools.OpenCVTools: Get filter coefficients for a 1D Gaussian (derivative) kernel.
getGeoJsonDataFormat() - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter: Get a DataFormat suitable for storing GeoJSON data on a clipboard.
getGeometry() - Method in class qupath.lib.roi.EllipseROI
getGeometry() - Method in class qupath.lib.roi.LineROI
getGeometry() - Method in class qupath.lib.roi.PointsROI
getGeometry() - Method in class qupath.lib.roi.PolylineROI
getGeometry() - Method in class qupath.lib.roi.RectangleROI
getGeometry() - Method in class qupath.lib.roi.AreaROI
getGeometry() - Method in class qupath.lib.roi.GeometryROI
getGeometry() - Method in interface qupath.lib.roi.interfaces.ROI: Returns a org.locationtech.jts.geom.Geometry object.
getGeometry() - Method in class qupath.lib.roi.PolygonROI
getGeometryFactory() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
getGitHubIssuesUrl() - Static method in class qupath.lib.gui.Urls: Get a URL pointing to the main GitHub issues page.
getGitHubRepoUrl() - Static method in class qupath.lib.gui.Urls: Get a URL pointing to the main QuPath GitHub repo.
getGreen() - Method in class qupath.lib.color.StainVector: Get the green component of the (normalized) stain vector.
getGreen() - Method in class qupath.lib.display.settings.ChannelColor: Get the green value.
getGreenOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
getGridHeight() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
getGridHeight() - Method in interface qupath.lib.objects.hierarchy.TMAGrid: Number of cores along the vertical axis of the grid.
getGridLines() - Method in class qupath.lib.gui.viewer.OverlayOptions
getGridWidth() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
getGridWidth() - Method in interface qupath.lib.objects.hierarchy.TMAGrid: Number of cores along the horizontal axis of the grid.
getHalo() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the 'halo' around the output.
getHandles() - Method in class qupath.lib.roi.RoiEditor: Get all the handles for the current ROI being edited, or an empty list if no handles are available.
getHazardRatio() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult: Get the calculated hazard ratio.
getHazardRatioLowerConfidence() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult: Get the lower bound of the hazard ratio confidence interval.
getHazardRatioUpperConfidence() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult: Get the upper bound of the hazard ratio confidence interval.
getHeight() - Method in class qupath.imagej.tools.PixelImageIJ
getHeight() - Method in interface qupath.lib.analysis.images.SimpleImage: Get the image height.
getHeight() - Method in class qupath.lib.geom.ImmutableDimension: Get the ImmutableDimension height.
getHeight() - Method in class qupath.lib.images.servers.AbstractImageServer
getHeight() - Method in interface qupath.lib.images.servers.ImageServer: Height of the full-resolution image in pixels.
getHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the full-resolution image height.
getHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel: Get the image height at this level.
getHeight() - Method in class qupath.lib.regions.ImageRegion: Get the height of the region bounding box.
getHelpText() - Method in class qupath.lib.plugins.parameters.BooleanParameter
getHelpText() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
getHelpText() - Method in class qupath.lib.plugins.parameters.DoubleParameter
getHelpText() - Method in class qupath.lib.plugins.parameters.EmptyParameter
getHelpText() - Method in class qupath.lib.plugins.parameters.IntParameter
getHelpText() - Method in class qupath.lib.plugins.parameters.NumericParameter
getHelpText() - Method in class qupath.lib.plugins.parameters.StringParameter
getHelpText() - Method in interface qupath.lib.plugins.parameters.Parameter: Get a description of the meaning of the Parameter; may be displayed e.g.
getHessian() - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder.FeatureMap: Get the MultiscaleFeatures.Hessian associated with these features.
getHideIfEmpty() - Method in class qupath.lib.gui.charts.HistogramChart: Query whether the chart is automatically hidden (visibility set to false) when there is no data.
getHierarchy() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the object hierarchy for the current image data, or null if no image data is available.
getHierarchy() - Method in class qupath.lib.images.ImageData: Get the object hierarchy.
getHierarchy() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: The hierarchy to which this event refers.
getHistogram() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData: Get the histogram.
getHistogram(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay: Returns a histogram for a ChannelInfo, or none if no histogram is available (e.g.
getHistogramData() - Method in class qupath.lib.gui.charts.HistogramChart: Get all histogram data objects.
getHistoryWorkflow() - Method in class qupath.lib.images.ImageData: Get a workflow representing a history of the processing steps applied to the ImageData.
getICCProfileBytes() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Request the bytes for an ICC profile.
getIcon() - Method in interface qupath.lib.gui.viewer.tools.PathTool: Get the icon of the tool.
getID() - Method in class qupath.lib.objects.PathObject: Get the ID for this object.
getID() - Method in interface qupath.lib.projects.ProjectImageEntry: Get a unique ID to represent this entry.
getID() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer: Layer ID.
getImage() - Method in class qupath.lib.experimental.pixels.Parameters: Get the image to process.
getImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the JavaFX image.
getImage() - Method in interface qupath.lib.images.PathImage: Get the pixel data (image).
getImage(Parameters<S, ?>) - Method in interface qupath.lib.experimental.pixels.ImageSupplier: Get the image to process.
getImageClass() - Method in class qupath.imagej.images.writers.TiffWriterIJ
getImageClass() - Method in class qupath.imagej.images.writers.ZipWriterIJ
getImageClass() - Method in class qupath.lib.images.servers.AbstractImageServer
getImageClass() - Method in interface qupath.lib.images.servers.ImageServer: Get the class of the image representation returned by this ImageServer.
getImageClass() - Method in class qupath.lib.images.writers.JpegWriter
getImageClass() - Method in class qupath.lib.images.writers.PngWriter
getImageClass() - Method in interface qupath.lib.images.writers.ImageWriter: Get the class of supported images.
getImageClass() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
getImageData() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Get the underlying ImageData used for classification.
getImageData() - Method in class qupath.lib.display.DirectServerChannelInfo
getImageData() - Method in class qupath.lib.display.ImageDisplay: Get the current image data
getImageData() - Method in class qupath.lib.experimental.pixels.Parameters: Get the image data.
getImageData() - Method in class qupath.lib.gui.QuPathGUI: Get the value of QuPathGUI.imageDataProperty().
getImageData() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the image data currently being displayed within thie viewer.
getImageData() - Method in class qupath.lib.scripting.ScriptParameters: Get the current ImageData that should be used with the script.
getImageData() - Method in interface qupath.opencv.ops.ImageDataServer: Get the ImageData wrapped by the ImageDataServer.
getImageDisplay() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the ImageDisplay object used to determine how the image is converted to RGB for display.
getImageHeight() - Method in class qupath.lib.images.servers.TileRequest: Get the height of the bounding box for this tile in the full resolution image.
getImageJIcon(int, int) - Static method in class qupath.imagej.gui.IJExtension: Try to read the ImageJ icon from its jar.
getImageJInstance() - Static method in class qupath.imagej.gui.IJExtension: Get an instance of ImageJ, or start one, for interactive use (with GUI displayed).
getImageJPath() - Static method in class qupath.imagej.gui.IJExtension: Get the path for a local ImageJ installation, if set.
getImageList() - Method in class qupath.lib.gui.tools.MeasurementExporter: Returns the list of images (ProjectImageEntry).
getImageList() - Method in interface qupath.lib.projects.Project: Get a list of image entries for the project.
getImageName() - Method in interface qupath.lib.projects.ProjectImageEntry: Get a name that may be used for this entry.
getImageObjectClassificationString(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Get a string representing the object classification x & y location in the viewer component, or an empty String if no object is found.
getImagePlane() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get the ImagePlane for this subdivision.
getImagePlane() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the ImagePlane currently being displayed, including z and t positions.
getImagePlane() - Method in class qupath.lib.images.servers.TileRequest: Get the ImagePlane for this request.
getImagePlane() - Method in class qupath.lib.regions.ImageRegion: Get the z-slice and time point for this region as an ImagePlane.
getImagePlane() - Method in class qupath.lib.roi.AreaROI
getImagePlane() - Method in class qupath.lib.roi.EllipseROI
getImagePlane() - Method in class qupath.lib.roi.GeometryROI
getImagePlane() - Method in class qupath.lib.roi.LineROI
getImagePlane() - Method in class qupath.lib.roi.PointsROI
getImagePlane() - Method in class qupath.lib.roi.PolygonROI
getImagePlane() - Method in class qupath.lib.roi.PolylineROI
getImagePlane() - Method in class qupath.lib.roi.RectangleROI
getImagePlane() - Method in interface qupath.lib.roi.interfaces.ROI: Get the ImagePlane, which contains the values for c, z and t in a single object.
getImagePlane(Roi, ImagePlus) - Static method in class qupath.imagej.tools.IJTools: Get the ImagePlane of an ImageJ Roi, based upon its stored positions.
getImageRegion() - Method in interface qupath.lib.images.PathImage: The region within the (original, possibly larger) image that this particular image corresponds to.
getImageRegion(Rectangle, int, int) - Static method in class qupath.lib.awt.common.AwtTools: Create an ImageRegion corresponding to a specified Rectangle bounding box.
getImageRegion(Shape, int, int) - Static method in class qupath.lib.awt.common.AwtTools: Create an ImageRegion corresponding to a the bounding box of a Shape.
getImageRegionStore() - Method in class qupath.lib.gui.QuPathGUI: Return the global DefaultImageRegionStore instance, used to cache and paint image tiles.
getImageRegionStore() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the region store used by this viewer for tile caching and painting.
getImages() - Method in interface qupath.lib.projects.ProjectImageEntry: Access additional images associated with the project entry, e.g.
getImageServer() - Method in class qupath.lib.display.DirectServerChannelInfo
getImageServerTypeAdapterFactory(boolean) - Static method in class qupath.lib.images.servers.ImageServers: Get a TypeAdapterFactory for ImageServers, optionally including metadata in the serialized form of the server.
getImageSupport(URI, String...) - Static method in class qupath.lib.images.servers.ImageServers: Get the ImageServerBuilder.UriImageSupport that is best able to open the specified image with optional args.
getImageSupport(ImageServerBuilder<BufferedImage>, URI, String...) - Static method in class qupath.lib.images.servers.ImageServers: Get the ImageServerBuilder.UriImageSupport associated with an ImageServerBuilder, or null if the builder does not support the image.
getImageType() - Method in class qupath.imagej.images.servers.ImageJServerBuilder
getImageType() - Method in class qupath.lib.images.ImageData: Get the image type
getImageType() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
getImageType() - Method in interface qupath.lib.images.servers.ImageServerBuilder: Returns the base class for the images supported by this server.
getImageType() - Method in class qupath.lib.images.servers.JsonImageServerBuilder
getImageType() - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
getImageWidth() - Method in class qupath.lib.images.servers.TileRequest: Get the width of the bounding box for this tile in the full resolution image.
getImageX() - Method in class qupath.lib.images.servers.TileRequest: Get the x-coordinate of the bounding box for this tile in the full resolution image.
getImageY() - Method in class qupath.lib.images.servers.TileRequest: Get the y-coordinate of the bounding box for this tile in the full resolution image.
getImportStatementGenerator() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Get an DefaultScriptLanguage.ImportStatementGenerator.
getImportStatementGenerator() - Method in class qupath.lib.gui.scripting.languages.GroovyLanguage
getImportStatements(Collection<Class<?>>) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Get the import statements as a String, to add at the beginning of the executed script.
getImportStatments(Collection<Class<?>>) - Method in interface qupath.lib.gui.scripting.languages.DefaultScriptLanguage.ImportStatementGenerator
getIncludeChildren() - Method in class qupath.lib.io.FeatureCollection: If true, include child objects nested within the output.
getIncludeColumns() - Method in class qupath.lib.gui.tools.MeasurementExporter: Returns the list of columns to include in the export.
getIndexColorModel(StainVector) - Static method in class qupath.lib.color.ColorToolsAwt: Create an IndexColorModel, ranging from white (low values) to a stain vector color (high values).
getIndexColorModel(StainVector, boolean) - Static method in class qupath.lib.color.ColorToolsAwt: Get an IndexColorModel representing a color deconvolution stain.
getIndexedClassificationColorModel(Map<Integer, PathClass>) - Static method in class qupath.lib.color.ColorModelFactory: Get a ColorModel suitable for showing output pixel classifications, using an 8-bit or 16-bit labeled image.
getInds() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel: Get the index array.
getInfoMessage() - Method in class qupath.lib.gui.commands.ContextHelpViewer: Get a message that may be used to create a badge indicating that info or warning messages are available.
getInfoMessage() - Method in class qupath.lib.gui.commands.LogViewerCommand: Get a string expression to draw attention to error messages.
getInputChannels() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the channels to extract from the image as input to the model.
getInputHeight() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Requested height of input image, or -1 if the classifier is not fussy
getInputLength() - Method in class qupath.opencv.ml.FeaturePreprocessor: Get the number of features required of the input.
getInputNumChannels() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Requested number of channels in input image; default is 3 (consistent with assuming RGB)
getInputPadding() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Requested input padding (above, below, left and right).
getInputResolution() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Requested pixel size for input.
getInputResolution() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the requested input resolution for the image.
getInputs() - Method in class qupath.opencv.dnn.DnnModelParams: Get the requested inputs and their shapes.
getInputs() - Method in interface qupath.opencv.dnn.PredictionFunction: Get the required inputs.
getInputShapes() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer: Layer input shape.
getInputWidth() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Requested width of input image, or -1 if the classifier is not fussy
getInsertion(String, int, String) - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion: Get the string to insert, given the provided text and position.
getInstallationUrl() - Static method in class qupath.lib.gui.Urls: Get a URL pointing to a page that explains how to install this version of QuPath.
getInstalledImageServerBuilders() - Static method in class qupath.lib.images.servers.ImageServerProvider: Request all available ImageServerBuilders.
getInstalledImageServerBuilders(Class<T>) - Static method in class qupath.lib.images.servers.ImageServerProvider: Request all available ImageServerBuilders supporting a given image class.
getInstance() - Static method in class qupath.lib.gui.BuildInfo: Get the shared BuildInfo instance.
getInstance() - Static method in class qupath.lib.gui.ExtensionClassLoader: Get a singleton instance of the ExtensionClassLoader.
getInstance() - Static method in class qupath.lib.gui.JavadocViewer: Get the main (singleton) instance of JavadocViewer.
getInstance() - Static method in class qupath.lib.gui.QuPathGUI: Get the static instance of the current QuPath GUI.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.CssLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.GroovyLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.JsonLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.MarkdownLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.PlainLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.PropertiesLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.XmlLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.YamlLanguage: Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.UserDirectoryManager: Get the singleton instance of the UserDirectoryManager.
getInstance() - Static method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Get the static instance of BioFormatsServerOptions, available to servers being constructed.
getInstance() - Static method in class qupath.lib.io.GsonTools: Get default Gson, capable of serializing/deserializing some key QuPath classes.
getInstance() - Static method in class qupath.lib.objects.DefaultPathObjectComparator: Get shared comparator instance to sort PathObjects repeatably.
getInstance() - Static method in class qupath.lib.roi.DefaultROIComparator: Get a static instance of this comparator, to avoid needing to construct it.
getInstance(boolean) - Static method in class qupath.lib.io.GsonTools: Get default Gson, optionally with pretty printing enabled.
getInstance(int, int) - Static method in class qupath.lib.geom.ImmutableDimension: Get an ImmutableDimension representing the specified width and height.
getInstance(String) - Static method in class qupath.lib.objects.classes.PathClass
getInstance(String, Integer) - Static method in class qupath.lib.images.servers.ImageChannel: Get a channel instance with the specified name and color.
getInstance(String, Integer) - Static method in class qupath.lib.objects.classes.PathClass: Get a base PathClass instance, without any parent PathClass.
getInstance(QuPathGUI) - Static method in class qupath.lib.gui.commands.ContextHelpViewer: Get the single ContextHelpViewer instance associated with a specific QuPath instance.
getInstance(QuPathGUI) - Static method in class qupath.lib.gui.WelcomeStage
getInstance(PathClass, String, Integer) - Static method in class qupath.lib.objects.classes.PathClass: Get a derived PathClass instance with the specified parent.
getInstance(LocalNormalization.SmoothingScale, double) - Static method in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType: Get an object containing the parameters necessary for normalization.
getInstance(LocalNormalization.SmoothingScale, LocalNormalization.SmoothingScale) - Static method in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType: Get an object containing the parameters necessary for normalization.
getInstanceLabels() - Method in class qupath.lib.images.servers.LabeledImageServer: Get a mapping between objects and instance labels.
getInterpolation() - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay: Get the preferred method of interpolation to use for display.
getIntParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Get a integer parameter value (or its default) for the specified key.
getItem() - Method in class qupath.lib.gui.SelectableItem: Get the current item.
getItems() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
getItems() - Method in interface qupath.lib.gui.measure.PathTableData: Get internal list of the items used to provide measurements.
getItems(UriUpdater.UriStatus) - Method in class qupath.lib.io.UriUpdater: Get all items with the specified status, or all items is status is null.
getKeyValueParameters(boolean) - Method in class qupath.lib.plugins.parameters.ParameterList: Returns a map of keys and their corresponding parameter values
getLabelMap() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining.ClassifierTrainingData: Get the map of classifications to labels.
getLabels() - Method in class qupath.lib.images.servers.LabeledImageServer: Get an unmodifiable map of classifications and their corresponding labels.
getLanguageFromExtension(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider: Return the first ScriptLanguage compatible with the specified extension (can be runnable or not).
getLanguageFromName(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider: Given a file name, determine the associated language - or null if no suitable (supported) language can be found.
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.GroovyStyler
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.JsonStyler
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.MarkdownStyler
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PlainStyler
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PropertiesStyler
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PythonStyler
getLanguageNames() - Method in interface qupath.lib.gui.scripting.richtextfx.stylers.ScriptStyler: Get a set of the scripting languages supported by this styler.
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.XmlStyler
getLanguageNames() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.YamlStyler
getLanguageNames() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Get a set of the scripting languages supported by this syntax.
getLaplacian() - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian: Get Laplacian of Gaussian image (calculated by summation without requiring eigenvalues).
getLaplacian() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
getLaplacian() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
getLargestImageHeight() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Get the height of the largest image, if known.
getLargestImageWidth() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Get the width of the largest image, if known.
getLastChangeTimestamp() - Method in class qupath.lib.display.ImageDisplay: Get a timestamp the last known changes for the object.
getLastChangeTimestamp() - Method in class qupath.lib.gui.images.stores.AbstractImageRenderer
getLastChangeTimestamp() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
getLastChangeTimestamp() - Method in interface qupath.lib.gui.images.stores.ImageRenderer: Timestamp of the last change (probably in milliseconds).
getLastResultsDescription() - Method in class qupath.imagej.detect.cells.SubcellularDetection
getLastResultsDescription() - Method in class qupath.imagej.detect.cells.WatershedCellDetection
getLastResultsDescription() - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
getLastResultsDescription() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
getLastResultsDescription() - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
getLastResultsDescription() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
getLastResultsDescription() - Method in class qupath.imagej.gui.ImageJMacroRunner
getLastResultsDescription() - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
getLastResultsDescription() - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
getLastResultsDescription() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
getLastResultsDescription() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
getLastResultsDescription() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
getLastResultsDescription() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
getLastResultsDescription() - Method in class qupath.lib.algorithms.TilerPlugin
getLastResultsDescription() - Method in interface qupath.lib.plugins.ObjectDetector: Get a String summarizing the result, which may be displayed to a user or logged.
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
getLastResultsDescription() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
getLastResultsDescription() - Method in interface qupath.lib.plugins.PathPlugin: (Optional) short one-line description of the results, e.g.
getLastResultsDescription() - Method in interface qupath.lib.plugins.PathTask: Get a description of the results from running this task, which may be used e.g.
getLastResultsDescription() - Method in class qupath.opencv.CellCountsCV
getLastResultsDescription() - Method in class qupath.opencv.DetectCytokeratinCV
getLastResultsDescription() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
getLastResultsDescription() - Method in class qupath.opencv.WatershedNucleiCV
getLastSavedPath() - Method in class qupath.lib.images.ImageData: Get the last path used to save this object;
getLastStep() - Method in class qupath.lib.plugins.workflow.Workflow: Get the last WorkflowStep in the workflow, or null if no steps are available.
getLastTime() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the time associated with the last recorded frame.
getLatestCommit() - Method in class qupath.lib.gui.BuildInfo: Get reference to the latest git commit, if known, or null if this has not be preserved.
getLayout() - Method in class qupath.opencv.dnn.DnnModelParams: Get a string representing the axes layout that the model expects as input.
getLength() - Method in class qupath.lib.roi.EllipseROI
getLength() - Method in class qupath.lib.roi.RectangleROI
getLength() - Method in class qupath.lib.roi.AreaROI
getLength() - Method in class qupath.lib.roi.GeometryROI
getLength() - Method in interface qupath.lib.roi.interfaces.ROI: Get ROI length.
getLength() - Method in class qupath.lib.roi.LineROI
getLength() - Method in class qupath.lib.roi.PointsROI
getLength() - Method in class qupath.lib.roi.PolygonROI
getLength() - Method in class qupath.lib.roi.PolylineROI
getLevel() - Method in class qupath.lib.images.servers.TileRequest: Get the resolution level.
getLevel() - Method in class qupath.lib.objects.PathObject: The level of the object in a hierarchy.
getLevel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata: Get resolution information for a specified pyramidal level.
getLevel0Height() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get the height of the full-resolution image (level 0).
getLevel0Width() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get the width of the full-resolution image (level 0).
getLevelCount() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get the total number of pyramid levels.
getLevelHeight(int) - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get the image height at the specified level.
getLevels() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get an unmodifiable list containing the resolution levels
getLevelWidth(int) - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get the image width at the specified level.
getLibraryVersion() - Static method in class qupath.lib.images.servers.openslide.jna.OpenSlideLoader: Get the version of the OpenSlide library.
getLineCommentString() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Get the String that represents the start of a comment line.
getLineObjects(Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools: Get a list of objects with line ROIs from a collection of objects.
getLineWidth() - Method in class qupath.lib.gui.charts.ChartThresholdPane: Get the threshold line width.
getLivePrediction() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Query whether live prediction is turned on.
getLoadedExtensions() - Method in class qupath.lib.gui.ExtensionManager
getLocalizationDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager: Get the path to where localization property files should be written.
getLocalizedResourceManager() - Static method in class qupath.lib.gui.localization.QuPathResources: Get a localized resource manager, which can be used to manage localized strings, and update these whenever the locale preferences are updated.
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in interface qupath.lib.gui.viewer.overlays.AbstractOverlay.LocationStringFunction: See PathOverlay.getLocationString(ImageData, double, double, int, int)
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in interface qupath.lib.gui.viewer.overlays.PathOverlay: Get a location string to display when showing a specified image.
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
getLocationStringFunction() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
getLogDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager: Get the path to where log files should be written.
getLoggableParameters(ImageData<T>) - Method in class qupath.lib.plugins.AbstractInteractivePlugin: Get a copy of the current parameter list (with empty parameters removed) suitable for logging.
getLogger() - Static method in class qupath.lib.scripting.QP: Get the logger associated with this class.
getLogMessageCounts() - Method in class qupath.lib.gui.commands.LogViewerCommand: Get the counts of all messages logged by the log viewer.
getLogStyling(String) - Static method in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Get styling for use with a logger.
getLogViewerCommand() - Method in class qupath.lib.gui.QuPathGUI: Get the log viewer associated with this QuPath instance.
getLongText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Get the long text (description) for the command, if available.
getLowerBound() - Method in enum class qupath.lib.images.servers.PixelType: Get a number representing the minimum value permitted by this type (may be negative).
getLowerBound() - Method in class qupath.lib.plugins.parameters.NumericParameter: Retrieve the lower bound.
getMagnification() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the magnification for the image within this viewer, or Double.NaN if no image is present.
getMagnification() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the magnification value, or Double.NaN if this is unavailable.
getMagnificationString(QuPathViewer) - Static method in class qupath.lib.gui.tools.GuiTools: Get an appropriate String to represent the magnification of the image currently in the viewer.
getMainObjectFilter() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters: Get the primary object filter.
getMajor() - Method in class qupath.lib.common.Version: Get the major version number (X.0.0).
getManager() - Method in class qupath.lib.images.servers.SparseImageServer: Get the manager, which defines from whence the regions originate.
getMask() - Method in class qupath.lib.experimental.pixels.Parameters: Get the mask associated with the main ROI or the parent object, or null if no mask is available.
getMask(Parameters<S, T>, ROI) - Method in interface qupath.lib.experimental.pixels.MaskSupplier: Get a mask corresponding to the image, depicting a specified ROI.
getMask(ROI) - Method in class qupath.lib.experimental.pixels.Parameters: Get the mask associated with any ROI, or null if no mask is available.
getMaskedPixels(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Extract all the masked pixels within an image.
getMaskImageNames() - Method in interface qupath.lib.projects.Project: Query whether 'true' or masked image names are being returned.
getMatrixInverse() - Method in class qupath.lib.color.ColorDeconvolutionStains: Get matrix inverse, as useful for color deconvolution.
getMax() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get the maximum non-NaN value added.
getMaxAllowed() - Method in class qupath.lib.display.DirectServerChannelInfo
getMaxAllowed() - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the max allowed display value.
getMaxBlue() - Method in class qupath.lib.color.ColorDeconvolutionStains: Get the maximum value for the blue channel (default = 255).
getMaxCount() - Method in class qupath.lib.analysis.stats.Histogram: Get the highest count found for any bin.
getMaxDecimalPlaces() - Method in class qupath.lib.common.Timeit: Get the maximum number of decimal places when reporting timings.
getMaxDisplay() - Method in class qupath.lib.display.DirectServerChannelInfo
getMaxDisplay() - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the max display value.
getMaxDisplay() - Method in class qupath.lib.display.settings.ChannelSettings: Get the requested maximum display value for the channel, This should be used with the last entry in any lookup table.
getMaxDownsample() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the maximum downsample value supported by this viewer.
getMaxFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Compute maximum features from all four rotations
getMaxGreen() - Method in class qupath.lib.color.ColorDeconvolutionStains: Get the maximum value for the green channel (default = 255).
getMaxHeight() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters: Get the maximum height of the density map.
getMaxNormalizedCount() - Method in class qupath.lib.analysis.stats.Histogram: Get the highest count found for any bin, divided by the total counts across the entire histogram.
getMaxRed() - Method in class qupath.lib.color.ColorDeconvolutionStains: Get the maximum value for the red channel (default = 255).
getMaxROIHandleSize() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the maximum size for which ROI handles may be drawn.
getMaxThreads() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Get the maximum number of threads that may be used during live prediction.
getMaxThreshold() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Get the maximum threshold value.
getMaxTime() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get the time of the last event, or -1 if there are no events.
getMaxValue() - Method in class qupath.lib.analysis.stats.Histogram: Get the maximum of all the values being histogrammed.
getMaxValue() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the minimum value supported by this image.
getMaxWidth() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters: Get the maximum width of the density map.
getMaxX() - Method in class qupath.lib.regions.ImageRegion: Get the x coordinate of the bottom right of the region bounding box.
getMaxY() - Method in class qupath.lib.regions.ImageRegion: Get the y coordinate of the bottom right of the region bounding box.
getMean() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get the mean of all non-NaN values that were added.
getMean() - Method in class qupath.opencv.dnn.OpenCVDnn: Get means which should be subtracted for preprocessing.
getMeanFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Compute averaged features over all four rotations
getMeanValue() - Method in class qupath.lib.analysis.stats.Histogram: Get the mean of all the values being histogrammed.
getMeasurementList() - Method in class qupath.lib.objects.PathObject: Retrieve the list stored measurements for the object.
getMeasurementMapper() - Method in class qupath.lib.gui.viewer.OverlayOptions
getMeasurementName(int) - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
since v0.4.0; using names is preferred over indexing but MeasurementList.getMeasurementNames() can still be used
getMeasurementNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
getMeasurementNames() - Method in interface qupath.lib.gui.measure.PathTableData: Get the names of all numeric measurements.
getMeasurementNames() - Method in interface qupath.lib.measurements.MeasurementList: Get the names of all measurements currently in the list.
getMeasurementNames() - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Get the names of all measurements that may be returned.
getMeasurements() - Method in class qupath.lib.objects.PathObject: Get a map-based view on PathObject.getMeasurementList().
getMeasurementValue(int) - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
since v0.4.0; using MeasurementList.get(String) is preferred over using an index
getMeasurementValue(String) - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
since v0.4.0; use MeasurementList.get(String) instead
getMeasurementValue(PathObject, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Get the value of a single measurement for a specified PathObject, computing it if it is unavailable.
getMeasurementValue(PathObject, String, boolean) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Deprecated.
use PixelClassificationMeasurementManager.getMeasurementValue(PathObject, String) or PixelClassificationMeasurementManager.getCachedMeasurementValue(PathObject, String) instead
getMeasurementValue(ROI, String) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Get the value of a single measurement for a specified ROI, computing it if it is unavailable.
getMeasurementValue(ROI, String, boolean) - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Deprecated.
use PixelClassificationMeasurementManager.getMeasurementValue(ROI, String) or PixelClassificationMeasurementManager.getCachedMeasurementValue(ROI, String) instead
getMeasurementValues(Collection<PathObject>, String) - Static method in class qupath.lib.analysis.stats.Histogram: Extract a specific measurement for each PathObject in a collection, storing the result in an array.
getMedianRGB(int[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Determine median of RGB values.
getMemoizationTimeMillis() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Returns the number of milliseconds that must elapse when opening an image before a memoization file is generated.
getMenu(String, boolean) - Method in class qupath.lib.gui.QuPathGUI: Get a reference to an existing menu from the main QuPath menubar, optionally creating a new menu if it is not present.
getMenu(List<Menu>, String, boolean) - Static method in class qupath.lib.gui.tools.MenuTools: Get a reference to an existing menu, optionally creating a new menu if it is not present.
getMenuBar() - Method in class qupath.lib.gui.QuPathGUI: Get the menubar for the main QuPath application.
getMenuItem() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Get the menu item corresponding to this command.
getMenuPath() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Get a String representation of the menu containing this command.
getMessageType() - Method in class qupath.lib.gui.actions.InfoMessage: Type of the message.
getMetadata() - Method in interface qupath.lib.classifiers.pixel.PixelClassifier: Get metadata that describes how the classifier should be called, and the kind of output it provides.
getMetadata() - Method in class qupath.lib.images.servers.AbstractImageServer
getMetadata() - Method in interface qupath.lib.images.servers.ImageServer: Get essential metadata associated with the ImageServer as a distinct object.
getMetadata() - Method in class qupath.lib.images.servers.ImageServerBuilder.AbstractServerBuilder
getMetadata() - Method in class qupath.lib.objects.PathDetectionObject: Get a map of metadata values.
getMetadata() - Method in class qupath.lib.objects.PathObject: Get a key/value pair map for object metadata.
getMetadataKeys() - Method in interface qupath.lib.objects.MetadataStore: Get all metadata keys.
getMetadataKeys() - Method in class qupath.lib.objects.TMACoreObject
getMetadataKeys() - Method in interface qupath.lib.projects.ProjectImageEntry: Get an unmodifiable collection of the metadata map's keys.
getMetadataMap() - Method in interface qupath.lib.objects.MetadataStore: Returns an unmodifiable map containing the metadata.
getMetadataMap() - Method in class qupath.lib.objects.TMACoreObject
getMetadataMap() - Method in interface qupath.lib.projects.ProjectImageEntry: Get an unmodifiable view of the underlying metadata map.
getMetadataNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Get the names of all columns corresponding to metadata (String) values.
getMetadataStore() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer: Get the MetadataStore, as used by Bio-Formats.
getMetadataString(String) - Method in interface qupath.lib.objects.MetadataStore: Get a metadata value, cast as a String if possible.
getMetadataString(String) - Method in class qupath.lib.objects.TMACoreObject
getMetadataSummaryString() - Method in interface qupath.lib.projects.ProjectImageEntry: Get a formatted string representation of the metadata map's contents.
getMetadataValue(String) - Method in interface qupath.lib.objects.MetadataStore: Get a metadata value of any kind.
getMetadataValue(String) - Method in class qupath.lib.objects.TMACoreObject
getMetadataValue(String) - Method in interface qupath.lib.projects.ProjectImageEntry: Request a metadata value.
getMethod() - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the ColorTransformer.ColorTransformMethod associated with this channel, or null if no method is relevant.
getMin() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get the minimum non-NaN value added.
getMinAllowed() - Method in class qupath.lib.display.DirectServerChannelInfo
getMinAllowed() - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the min allowed display value.
getMinDisplay() - Method in class qupath.lib.display.DirectServerChannelInfo
getMinDisplay() - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the min display value.
getMinDisplay() - Method in class qupath.lib.display.settings.ChannelSettings: Get the requested minimum display value for the channel.
getMinDownsample() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the minimum downsample value supported by this viewer.
getMinFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Compute minimum features from all four rotations
getMinor() - Method in class qupath.lib.common.Version: Get the minor version number (0.X.0).
getMinSizeForTiling() - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand: Query the default minimum image size when writing OME-TIFF images.
getMinThreshold() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold: Get the minimum threshold value.
getMinValue() - Method in class qupath.lib.analysis.stats.Histogram: Get the minimum of all the values being histogrammed.
getMinValue() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the minimum value supported by this image.
getMinX() - Method in class qupath.lib.regions.ImageRegion: Get the x coordinate of the top left of the region bounding box.
getMinY() - Method in class qupath.lib.regions.ImageRegion: Get the y coordinate of the top left of the region bounding box.
getMissingFeatures(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.opencv.dnn.DnnObjectClassifier
getMissingFeatures(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
getMissingFeatures(ImageData<T>, Collection<? extends PathObject>) - Method in interface qupath.lib.classifiers.object.ObjectClassifier: Check for missing features, returning the names and number of input objects missing the specified features.
getMissingFeatures(ImageData<T>, Collection<? extends PathObject>) - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
getMissingFeatures(ImageData<T>, PathObject) - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor: Check for missing features, returning the names.
getMissingItems() - Method in class qupath.lib.io.UriUpdater: Get all missing items.
getMissingValue() - Method in class qupath.opencv.ml.objects.features.Normalizer: Return the value that will be output after normalization if the computed value is not finite.
getModelType() - Method in class qupath.opencv.dnn.OpenCVDnn: Get the type of the model that would be built with OpenCVDnn.buildModel().
getModelUri() - Method in class qupath.opencv.dnn.OpenCVDnn: Get the path to the model.
getModeRGB(int[]) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors: Get the mode from an array of (packed) RGB pixel values.
getModificationTimestamp() - Method in interface qupath.lib.projects.Project: Request a timestamp from when the project was last synchronized.
getMoreTranslucentColor(Color) - Static method in class qupath.lib.color.ColorToolsAwt: Get a (slightly more) translucent version of the specified color.
getMousePointIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
getMousePosition() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the current cursor position within this viewer, or null if the cursor is outside the viewer.
getName() - Method in class qupath.ext.openslide.OpenSlideExtension
getName() - Method in class qupath.imagej.detect.cells.PositiveCellDetection
getName() - Method in class qupath.imagej.detect.cells.SubcellularDetection
getName() - Method in class qupath.imagej.detect.cells.WatershedCellDetection
getName() - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
getName() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
getName() - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
getName() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
getName() - Method in class qupath.imagej.gui.IJExtension
getName() - Method in class qupath.imagej.gui.ImageJMacroRunner
getName() - Method in class qupath.imagej.images.servers.ImageJServerBuilder
getName() - Method in class qupath.imagej.images.writers.TiffWriterIJ
getName() - Method in class qupath.imagej.images.writers.ZipWriterIJ
getName() - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
getName() - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
getName() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
getName() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
getName() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
getName() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
getName() - Method in class qupath.lib.algorithms.TilerPlugin
getName() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get the name of this data, generally used for display.
getName() - Method in class qupath.lib.color.ColorDeconvolutionStains: Get the stains name.
getName() - Method in interface qupath.lib.color.ColorMaps.ColorMap: Get the name of the colormap.
getName() - Method in class qupath.lib.color.StainVector: Returns the name of the stain vector.
getName() - Method in class qupath.lib.common.Timeit.Checkpoint: Get the checkpoint name.
getName() - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the channel name.
getName() - Method in class qupath.lib.display.DirectServerChannelInfo
getName() - Method in class qupath.lib.display.settings.ChannelSettings: Get the name of the channel.
getName() - Method in class qupath.lib.display.settings.ImageDisplaySettings: Get the name of the settings.
getName() - Method in interface qupath.lib.experimental.pixels.MeasurementProcessor.CustomMeasurement
getName() - Method in class qupath.lib.extension.svg.SvgExtension
getName() - Method in class qupath.lib.gui.actions.menus.AnalyzeMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.AutomateMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.ClassifyMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.EditMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.ExtensionsMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.FileMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.HelpMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.MeasureMenuActions
getName() - Method in interface qupath.lib.gui.actions.menus.MenuActions: Get the name of the menu.
getName() - Method in class qupath.lib.gui.actions.menus.ObjectsMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.TMAMenuActions
getName() - Method in class qupath.lib.gui.actions.menus.ViewMenuActions
getName() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo: Get the name.
getName() - Method in interface qupath.lib.gui.extensions.QuPathExtension: A readable name for the extension.
getName() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion: Get the release name (any text).
getName() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the name of the image.
getName() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption: Get a user-friendly name for the style.
getName() - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditorExtension
getName() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the name of this ViewTracker.
getName() - Method in interface qupath.lib.gui.viewer.tools.PathTool: Get the name of the tool
getName() - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
getName() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
getName() - Method in interface qupath.lib.images.servers.ColorTransforms.ColorTransform: Get a displayable name for the transform.
getName() - Method in class qupath.lib.images.servers.ImageChannel: Name of the output channel.
getName() - Method in interface qupath.lib.images.servers.ImageServerBuilder: Get a human-readable name for the kind of ImageServer this builds.
getName() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the image name.
getName() - Method in class qupath.lib.images.servers.JsonImageServerBuilder
getName() - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
getName() - Method in interface qupath.lib.images.writers.ImageWriter: Get the name of the image writer.
getName() - Method in class qupath.lib.images.writers.JpegWriter
getName() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
getName() - Method in class qupath.lib.images.writers.PngWriter
getName() - Method in interface qupath.lib.measurements.Measurement: Get the name of the measurement.
getName() - Method in class qupath.lib.objects.classes.PathClass: Get the name of this classification.
getName() - Method in class qupath.lib.objects.PathObject: Request the stored object name.
getName() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
getName() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
getName() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
getName() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
getName() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
getName() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
getName() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
getName() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
getName() - Method in interface qupath.lib.plugins.PathPlugin: Get the name of the plugin for display.
getName() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
getName() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
getName() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
getName() - Method in interface qupath.lib.plugins.workflow.WorkflowStep: Get the name of the workflow step.
getName() - Method in interface qupath.lib.projects.Project: Get the name of the project.
getName() - Method in class qupath.lib.scripting.languages.ScriptLanguage: Get the name of this language
getName() - Method in class qupath.opencv.CellCountsCV
getName() - Method in class qupath.opencv.DetectCytokeratinCV
getName() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer: Layer name.
getName() - Method in class qupath.opencv.dnn.OpenCVDnn: Get a user-readable name for this model, or null if no name is specified.
getName() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
getName() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: User-friendly, readable name for the classifier
getName() - Method in class qupath.opencv.WatershedNucleiCV
getName() - Method in class qupath.process.gui.commands.ml.ClassificationResolution: Get the simple name for this resolution.
getName() - Method in class qupath.process.gui.ProcessingExtension
getNameFromURI(URI) - Static method in interface qupath.lib.projects.Project: Extract a usable project name from a URI.
getNames() - Method in interface qupath.lib.projects.ResourceManager.Manager: Get a list of the available resources.
getNameWithoutExtension(File) - Static method in class qupath.lib.common.GeneralTools: Get the file name with extension removed.
getNameWithoutExtension(String) - Static method in class qupath.lib.common.GeneralTools: Deprecated.
v0.5.0 in favor of GeneralTools.stripExtension(String), which does the same thing but has a more descriptive name. See https://github.com/qupath/qupath/pull/1275 for details.
getNanoseconds() - Method in class qupath.lib.common.Timeit.Checkpoint: Get the checkpoint timestamp in nanoseconds.
getNavigationAccelerationProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get whether to apply the navigation acceleration (& deceleration) effects or not.
getNearest(double, double, double) - Method in class qupath.lib.roi.PointsROI: Identify the closest point within a specified distance to coordinates x,y - or null if no points are found.
getNearestNeighbor(PathObject) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get the nearest neighbor for the specified object.
getNearestNeighbor(PathObject, BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get the nearest neighbor for the specified object, filtered by a predicate.
getNegative(PathClass) - Static method in class qupath.lib.objects.classes.PathClass: Get a standalone or derived Negative classification
getNegative(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use PathClass.getNegative(PathClass)
getNeighbors(PathObject) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get all neighbors for a specified object.
getNewConsole() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
getNewConsole() - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditor
getNewEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
getNewEditor() - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditor
getNode() - Method in class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane: Get the node to display.
getNonIntensityAncestorClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Get the first ancestor class that is not an intensity class (i.e.
getNonIntensityAncestorPathClass(PathObject) - Static method in class qupath.lib.scripting.QP: Get the first ancestor class of pathObject.getPathClass() that is not an intensity class (i.e.
getNormalizedCountsForBin(int) - Method in class qupath.lib.analysis.stats.Histogram: Get the normalized histogram count for the specified bin.
getNucleusOrMainROI(PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Get the nucleus ROI for a cell, or the main ROI if no nucleus is found.
getNucleusROI() - Method in class qupath.lib.objects.PathCellObject: Get the nucleus ROI for this cell.
getNucleusROI(PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Get the nucleus ROI for a cell, or null if the input is not a cell or no nucleus is found.
getNullClass() - Static method in class qupath.lib.objects.classes.PathClass: Get the value of PathClass.NULL_CLASS, used to represent no classification.
getNumBins() - Method in class qupath.lib.gui.charts.HistogramDisplay: Get the requested number of bins used for the histogram.
getNumericValue(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
getNumericValue(T, String) - Method in interface qupath.lib.gui.measure.PathTableData: Get the numeric value from an object for the specific measurement.
getNumNaNs() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get count of the number of NaN values added.
getNumPoints() - Method in class qupath.lib.roi.AreaROI: Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.GeometryROI: Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.PolygonROI: Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.PolylineROI: Default implementation, calls ROI.getAllPoints() and then caches the result.
getNumPoints() - Method in class qupath.lib.roi.EllipseROI: Returns 4 (since the ellipse is defined by its bounding box).
getNumPoints() - Method in interface qupath.lib.roi.interfaces.ROI: Get the number of points, as would be returned by ROI.getAllPoints().
getNumPoints() - Method in class qupath.lib.roi.LineROI: Returns 2 (since the line is defined by its end points).
getNumPoints() - Method in class qupath.lib.roi.PointsROI
getNumPoints() - Method in class qupath.lib.roi.RectangleROI: Returns 4 (since the rectangle is defined by its bounding box).
getNumThreads() - Static method in class qupath.lib.common.Prefs: Get the requested number of threads to use for parallelization.
getObjectClassificationString(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Get a string representing the object classification x & y location in the viewer component, or an empty String if no object is found.
getObjectClassifiers() - Method in interface qupath.lib.projects.Project: Get a manager for object classifiers saved within this project.
getObjectFileExtensions() - Static method in class qupath.lib.io.PathIO: Deprecated.
use PathIO.getObjectFileExtensions(boolean) instead
getObjectFileExtensions(boolean) - Static method in class qupath.lib.io.PathIO: Get a list of known file extensions that may contain objects, optionally including compressed files.
getObjects(Collection<PathObject>, Class<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get all objects in the hierarchy, optionally filtering to return only objects that are instances of a specific class.
getObjects(Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP: Get a list of all objects in the current hierarchy according to a specified predicate.
getObjects(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP: Get a list of all objects in the specified hierarchy according to a specified predicate.
getObjectsForLocation(PathObjectHierarchy, double, double, int, int, double) - Static method in class qupath.lib.objects.PathObjectTools: Get a collection of objects that overlap a specified pixel location.
getObjectsForRegion(Class<? extends PathObject>, ImageRegion, Collection<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get the objects overlapping or close to a specified region.
getObjectsForRegion(ImageRegion) - Method in class qupath.lib.images.servers.LabeledImageServer: Get the objects to be painted that fall within a specified region.
getObjectsForROI(Class<? extends PathObject>, ROI) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get the objects within a specified ROI, as defined by the general rules for resolving the hierarchy.
getObjectsOfClass(Collection<PathObject>, Class<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Get the PathObjects in a collection that are instances of a specified class.
getODNormalizedColor(int, double, float, float) - Static method in class qupath.lib.color.ColorTransformer: Create a 'normalized' color for visualization.
getOffset(int) - Method in class qupath.opencv.ml.objects.features.Normalizer: Get the offset for the specified feature
getOMEString(ImageServer<?>) - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Get the String representation understood by OMETiffWriter.
getOnePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClass: Get a standalone or derived 1+ classification, indicating weak positivity
getOnePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use PathClass.getOnePlus(PathClass)
getOpacity() - Method in class qupath.lib.gui.viewer.OverlayOptions: Get the global opacity for overlay drawing.
getOpacity() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay: Get opacity, between 0 (completely transparent) and 1 (completely opaque).
getOpenCVPixelType(PixelType) - Static method in class qupath.opencv.tools.OpenCVTools: Get the OpenCV type code corresponding to a PixelType.
getOpenCVTypeAdaptorFactory() - Static method in class qupath.opencv.io.OpenCVTypeAdapters: Get a TypeAdapterFactory to pass to a GsonBuilder to aid with serializing OpenCV objects (e.g.
getOrDefault(String, double) - Method in interface qupath.lib.measurements.MeasurementList: Get the specified measurement, or the provided default value if it is not contained in the list.
getOriginalImageName() - Method in interface qupath.lib.projects.ProjectImageEntry: Get the original image name, without any randomization.
getOriginalMetadata() - Method in class qupath.imagej.images.servers.ImageJServer
getOriginalMetadata() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.AffineTransformImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.CroppedImageServer
getOriginalMetadata() - Method in interface qupath.lib.images.servers.ImageServer: Get the original metadata read during creation of the server.
getOriginalMetadata() - Method in class qupath.lib.images.servers.LabeledImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.RotatedImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.SparseImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.TransformingImageServer
getOriginalMetadata() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
getOutputChannels() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: List representing the names & display colors for each output channel, or for the output classifications if outputType == OutputType.Classification
getOutputChannelType() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the requested output channel type.
getOutputClasses() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the classifications for the output.
getOutputLayerNames(Net) - Static method in class qupath.opencv.dnn.DnnTools: Get the names of all unconnected output layers.
getOutputLayers(Net, DnnShape...) - Static method in class qupath.opencv.dnn.DnnTools: Get the names of all unconnected output layers.
getOutputLength() - Method in class qupath.opencv.ml.FeaturePreprocessor: Get the number of features expected in the output.
getOutputPixelType() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Pixel type of output; default is null indicating the pixel type is unknown.
getOutputs() - Method in class qupath.opencv.dnn.DnnModelParams: Get the expected outputs and their shapes.
getOutputs(DnnShape...) - Method in interface qupath.opencv.dnn.PredictionFunction: Get the output names mapped to the output shapes.
getOutputShapes() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer: Layer output shape.
getOutputType() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata: Channel type of output; default is ImageServerMetadata.ChannelType.CLASSIFICATION
getOutputType(PixelType) - Method in interface qupath.opencv.ops.ImageDataOp: Get the output pixel type.
getOutputType(PixelType) - Method in interface qupath.opencv.ops.ImageOp: Get the output pixel type.
getOverlayActions() - Method in class qupath.lib.gui.QuPathGUI: Get the actions associated with the viewer overlay options.
getOverlayLayers() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get an unmodifiable list containing the overlay layers, in order.
getOverlayOptions() - Method in class qupath.lib.gui.actions.OverlayActions: Get the overlay options controlled by these actions.
getOverlayOptions() - Method in class qupath.lib.gui.QuPathGUI: Return the global OverlayOptions instance, used to control display within viewers by default.
getOverlayOptions() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay: Get the overlay options, which may influence the display of this overlay.
getOverlayOptions() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the overlay options that control the viewer display.
getOverlayOptions() - Method in class qupath.lib.gui.viewer.ViewerManager: Get the overlay options shared by all viewers created by this manager.
getOverrideSystemMenuBar() - Static method in class qupath.lib.gui.prefs.SystemMenuBar: Get the current value of the override property, which specifies whether the system menubar should not be used by any window - no matter what the value of SystemMenuBar.systemMenubarProperty().
getOwner() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo: Get the owner.
getPackageVersion(Class<?>) - Static method in class qupath.lib.common.GeneralTools: Try to determine the version of a jar containing a specified class.
getPaddedRequest(ImageServer<BufferedImage>, RegionRequest, Padding) - Static method in class qupath.lib.images.servers.ServerTools: Get a raster, padded by the specified amount, to the left, right, above and below.
getPadding() - Method in interface qupath.opencv.ops.ImageOp: Get the padding requested for this operation.
getPadding() - Method in class qupath.opencv.ops.ImageOps.PaddedOp
getPadding(int, int) - Static method in class qupath.lib.regions.Padding: Get an padding object 'x' pixels to the left and right, and 'y' pixels above and below.
getPadding(int, int, int, int) - Static method in class qupath.lib.regions.Padding: Get a padding object that may have different padding on each side.
getPane() - Method in class qupath.lib.gui.charts.HistogramDisplay: Get the pane containing the histogram and associated UI components, for addition to a scene.
getPane() - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager: Get the pane containing all mini viewers, which can be added to a scene for display.
getPane() - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Get the Pane that can be displayed.
getPane() - Method in class qupath.lib.gui.panes.AnnotationPane: Get the pane for display.
getPane() - Method in class qupath.lib.gui.panes.ImageDetailsPane: Get the Pane component for addition to a scene.
getPane() - Method in class qupath.lib.gui.panes.MeasurementMapPane: Get the pane, which can be added to a scene for display.
getPane() - Method in class qupath.lib.gui.panes.PathObjectHierarchyView: Get the pane for display.
getPane() - Method in class qupath.lib.gui.panes.PreferencePane: Get a pane to display.
getPane() - Method in class qupath.lib.gui.panes.ProjectBrowser: Get the Pane component for addition to a scene.
getPane() - Method in class qupath.lib.gui.panes.WorkflowCommandLogView: Get the pane to add to a scene.
getParallelism() - Static method in class qupath.lib.common.ThreadTools: Get the requested level of parallelism.
getParameterEnabled(String) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Returns true if a parameter exists with the given key and is enabled (and is therefore editable).
getParameterEnabled(Parameter<?>) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Returns true if a parameter is enabled (and is therefore editable).
getParameterList() - Method in interface qupath.lib.plugins.parameters.Parameterizable: Get the parameter list associated with the class.
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
getParameterList() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Retrieve a list of adjustable parameter that can be used to customize the classifier.
getParameterList(ImageData<T>) - Method in class qupath.lib.plugins.AbstractInteractivePlugin: Get a reference to a ParameterList stored internally, and which will be used for analysis.
getParameterListJSON(Map<String, ?>, String) - Static method in class qupath.lib.plugins.parameters.ParameterList: Deprecated.
use ParameterList.convertToJson(Map) instead.
getParameterListJSON(ParameterList, String) - Static method in class qupath.lib.plugins.parameters.ParameterList: Deprecated.
use ParameterList.convertToJson(ParameterList) instead.
getParameterMap() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
getParameterMap() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
getParameterMap() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
getParameterMap() - Method in interface qupath.lib.plugins.workflow.WorkflowStep: Get a map of parameters required for this step.
getParameters() - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Get the ParameterList displayed in this panel.
getParameters() - Method in class qupath.lib.plugins.parameters.ParameterList: Returns a map of keys and their corresponding parameters
getParent() - Method in class qupath.lib.experimental.pixels.Parameters: Get the parent object.
getParent() - Method in class qupath.lib.objects.PathObject: Request the parent object.
getParentClass() - Method in class qupath.lib.objects.classes.PathClass: Get the parent classification, or null if this classification has no parent.
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.cells.SubcellularDetection
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.gui.ImageJMacroRunner
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.AbstractDetectionPlugin: Get all selected objects that are instances of a supported class.
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin: Get a collection of objects to process, based on the contents of the PluginRunner.
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
getParentObjects(ImageData<T>) - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
getParentObjects(ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
getParentOrProxy() - Method in class qupath.lib.experimental.pixels.Parameters: Get the parent, or a proxy parent if one has been specified.
getPatch() - Method in class qupath.lib.common.Version: Get the patch version number (0.0.X).
getPatchHeight() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the height of a patch, in pixels.
getPatchWidth() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the width of a patch, in pixels.
getPath() - Method in class qupath.lib.images.servers.AbstractImageServer: Default implementation lazily calls AbstractImageServer.createID() on demand.
getPath() - Method in interface qupath.lib.images.servers.ImageServer: Get a String path that can uniquely identify this image.
getPath() - Method in class qupath.lib.io.UriUpdater.SingleUriItem: Get the Path corresponding to the URI, or none if the URI does not refer to a file.
getPath() - Method in interface qupath.lib.projects.Project: Get a path to this project, or null if this project is not on a local file system.
getPath() - Method in class qupath.lib.regions.RegionRequest: Get the requested ImageServer path, used as an identifier.
getPathClass() - Method in class qupath.lib.objects.PathObject: Get the classification of the object.
getPathClass() - Method in class qupath.lib.objects.PathROIObject
getPathClass() - Method in class qupath.lib.objects.PathRootObject
getPathClass(String) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.

Get a PathClass, without specifying any color.
getPathClass(String) - Static method in class qupath.lib.scripting.QP: Get a PathClass with the specified name.
getPathClass(String, Integer) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0 in favor of PathClass.getInstance(String, Integer) or PathClass.fromString(String, Integer)
getPathClass(String, Integer) - Static method in class qupath.lib.scripting.QP: Get a PathClass with the specified name and color.
getPathClass(String, String...) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0 in favor of PathClass.fromArray(String...)
getPathClass(List<String>) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0 in favor of PathClass.fromCollection(java.util.Collection)
getPathClass(PathClassFactory.StandardPathClasses) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use PathClass.StandardPathClasses
getPathClassColor(PathClass) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get a Color appropriate for displaying a PathClass.
getPathClasses() - Method in interface qupath.lib.classifiers.object.ObjectClassifier: Get the classifications set by this classifier.
getPathClasses() - Method in interface qupath.lib.projects.Project: Get an unmodifiable list representing the PathClasses associated with this project.
getPathClasses() - Method in class qupath.opencv.dnn.DnnObjectClassifier
getPathClasses() - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
getPathClasses() - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
getPathClassUnclassified() - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use instead PathClass.NULL_CLASS
getPathMemoization() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Get the path to the directory where memoization files should be written, or null if no path is set.
getPathObject() - Method in class qupath.lib.objects.classes.Reclassifier: Get the stored PathObject for which the PathClass may be set.
getPathObjects() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get all the objects associated with this subdivision.
getPathObjects() - Method in class qupath.lib.io.FeatureCollection: Get the objects being wrapped.
getPathObjects() - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
getPathObjects() - Method in interface qupath.lib.objects.PathObjectConnectionGroup: Get an unmodifiable collection containing all the PathObjects contained within this group.
getPathObjects() - Method in class qupath.opencv.features.DelaunayTriangulation
getPathObjectsForRegion(ImageRegion) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
getPathObjectsForRegion(ImageRegion) - Method in interface qupath.lib.objects.PathObjectConnectionGroup: Get all the objects with connections that may intersect the specified region.
getPenManager() - Static method in class qupath.lib.gui.viewer.tools.QuPathPenManager: Get the current PenInputManager.
getPixelCalibration() - Method in interface qupath.lib.images.PathImage: Get the PixelCalibration representing actual pixel sizes in this image, with downsampling applied if necessary.
getPixelCalibration() - Method in interface qupath.lib.images.servers.ImageServer: Get the PixelCalibration object from the current metadata.
getPixelCalibration() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get a PixelCalibration object representing the pixel size information for this metadata object.
getPixelCalibration() - Method in class qupath.process.gui.commands.ml.ClassificationResolution: Get the PixelCalibration used to apply this resolution.
getPixelClassificationRegionFilter() - Method in class qupath.lib.gui.viewer.OverlayOptions
getPixelClassificationServer(ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Get the ImageServer that would be used by this overlay for the specified ImageData.
getPixelClassifiers() - Method in interface qupath.lib.projects.Project: Get a manager for pixel classifiers saved within this project.
getPixelHeight() - Method in class qupath.lib.images.servers.PixelCalibration: Get the numeric value representing the pixel height, in the stored units.
getPixelHeightMicrons() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the pixel height in microns, if available - or Double.NaN otherwise.
getPixelHeightMicrons() - Method in class qupath.lib.images.servers.PixelCalibration: Get the pixel height in microns, or Double.NaN if this is unknown.
getPixelHeightUnit() - Method in class qupath.lib.images.servers.PixelCalibration: Get a String representation of the preferred pixel height unit.
getPixelLayer(ImageData<?>) - Static method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Request the pixel layer from an ImageData.
getPixels(SimpleImage, boolean) - Static method in class qupath.lib.analysis.images.SimpleImages: Get the pixel values for the image.
getPixelSize() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters: Get the requested pixel size for the density map.
getPixelType() - Method in class qupath.lib.images.servers.AbstractImageServer
getPixelType() - Method in interface qupath.lib.images.servers.ImageServer: The bit-depth and type of the image.
getPixelType() - Method in class qupath.lib.images.servers.ImageServerMetadata: Returns the bit-depth for individual pixels in the image.
getPixelValue(int, ColorTransformer.ColorTransformMethod) - Static method in class qupath.lib.color.ColorTransformer: Get the value of a single packed RGB pixel after applying a specified color transform method.
getPixelValue(int, ColorTransformer.ColorTransformMethod, ColorDeconvolutionStains) - Static method in class qupath.lib.color.ColorTransformer: Get the value of a single packed RGB pixel after applying a specified color transform method, with color deconvolution stains provided.
getPixelWidth() - Method in class qupath.lib.images.servers.PixelCalibration: Get the numeric value representing the pixel width, in the stored units.
getPixelWidthMicrons() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the pixel width in microns, if available - or Double.NaN otherwise.
getPixelWidthMicrons() - Method in class qupath.lib.images.servers.PixelCalibration: Get the pixel width in microns, or Double.NaN if this is unknown.
getPixelWidthUnit() - Method in class qupath.lib.images.servers.PixelCalibration: Get a String representation of the preferred pixel width unit.
getPlaceholderText() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the placeholder text to show if no image is available.
getPlainStyling(String) - Static method in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Get simple styling that does not apply any classes.
getPlane() - Method in class qupath.lib.images.servers.TileRequest: Deprecated.
v0.4.0 use TileRequest.getImagePlane() instead (changed for better consistency with other classes)
getPlane() - Method in class qupath.lib.regions.ImageRegion: Deprecated.
v0.4.0 use ImageRegion.getImagePlane() instead (changed for better consistency with other classes)
getPlane(int, int) - Static method in class qupath.lib.regions.ImagePlane: Returns an ImagePlus, where the z-slice and time point can be specified and channel is ignored (i.e.
getPlane(ImageRegion) - Static method in class qupath.lib.regions.ImagePlane: Returns an ImagePlane with channel -1 and z and t set from an existing ImageRegion.
getPlane(ROI) - Static method in class qupath.lib.regions.ImagePlane: Returns an ImagePlane with channel -1, and z and t set from an existing ROI.
getPlaneWithChannel(int, int, int) - Static method in class qupath.lib.regions.ImagePlane: Returns an ImagePlane, where the channel, z-slice and time point can be specified.
getPlaneWithChannel(ROI) - Static method in class qupath.lib.regions.ImagePlane: Returns an ImagePlane with channel, z and t set from an existing ROI.
getPluginClass() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep: Get the full name of the plugin class.
getPointObjects(Class<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get objects that contain Point ROIs.
getPointObjects(Collection<T>) - Static method in class qupath.lib.objects.PathObjectTools: Get a list of objects with point ROIs from a collection of objects.
getPoolSizeProp() - Method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager
getPositive(PathClass) - Static method in class qupath.lib.objects.classes.PathClass: Get a standalone or derived Positive classification
getPositive(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use PathClass.getPositive(PathClass)
getPostprocessing() - Method in class qupath.opencv.ml.PatchClassifierParams: Get any postprocessing steps that should be applied after prediction.
getPredictionFunction() - Method in class qupath.opencv.dnn.AbstractDnnModel: Get the prediction function that can apply a prediction with one or more blobs as input.
getPredictionFunction() - Method in class qupath.opencv.dnn.OpenCVDnn
getPredictionOp() - Method in class qupath.opencv.ml.PatchClassifierParams: Get the image op used for prediction only.
getPreferencePane() - Method in class qupath.lib.gui.QuPathGUI: Get a reference to the PreferencePane.
getPreferredDownsampleFactor(ImageServer<?>, double) - Static method in class qupath.lib.images.servers.ServerTools: Get the downsample factor supported by the server that is the best match for the requested downsample.
getPreferredDownsamples() - Method in class qupath.lib.images.servers.AbstractImageServer: Request the preferred downsamples from the image metadata.
getPreferredDownsamples() - Method in interface qupath.lib.images.servers.ImageServer: Get an array of downsample factors supported by the server
getPreferredDownsamplesArray() - Method in class qupath.lib.images.servers.ImageServerMetadata: Request the preferred downsamples from the image metadata.
getPreferredOverlayColor() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay: Return the preferred overlay color.
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.CellCountsCV
getPreferredPixelSizeMicrons(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.WatershedNucleiCV
getPreferredPixelSizeMicrons(ImageData<T>, ParameterList) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin: Get the preferred pixel size that would be used for the specified ImageData and ParameterList.
getPreferredResolutionLevel(ImageServer<?>, double) - Static method in class qupath.lib.images.servers.ServerTools: Get the preferred resolution level to request regions from an ImageServer at a specified downsample level.
getPreferredTileHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the preferred tile height, which can be used to optimize pixel requests for large images.
getPreferredTileWidth() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the preferred tile width, which can be used to optimize pixel requests for large images.
getPreferredUriImageSupport(Class<T>, String, String...) - Static method in class qupath.lib.images.servers.ImageServerProvider: Get the preferred ImageServerBuilder.UriImageSupport for a specified image path.
getPreprocessing() - Method in class qupath.opencv.ml.PatchClassifierParams: Get any preprocessing steps that should be applied.
getPressure() - Method in interface qupath.lib.gui.viewer.tools.QuPathPenManager.PenInputManager: Returns a pressure value, between 0 and 1.
getPreviousSelectedTool() - Method in class qupath.lib.gui.ToolManager: Get the value of ToolManager.selectedToolProperty().
getPreviousURI() - Method in interface qupath.lib.projects.Project: Sometimes projects move (unfortunately).
getProbabilityColorModel32Bit(List<ImageChannel>) - Static method in class qupath.lib.color.ColorModelFactory: Get a ColorModel suitable for showing 32-bit (pseudo-)probabilities for multiple channels.
getProbabilityColorModel8Bit(List<ImageChannel>) - Static method in class qupath.lib.color.ColorModelFactory: Get a ColorModel suitable for showing 8-bit pseudo-probabilities for multiple channels.
getProbabilityThreshold(WritableRaster) - Static method in class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Get a suitable threshold assuming a raster contains probability values.
getProject() - Method in class qupath.lib.gui.QuPathGUI: Get the value of QuPathGUI.projectProperty().
getProject() - Static method in class qupath.lib.scripting.QP: Get the current project.
getProject() - Method in class qupath.lib.scripting.ScriptParameters: Get the current project that should be used with the script.
getProjectEntry() - Static method in class qupath.lib.scripting.QP: Get the project entry for the currently-open image within the current project, or null if no project/image is open.
getProjectEntryMetadataValue(String) - Static method in class qupath.lib.scripting.QP: Get the metadata value from the current project entry for the specified key, or null if no such metadata value exists (or no project entry is open).
getProjectExtension() - Static method in class qupath.lib.projects.ProjectIO: Get the default extension for a QuPath project file, without the 'dot'.
getProjectExtension(boolean) - Static method in class qupath.lib.projects.ProjectIO: Get the default extension for a QuPath project file.
getPrompt() - Method in class qupath.lib.plugins.parameters.BooleanParameter
getPrompt() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
getPrompt() - Method in class qupath.lib.plugins.parameters.DoubleParameter
getPrompt() - Method in class qupath.lib.plugins.parameters.EmptyParameter
getPrompt() - Method in class qupath.lib.plugins.parameters.IntParameter
getPrompt() - Method in class qupath.lib.plugins.parameters.NumericParameter
getPrompt() - Method in class qupath.lib.plugins.parameters.StringParameter
getPrompt() - Method in interface qupath.lib.plugins.parameters.Parameter: Get some prompt text that may be displayed to a user.
getProperties() - Method in class qupath.lib.images.ImageData: Get an unmodifiable map representing all known properties for this ImageData.
getProperties() - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide: Get an unmodifiable map of all available properties.
getProperty(String) - Method in class qupath.lib.images.ImageData: Get a specified property.
getPropertySheet() - Method in class qupath.lib.gui.panes.PreferencePane: Get the property sheet for this PreferencePane.
getProviderClass() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport: Get the class of the associated ImageServerBuilder.
getPValue() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult: Get the calculated p-value.
getQuartiles(double[]) - Static method in class qupath.lib.analysis.stats.StatisticsHelper: Determine thresholds for dividing an array of double values into quartiles.
getQuPath() - Method in class qupath.lib.gui.actions.CommonActions: Get the QuPath instance associated with these actions.
getQuPath() - Static method in class qupath.lib.gui.scripting.QPEx: Get the current QuPath instance.
getQuPathVersion() - Method in class qupath.imagej.gui.IJExtension: Returns the version stored within this jar, because it is matched to the QuPath version.
getQuPathVersion() - Method in class qupath.lib.extension.svg.SvgExtension: Returns the version stored within this jar, because it is matched to the QuPath version.
getQuPathVersion() - Method in interface qupath.lib.gui.extensions.QuPathExtension: Get a QuPath version for which this extension was written.
getQuPathVersion() - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditorExtension: Returns the version stored within this jar, because it is matched to the QuPath version.
getQuPathVersion() - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension: Returns the version stored within this jar, because it is matched to the QuPath version.
getQuPathVersion() - Method in class qupath.process.gui.ProcessingExtension: Returns the version stored within this jar, because it is matched to the QuPath version.
getRadius() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters: Get the radius for the density map, in calibrated units.
getRange() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get the range, i.e.
getReaderOptions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Get a map representing additional arguments that should be passed to readers.
getRecentProjectList() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get a list of the most recent projects that were opened.
getRecentScriptsList() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get a list of the most recent scripts that were opened.
getRed() - Method in class qupath.lib.color.StainVector: Get the red component of the (normalized) stain vector.
getRed() - Method in class qupath.lib.display.settings.ChannelColor: Get the red value.
getRedOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
getRegion() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
getRegion() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Get the region representing this control, so it may be added to a scene.
getRegion() - Method in class qupath.lib.gui.scripting.TextAreaControl
getRegion() - Method in class qupath.lib.gui.viewer.ViewerManager: Get the region node that can be added to a scene graph to display the viewers.
getRegionMap() - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Get an unmodifiable Map containing image regions to paint on this overlay.
getRegionRequest() - Method in class qupath.lib.experimental.pixels.Parameters: Get the region request.
getRegionRequest() - Method in class qupath.lib.images.servers.TileRequest: Get the RegionRequest that this tile represents.
getRegions() - Method in class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager: Get an unmodifiable collection for all available regions.
getRelativePathOrNull(String) - Method in class qupath.lib.gui.UserDirectoryManager
getRenderer() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Get the ImageRenderer used with this overlay, which may be null.
getRenderer() - Method in class qupath.lib.gui.viewer.QuPathViewer: Request a renderer that converts image tiles into RGB images.
getReplacements() - Method in class qupath.lib.io.UriUpdater: Get a map of all replacements.
getRepo() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo: Get the repo.
getRepository() - Method in interface qupath.lib.gui.extensions.GitHubProject: Get the GitHub repository associated with the project.
getRepresentedPathClasses(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Get a set of the represented path classes, i.e.
getRequestedCursor() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
getRequestedDataFileVersion() - Static method in class qupath.lib.io.PathIO: Get the requested version for .qpdata files.
getResolution() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Get the resolution at which the training should occur.
getResources(String, Class<S>, String) - Method in interface qupath.lib.projects.Project: Get a manager for objects of a specified class within this project.
getResourcesForProject(Project<?>) - Static method in class qupath.lib.display.settings.DisplaySettingUtils: Get the resource manager for image display settings from a project.
getResultString() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult: Returns a presentable representation of the log-rank test result, including hazard ratio and confidence interval.
getRGB(float, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo: Get a suitable RGB value for displaying a pixel with the specified value
getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the RGB values that would be used to display all the pixels of an image
getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo: Get the RGB value that would be used to display a particular pixel
getRGB(Color) - Static method in class qupath.lib.gui.tools.ColorToolsFX: Get a packed int (ARGB) representation of a Color object, omitting the alpha component.
getRGBThumbnail() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get a thumbnail representing the image as displayed by this viewer.
getROI() - Method in class qupath.lib.objects.PathObject: Get the region of interest (ROI) for the object.
getROI() - Method in class qupath.lib.objects.PathROIObject
getROI() - Method in class qupath.lib.objects.PathRootObject
getROI() - Method in class qupath.lib.roi.RoiEditor: Retrieve the ROI currently being edited (may be null).
getROI(PathObject, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Get the ROI for a PathObject, with a preference for the nucleus ROI of a cell.
getROIEditor() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the RoiEditor used by this viewer.
getRoiName() - Method in class qupath.lib.roi.AreaROI
getRoiName() - Method in class qupath.lib.roi.EllipseROI
getRoiName() - Method in class qupath.lib.roi.GeometryROI
getRoiName() - Method in interface qupath.lib.roi.interfaces.ROI: Get a String representation of the kind of ROI we have, e.g.
getRoiName() - Method in class qupath.lib.roi.LineROI
getRoiName() - Method in class qupath.lib.roi.PointsROI
getRoiName() - Method in class qupath.lib.roi.PolygonROI
getRoiName() - Method in class qupath.lib.roi.PolylineROI
getRoiName() - Method in class qupath.lib.roi.RectangleROI
getRoiType() - Method in class qupath.lib.roi.AreaROI
getRoiType() - Method in class qupath.lib.roi.EllipseROI
getRoiType() - Method in class qupath.lib.roi.GeometryROI
getRoiType() - Method in interface qupath.lib.roi.interfaces.ROI: Get the RoiType, used to distinguish between points, lines and areas.
getRoiType() - Method in class qupath.lib.roi.LineROI
getRoiType() - Method in class qupath.lib.roi.PointsROI
getRoiType() - Method in class qupath.lib.roi.PolygonROI
getRoiType() - Method in class qupath.lib.roi.PolylineROI
getRoiType() - Method in class qupath.lib.roi.RectangleROI
getRootLogLevel() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level, as set by this manager.
getRootObject() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get the root object.
getRotatedBuilder(ImageServerBuilder.ServerBuilder<BufferedImage>, RotatedImageServer.Rotation) - Static method in class qupath.lib.images.servers.RotatedImageServer: Get a ServerBuilder that applies a rotation to another server.
getRotation() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the current rotation; angle in radians.
getRotation() - Method in class qupath.lib.images.servers.RotatedImageServer: Get the rotation applied by this server.
getSaturationPercent() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the percentage of pixels to use when applying auto contrast settings to a non-8-bit image.
getScale() - Method in class qupath.opencv.dnn.OpenCVDnn: Get scale factors to be applied to preprocess input.
getScale(int) - Method in class qupath.opencv.ml.objects.features.Normalizer: Get the scale factor for the specified feature
getScaledArea(double, double) - Method in class qupath.lib.roi.AreaROI
getScaledArea(double, double) - Method in class qupath.lib.roi.EllipseROI
getScaledArea(double, double) - Method in class qupath.lib.roi.GeometryROI
getScaledArea(double, double) - Method in interface qupath.lib.roi.interfaces.ROI: Get scaled area of the ROI, for use with calibrated pixel sizes.
getScaledArea(double, double) - Method in class qupath.lib.roi.LineROI
getScaledArea(double, double) - Method in class qupath.lib.roi.PointsROI
getScaledArea(double, double) - Method in class qupath.lib.roi.PolygonROI
getScaledArea(double, double) - Method in class qupath.lib.roi.PolylineROI
getScaledArea(double, double) - Method in class qupath.lib.roi.RectangleROI
getScaledLength(double, double) - Method in class qupath.lib.roi.AreaROI
getScaledLength(double, double) - Method in class qupath.lib.roi.EllipseROI
getScaledLength(double, double) - Method in class qupath.lib.roi.GeometryROI
getScaledLength(double, double) - Method in interface qupath.lib.roi.interfaces.ROI: Get the scaled length, for use with calibrated pixel sizes.
getScaledLength(double, double) - Method in class qupath.lib.roi.LineROI
getScaledLength(double, double) - Method in class qupath.lib.roi.PointsROI
getScaledLength(double, double) - Method in class qupath.lib.roi.PolygonROI
getScaledLength(double, double) - Method in class qupath.lib.roi.PolylineROI
getScaledLength(double, double) - Method in class qupath.lib.roi.RectangleROI
getScaledNavigationSpeed() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get navigation speed scaled as a proportion and forced to be in the range 0-1.
getScaledRGBInstance(BufferedImage, int, int) - Static method in class qupath.lib.gui.tools.GuiTools: Get a scaled (RGB or ARGB) image, achieving reasonable quality even when scaling down by a considerably amount.
getScaledScrollSpeed() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get scroll speed scaled as a proportion and forced to be in the range 0-1.
getScript() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
getScript() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
getScript() - Method in interface qupath.lib.plugins.workflow.ScriptableWorkflowStep: Get one or more script lines that may be used to apply the step.
getScript() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
getScript() - Method in class qupath.lib.scripting.ScriptParameters: Get the text of the script.
getScriptEditor() - Method in class qupath.lib.gui.QuPathGUI: Get a reference to the current ScriptEditor (which may or may not be open at the moment).
getScripts() - Method in interface qupath.lib.projects.Project: Get a manager for scripts saved within this project.
getScriptsDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager: Get the path to where shared script files should be written.
getSecondaryObjectFilters() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters: Get the secondary object filters.
getSelectedObject() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the currently-selected object from the hierarchy.
getSelectedObject() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Get the current primary selected object.
getSelectedObject() - Static method in class qupath.lib.scripting.QP: Get the primary selected object within the current PathObjectHierarchy.
getSelectedObjects() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Get an unmodifiable set containing all the currently-selected objects.
getSelectedObjects() - Static method in class qupath.lib.scripting.QP: Get the selected objects within the current PathObjectHierarchy.
getSelectedROI() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Get the ROI of the selected object, if available, or null
getSelectedROI() - Static method in class qupath.lib.scripting.QP: Get the ROI for the primary selected object within the current PathObjectHierarchy.
getSelectedText() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
getSelectedText() - Method in interface qupath.lib.gui.scripting.EditableText: Get the selected text as a string.
getSelectedText() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl: Gets the value of the selectedText property.
getSelectedText() - Method in class qupath.lib.gui.scripting.TextAreaControl: Gets the value of the selectedText property.
getSelectedTool() - Method in class qupath.lib.gui.ToolManager: Get the value of ToolManager.selectedToolProperty().
getSelection() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
getSelection() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Get the range of the currently-selected text.
getSelection() - Method in class qupath.lib.gui.scripting.TextAreaControl
getSelectionEnd() - Method in interface qupath.lib.gui.scripting.EditableText: Get the ending position for any selection (exclusive).
getSelectionEnd() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
getSelectionLength() - Method in interface qupath.lib.gui.scripting.EditableText: Get the selection length, or 0 if there is no selection.
getSelectionModeAction() - Method in class qupath.lib.gui.ToolManager: Return the action associated with 'selection mode'.
getSelectionModel() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Get the selection model for the channels.
getSelectionModel() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get the selection model, which handles the selection status of objects.
getSelectionStart() - Method in interface qupath.lib.gui.scripting.EditableText: Get the starting position for any selection (inclusive).
getSelectionStart() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
getSemanticVersion() - Static method in class qupath.lib.common.GeneralTools: Get a representation of QuPath's version, parsed according to the rules of semantic versioning if possible.
getSeparator() - Method in class qupath.lib.gui.tools.MeasurementExporter: Returns the separator used in between measurements.
getSerializationExtension() - Static method in class qupath.lib.gui.prefs.PathPrefs: File extension used for serialization of ImageData (without the dot)
getSeries() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer: Get the series index, as used by Bio-Formats.
getServer() - Method in class qupath.lib.experimental.pixels.Parameters: Get the server.
getServer() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the ImageServer for the current image displayed within the viewer, or null if no image is displayed.
getServer() - Method in class qupath.lib.images.ImageData: Get the ImageServer.
getServer(ImageRegion, double) - Method in class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager: Request the server for a specific downsample.
getServerBounds() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get an ImageRegion representing the full width and height of the current image.
getServerBuilder() - Method in interface qupath.lib.projects.ProjectImageEntry: Get a ImageServerBuilder.ServerBuilder that can be used to open this image.
getServerBuilderFactory() - Static method in class qupath.lib.images.servers.ImageServers: Get a TypeAdapterFactory to handle ServerBuilders.
getServerHeight() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the height in pixels of the full resolution of the current image, or 0 if no image is currently open.
getServerPath() - Method in class qupath.lib.images.ImageData: Get the path of the ImageServer.
getServerType() - Method in class qupath.imagej.images.servers.ImageJServer
getServerType() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
getServerType() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
getServerType() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
getServerType() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
getServerType() - Method in class qupath.lib.images.servers.AffineTransformImageServer
getServerType() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
getServerType() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
getServerType() - Method in class qupath.lib.images.servers.CroppedImageServer
getServerType() - Method in interface qupath.lib.images.servers.ImageServer: A string describing the type of server, for example the name of the library used (Openslide, Bioformats...)
getServerType() - Method in class qupath.lib.images.servers.LabeledImageServer
getServerType() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
getServerType() - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
getServerType() - Method in class qupath.lib.images.servers.RotatedImageServer
getServerType() - Method in class qupath.lib.images.servers.SparseImageServer
getServerType() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
getServerURIs() - Method in interface qupath.lib.projects.ProjectImageEntry: Deprecated.
use instead UriResource.getURIs()
getServerWidth() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the width in pixels of the full resolution of the current image, or 0 if no image is currently open.
getShape() - Method in class qupath.lib.roi.AreaROI
getShape() - Method in class qupath.lib.roi.EllipseROI
getShape() - Method in class qupath.lib.roi.GeometryROI
getShape() - Method in interface qupath.lib.roi.interfaces.ROI: Returns a java.awt.Shape representing this ROI, if possible.
getShape() - Method in class qupath.lib.roi.LineROI
getShape() - Method in class qupath.lib.roi.PointsROI: It is not possible to convert a PointROI to a java.awt.Shape.
getShape() - Method in class qupath.lib.roi.PolygonROI
getShape() - Method in class qupath.lib.roi.PolylineROI
getShape() - Method in class qupath.lib.roi.RectangleROI
getShape() - Method in class qupath.opencv.dnn.DnnShape: Get a copy of the internal dimensions array.
getShape(ROI) - Static method in class qupath.lib.roi.RoiTools: Get a Shape object representing a ROI.
getShapeROI(Area, ImagePlane) - Static method in class qupath.lib.roi.RoiTools: Create a ROI from an Shape.
getShapeROI(Shape, ImagePlane, double) - Static method in class qupath.lib.roi.RoiTools: Create a ROI from an Shape with a specified 'flatness'.
getShowAllRGBTransforms() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request that all available color transforms are shown for RGB images.
getShowAnnotations() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowCellBoundaries() - Method in class qupath.lib.gui.viewer.OverlayOptions: Query the current OverlayOptions.DetectionDisplayMode to see if cell boundary ROIs should be drawn.
getShowCellNuclei() - Method in class qupath.lib.gui.viewer.OverlayOptions: Query the current OverlayOptions.DetectionDisplayMode to see if nuclei ROIs should be drawn.
getShowConnections() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowDetections() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowGrid() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowLocation() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Get the value of ViewerPlusDisplayOptions.showLocationProperty().
getShowNames() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowOverview() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Get the value of ViewerPlusDisplayOptions.showOverviewProperty().
getShowPixelClassification() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowScalebar() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Get the value of ViewerPlusDisplayOptions.showScalebarProperty().
getShowTMACoreLabels() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowTMAGrid() - Method in class qupath.lib.gui.viewer.OverlayOptions
getSigma() - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale: Get the sigma value.
getSigmaZ(PixelCalibration) - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale: Get the sigma value for the z dimension.
getSimpleTransformedPixels(int[], ColorTransformer.ColorTransformMethod, float[]) - Static method in class qupath.lib.color.ColorTransformer: Apply a color transform to all pixels in a packed (A)RGB array.
getSingleThreadExecutor(Object) - Method in class qupath.lib.gui.SharedThreadPoolManager: Get a reusable executor using a single thread, creating a new executor if needed.
getSingleton(PathClass) - Static method in class qupath.lib.objects.classes.PathClass: Get the singleton PathClass that is equivalent to the PathClass provided.
getSingletonPathClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0 in favor of PathClass.getSingleton(PathClass)
getSize() - Method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
getSizeC() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the number of image channels.
getSizeT() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the number of time points.
getSizeZ() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the number of z-slices.
getSkipAlwaysExtensions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Query the set of file extensions for which Bio-Formats should not be used.
getSkipBoundaryStrategy() - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy: Create a boundary strategy that ignores boundaries, not using them for classifier training.
getSkipMissingCoresProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Return whether the viewer skips missing TMA cores when navigating TMA grids with arrow keys.
getSolidity() - Method in class qupath.lib.roi.AreaROI
getSolidity() - Method in class qupath.lib.roi.EllipseROI
getSolidity() - Method in class qupath.lib.roi.GeometryROI
getSolidity() - Method in class qupath.lib.roi.LineROI
getSolidity() - Method in class qupath.lib.roi.PointsROI
getSolidity() - Method in class qupath.lib.roi.PolygonROI
getSolidity() - Method in class qupath.lib.roi.PolylineROI
getSolidity() - Method in class qupath.lib.roi.RectangleROI
getSolidity() - Method in interface qupath.lib.roi.interfaces.ROI: Calculate the solidity, defined as ROI area / convex hull area.
getSource() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Get the source that triggered the event.
getSpaceX() - Method in class qupath.lib.gui.viewer.GridLines: Horizontal spacing between lines for any counting grid.
getSpaceY() - Method in class qupath.lib.gui.viewer.GridLines: Vertical spacing between lines for any counting grid.
getStage() - Method in class qupath.lib.gui.commands.ContextHelpViewer: Get the help viewer stage.
getStage() - Method in class qupath.lib.gui.commands.PathObjectGridView: Get the stage used to show the grid view.
getStage() - Method in class qupath.lib.gui.JavadocViewer: Get the stage used to show the javadocs.
getStage() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the stage used to display the image.
getStage() - Method in class qupath.lib.gui.QuPathGUI: Get the main QuPath stage.
getStage() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Get the stage for this script editor.
getStage() - Method in class qupath.lib.gui.tma.TMASummaryViewer: Deprecated.

Get the stage for display.
getStage() - Method in class qupath.process.gui.commands.density.DensityMapDialog: Get the stage.
getStain(int) - Method in class qupath.lib.color.ColorDeconvolutionStains: Get a specified color deconvolution stain vector, where n should be 1, 2 or 3 (because color deconvolution on a 3-channel image can recover [to some extent] up to 3 stains).
getStainNumber(StainVector) - Method in class qupath.lib.color.ColorDeconvolutionStains: Get the number for a specific stain (1, 2 or 3).
getStainProjection(int, double, double, double, double[], double[], double[]) - Static method in class qupath.lib.color.ColorTransformer: Calculate magnitude of projection of pixel OD onto stain OD.
getStainRejection(int, double, double, double, double[], double[], double[]) - Static method in class qupath.lib.color.ColorTransformer: Calculate magnitude of rejection of pixel OD onto stain OD.
getStains(boolean) - Method in class qupath.lib.color.ColorDeconvolutionStains: Get a collection of all the stains.
getStartTime() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the time associated with the first recorded frame.
getStartX() - Method in class qupath.lib.gui.viewer.GridLines: Starting x coordinate for any counting grid (usually 0).
getStartY() - Method in class qupath.lib.gui.viewer.GridLines: Starting y coordinate for any counting grid (usually 0).
getStaticImportStatements(Collection<Class<?>>) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Get the static import statements as a String, to add at the beginning of the executed script.
getStaticImportStatments(Collection<Class<?>>) - Method in interface qupath.lib.gui.scripting.languages.DefaultScriptLanguage.ImportStatementGenerator
getStatistic() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Retrieve a sorted array containing the value corresponding to a time from KaplanMeierData.getAllTimes().
getStatus() - Method in class qupath.lib.io.UriUpdater.SingleUriItem: Get the URI status.
getStatus() - Method in class qupath.lib.plugins.ParallelTileObject: Get the current status (pending, processing or done).
getStdDev() - Method in class qupath.lib.analysis.stats.Histogram: Get the standard deviation of all the values being histogrammed.
getStdDev() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get the standard deviation of all non-NaN values that were added.
getSteps() - Method in class qupath.lib.plugins.workflow.Workflow: Get an unmodifiable list of the steps.
getString(String) - Static method in class qupath.lib.gui.localization.QuPathResources: Get a string from the main ResourceBundle used for the QuPath user interface.
getString(String, String) - Static method in class qupath.lib.gui.localization.QuPathResources
getStringParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Get a String parameter value (or its default) for the specified key.
getStringValue(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
getStringValue(PathObject, String, int) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
getStringValue(T, String) - Method in interface qupath.lib.gui.measure.PathTableData: Get a string representation of the value.
getStringValue(T, String, int) - Method in interface qupath.lib.gui.measure.PathTableData: Get a string value, converting to a fixed number of decimal places if the column is numeric.
getStroke() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData: Get the histogram stroke color.
getStructureChangeBase() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: If this is a structure change event, return the base object, i.e.
getStylerFromLanguage(ScriptLanguage) - Static method in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Get the ScriptStyler object corresponding to the specified ScriptLanguage.
getStyles() - Method in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
getSuffix() - Method in class qupath.lib.common.Version: Get the (optional) suffix, which may be appended at the end of the version number to indicate a pre-release (0.0.0-X).
getSuitableName(Class<? extends PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Get a user-friendly name for a specific type of PathObject, based on its Java class.
getSum() - Method in class qupath.lib.analysis.stats.Histogram: Get the sum of all the values being histogrammed.
getSum() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get the sum of all non-NaN values that were added.
getSummary() - Method in interface qupath.lib.projects.ProjectImageEntry: Get a summary string representing this image entry.
getSupportedObjects(Collection<? extends PathObject>, Collection<Class<? extends PathObject>>) - Static method in class qupath.lib.objects.PathObjectTools: From a collection of available objects, extract those that are instances of specified supported classes.
getSupportedParentObjectClasses() - Method in class qupath.imagej.detect.cells.SubcellularDetection
getSupportedParentObjectClasses() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
getSupportedParentObjectClasses() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
getSupportedParentObjectClasses() - Method in class qupath.imagej.gui.ImageJMacroRunner
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.algorithms.TilerPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.AbstractDetectionPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
getSupportedParentObjectClasses() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
getSupportedParentObjectClasses() - Method in interface qupath.lib.plugins.PathInteractivePlugin: Get a collection of possible parent objects that the plugin could have.
getSupportedParentObjectClasses() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
getSupportLevel() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport: Estimated 'support level' for a given file path, where support level is a summary of the likelihood that pixel values and metadata will be returned correctly and in a way that achieves good performance.
getSwapRedBlueBuilder(ImageServerBuilder.ServerBuilder<BufferedImage>, String) - Static method in class qupath.lib.images.servers.RearrangeRGBImageServer: Get a ServerBuilder that swaps red and blue channels for another (RGB) server.
getSwitchToGrayscaleChannel() - Method in class qupath.lib.display.ImageDisplay: Get the value of ImageDisplay.switchToGrayscaleChannelProperty().
getSynchronizeViewers() - Method in class qupath.lib.gui.viewer.ViewerManager: Gets the value of the synchronizeViewers property.
getSyntaxFromName(String) - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider: Get a script syntax from a specified language name.
getT() - Method in class qupath.lib.images.servers.TileRequest: Get the time point index for this request.
getT() - Method in class qupath.lib.regions.ImagePlane: Get the time point index.
getT() - Method in class qupath.lib.regions.ImageRegion: Get the time point index for the region.
getT() - Method in class qupath.lib.roi.AreaROI
getT() - Method in class qupath.lib.roi.EllipseROI
getT() - Method in class qupath.lib.roi.GeometryROI
getT() - Method in class qupath.lib.roi.LineROI
getT() - Method in class qupath.lib.roi.PointsROI
getT() - Method in class qupath.lib.roi.PolygonROI
getT() - Method in class qupath.lib.roi.PolylineROI
getT() - Method in class qupath.lib.roi.RectangleROI
getT() - Method in interface qupath.lib.roi.interfaces.ROI: Get time point index.
getTable() - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView: Get the TableView.
getTableModelString(PathTableData<T>, String, Collection<String>) - Static method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand: Get a single String representing the data in a table.
getTableModelStrings(PathTableData<T>, String, Collection<String>) - Static method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand: Get a list of Strings representing table data.
getTabString() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: String to insert when tab key pressed
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin: Get a collection of tasks to perform.
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
getTasks(ImageData<T>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
getTertiles(double[]) - Static method in class qupath.lib.analysis.stats.StatisticsHelper: Determine thresholds for dividing an array of double values into tertiles.
getText() - Method in class qupath.lib.gui.actions.InfoMessage: Text of the message.
getText() - Method in interface qupath.lib.gui.scripting.EditableText: Get all the text in the editor;
getText() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl: Gets the value of the text property.
getText() - Method in class qupath.lib.gui.scripting.TextAreaControl: Gets the value of the text property.
getText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Get the name of the command.
getTextField(Parameter<?>, int) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
getThickStrokeWidth(double) - Method in class qupath.lib.gui.viewer.OverlayOptions: Get the requested stroke thickness to use when drawing ROIs that should be represented with 'thick' lines (annotations, TMA cores).
getThis() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
getThis() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
getThis() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
getThreadPoolManager() - Method in class qupath.lib.gui.QuPathGUI: Get a SharedThreadPoolManager to help with submitting tasks in other threads.
getThreePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClass: Get a standalone or derived 3+ classification, indicating strong positivity
getThreePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use PathClass.getThreePlus(PathClass)
getThresholds() - Method in class qupath.lib.gui.charts.ChartThresholdPane: Get a list of all thresholds.
getThumbnail() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get a thumbnail representing the image as displayed by this viewer.
getThumbnail() - Method in interface qupath.lib.projects.ProjectImageEntry: Request a thumbnail for the image.
getThumbnail(ImageServer<BufferedImage>, int, int, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
getThumbnailDownsampleFactor(int, int) - Method in class qupath.lib.images.servers.AbstractImageServer
getThumbnailRGB(ImageServer<BufferedImage>) - Static method in class qupath.lib.gui.commands.ProjectCommands: Get an RGB thumbnail for an image server, suitable for showing as a project thumbnail.
getTile(TileRequest) - Method in class qupath.lib.images.servers.AbstractTileableImageServer: Get a tile for the request - ideally from the cache, but otherwise read it and then add it to the cache.
getTileCacheSize() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Get the tile cache size, in bytes.
getTileHeight() - Method in class qupath.lib.images.servers.TileRequest: Get the height of the bounding box for this tile at the tile resolution.
getTileHeight() - Method in class qupath.lib.objects.utils.Tiler: Get the height of output tiles
getTileObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get all tile objects in the hierarchy.
getTileObjects() - Static method in class qupath.lib.scripting.QP: Get a list of the current tile objects.
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.CellCountsCV: Returns zero - indicating no overlap...
getTileOverlap(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.WatershedNucleiCV
getTileOverlap(ImageData<T>, ParameterList) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin: Get an appropriate overlap, in pixels, if analysis of the specified ImageData will be tiled.
getTileRequest() - Method in class qupath.lib.experimental.pixels.Parameters: Get the tile request, if available.
getTileRequest(int, int, int, int, int) - Method in interface qupath.lib.images.servers.TileRequestManager: Get the single TileRequest containing a specified pixel, or null if no such request exists.
getTileRequest(ImageServer<BufferedImage>, double, double, double, int, int) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreHelpers: Given an ImageServer, determine the boundaries of the image tile that contains specified x, y coordinates.
getTileRequestManager() - Method in class qupath.lib.images.servers.AbstractImageServer
getTileRequestManager() - Method in interface qupath.lib.images.servers.ImageServer: Get a TileRequestManager that can be used to identify image tiles that may be efficiently requested from this ImageServer.
getTileRequests(RegionRequest) - Method in interface qupath.lib.images.servers.TileRequestManager: Get a collection of TileRequest objects necessary to fulfil a specific RegionRequest.
getTileRequestsForLevel(int) - Method in interface qupath.lib.images.servers.TileRequestManager: Get TileRequest objects for all tiles that this server supports at the specified resolution level.
getTilesToRequest(ImageServer<?>, Shape, double, int, int, List<RegionRequest>) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreHelpers: Given ImageServer, determine the boundaries of the image tiles that would be needed to paint a specified shape (defined by coordinates in the full-resolution image space).
getTileWidth() - Method in class qupath.lib.images.servers.TileRequest: Get the width of the bounding box for this tile at the tile resolution.
getTileWidth() - Method in class qupath.lib.objects.utils.Tiler: Get the width of output tiles
getTileX() - Method in class qupath.lib.images.servers.TileRequest: Get the x-coordinate of the bounding box for this tile at the tile resolution.
getTileY() - Method in class qupath.lib.images.servers.TileRequest: Get the y-coordinate of the bounding box for this tile at the tile resolution.
getTimepoint(int) - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the time point, defined in ImageServerMetadata.getTimeUnit(), or Double.NaN if this is unknown.
getTimepoint(int) - Method in class qupath.lib.images.servers.PixelCalibration: Get the time for the specified time point, or Double.NaN if this is unknown.
getTimeToEvent() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent: Get the stored time to event (units are unspecified).
getTimeUnit() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the time unit for a time series.
getTimeUnit() - Method in class qupath.lib.images.servers.PixelCalibration: Get the time unit for a time series.
getTMACore(int, int) - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
getTMACore(int, int) - Method in interface qupath.lib.objects.hierarchy.TMAGrid: Get the TMACoreObject for a specified grid location.
getTMACore(String) - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
getTMACore(String) - Method in interface qupath.lib.objects.hierarchy.TMAGrid: Retrieve a TMA core based upon its name.
getTMACoreForPixel(TMAGrid, double, double) - Static method in class qupath.lib.objects.PathObjectTools: Get the TMA core that contains the specified x & y coordinate, or null if no core is available for the coordinates give.
getTMACoreList() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
getTMACoreList() - Method in interface qupath.lib.objects.hierarchy.TMAGrid: Get an unmodifiable list of all TMA core objects.
getTMACoreList() - Static method in class qupath.lib.scripting.QP: Get the list of TMA core objects for the current hierarchy.
getTMACoreObjects(PathObjectHierarchy, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Extract a list of TMA cores from an object hierarchy.
getTMAGrid() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Get the TMAGrid, or null if there is no TMA grid associated with this hierarchy.
getToken(String, int) - Method in interface qupath.lib.scripting.languages.AutoCompletions.CompletionTokenizer: Get the token needed for the completion.
getTokenizer() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion: Get the tokenizer needed to extract the relevant bit of the text to determine the validity and/or insertion for the completion.
getTool(String) - Static method in class qupath.lib.gui.viewer.tools.PathTools: Return the PathTool corresponding to the specified String.
getToolAction(PathTool) - Method in class qupath.lib.gui.ToolManager: Get the action that corresponds to a specific PathTool, creating a new action if one does not already exist.
getToolBar() - Method in class qupath.lib.gui.QuPathGUI: Get the main toolbar.
getToolManager() - Method in class qupath.lib.gui.QuPathGUI: Get the ToolManager that handles available and selected tools.
getTools() - Method in class qupath.lib.gui.ToolManager: Get a read-only list of all available tools.
getTPosition() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the currently-visible time point.
getTrainData() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining.ClassifierTrainingData: Get training data.
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
getTrainFlags() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
getTransform() - Method in class qupath.lib.images.servers.AffineTransformImageServer: Get the affine transform for this server.
getTransformedPixels(int[], ColorTransformer.ColorTransformMethod, float[], ColorDeconvolutionStains) - Static method in class qupath.lib.color.ColorTransformer: Apply a color transform to all pixels in a packed (A)RGB array.
getTransformedValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.ImageDisplay: Get a string representation of a transformed pixel value, using the currently-selected channels.
getTranslucentColor(Color) - Static method in class qupath.lib.color.ColorToolsAwt: Get a (slightly) translucent version of the specified color.
getTwoPlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClass: Get a standalone or derived 2+ classification, indicating moderate positivity
getTwoPlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassFactory: Deprecated.
since v0.4.0, use PathClass.getTwoPlus(PathClass)
getType() - Method in class qupath.lib.gui.tools.MeasurementExporter: Returns the type of path objects used in the export.
getTypeAdapterFactory() - Static method in class qupath.lib.classifiers.object.ObjectClassifiers: Get a TypeAdapterFactory to handle ObjectClassifier instances.
getTypeAdapterFactory() - Static method in class qupath.opencv.ml.objects.features.FeatureExtractors: Get the TypeAdapterFactory default used for FeatureExtractor objects.
getTypeAdapterFactory() - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Get the TypeAdapterFactory default used for PixelClassifier objects.
getTypeAdaptor(Class<T>) - Static method in class qupath.opencv.io.OpenCVTypeAdapters: Get a TypeAdapter to pass to a GsonBuilder for a specific supported OpenCV class, i.e.
getUndoRedoManager() - Method in class qupath.lib.gui.QuPathGUI: Get the UndoRedoManager, which can be useful if needing to clear it in cases where available memory is low.
getUniqueID() - Method in class qupath.lib.gui.images.stores.AbstractImageRenderer
getUniqueID() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
getUniqueID() - Method in interface qupath.lib.gui.images.stores.ImageRenderer: Get a unique key, which will be used for caching.
getUnit() - Method in class qupath.lib.plugins.parameters.NumericParameter: Get the unit to display for this parameter (may be null if no unit is available).
getUnmodifiableMetadataMap() - Method in class qupath.lib.objects.PathObject: Get an unmodifiable map of the metadata.
getUpperBound() - Method in enum class qupath.lib.images.servers.PixelType: Get a number representing the maximum value permitted by this type.
getUpperBound() - Method in class qupath.lib.plugins.parameters.NumericParameter: Retrieve the upper bound.
getUri() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion: Get a URI to download the release (may be null if no URI is available).
getURI() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder: Get the URI used by this builder.
getURI() - Method in class qupath.lib.io.UriUpdater.SingleUriItem: Get the URI.
getURI() - Method in interface qupath.lib.projects.Project: Get a URI that can be used when saving/reloading this project.
getUris() - Method in interface qupath.lib.io.UriResource
getURIs() - Method in class qupath.imagej.images.servers.ImageJServer
getURIs() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
getURIs() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
getURIs() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
getURIs() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
getURIs() - Method in interface qupath.lib.images.servers.ImageServer: Get the URIs for images required for this server.
getURIs() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
getURIs() - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder: Get a list of URIs required by this builder.
getURIs() - Method in class qupath.lib.images.servers.LabeledImageServer
getURIs() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
getURIs() - Method in class qupath.lib.images.servers.SparseImageServer
getURIs() - Method in class qupath.lib.images.servers.TransformingImageServer
getURIs() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
getURIs() - Method in interface qupath.lib.io.UriResource: Get all the URIs required for this resource.
getURIs() - Method in class qupath.opencv.dnn.DnnModelParams: Get the URIs associated with the model (e.g.
getURIs() - Method in class qupath.opencv.dnn.DnnObjectClassifier
getURIs() - Method in class qupath.opencv.dnn.OpenCVDnn
getURIs() - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
getURIs() - Method in interface qupath.opencv.ops.ImageOp: Default implementation returns an empty list; classes should override this if necessary.
getUrlString() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo: Get the URL for the main repo.
getUseAlwaysExtensions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Query the set of file extensions for which Bio-Formats should always be used.
getUsefulValue(PathObject, double) - Method in class qupath.lib.gui.tools.MeasurementMapper
getUserForumUrl() - Static method in class qupath.lib.gui.Urls: Get a URL pointing to the main QuPath user forum.
getUserPath() - Method in class qupath.lib.gui.UserDirectoryManager: Get the user path where additional files may be stored.
getUserPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs: Deprecated.
since v0.5.0 - avoid direct use of the Preferences object, since this may be invalidated by a call to PathPrefs.resetPreferences()
getValue() - Method in interface qupath.lib.measurements.Measurement: Get the numeric value of the measurement.
getValue() - Method in class qupath.lib.plugins.parameters.BooleanParameter
getValue() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
getValue() - Method in class qupath.lib.plugins.parameters.DoubleParameter
getValue() - Method in class qupath.lib.plugins.parameters.EmptyParameter
getValue() - Method in class qupath.lib.plugins.parameters.IntParameter
getValue() - Method in class qupath.lib.plugins.parameters.NumericParameter
getValue() - Method in class qupath.lib.plugins.parameters.StringParameter
getValue() - Method in interface qupath.lib.plugins.parameters.Parameter: Get the current set value (may be null).
getValue() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel: Get the value stored internally for this pixel.
getValue(int, int) - Method in class qupath.imagej.tools.PixelImageIJ
getValue(int, int) - Method in interface qupath.lib.analysis.images.SimpleImage: Get the value of a single pixel as a float.
getValue(BufferedImage, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
getValue(BufferedImage, int, int) - Method in interface qupath.lib.display.SingleChannelDisplayInfo: Extract the value for a single pixel of an image.
getValue(Indexer) - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel: Get the value from another image via its Indexer.
getValue(Parameters<S, T>) - Method in interface qupath.lib.experimental.pixels.MeasurementProcessor.CustomMeasurement
getValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
getValueAsString(BufferedImage, int, int) - Method in interface qupath.lib.display.ChannelDisplayInfo: Get a string representation of a pixel's value.
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.BooleanParameter
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.DoubleParameter
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.EmptyParameter
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.IntParameter
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.NumericParameter
getValueOrDefault() - Method in class qupath.lib.plugins.parameters.StringParameter
getValueOrDefault() - Method in interface qupath.lib.plugins.parameters.Parameter: Get the current set value, or any default if no value has been set.
getValues(BufferedImage, int, int, int, int, float[]) - Method in class qupath.lib.display.DirectServerChannelInfo
getValues(BufferedImage, int, int, int, int, float[]) - Method in interface qupath.lib.display.SingleChannelDisplayInfo: Extract values for a square of pixels from an image.
getVariance() - Method in class qupath.lib.analysis.stats.Histogram: Get the variance of all the values being histogrammed.
getVariance() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get the variance of all non-NaN values that were added.
getVersion() - Static method in class qupath.lib.common.GeneralTools: Get a String representation of QuPath's version, if known.
getVersion() - Method in class qupath.lib.gui.BuildInfo: Get the version, or null if the version is unknown.
getVersion() - Method in interface qupath.lib.gui.extensions.QuPathExtension: Get the version of the current extension.
getVersion() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion: Get the semantic version.
getVersion() - Static method in class qupath.lib.gui.QuPathGUI: Get the current QuPath version.
getVersion() - Method in interface qupath.lib.projects.Project: The version string for this project, which can be used to distinguish new and older project (which may contain different information).
getVersion() - Method in class qupath.process.gui.ProcessingExtension
getVersionedDocsUrl() - Static method in class qupath.lib.gui.Urls: Get the base URL for the QuPath documentation, specifically for this software version.
getVersionedDocsUrl(String) - Static method in class qupath.lib.gui.Urls: Get the base URL for the QuPath documentation for this software version, including a relative component to link to a specific page (without leading slash).
getView() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the main JavaFX component representing this viewer.
getViewer() - Method in class qupath.lib.gui.QuPathGUI: Get the currently active viewer.
getViewer() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
getViewer() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
getViewer() - Method in class qupath.process.gui.WandToolEventHandler
getViewerActions() - Method in class qupath.lib.gui.QuPathGUI: Get the associations associated with QuPath image viewers.
getViewerManager() - Method in class qupath.lib.gui.actions.ViewerActions
getViewerManager() - Method in class qupath.lib.gui.QuPathGUI: Get the viewer manager, which gives access to all the viewers available within this QuPath instance.
getVoronoiFaces() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get a map of Voronoi faces as JTS Geometry objects.
getVoronoiROIs(Geometry) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision: Get a map of Voronoi faces, convered to ROI objects.
getWandSensitivity() - Static method in class qupath.process.gui.WandToolEventHandler: Query the wand sensitivity value, which influences how similar local intensity values must be for the wand region growing.
getWandSigmaPixels() - Static method in class qupath.process.gui.WandToolEventHandler: Query the Gaussian sigma value used to smooth the image when applying the wand.
getWandUseOverlays() - Static method in class qupath.process.gui.WandToolEventHandler: Query whether the wand tool should be influenced by pixel values painted on image overlays.
getWidth() - Method in class qupath.imagej.tools.PixelImageIJ
getWidth() - Method in interface qupath.lib.analysis.images.SimpleImage: Get the image width.
getWidth() - Method in class qupath.lib.geom.ImmutableDimension: Get the ImmutableDimension width.
getWidth() - Method in class qupath.lib.images.servers.AbstractImageServer
getWidth() - Method in interface qupath.lib.images.servers.ImageServer: Width of the full-resolution image in pixels.
getWidth() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the full-resolution image width.
getWidth() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel: Get the image width at this level.
getWidth() - Method in class qupath.lib.regions.ImageRegion: Get the width of the region bounding box.
getWindow(String) - Static method in class qupath.lib.gui.scripting.QPEx: Access a window currently open within QuPath by its title.
getWrappedServer() - Method in class qupath.lib.images.servers.TransformingImageServer: Get underlying ImageServer, i.e.
getWriter() - Method in class qupath.lib.scripting.ScriptParameters: Get the main writer for script output.
getX() - Method in class qupath.lib.geom.Point2: Get the x coordinate of this point.
getX() - Method in class qupath.lib.regions.ImageRegion: Get the x coordinate of the region bounding box (top left).
getX() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel: Get x index.
getX1() - Method in class qupath.lib.regions.Padding: Get the first horizontal padding (left of the image), in pixels.
getX1() - Method in class qupath.lib.roi.LineROI: Get the first x co-ordinate (start of the line).
getX2() - Method in class qupath.lib.regions.Padding: Get the second horizontal padding (right of the image), in pixels.
getX2() - Method in class qupath.lib.roi.LineROI: Get the second x co-ordinate (end of the line).
getXSum() - Method in class qupath.lib.regions.Padding: Get the total horizontal padding (sum of x1 and x2).
getY() - Method in class qupath.lib.geom.Point2: Get the y coordinate of this point.
getY() - Method in class qupath.lib.regions.ImageRegion: Get the y coordinate of the region bounding box (top left).
getY() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel: Get y index.
getY1() - Method in class qupath.lib.regions.Padding: Get the first vertical padding (top of the image), in pixels.
getY1() - Method in class qupath.lib.roi.LineROI: Get the first y co-ordinate (start of the line).
getY2() - Method in class qupath.lib.regions.Padding: Get the second vertical padding (bottom of the image), in pixels.
getY2() - Method in class qupath.lib.roi.LineROI: Get the second y co-ordinate (end of the line).
getYouTubeUrl() - Static method in class qupath.lib.gui.Urls: Get a URL pointing to the QuPath YouTube channel.
getYSum() - Method in class qupath.lib.regions.Padding: Get the total vertical padding (sum of x1 and x2).
getZ() - Method in class qupath.lib.images.servers.TileRequest: Get the z-slice index for this request.
getZ() - Method in class qupath.lib.regions.ImagePlane: Get the z-slice index.
getZ() - Method in class qupath.lib.regions.ImageRegion: Get the z-slice index for the region.
getZ() - Method in class qupath.lib.roi.AreaROI
getZ() - Method in class qupath.lib.roi.EllipseROI
getZ() - Method in class qupath.lib.roi.GeometryROI
getZ() - Method in class qupath.lib.roi.LineROI
getZ() - Method in class qupath.lib.roi.PointsROI
getZ() - Method in class qupath.lib.roi.PolygonROI
getZ() - Method in class qupath.lib.roi.PolylineROI
getZ() - Method in class qupath.lib.roi.RectangleROI
getZ() - Method in interface qupath.lib.roi.interfaces.ROI: Get z-stack slice index.
getZoomToFitDownsampleFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
getZPosition() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the currently-visible z-slice.
getZSpacing() - Method in class qupath.lib.images.servers.PixelCalibration: Get the numeric value representing the z-spacing, in the stored units.
getZSpacingMicrons() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the z-spacing in microns, if available - or Double.NaN otherwise.
getZSpacingMicrons() - Method in class qupath.lib.images.servers.PixelCalibration: Get the z-spacing in microns, or Double.NaN if this is unknown.
getZSpacingUnit() - Method in class qupath.lib.images.servers.PixelCalibration: Get a String representation of the preferred z-spacing unit.
GITHUB - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
GitHubProject - Interface in qupath.lib.gui.extensions: Helper class to represent a project hosted on GitHub.
GitHubProject.GitHubRepo - Class in qupath.lib.gui.extensions: Helper class to represent a GitHub repository.
grabHandle(double, double, double, boolean) - Method in class qupath.lib.roi.RoiEditor: Try to grab a ROI handle.
GRADIENT_MAGNITUDE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Gradient magnitude
gradientMagnitude(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate the gradient magnitude.
graphic(ObservableValue<Node>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Bind the graphic property of the action to an ObservableValue, bidirectionally if possible.
graphic(Node) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Set the graphic property of the action.
GRAY - Enum constant in enum class qupath.process.gui.WandToolEventHandler.WandType: Grayscale image
grayscale() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Use grayscale LUT, rather than deriving colors from classifications.
grayscale(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Optionally use grayscale LUT, rather than deriving colors from classifications.
GRAYSCALE - Enum constant in enum class qupath.lib.display.ChannelDisplayMode: Show using a grayscale LUT (black to white)
greaterThan(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by thresholding pixels to find where ip1 > ip2
greaterThanOrEqual(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by thresholding pixels to find where ip1 >= ip2
green(int) - Static method in class qupath.lib.common.ColorTools: Extract the 8-bit green value from a packed RGB value.
Green - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Green channel only
GREEN - Static variable in class qupath.lib.common.ColorTools: Packed int representing green.
GREEN - Static variable in class qupath.lib.images.servers.ImageChannel: Default green channel for RGB images.
Green_chromaticity - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Green chromaticity value, green / max(1, red + green + blue)
Green_divided_by_blue - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Green value divided by blue value
Green_OD - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Green channel optical densities
greenChromaticity(int) - Static method in class qupath.lib.color.ColorTransformer: Extract green chromaticity value from a packed RGB pixel, green / max(1, red + green + blue)
greenOverBlue(int) - Static method in class qupath.lib.color.ColorTransformer: Extract green over blue value from a packed RGB pixel, green / max(1, blue)
GRID - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
GRID_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
GRID_SPACING - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
GRID_SPACING - Variable in class qupath.lib.gui.actions.OverlayActions
GRID_TMA - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
GridLines - Class in qupath.lib.gui.viewer: Simple class used for storing information related to GridLines that may be painted over an image.
GridLines() - Constructor for class qupath.lib.gui.viewer.GridLines
gridLinesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
GridOverlay - Class in qupath.lib.gui.viewer.overlays: An overlay used to show a (counting) grid on top of an image.
GridOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.GridOverlay: Constructor.
gridScaleMicrons - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
gridScaleMicronsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Define counting grid optionally displayed on any viewer using microns rather than pixel coordinates.
gridSpacingX - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
gridSpacingXProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Horizontal spacing between lines for any counting grid.
gridSpacingY - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
gridSpacingYProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Vertical spacing between lines for any counting grid.
gridStartXProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Starting x coordinate for any counting grid (usually 0).
gridStartYProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Starting y coordinate for any counting grid (usually 0).
GROOVY - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for Groovy
GROOVY - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
GroovyAutoCompletor - Class in qupath.lib.gui.scripting.completors: Auto completion support for Groovy.
GroovyAutoCompletor(boolean) - Constructor for class qupath.lib.gui.scripting.completors.GroovyAutoCompletor: Constructor.
GroovyCV - Class in qupath.opencv.tools: Category class for enhanced Groovy scripting with OpenCV.
GroovyCV() - Constructor for class qupath.opencv.tools.GroovyCV
GroovyLanguage - Class in qupath.lib.gui.scripting.languages: Class for the representation of the Groovy programming language in QuPath.
GroovyLanguage() - Constructor for class qupath.lib.gui.scripting.languages.GroovyLanguage: Constructor for Groovy Language.
GroovyStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling to apply to a CodeArea, based on Groovy or Java syntax.
GsonTools - Class in qupath.lib.io: Helper class providing Gson instances with type adapters registered to serialize several key classes.
GsonTools() - Constructor for class qupath.lib.io.GsonTools
GsonTools.SubTypeAdapterFactory<T> - Class in qupath.lib.io: A TypeAdapterFactory that is suitable for handling class hierarchies.
gt(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Apply a greater than threshold.
gt(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Apply a greater than threshold between two arrays.
GuiTools - Class in qupath.lib.gui.tools: Assorted static methods to help with JavaFX and QuPath GUI-related tasks.
GuiTools() - Constructor for class qupath.lib.gui.tools.GuiTools
GuiTools.SnapshotType - Enum Class in qupath.lib.gui.tools: Kinds of snapshot image that can be created for QuPath.

H

H_DAB - Enum constant in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains: Hematoxylin and DAB
H_E - Enum constant in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains: Hematoxylin and eosin
halo(int) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define a halo that is symmetric in x and y.
halo(Padding) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define a halo using a padding object.
handle(DragEvent) - Method in class qupath.lib.gui.viewer.DragDropImportListener
handle(MouseEvent) - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
handle(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
handle(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
handle(MouseEvent) - Method in class qupath.process.gui.WandToolEventHandler
handleBackspace(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Handle a backspace.
handleDrop(QuPathViewer, List<T>) - Method in interface qupath.lib.gui.viewer.DragDropImportListener.DropHandler: Handle drop onto a viewer.
handleGitHubURL(String) - Static method in class qupath.lib.gui.ExtensionControlPane: Handle a URL that might be an extension hosted on GitHub.
handleLeftParenthesis(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Handle left parentheses (.
handleLineComment(EditableText) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Handle line comments.
handleNewLine(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Handle a new line.
handleOutput(Parameters<S, T>, U) - Method in interface qupath.lib.experimental.pixels.OutputHandler: Optional method to handle the output of a Processor.
handleOutput(Parameters<S, T>, U) - Method in class qupath.lib.experimental.pixels.OutputHandler.ObjectOutputHandler
handleOutputClassification(Parameters<?, ?>, String) - Static method in interface qupath.lib.experimental.pixels.OutputHandler: Handle the output of a pixel processor by setting a PathClass, given by its name.
handleOutputClassification(Parameters<?, ?>, PathClass) - Static method in interface qupath.lib.experimental.pixels.OutputHandler: Handle the output of a pixel processor by setting a PathClass.
handleOutputMeasurements(Parameters<?, ?>, Map<String, ? extends Number>) - Static method in interface qupath.lib.experimental.pixels.OutputHandler: Handle the output of a pixel processor by adding measurements to the path object.
handleQuotes(EditableText, boolean, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Handle single/double quotes.
handleRightParenthesis(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Handle right parentheses ).
handleTabPress(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax: Handle tab key.
HaralickFeatureComputer - Class in qupath.lib.analysis.features: Static methods for computing Haralick texture features.
HaralickFeatureComputer() - Constructor for class qupath.lib.analysis.features.HaralickFeatureComputer
HaralickFeatures - Class in qupath.lib.analysis.features: Helper class for computing Haralick features given a cooccurrence matrix.
HaralickFeaturesPlugin - Class in qupath.lib.algorithms: Plugin for calculating Haralick texture features, within or around detections or tiles.
HaralickFeaturesPlugin() - Constructor for class qupath.lib.algorithms.HaralickFeaturesPlugin: Default constructor.
hasActiveHandle() - Method in class qupath.lib.roi.RoiEditor: Returns true if a handle is currently active, for example being reposition.
hasActiveToolTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return whether this ViewTracker tracks the active tool.
hasAlpha() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
hasBundleForLocale(String, Locale) - Static method in class qupath.lib.gui.localization.QuPathResources
hasChildObjects() - Method in class qupath.lib.objects.PathObject: Check if this object has children, or if its child object list is empty.
hasChildren() - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, replaced by PathObject.hasChildObjects()
hasCursorTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return whether this ViewTracker tracks the cursor.
hasDefaultBundleForLocale(Locale) - Static method in class qupath.lib.gui.localization.QuPathResources
hasEyeTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return whether this ViewTracker tracks the eye.
hasFeatureImportance() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier: Check if the last time train was called, variable (feature) importance was calculated.
hashCode() - Method in class qupath.lib.common.Version
hashCode() - Method in class qupath.lib.geom.Point2
hashCode() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
hashCode() - Method in class qupath.lib.images.servers.ImageChannel
hashCode() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
hashCode() - Method in class qupath.lib.images.servers.ImageServerMetadata
hashCode() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
hashCode() - Method in class qupath.lib.images.servers.PixelCalibration
hashCode() - Method in class qupath.lib.images.servers.TileRequest
hashCode() - Method in class qupath.lib.io.UriUpdater.SingleUriItem
hashCode() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
hashCode() - Method in class qupath.lib.regions.ImagePlane
hashCode() - Method in class qupath.lib.regions.ImageRegion
hashCode() - Method in class qupath.lib.regions.RegionRequest
hashCode() - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
hashCode() - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
hashCode() - Method in class qupath.process.gui.commands.ml.ClassificationResolution
hasHelpText() - Method in class qupath.lib.plugins.parameters.BooleanParameter
hasHelpText() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
hasHelpText() - Method in class qupath.lib.plugins.parameters.DoubleParameter
hasHelpText() - Method in class qupath.lib.plugins.parameters.EmptyParameter
hasHelpText() - Method in class qupath.lib.plugins.parameters.IntParameter
hasHelpText() - Method in class qupath.lib.plugins.parameters.NumericParameter
hasHelpText() - Method in class qupath.lib.plugins.parameters.StringParameter
hasHelpText() - Method in interface qupath.lib.plugins.parameters.Parameter: Query whether getHelpText() returns a meaningful String (as opposed to null).
hasImageData() - Method in interface qupath.lib.projects.ProjectImageEntry: Check if this entry has saved ImageData already available.
hasJavaPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs: Attempt to load user JVM defaults - may fail if packager.jar (and any required native library) isn't found.
hasLowerAndUpperBounds() - Method in class qupath.lib.plugins.parameters.NumericParameter: Returns true if this parameter has both lower and upper bounds constraining valid values.
hasLowerBound() - Method in class qupath.lib.plugins.parameters.NumericParameter: Returns true if the parameter has a valid lower bound.
hasMeasurement(PathObject, String) - Static method in class qupath.lib.scripting.QP: Test whether a PathObject has a specified measurement in its measurement list.
hasMeasurements() - Method in class qupath.lib.objects.PathObject: Returns true if the measurement list for this object is not empty.
hasNucleus() - Method in class qupath.lib.objects.PathCellObject: Returns true if a nucleus ROI is stored for this cell.
hasObjectsForRegion(Class<? extends PathObject>, ImageRegion) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Returns true if the hierarchy contains objects overlapping a specific region, optionally filtering to identify only objects of a specific class.
hasPixelSizeMicrons() - Method in class qupath.lib.images.servers.PixelCalibration: Returns true if the pixel width and height information in microns is known.
hasPointROI(PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Returns true if a PathObject has a Point ROI.
hasROI() - Method in class qupath.lib.objects.PathObject: Returns true if this object has a ROI.
hasROI() - Method in class qupath.lib.roi.RoiEditor: Returns true if this editor currently has a ROI.
hasServer() - Method in class qupath.lib.gui.viewer.QuPathViewer: Returns true if there is currently an ImageServer being displayed in this viewer.
hasString(String) - Static method in class qupath.lib.gui.localization.QuPathResources
hasString(String, String) - Static method in class qupath.lib.gui.localization.QuPathResources
hasSuffix() - Method in class qupath.lib.common.Version: Returns true if the version has a suffix, which typically indicates that it does not refer to a final stable version.
hasUnseenErrors() - Method in class qupath.lib.gui.commands.LogViewerCommand: Boolean binding indicating whether there are any unseen errors.
hasUpperBound() - Method in class qupath.lib.plugins.parameters.NumericParameter: Returns true if the parameter has a valid upper bound.
hasZAndT() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return whether this ViewTracker has Z and T information.
hasZSpacingMicrons() - Method in class qupath.lib.images.servers.PixelCalibration: Returns true if the z-spacing is known in microns.
hConcat(Collection<? extends Mat>, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Horizontal concatenation for a Mat.
headerText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the dialog header text.
height - Variable in class qupath.lib.geom.ImmutableDimension: Height of the ImmutableDimension.
height - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
height - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
height - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
height(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Set the preferred height of the chart.
height(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Set the preferred height of the chart.
height(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the preferred height of the chart.
height(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the dialog height.
height(int) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Export image height.
height(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the full-resolution image height.
HELP - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
HELP_VIEWER - Variable in class qupath.lib.gui.actions.CommonActions
HELP_VIEWER - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
HelpMenuActions - Class in qupath.lib.gui.actions.menus
HelpMenuActions.Actions - Class in qupath.lib.gui.actions.menus
HEMATOXYLIN - Enum constant in enum class qupath.lib.color.StainVector.DefaultStains: Hematoxylin
HEMATOXYLIN - Static variable in class qupath.lib.color.ColorDeconvolutionStains: Default name (and spelling) for hematoxylin stain
Hematoxylin_H_DAB - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Hematoxylin after color deconvolution with default H-DAB stains
Hematoxylin_H_DAB_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Hematoxylin after color deconvolution with default H-DAB stains and conversion to 8-bit
Hematoxylin_H_E - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Hematoxylin after color deconvolution with default H&E stains
Hematoxylin_H_E_8_bit - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Hematoxylin after color deconvolution with default H&E stains and conversion to 8-bit
HESSIAN_DETERMINANT - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Determinant of the Hessian matrix, calculated per pixel
HESSIAN_EIGENVALUE_MAX - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Maximum eigenvalue of the 2x2 or 3x3 Hessian matrix, calculated per pixel (by value, not absolute value)
HESSIAN_EIGENVALUE_MIDDLE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Middle eigenvalue of the 3x3 Hessian matrix, calculated per pixel (by value, not absolute value)
HESSIAN_EIGENVALUE_MIN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Minimum eigenvalue of the 2x2 or 3x3 Hessian matrix, calculated per pixel (by value, not absolute value)
hessianDeterminant(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate the determinant of the Hessian matrix per pixel.
hessianEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate the eigenvalues of the Hessian matrix per pixel.
hiddenClassesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
hideIfEmptyProperty() - Method in class qupath.lib.gui.charts.HistogramChart: Property controlling whether the chart should be hidden if there is no data.
hierarchy(PathObjectHierarchy) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify the PathObjectHierarchy.
HIERARCHY_COMPARATOR - Static variable in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Comparator to use when looking for a parent annotation in the hierarchy.
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.commands.PathObjectGridView
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.AnnotationPane
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.UndoRedoManager
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.viewer.QuPathViewer
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.images.ImageData
hierarchyChanged(PathObjectHierarchyEvent) - Method in interface qupath.lib.objects.hierarchy.events.PathObjectHierarchyListener: Notify listeners of a change in the hierarchy or its objects.
hierarchyContainsObject(PathObjectHierarchy, PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Check if a hierarchy contains a specified PathObject.
hierarchyDisplayMode - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
HierarchyOverlay - Class in qupath.lib.gui.viewer.overlays: An overlay capable of painting a PathObjectHierarchy, except for any TMA grid (which is handled by TMAGridOverlay).
HierarchyOverlay(DefaultImageRegionStore, OverlayOptions, ImageData<BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.HierarchyOverlay: Constructor.
Histogram - Class in qupath.lib.analysis.stats: Class for storing histogram data & basic statistics.
Histogram(double[], int) - Constructor for class qupath.lib.analysis.stats.Histogram: Create histogram from a double array, using a specified number of bins and the data min/max as the min/max edges.
Histogram(double[], int, double, double) - Constructor for class qupath.lib.analysis.stats.Histogram: Create a histogram from an array of values, optionally specifying the minimum & maximum values to include.
Histogram(float[], int) - Constructor for class qupath.lib.analysis.stats.Histogram: Create histogram from a float array, using a specified number of bins and the data min/max as the min/max edges.
Histogram(float[], int, double, double) - Constructor for class qupath.lib.analysis.stats.Histogram: Create a histogram from an array of values, optionally specifying the minimum & maximum values to include.
Histogram(int[], int, double, double) - Constructor for class qupath.lib.analysis.stats.Histogram: Create a histogram from an array of values, optionally specifying the minimum & maximum values to include.
HistogramChart - Class in qupath.lib.gui.charts: JavaFX chart for displaying histograms.
HistogramChart() - Constructor for class qupath.lib.gui.charts.HistogramChart
HistogramChart.CountsTransformMode - Enum Class in qupath.lib.gui.charts: Enum to specify how the counts are displayed.
HistogramChart.DisplayMode - Enum Class in qupath.lib.gui.charts: Display mode for the histogram.
HistogramChart.HistogramData - Class in qupath.lib.gui.charts: Helper class for representing data that may be visualized with a HistogramChart.
HistogramData(Histogram, Color) - Constructor for class qupath.lib.gui.charts.HistogramChart.HistogramData: Wrapper for histogram & data relevant to its display.
HistogramDisplay - Class in qupath.lib.gui.charts: Wrapper close to enable the generation and display of histograms relating to a data table.
HistogramDisplay(PathTableData<?>, boolean) - Constructor for class qupath.lib.gui.charts.HistogramDisplay: Constructor.
HISTORY_SCRIPT - Variable in class qupath.lib.gui.actions.AutomateActions
HISTORY_SCRIPT - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
HISTORY_SHOW - Variable in class qupath.lib.gui.actions.AutomateActions
HISTORY_SHOW - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
homogenizeGeometryCollection(Geometry) - Static method in class qupath.lib.roi.GeometryTools: Ensure a GeometryCollection contains only Geometries of the same type (Polygonal, Lineal or Puntal).
HOVER - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay: Display only when the cursor hovers nearby
HtmlRenderer - Interface in qupath.lib.gui.scripting.languages: Marker interface that indicates an executable language renders HTML.
hue(int) - Static method in class qupath.lib.color.ColorTransformer: Extract hue value from RGB-to-HSB transform.
Hue - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Hue value (from RGB-HSB transform)
HUGE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize

I

IconFactory - Class in qupath.lib.gui.tools: Factory class for creating icons.
IconFactory() - Constructor for class qupath.lib.gui.tools.IconFactory
IconFactory.PathIcons - Enum Class in qupath.lib.gui.tools: Default icons for QuPath commands.
iconProperty() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
iconProperty() - Method in interface qupath.lib.gui.viewer.tools.PathTool: Property giving the icon that should be used for the tool
identity() - Static method in class qupath.lib.awt.common.AffineTransforms: Create an affine transform representing the identity transform.
identity() - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that returns its input unchanged.
IGNORE - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Ignore classification, indicating what should not be further measured (e.g.
IGNORE - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Ignore classification, indicating what should not be further measured (e.g.
IJExtension - Class in qupath.imagej.gui: QuPath extension & associated static helper methods used to support integration of ImageJ with QuPath.
IJExtension() - Constructor for class qupath.imagej.gui.IJExtension
IJExtension.IJExtensionCommands - Class in qupath.imagej.gui: Commands to install with the ImageJ extension.
IJTools - Class in qupath.imagej.tools: Collection of static methods to help with using ImageJ with QuPath.
IJTools() - Constructor for class qupath.imagej.tools.IJTools
IMAGE - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Accept all requests for the image where the region is non-empty
IMAGE_ROOT - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Root object classification
IMAGE_ROOT - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Root object classification
ImageChannel - Class in qupath.lib.images.servers: The name and display color for a single image channel.
imageData - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
imageData - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
imageData - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify an ImageData object.
imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify an ImageData object.
imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify an ImageData object.
imageData(ImageData<BufferedImage>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Set the image data.
imageData(ImageData<BufferedImage>) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify the ImageData.
ImageData<T> - Class in qupath.lib.images: Class that brings together the main data in connection with the analysis of a single image.
ImageData(ImageServer<T>) - Constructor for class qupath.lib.images.ImageData: Create a new ImageData with ImageType.UNKNOWN and a new PathObjectHierarchy.
ImageData(ImageServer<T>, ImageData.ImageType) - Constructor for class qupath.lib.images.ImageData: Create a new ImageData with a specified type and creating a new object hierarchy.
ImageData(ImageServer<T>, PathObjectHierarchy) - Constructor for class qupath.lib.images.ImageData: Create a new ImageData with ImageType.UNKNOWN.
ImageData(ImageServer<T>, PathObjectHierarchy, ImageData.ImageType) - Constructor for class qupath.lib.images.ImageData: Create a new ImageData with a specified object hierarchy and type.
ImageData.ImageType - Enum Class in qupath.lib.images: Enum representing possible image types.
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.UndoRedoManager
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener: Called with the image data within a viewer has changed.
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.ViewerManager
ImageDataOp - Interface in qupath.opencv.ops: Request pixels from an image, potentially applying further transforms.
imageDataProperty() - Method in class qupath.lib.gui.commands.PathObjectGridView
imageDataProperty() - Method in class qupath.lib.gui.QuPathGUI: Read-only property containing the image open within the currently-active viewer.
imageDataProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer: Property for the image data currently being displayed within this viewer.
imageDataProperty() - Method in class qupath.lib.gui.viewer.ViewerManager: Read-only property containing the image open within the currently-active viewer.
ImageDataServer<T> - Interface in qupath.opencv.ops: An ImageServer that wraps an ImageData.
ImageDetailsPane - Class in qupath.lib.gui.panes: A panel used for displaying basic info about an image, e.g.
ImageDetailsPane(ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.ImageDetailsPane: Constructor.
ImageDisplay - Class in qupath.lib.display: Class used to look after the color transforms that may be applied to an image, including brightness/contrast settings.
ImageDisplay() - Constructor for class qupath.lib.display.ImageDisplay: Constructor.
imageDisplayObjectProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane: The current image display.
imageDisplayProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Property for the image display that should be shown and managed by this pane.
imageDisplayProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: The image display to which the sliders are applied.
ImageDisplaySettings - Class in qupath.lib.display.settings: A simple class to store the main information needed by QuPath to display an image, in a JSON-friendly form.
ImageDisplaySettings() - Constructor for class qupath.lib.display.settings.ImageDisplaySettings
imageExtension(String) - Method in class qupath.lib.images.writers.TileExporter: Specify a file extension for the original pixels, which determines the export file format.
imageFunction(ImageSupplier<S>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Function used ot lazily read the image.
ImageInterpolation - Enum Class in qupath.lib.gui.viewer: Supported interpolation methods when displaying images.
ImageJMacroRunner - Class in qupath.imagej.gui: QuPath plugin for running ImageJ macros & returning detected regions.
ImageJMacroRunner(QuPathGUI) - Constructor for class qupath.imagej.gui.ImageJMacroRunner: Constructor.
imageJPathProperty() - Static method in class qupath.imagej.gui.IJExtension: Property representing the path to a local ImageJ installation, or null if no path has been set.
ImageJProcessor - Class in qupath.lib.experimental.pixels: Class to generate a PixelProcessor when using ImageJ for the primary image representation.
ImageJProcessor() - Constructor for class qupath.lib.experimental.pixels.ImageJProcessor
ImageJServer - Class in qupath.imagej.images.servers: ImageServer that uses ImageJ's image-reading capabilities.
ImageJServer(URI, String...) - Constructor for class qupath.imagej.images.servers.ImageJServer: Constructor.
ImageJServerBuilder - Class in qupath.imagej.images.servers: Builder for ImageServers that use ImageJ to read images.
ImageJServerBuilder() - Constructor for class qupath.imagej.images.servers.ImageJServerBuilder
imageList(List<ProjectImageEntry<BufferedImage>>) - Method in class qupath.lib.gui.tools.MeasurementExporter: Specify the list of images (ProjectImageEntry) to export.
imageNameProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get a read-only property indicating the name of the image.
ImageOp - Interface in qupath.opencv.ops: An operation that may be applied to a Mat.
ImageOps - Class in qupath.opencv.ops: Create and use ImageOp and ImageDataOp objects.
ImageOps() - Constructor for class qupath.opencv.ops.ImageOps
ImageOps.Channels - Class in qupath.opencv.ops: Channel and color operations.
ImageOps.Core - Class in qupath.opencv.ops: Core operations.
ImageOps.Filters - Class in qupath.opencv.ops: Filtering operations.
ImageOps.ML - Class in qupath.opencv.ops: Machine learning operations.
ImageOps.Normalize - Class in qupath.opencv.ops: Normalization operations.
ImageOps.PaddedOp - Class in qupath.opencv.ops: Abstract ImageOp to simplify the process of handling padding.
ImageOps.Threshold - Class in qupath.opencv.ops: Thresholding operations.
ImagePlane - Class in qupath.lib.regions: Helper class to store z-slice and time point indices, optionally along with a channel index as well.
imagePointToComponentPoint(Point2D, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Convert a coordinate from the the full-resolution image into the corresponding pixel coordinate in the viewer - optionally constraining it to any viewer component bounds.
imageProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get a read-only property representing the JavaFX image.
ImageRegion - Class in qupath.lib.regions: Class for defining an image region.
ImageRegionRenderer - Interface in qupath.lib.gui.images.stores: Interface for painting regions of an ImageServer onto a Graphics object.
ImageRegionStoreFactory - Class in qupath.lib.gui.images.stores: Factory for creating an ImageRegionStore.
ImageRegionStoreFactory() - Constructor for class qupath.lib.gui.images.stores.ImageRegionStoreFactory
ImageRegionStoreHelpers - Class in qupath.lib.gui.images.stores: Helper methods related to image region storage.
ImageRegionStoreHelpers() - Constructor for class qupath.lib.gui.images.stores.ImageRegionStoreHelpers
ImageRenderer - Interface in qupath.lib.gui.images.stores: Interface for objects capable of converting a BufferedImage for rendering using Graphics2D.
images(SvgTools.SvgBuilder.ImageIncludeType) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify if/how raster images should be included in the SVG.
IMAGES - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType: Channels are stored as separate images (this is not yet supported!).
imagesEqual(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by identifying pixels where ip1 == ip2
ImageServer<T> - Interface in qupath.lib.images.servers: Generic ImageServer, able to return pixels and metadata.
ImageServerBuilder<T> - Interface in qupath.lib.images.servers: Helper class for creating ImageServers from a given URI and optional argument list.
ImageServerBuilder.AbstractServerBuilder<T> - Class in qupath.lib.images.servers: Abstract ServerBuilder implementation that handles metadata.
ImageServerBuilder.DefaultImageServerBuilder<T> - Class in qupath.lib.images.servers: Default ImageServerBuilder.ServerBuilder that requires a URI and (optional) array of String arguments to create an ImageServer with the help of a ImageServerBuilder.
ImageServerBuilder.ServerBuilder<T> - Interface in qupath.lib.images.servers: Interface that defines a class encapsulating all that is required to build an ImageServer.
ImageServerBuilder.UriImageSupport<T> - Class in qupath.lib.images.servers: Helper class to summarize which ImageServers can be build by a particular ImageServerBuilder for a given URI, and a level of confidence.
ImageServerMetadata - Class in qupath.lib.images.servers: Class for storing primary ImageServer metadata fields.
ImageServerMetadata.Builder - Class in qupath.lib.images.servers: Builder to create a new ImageServerMetadata object.
ImageServerMetadata.ChannelType - Enum Class in qupath.lib.images.servers: Enum representing possible channel (band) types for an image.
ImageServerMetadata.ImageResolutionLevel - Class in qupath.lib.images.servers: Width and height of each resolution in a multi-level image pyramid.
ImageServerMetadata.ImageResolutionLevel.Builder - Class in qupath.lib.images.servers: Builder to create a list of ImageServerMetadata.ImageResolutionLevel to represent pyramidal resolutions.
ImageServerProvider - Class in qupath.lib.images.servers: Service provider for creating ImageServers from a given path - which may be a file path or URL.
ImageServerProvider() - Constructor for class qupath.lib.images.servers.ImageServerProvider
ImageServers - Class in qupath.lib.images.servers: Helper class for working with ImageServer objects.
ImageServers() - Constructor for class qupath.lib.images.servers.ImageServers
imagesFromBlob(Mat) - Static method in class qupath.opencv.dnn.DnnTools: Extract images from an OpenCV blob.
imageSubDir(String) - Method in class qupath.lib.images.writers.TileExporter: Specify a subdirectory within which image tiles should be saved.
imageSupplier(ImageSupplier<S>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the image supplier.
ImageSupplier<S> - Interface in qupath.lib.experimental.pixels: A functional interface for supplying an image region for processing.
imageToMat(BufferedImage) - Static method in class qupath.opencv.tools.OpenCVTools: Convert a BufferedImage to an OpenCV Mat.
imageToMatBGR(BufferedImage, boolean) - Static method in class qupath.opencv.tools.OpenCVTools: Extract 8-bit unsigned pixels from a BufferedImage as a multichannel BGR(A) Mat.
imageToMatRGB(BufferedImage, boolean) - Static method in class qupath.opencv.tools.OpenCVTools: Extract 8-bit unsigned pixels from a BufferedImage as a multichannel RGB(A) Mat.
imageTypeSettingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Specify how setting the image type should be handled for images when they are opened for the first time.
imageUpdated - Variable in class qupath.lib.gui.viewer.QuPathViewer: Flag used to indicate that the image was updated for a repaint (otherwise it's assumed only the overlay may have changed)
ImageWriter<T> - Interface in qupath.lib.images.writers: Interface for defining class that can write images.
ImageWriterTools - Class in qupath.lib.images.writers: Static methods to access ImageWriter objects and write images.
ImageWriterTools() - Constructor for class qupath.lib.images.writers.ImageWriterTools
IMMUNE_CELLS - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Immune cell classification
IMMUNE_CELLS - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Immune cell classification
ImmutableDimension - Class in qupath.lib.geom: An immutable alternative to Java's AWT Dimension.
IMPORT_IMAGES - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
IMPORT_IMAGES_LEGACY - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
importDearrayedTMAData(File) - Static method in class qupath.lib.gui.tma.TMADataIO: Import a TMA grid from an exported TMA analysis file, i.e.
importFromCSV(File, PathObjectHierarchy) - Static method in class qupath.lib.io.TMAScoreImporter: Import TMA scores from a file into the TMAGrid of an object hierarchy.
importFromCSV(String, PathObjectHierarchy) - Static method in class qupath.lib.io.TMAScoreImporter: Import TMA scores from a String into the TMAGrid of an object hierarchy.
importObjectsFromFile(String) - Static method in class qupath.lib.scripting.QP: Import all PathObjects from the given file.
importPreferences(InputStream) - Static method in class qupath.lib.gui.prefs.PathPrefs: Import preferences from a stream.
imposeMaxima(FloatProcessor, Roi) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Ensure that a FloatProcessor only has region maxima within a specified Roi, using morphological reconstruction.
imposeMaxima(FloatProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Ensure that a FloatProcessor only has region maxima within a specified mask, using morphological reconstruction.
imposeMinima(FloatProcessor, Roi) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Ensure that a FloatProcessor only has region minima within a specified Roi, using morphological reconstruction.
INACTIVE_SERVER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
INCLUDE_IGNORED - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions: Generate objects for ignored classes (default is not to)
includeOnlyColumns(String...) - Method in class qupath.lib.gui.tools.MeasurementExporter: Specify the columns that will be included in the export.
includeOverlays(boolean) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify whether overlays should be included.
includePartialTiles(boolean) - Method in class qupath.lib.images.writers.TileExporter: Specify whether incomplete tiles at image boundaries should be included.
info(String) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an information message with static text.
info(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an information message with static text and a count.
info(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage: Create a information message to show a count of messages.
info(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an information message.
info(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage: Create an information message with a count.
INFO - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType: Information only.
INFO - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: Info logging (default)
INFO - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
INFO - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
infoMessage() - Method in class qupath.lib.gui.commands.BrightnessContrastCommand: Get a string expression to draw attention to any warnings associated with the current display settings.
InfoMessage - Class in qupath.lib.gui.actions: An informative message that should be shown to the user.
InfoMessage.MessageType - Enum Class in qupath.lib.gui.actions: The type of message, which can be used for styling.
information() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Create an information alert dialog.
initializeForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
initializeForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
initializeModel(Model) - Method in class qupath.opencv.dnn.OpenCVDnn: Initialize the model with the same preprocessing defined here (i.e.
input(String, long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shape as a long array for a single input with a specified name.
input(String, DnnShape) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shape for a single input with a specified name.
INPUT_DISPLAY - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
inputChannels(int...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the input channels using (zero-based) channel numbers.
inputChannels(String...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the input channels using channel names.
inputChannels(Collection<? extends ColorTransforms.ColorTransform>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the input channels from a collection of color transforms.
inputFiles(Collection<File>) - Method in class qupath.lib.gui.FileCopier: Collection of files to copy.
InputOutputPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
inputPadding(int) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Amount of padding requested for the left, right, top and bottom of the image tile being classified.
inputPaths(Collection<Path>) - Method in class qupath.lib.gui.FileCopier: Collection of paths representing files to copy.
inputResolution(PixelCalibration) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Pixel size defining the resolution at which the classifier should operate.
inputResolution(PixelCalibration) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the input resolution using a pixel calibration object.
inputResolution(PixelCalibration, double) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the input resolution using a pixel calibration and a scaling factor.
inputs(Map<String, DnnShape>) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shapes for one or more inputs.
inputShape(int, int) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Preferred input image width and height.
inputShape(long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shape for a single input, with the default input name.
INSERT_INTO_HIERARCHY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
insertAllDefaultImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
insertDetectionMeasurementsAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
insertMuAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
insertObjectClassifiersAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
insertObjects(Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Insert objects into the hierarchy, resolving their location and setting parent/child relationships.
insertObjects(PathObject) - Static method in class qupath.lib.scripting.QP: Insert object into the hierarchy, resolving its location and setting parent/child relationships.
insertPathObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Insert an object into the hierarchy.
insertPathObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Insert a collection of objects into the hierarchy, firing a change event on completion.
insertPixelClassifiersAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
insertQPExImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
insertQPImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
insertSelectedObjectsInHierarchy(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Insert the selected objects in the hierarchy, resolving positions accordingly.
insertText(int, String) - Method in interface qupath.lib.gui.scripting.EditableText: Request inserting the specified text.
insertText(int, String) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
insertText(int, String) - Method in class qupath.lib.gui.scripting.TextAreaControl
installActions(Collection<? extends Action>) - Method in class qupath.lib.gui.QuPathGUI: Install the specified actions.
installColorMaps(Path...) - Static method in class qupath.lib.color.ColorMaps: Install colormaps from the specified paths.
installColorMaps(ColorMaps.ColorMap...) - Static method in class qupath.lib.color.ColorMaps: Install colormaps.
installCommand(String, Runnable) - Method in class qupath.lib.gui.QuPathGUI: Install a new command in QuPath.
installDefaultFeatureClassificationBuilder(ImageDataTransformerBuilder) - Static method in class qupath.process.gui.commands.ml.PixelClassifierPane: Add to the list of default feature calculator builders that will be available when this pane is opened.
installDragAndDropHandler(QuPathGUI) - Static method in class qupath.lib.gui.commands.TMACommands: Command to install a drag and drop file handler for exported TMA data.
installExtension(QuPathGUI) - Method in class qupath.ext.openslide.OpenSlideExtension
installExtension(QuPathGUI) - Method in class qupath.imagej.gui.IJExtension
installExtension(QuPathGUI) - Method in class qupath.lib.extension.svg.SvgExtension
installExtension(QuPathGUI) - Method in interface qupath.lib.gui.extensions.QuPathExtension: Install the extension for a QuPathGUI instance.
installExtension(QuPathGUI) - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditorExtension
installExtension(QuPathGUI) - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
installExtension(QuPathGUI) - Method in class qupath.process.gui.ProcessingExtension
installGroovyCommand(String, File) - Method in class qupath.lib.gui.QuPathGUI: Install a Groovy script as a new command in QuPath.
installGroovyCommand(String, String) - Method in class qupath.lib.gui.QuPathGUI: Install a Groovy script as a new command in QuPath.
installImageDataCommand(String, Consumer<ImageData<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI: Install a new command in QuPath that takes the current ImageData as input.
installInfoMessage(Action, ObjectExpression<InfoMessage>) - Static method in class qupath.lib.gui.actions.ActionTools: Install an optional info message to the action.
installRangePrompt(Slider) - Static method in class qupath.lib.gui.tools.GuiTools: Install a mouse click listener to prompt the user to input min/max values for a slider.
installStyles(Collection<File>) - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Handle installing CSS files (which can be used to style QuPath).
installTool(PathTool, KeyCodeCombination) - Method in class qupath.lib.gui.ToolManager: Install a new tool for interacting with viewers.
INT16 - Enum constant in enum class qupath.lib.images.servers.PixelType: 16-bit signed integer
INT32 - Enum constant in enum class qupath.lib.images.servers.PixelType: 32-bit signed integer
INT8 - Enum constant in enum class qupath.lib.images.servers.PixelType: 8-bit signed integer
INTENSITY_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
IntensityFeaturesPlugin - Class in qupath.lib.algorithms: Plugin for calculating intensity-based features, including Haralick textures, within or around detections or tiles.
IntensityFeaturesPlugin() - Constructor for class qupath.lib.algorithms.IntensityFeaturesPlugin
InteractiveObjectImporter - Class in qupath.lib.gui.commands: Static methods to import object(s) from different sources.
INTERLEAVED - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType: Channels are interleaved ('PLANARCONFIG_CONTIG').
interp2D(Indexer, double, double) - Static method in class qupath.opencv.tools.Interpolation: Request a value from an Indexer using bilinear interpolation.
interp3D(Indexer, double, double, double) - Static method in class qupath.opencv.tools.Interpolation: Request a value from an Indexer using trilinear interpolation.
interpolateBilinear - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
Interpolation - Class in qupath.opencv.tools: Methods to help with requesting interpolated values.
Interpolation() - Constructor for class qupath.opencv.tools.Interpolation
interpolationProperty() - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay: The preferred method of interpolation to use for display.
INTERSECT - Enum constant in enum class qupath.lib.roi.RoiTools.CombineOp: Calculate intersection (overlap) between ROIs.
intersect2D(int, int, int, int) - Method in class qupath.lib.regions.RegionRequest: Intersect to the specified 2D region.
intersect2D(ImageRegion) - Method in class qupath.lib.regions.RegionRequest: Intersect to the specified 2D region, ignoring z and t.
intersection(Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools: Create intersection of multiple ROIs from a collection.
intersection(ROI...) - Static method in class qupath.lib.roi.RoiTools: Create intersection of multiple ROIs.
intersects(double, double, double, double) - Method in class qupath.lib.regions.ImageRegion: Query if this region intersects with a specified bounding box, ignoring z-slice and time point information.
intersects(ImageRegion) - Method in class qupath.lib.regions.ImageRegion: Returns true if the region specified by this region overlaps with another.
intersectsRegion(ROI, ImageRegion) - Static method in class qupath.lib.roi.RoiTools: Test whether a ROI and an ImageRegion intersect.
IntParameter - Class in qupath.lib.plugins.parameters: Parameter to represent an integer numeric value.
inverse() - Method in class qupath.lib.color.ColorDeconvMatrix3x3: Calculate the 3x3 matrix inverse.
invertBackground() - Method in class qupath.lib.display.settings.ImageDisplaySettings: Get whether the background should be shown 'inverted'.
invertBinary(Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Invert a binary image.
invertColors() - Method in enum class qupath.lib.display.ChannelDisplayMode
INVERTED_COLOR - Enum constant in enum class qupath.lib.display.ChannelDisplayMode: Show using color LUT with an inverted background
INVERTED_GRAYSCALE - Enum constant in enum class qupath.lib.display.ChannelDisplayMode: Show using an inverted grayscale LUT (white to black)
invertScrolling - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
invertScrollingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Invert the scrolling direction of the mouse applied to the viewer.
invertZSlider - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
invertZSliderProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Invert the z-slider for the viewer.
is8bitColorType(int) - Static method in class qupath.lib.awt.common.BufferedImageTools: Returns true if a BufferedImage type represents an 8-bit color image.
isAddedOrRemovedEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Returns true if objects have been added or removed from the hierarchy.
isAdditive() - Method in interface qupath.lib.display.ChannelDisplayInfo: Returns true if this channel can be used additively to create a composite image display; returns false if this channel wants all the color information to itself, so can't be displayed with others.
isAdditive() - Method in class qupath.lib.display.DirectServerChannelInfo
isAncestor(PathObject, PathObject) - Static method in class qupath.lib.objects.PathObjectTools: Query if one object is the ancestor of another.
isAncestorOf(PathClass) - Method in class qupath.lib.objects.classes.PathClass: Returns true if this class is equal to the specified child class, or an ancestor of that class.
isAnnotation() - Method in class qupath.lib.objects.PathObject: Returns true if the object is an annotation.
isArea() - Method in class qupath.lib.roi.AreaROI
isArea() - Method in class qupath.lib.roi.EllipseROI
isArea() - Method in class qupath.lib.roi.GeometryROI
isArea() - Method in class qupath.lib.roi.LineROI
isArea() - Method in class qupath.lib.roi.PointsROI
isArea() - Method in class qupath.lib.roi.PolygonROI
isArea() - Method in class qupath.lib.roi.PolylineROI
isArea() - Method in class qupath.lib.roi.RectangleROI
isArea() - Method in interface qupath.lib.roi.interfaces.ROI: Returns true if this ROI encloses an area.
isBigTiff() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Returns true if URI is for a local file known/expected to be a BigTIFF image.
isBrightfield() - Method in class qupath.lib.images.ImageData: Returns true if the image type is set to brightfield.
isBrightnessContrastRescaled() - Method in class qupath.lib.display.DirectServerChannelInfo
isBrightnessContrastRescaled() - Method in interface qupath.lib.display.ChannelDisplayInfo: Returns true if rescaling according to min & max display levels is applied, false if the full display range is used.
isCancelled() - Method in class qupath.lib.plugins.AbstractTaskRunner
isCancelled() - Method in interface qupath.lib.plugins.TaskRunner: Query if the plugin can be cancelled while running.
isCell() - Method in class qupath.lib.objects.PathObject: Returns true if the object is a cell object (a special type of detection, which can contain second ROI for the nucleus).
isCensored() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent: Returns true if the event should be considered right-censored.
isChanged() - Method in class qupath.lib.images.ImageData: Returns true if changes have been recorded since the last time this object was notified that it was saved.
isChanging() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Returns true if changes are still being made, so more events will be fired.
isCircle() - Method in class qupath.lib.roi.EllipseROI: Query if the width and height of the ellipse bounding box are the same, assuming 'square' pixels.
isCircle(double, double) - Method in class qupath.lib.roi.EllipseROI: Query if the width and height of the ellipse bounding box are the same, optionally using 'non-square' pixels.
isCompatible(String, int, String) - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion: Test if this completion is compatible with the provided text.
isCompatible(ImageDisplay) - Method in class qupath.lib.display.ImageDisplay: Check if an image display is 'compatible' with this one.
isCompatibleMetadata(ImageServerMetadata) - Method in class qupath.lib.images.servers.ImageServerMetadata: Returns true if a specified ImageServerMetadata is compatible with this one, that is it has the same path and dimensions (but possibly different pixel sizes, magnifications etc.).
isComplete() - Method in class qupath.lib.plugins.ParallelTileObject: Returns true if setComplete() has been called.
isCudaAvailable() - Static method in class qupath.opencv.dnn.DnnTools: Query whether CUDA is reported as available by OpenCV.
isDAB(StainVector) - Static method in class qupath.lib.color.ColorDeconvolutionStains: Check if the name of a StainVector is "dab" or "d" (ignoring case)
isDefaultStyle() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Check if the default JavaFX style is used.
isDerivedClass() - Method in class qupath.lib.objects.classes.PathClass: Returns true if #getParentClass() != null.
isDerivedFrom(PathClass) - Method in class qupath.lib.objects.classes.PathClass: Returns true if this class, or any ancestor class, is equal to the specified parent class.
isDetection() - Method in class qupath.lib.objects.PathObject: Returns true if the object is a detection.
isDirectory(String) - Static method in class qupath.lib.scripting.QP: Query if a file path corresponds to a directory.
isDynamic() - Method in interface qupath.lib.measurements.Measurement: Deprecated.
isEditable() - Method in class qupath.lib.objects.PathDetectionObject: Always returns false - detection objects shouldn't be edited.
isEditable() - Method in class qupath.lib.objects.PathObject: Flag indicating that the object is editable.
isEditable() - Method in class qupath.lib.objects.PathROIObject: Deprecated.
since v0.4.0
isEditable() - Method in class qupath.lib.objects.PathRootObject: The root object is never locked.
isEmpty() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Returns true if there are no events included.
isEmpty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Query if the table is empty, i.e.
isEmpty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return whether the collection of recorded frames is empty.
isEmpty() - Method in interface qupath.lib.measurements.MeasurementList: Returns true if the list does not contain any measurements.
isEmpty() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Check if the hierarchy is empty (i.e.
isEmpty() - Method in class qupath.lib.objects.PathObjectConnections: Returns true if the group is empty.
isEmpty() - Method in class qupath.lib.plugins.workflow.Workflow: Returns true if the workflow does not contain any steps.
isEmpty() - Method in interface qupath.lib.projects.Project: Test if the project contains any images.
isEmpty() - Method in class qupath.lib.regions.Padding: Returns true of the padding is zero.
isEmpty() - Method in class qupath.lib.roi.EllipseROI
isEmpty() - Method in class qupath.lib.roi.RectangleROI
isEmpty() - Method in class qupath.lib.roi.AreaROI: True if the bounding box has zero area
isEmpty() - Method in class qupath.lib.roi.GeometryROI: True if the bounding box has zero area
isEmpty() - Method in class qupath.lib.roi.PolygonROI: True if the bounding box has zero area
isEmpty() - Method in class qupath.lib.roi.PolylineROI: True if the bounding box has zero area
isEmpty() - Method in interface qupath.lib.roi.interfaces.ROI: Returns true if the ROI bounds have zero width and height.
isEmpty() - Method in class qupath.lib.roi.LineROI
isEmpty() - Method in class qupath.lib.roi.PointsROI: A Points ROI is empty if it contains no points (*not* if its bounds have no width or height...
isEmptyRegion(RegionRequest) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer: Returns true if there are no objects to be painted within the requested region.
isEmptyRegion(RegionRequest) - Method in class qupath.lib.images.servers.AbstractImageServer: Always returns false.
isEmptyRegion(RegionRequest) - Method in interface qupath.lib.images.servers.ImageServer: Test whether a region is empty, i.e.
isEmptyRegion(RegionRequest) - Method in class qupath.lib.images.servers.LabeledImageServer: Returns true if there are no objects to be painted within the requested region.
isEosin(StainVector) - Static method in class qupath.lib.color.ColorDeconvolutionStains: Check if the name of a StainVector is "eosin", "eos" or "e" (ignoring case)
isEraser() - Method in interface qupath.lib.gui.viewer.tools.QuPathPenManager.PenInputManager: Query if there is a pen currently being used as an eraser.
iseScrollGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
isFloat(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Returns true if a Mat is a floating point (rather than int) type.
isFloatingPoint() - Method in enum class qupath.lib.images.servers.PixelType: Returns true if the type is a floating point representation.
isFluorescence() - Method in class qupath.lib.images.ImageData: Returns true if the image type is set to fluorescence.
isGradedIntensityClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the PathClass represents a built-in intensity class.
isH_DAB() - Method in class qupath.lib.color.ColorDeconvolutionStains: Check if we have H-DAB staining, by checking the names of the first two stains and confirming that the third stain is a residual.
isH_E() - Method in class qupath.lib.color.ColorDeconvolutionStains: Check if we have H&E staining, by checking the names of the first two stains and confirming that the third stain is a residual.
isHematoxylin(StainVector) - Static method in class qupath.lib.color.ColorDeconvolutionStains: Check if the name of a StainVector is "haematoxylin", "hematoxylin", "haem" or "h" (ignoring case)
isHidden() - Method in class qupath.lib.plugins.parameters.BooleanParameter
isHidden() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
isHidden() - Method in class qupath.lib.plugins.parameters.DoubleParameter
isHidden() - Method in class qupath.lib.plugins.parameters.EmptyParameter
isHidden() - Method in class qupath.lib.plugins.parameters.IntParameter
isHidden() - Method in class qupath.lib.plugins.parameters.NumericParameter
isHidden() - Method in class qupath.lib.plugins.parameters.StringParameter
isHidden() - Method in interface qupath.lib.plugins.parameters.Parameter: Test is the 'hidden' flag is set for the parameter.
isIdentity() - Method in class qupath.opencv.ml.objects.features.Normalizer: Returns true if this normalizer does not actually do anything.
isIgnoredClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the PathClass should be ignored from some operations, or is null.
isImageDataChanging() - Method in class qupath.lib.gui.viewer.QuPathViewer: Returns true between the time setImageData has been called, and before the first repaint has been completed.
isInteger() - Method in class qupath.lib.analysis.stats.Histogram: Check if the histogram has been generated from integer values only.
isIntegerWrapper() - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper: Returns true if the array wrapper only supports integer values.
isInteractive() - Method in class qupath.lib.gui.charts.ChartThresholdPane: Returns the value of ChartThresholdPane.isInteractiveProperty().
isInteractiveProperty() - Method in class qupath.lib.gui.charts.ChartThresholdPane: Property indicating whether thresholds can be adjusted interactively.
isInterleaved(boolean) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
isLastFrame(ViewRecordingFrame) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return whether the specified frame is the last one recorded.
isLine() - Method in class qupath.lib.roi.AreaROI
isLine() - Method in class qupath.lib.roi.EllipseROI
isLine() - Method in class qupath.lib.roi.GeometryROI
isLine() - Method in class qupath.lib.roi.LineROI
isLine() - Method in class qupath.lib.roi.PointsROI
isLine() - Method in class qupath.lib.roi.PolygonROI
isLine() - Method in class qupath.lib.roi.PolylineROI
isLine() - Method in class qupath.lib.roi.RectangleROI
isLine() - Method in interface qupath.lib.roi.interfaces.ROI: Returns true if this ROI consists of line segments and does not enclose an area.
isLinux() - Static method in class qupath.lib.common.GeneralTools: Return true if running on Linux.
isLocationVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus: Returns true if the cursor location is visible, false otherwise.
isLocked() - Method in class qupath.lib.objects.PathObject: Query the locked status.
isLocked() - Method in class qupath.lib.objects.PathROIObject: Query the locked status for the object, indicating whether it should be editable or not.
isMac() - Static method in class qupath.lib.common.GeneralTools: Return true if running on macOS.
isMemorySufficient(RegionRequest, ImageData<BufferedImage>) - Static method in class qupath.imagej.tools.IJTools: Check if sufficient memory is available to request pixels for a specific region, and the number of pixels is less than the maximum length of a Java array.
isMissing() - Method in class qupath.lib.objects.TMACoreObject: Query the 'missing' flag for this core.
isModified() - Method in class qupath.lib.gui.scripting.ScriptTab: Return
isModifiedProperty() - Method in class qupath.lib.gui.scripting.ScriptTab: Return the isModifiedProperty of this script tab (true if the script is modified, i.e.
isMultipartExtension(String) - Static method in class qupath.lib.common.GeneralTools: Returns true for file extensions containing multiple parts (or 'dots').
isMutable() - Method in class qupath.lib.display.DirectServerChannelInfo
isMutable() - Method in interface qupath.lib.display.SingleChannelDisplayInfo: Check if SingleChannelDisplayInfo.getValue(BufferedImage, int, int) returns fixed values, or if they are dependent on other properties of the ImageData.
isNegativeClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the PathClass has the name "Negative".
isNotRGB() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Returns true if we can say with reasonable confidence that the image is not RGB.
isNullClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the PathClass is null, its name is null or if it is equal to the special case of 'Unclassified' path object.
isNumericMeasurement(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Query whether a named measurement returns a numeric value only.
isObjectClassificationEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Returns true if the event indicates that object classifications have changed.
isObjectMeasurementEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Returns true if the event indicates that object measurements have changed.
isOnePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Returns true if the name of the class is "1+", indicating a weakly-positive staining.
isOpenSlideAvailable() - Static method in class qupath.lib.images.servers.openslide.jna.OpenSlideLoader: Query whether OpenSlide has already been loaded.
isOverviewVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus: Returns true if the image overview is visible, false otherwise.
isPathClassHidden(PathClass) - Method in class qupath.lib.gui.viewer.OverlayOptions: Query whether objects with a specified classification should be displayed or hidden.
isPoint() - Method in class qupath.lib.roi.AreaROI
isPoint() - Method in class qupath.lib.roi.EllipseROI
isPoint() - Method in class qupath.lib.roi.GeometryROI
isPoint() - Method in class qupath.lib.roi.LineROI
isPoint() - Method in class qupath.lib.roi.PointsROI
isPoint() - Method in class qupath.lib.roi.PolygonROI
isPoint() - Method in class qupath.lib.roi.PolylineROI
isPoint() - Method in class qupath.lib.roi.RectangleROI
isPoint() - Method in interface qupath.lib.roi.interfaces.ROI: Returns true if this ROI represents distinct (unconnected) points.
isPositiveClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the PathClass has the name "Positive".
isPositiveOrGradedIntensityClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the name of the class is "Positive", "1+", "2+" or "3+", indicating positive staining.
isProcessing() - Method in class qupath.lib.plugins.ParallelTileObject: Returns true if setIsProcessing(true) has recently been called.
isReadOnly() - Method in class qupath.lib.gui.QuPathGUI: Query whether QuPath is in 'read-only' mode.
isRecording() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return whether this is currently recording.
isRedoable() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
isRedoable() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Returns true if 'redo' can be applied to the control.
isRedoable() - Method in class qupath.lib.gui.scripting.TextAreaControl
isResidual() - Method in class qupath.lib.color.StainVector: Returns true if this vector represents the residual (orthogonal) stain, used whenever color deconvolution is required with two stains only.
isResizable() - Method in class qupath.lib.gui.ColorMapCanvas
isRGB() - Method in class qupath.lib.images.servers.AbstractImageServer
isRGB() - Method in interface qupath.lib.images.servers.ImageServer: True if the image has 8-bit red, green & blue channels (and nothing else), false otherwise.
isRGB() - Method in class qupath.lib.images.servers.ImageServerMetadata: Returns true if the pixels are stored in (A)RGB form.
isRootObject() - Method in class qupath.lib.objects.PathObject: Returns true if the object is the 'root' of an object hierarchy.
isRootObject() - Method in class qupath.lib.objects.PathRootObject
isRotated() - Method in class qupath.lib.gui.viewer.QuPathViewer: Returns true if viewer.getRotation() != 0.
isScalebarVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus: Returns true if the scalebar is visible, false otherwise.
isSelectable(Action) - Static method in class qupath.lib.gui.actions.ActionTools: Specify that an Action has a meaningful 'selected' status.
isSelected() - Method in class qupath.lib.gui.SelectableItem: Returns true if the value of the selected property equals SelectableItem.getItem().
isSelected(PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Query whether a specific object is selected.
isShapeROI(ROI) - Static method in class qupath.lib.roi.RoiTools: Returns true if the ROI is not null and is not a point ROI.
isShowing() - Method in class qupath.lib.display.settings.ChannelSettings: Get whether the channel should be displayed.
isShowing() - Method in class qupath.lib.gui.viewer.QuPathViewer: Returns true if the viewer is visible, and attached to a scene.
isSignedInteger() - Method in enum class qupath.lib.images.servers.PixelType: Returns true if the type is a signed integer representation.
isSpaceDown() - Method in class qupath.lib.gui.viewer.QuPathViewer: Returns true if the spacebar was pressed when this component was focussed, and is still being held down.
isStandalone() - Method in class qupath.lib.gui.QuPathGUI: Query whether this is a standalone QuPathGUI instance, as flagged during startup.
isStringMeasurement(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Query whether a named measurement returns a String value only.
isStructureChangeEvent() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent: Returns true if the hierarchy structure has changed, e.g.
isSubtractMode(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
isSymmetric() - Method in class qupath.lib.regions.Padding: Returns true of the padding is identical on all sides (x1 == x2 == y1 == y2).
isThreePlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the name of the class is "3+", indicating a weakly-positive staining.
isTiff() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Returns true if URI is for a local file known/expected to be a TIFF image.
isTile() - Method in class qupath.lib.objects.PathObject: Returns true if this object represents an image tile.
isTitle - Variable in class qupath.lib.plugins.parameters.EmptyParameter
isTitle() - Method in class qupath.lib.plugins.parameters.EmptyParameter: Returns true if the parameter should be considered a title.
isTMACore() - Method in class qupath.lib.objects.PathObject: Returns true if this object represents a TMA core.
isTMADearrayed() - Static method in class qupath.lib.scripting.QP: Returns true if TMA cores are available.
isToolSwitchingEnabled() - Method in class qupath.lib.gui.ToolManager: Returns true if the user is able to activate another PathTool, false otherwise.
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
isTrained() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Classifier has already been trained and is ready to predict.
isTranslating() - Method in class qupath.lib.roi.RoiEditor: Query if a ROI is currently being translated through this editor.
isTransparent() - Method in class qupath.lib.images.servers.ImageChannel: Check if the color is 'transparent'; this is used for background/ignored channels.
isTwoPlus(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Return true if the name of the class is "2+", indicating a moderately-positive staining.
isUnbounded() - Method in class qupath.lib.plugins.parameters.NumericParameter: Returns true if this neither a lower nor an upper bound constraining valid values.
isUndoable() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
isUndoable() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Returns true if 'undo' can be applied to the control.
isUndoable() - Method in class qupath.lib.gui.scripting.TextAreaControl
isUnknown() - Method in class qupath.opencv.dnn.DnnShape: Returns true if the shape is unknown.
isUnsignedInteger() - Method in enum class qupath.lib.images.servers.PixelType: Returns true if the type is an unsigned integer representation.
isURL() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Return true if URI has a scheme beginning with http.
isValid() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult: Returns true if the p-value is not NaN.
isValid() - Method in class qupath.lib.gui.tools.MeasurementMapper: Query if the mapper is valid.
isValid() - Method in class qupath.lib.objects.classes.PathClass: A PathClass is valid if its name is not null.
isValidClass(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Returns true if the PathClass represents a valid (non-null) classification.
isValidFilename(String) - Static method in class qupath.lib.common.GeneralTools: Returns true if the output of GeneralTools.stripInvalidFilenameChars(String) matches the provided name, and the name is not null or blank.
isValidInput(Boolean) - Method in class qupath.lib.plugins.parameters.BooleanParameter
isValidInput(String) - Method in class qupath.lib.plugins.parameters.EmptyParameter: Always returns false
isValidInput(String) - Method in class qupath.lib.plugins.parameters.StringParameter
isValidInput(S) - Method in class qupath.lib.plugins.parameters.ChoiceParameter
isValidInput(S) - Method in class qupath.lib.plugins.parameters.NumericParameter: Numbers are considered valid if they are not NaN
isValidInput(S) - Method in interface qupath.lib.plugins.parameters.Parameter: Query if a specified value would be valid for this parameter.
isVisible() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay: Check overlay visibility status.
isVisible() - Method in class qupath.lib.gui.viewer.overlays.GridOverlay
isVisible() - Method in class qupath.lib.gui.viewer.overlays.TMAGridOverlay
isWindows() - Static method in class qupath.lib.common.GeneralTools: Return true if running on Windows.

J

J2K - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Lossless JPEG-2000 compression.
J2K_LOSSY - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Lossy JPEG-2000 compression.
JAVA - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for Java
JAVA_IMPORTER - Static variable in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Java-like import statements
JAVA_TOKENIZER - Static variable in class qupath.lib.scripting.languages.AutoCompletions: A completion tokenizer that extracts a token used to determine Java completions.
JavadocViewer - Class in qupath.lib.gui: Command to show javadocs in a WebView.
JPEG - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: JPEG compression (only for single channel or RGB 8-bit images).
JpegWriter - Class in qupath.lib.images.writers: ImageWriter implementation to write JPEG images using ImageIO.
JpegWriter() - Constructor for class qupath.lib.images.writers.JpegWriter
JSON - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for JSON
JSON - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
JsonImageServerBuilder - Class in qupath.lib.images.servers: ImageServerBuilder that constructs an ImageServer from a JSON representation.
JsonImageServerBuilder() - Constructor for class qupath.lib.images.servers.JsonImageServerBuilder
JsonLanguage - Class in qupath.lib.gui.scripting.languages: Class for the representation of JSON syntax in QuPath.
JsonLanguage() - Constructor for class qupath.lib.gui.scripting.languages.JsonLanguage: Constructor for JSON language.
jsonRegion(ImageRegion, double, ImageServerBuilder.ServerBuilder<BufferedImage>) - Method in class qupath.lib.images.servers.SparseImageServer.Builder: Add a region based on a JSON representation of an ImageServer.
JsonStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling to apply to a CodeArea, based on JSON syntax.

K

KaplanMeierData - Class in qupath.lib.analysis.stats.survival: Structure used to store data related to generating Kaplan-Meier survival curves.
KaplanMeierData(String) - Constructor for class qupath.lib.analysis.stats.survival.KaplanMeierData: Create a new KaplanMeierData object with the specified display name.
KaplanMeierData(String, Collection<KaplanMeierData.KaplanMeierEvent>) - Constructor for class qupath.lib.analysis.stats.survival.KaplanMeierData: Create a new KaplanMeierData object with the specified display name and events.
KaplanMeierData.KaplanMeierEvent - Class in qupath.lib.analysis.stats.survival: Simple class to store event time and censored flag.
keepDisplaySettings - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
keepDisplaySettingsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Retain display settings (channel colors, brightness/contrast) when opening new images that have the same properties (channels, channel names, bit-depths).
KEY_CASE_ID - Static variable in class qupath.lib.objects.TMACoreObject: Metadata key to store a case identify for the TMA core.
KEY_OBJECT_CONNECTIONS - Static variable in class qupath.lib.objects.DefaultPathObjectConnectionGroup: Key to use when storing object connections as a property of an ImageData object.
KEY_OS_CENSORED - Static variable in class qupath.lib.objects.TMACoreObject: Metadata key for an overall survival censored flag.
KEY_OVERALL_SURVIVAL - Static variable in class qupath.lib.objects.TMACoreObject: Metadata key for an overall survival (temporal) value.
KEY_RECURRENCE_FREE_SURVIVAL - Static variable in class qupath.lib.objects.TMACoreObject: Metadata key for an recurrence-free survival (temporal) value.
KEY_RFS_CENSORED - Static variable in class qupath.lib.objects.TMACoreObject: Metadata key for an recurrence-free survival censored flag.
KEYPOINTS - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Refers to KeypointsModel.
keySet() - Method in interface qupath.lib.measurements.MeasurementList: Get all available names as a set.
killRunningScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor

L

LAB_DISTANCE - Enum constant in enum class qupath.process.gui.WandToolEventHandler.WandType: Color image converted to CIELAB, Euclidean distance calculated
label(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Label connected components for non-zero pixels in an image.
label(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Label connected components for non-zero pixels in an image.
labeledImageExtension(String) - Method in class qupath.lib.images.writers.TileExporter: Specify a file extension for the labelled image, which determines the export file format.
labeledImageId(String) - Method in class qupath.lib.images.writers.TileExporter: Specify an identifier appended to the filename for labeled images.
LabeledImageServer - Class in qupath.lib.images.servers: A special ImageServer implementation that doesn't have a backing image, but rather constructs tiles from a PathObjectHierarchy where pixel values are integer labels corresponding stored and classified annotations.
LabeledImageServer.Builder - Class in qupath.lib.images.servers: Helper class for building a LabeledImageServer.
labeledImageSubDir(String) - Method in class qupath.lib.images.writers.TileExporter: Specify a subdirectory within which labeled image tiles should be saved.
labeledServer(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.TileExporter: Optional server providing image labels.
labelImage(ImageProcessor, float, boolean) - Static method in class qupath.imagej.processing.RoiLabeling: Create a labelled image from above-threshold pixels for an image.
labelImage(Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Deprecated.
Use OpenCVTools.label(Mat, Mat, int) instead.
labelROIs(ImageProcessor, List<? extends Roi>) - Static method in class qupath.imagej.processing.RoiLabeling: Label ROIs by filling each pixel with an integer value corresponding to the index of the Roi in the list + 1.
labelsToAnnotations(Path, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing: Convert a labeled image to annotation objects.
labelsToAnnotations(Collection<Path>, boolean) - Static method in class qupath.lib.analysis.images.ContourTracing: Convert labeled images to annotation objects, determining the region from the filename if possible.
labelsToCells(Path, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing: Convert a 2-channel labeled image to cell objects.
labelsToCells(Collection<Path>, boolean) - Static method in class qupath.lib.analysis.images.ContourTracing: Convert 2-channel labeled images to cell objects, determining the region from the filename if possible.
labelsToConnectedROIs(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling: Create ROIs from labels in an image.
labelsToDetections(Path, RegionRequest) - Static method in class qupath.lib.analysis.images.ContourTracing: Convert a labeled image to detection objects.
labelsToDetections(Collection<Path>, boolean) - Static method in class qupath.lib.analysis.images.ContourTracing: Convert labeled images to detection objects, determining the region from the filename if possible.
labelsToFilledRoiList(ImageProcessor, boolean) - Static method in class qupath.imagej.processing.RoiLabeling: Convert a labelled image into a list of PolygonRois by tracing.
labelsToFilledROIs(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling: Convert a labelled image into a list of PolygonRois by tracing.
labelsToObjects(Path, RegionRequest, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing: Convert a labeled image to objects.
labelText(String) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Prompt to include beside the resource name text field
LAPLACIAN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Laplacian of Gaussian filter
laplacianOfGaussian(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate the Laplacian of Gaussian image.
LARGE - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
LARGE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
lastChangeTimestamp() - Method in class qupath.lib.gui.viewer.OverlayOptions: Get a property representing the timestamp of the last recorded change for any property.
lastValue - Variable in class qupath.lib.plugins.parameters.BooleanParameter
lastValue - Variable in class qupath.lib.plugins.parameters.ChoiceParameter
lastValue - Variable in class qupath.lib.plugins.parameters.DoubleParameter
lastValue - Variable in class qupath.lib.plugins.parameters.EmptyParameter
lastValue - Variable in class qupath.lib.plugins.parameters.IntParameter
lastValue - Variable in class qupath.lib.plugins.parameters.NumericParameter
lastValue - Variable in class qupath.lib.plugins.parameters.StringParameter
launchInstanceFromSwing() - Static method in class qupath.lib.gui.QuPathGUI: Static method to launch QuPath from within a Swing/AWT application.
launchTMADataViewer(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Open new window with the TMA data viewer.
layers(Collection<PathOverlay>) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify one or more overlay layers as a collection.
layers(PathOverlay...) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify one or more overlay layers.
layout(String) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify a string representing the axes layout that the model expects as input.
lazyInitialize(boolean) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Optionally request lazy initialization.
LEGACY_KEY_UNIQUE_ID - Static variable in class qupath.lib.objects.TMACoreObject: Deprecated.
legacyPathToURI(String) - Static method in class qupath.lib.images.servers.ImageServerProvider: Method to help with converting legacy image paths to URIs.
legend(boolean) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify whether the legend should be shown or not.
legend(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify whether the legend should be shown or not.
legend(boolean) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify whether the legend should be shown or not.
legend(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify the side of the chart where the legend should be shown.
legend(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify the side of the chart where the legend should be shown.
legend(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify the side of the chart where the legend should be shown.
legend(Side) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify the side of the chart where the legend should be shown.
legend(Side) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify the side of the chart where the legend should be shown.
legend(Side) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify the side of the chart where the legend should be shown.
legendSide - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
legendSide - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
legendSide - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
legendVisible - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
legendVisible - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
legendVisible - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
LENGTH - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Length of the shape; for area geometries, this provides the perimeter.
leq(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Apply a less than or equal to threshold.
leq(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Apply a less than or equal to threshold between two arrays.
levels(Collection<ImageServerMetadata.ImageResolutionLevel>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify resolution levels, where the largest image should come first.
levelsFromDownsamples(double...) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify downsample values for pyramidal levels.
LICENSE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
limitDatapoints(int) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Choose the maximum number of supported datapoints.
LINE - Enum constant in enum class qupath.lib.roi.interfaces.ROI.RoiType: ROI represents a line or polyline.
LINE - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Line drawing tool
LINE_OR_ARROW - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Extended PathTool that can switch between drawing lines or arrows.
LINE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
LINE_TOOL - Variable in class qupath.lib.gui.ToolManager
LineROI - Class in qupath.lib.roi: ROI representing a straight line, defined by its end points.
lineThickness(float) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Thickness of boundary lines and line annotations, defined in terms of pixels at the resolution specified by the downsample value of the server.
lineWidthProperty() - Method in class qupath.lib.gui.charts.ChartThresholdPane: Line width property used for displaying threshold lines.
LINK - Enum constant in enum class qupath.lib.extension.svg.SvgTools.SvgBuilder.ImageIncludeType: Link the image (to a separate PNG).
linkImages() - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify whether the underlying (raster) image should be included in any export.
loadDensityMap(String) - Static method in class qupath.lib.scripting.QP: Load a density map for a project or file path.
loadDensityMap(Path) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps: Load a DensityMaps.DensityMapBuilder from the specified path.
loadDisplaySettings(String) - Static method in class qupath.lib.gui.scripting.QPEx: Load a display settings object from a file path or from the current project.
loadImageData(String, boolean) - Static method in class qupath.lib.scripting.QP: Deprecated.
loadObjectClassifier(String...) - Static method in class qupath.lib.scripting.QP: Load an object classifier for a project or file path.
loadPixelClassifier(String) - Static method in class qupath.lib.scripting.QP: Load a pixel classifier for a project or file path.
loadProject(File, Class<T>) - Static method in class qupath.lib.projects.ProjectIO: Load a project from a local file.
loadProject(URI, Class<T>) - Static method in class qupath.lib.projects.ProjectIO: Read project from URI.
LoadResourceCommand<S> - Class in qupath.process.gui.commands.ui: Create commands for displaying pixel classifiers and density maps.
LocalBinaryPatterns - Class in qupath.lib.analysis.features: Initial test implementation of Local Binary Patterns.
LocalBinaryPatterns() - Constructor for class qupath.lib.analysis.features.LocalBinaryPatterns
LocalBinaryPatternsPlugin - Class in qupath.lib.algorithms: Calculate local binary pattern features.
LocalBinaryPatternsPlugin() - Constructor for class qupath.lib.algorithms.LocalBinaryPatternsPlugin: Default constructor.
localeDefault - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
localeDisplay - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
localeFormat - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
LocalePreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.LocalePreferences
localizationDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager: Read only property representing the localization directory.
localNormalization(double, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Apply local 2D normalization using Gaussian-weighted mean subtraction and (optionally) variance estimation.
LocalNormalization - Class in qupath.opencv.tools: Methods to normalize the local image intensity within an image, to have (approximately) zero mean and unit variance.
LocalNormalization() - Constructor for class qupath.opencv.tools.LocalNormalization
LocalNormalization.LocalNormalizationType - Class in qupath.opencv.tools: Helper class to store local normalization parameters.
LocalNormalization.NormalizationType - Enum Class in qupath.opencv.tools: Local normalization type.
LocalNormalization.SmoothingScale - Class in qupath.opencv.tools: 2D or 3D Gaussian scale.
locateFile(String) - Static method in class qupath.lib.gui.scripting.QPEx: Locate a specified file based upon its name or path, with a search depth of 4.
locateFile(String) - Static method in class qupath.lib.scripting.QP: Locate a specified file based upon its name or path, with a search depth of 4.
locateFile(String, int) - Static method in class qupath.lib.gui.scripting.QPEx: Locate a specified file based upon its name or path.
locateFile(String, int) - Static method in class qupath.lib.scripting.QP: Locate a specified file based upon its name or path.
locateFile(String, int, Path...) - Static method in class qupath.lib.io.UriUpdater: Attempt to update a file using the specified search paths.
locateFile(URI, int, Path...) - Static method in class qupath.lib.io.UriUpdater: Attempt to update a URI to find an existing file using the specified search paths.
LOCATION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
locationFontSize - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
locationFontSizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Preferred font size for the location text in the viewer.
locationUpdated - Variable in class qupath.lib.gui.viewer.QuPathViewer: Flag used to indicate that the visible region in the viewer has changed
LOCK_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
lockActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
LockActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
lockObjects(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Set specified objects to be 'locked'.
lockSelectedObjects(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools: Set selected objects to be 'locked', firing an update event if the status of any object is changed.
lockSelectedToolProperty() - Method in class qupath.lib.gui.ToolManager: Property to request that the selected tool be locked.
log() - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that returns the natural logarithm of values.
LOG_DELIMITER - Static variable in class qupath.lib.gui.viewer.recording.ViewTracker
LOG_VIEWER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
LOGARITHM - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode: Natural logarithm of raw bin counts.
logDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager: Read only property representing the log file directory.
LoggingTools - Class in qupath.lib.scripting
LoggingTools() - Constructor for class qupath.lib.scripting.LoggingTools
logLevel - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
LogManager - Class in qupath.lib.gui.logging: Manage logging levels.
LogManager() - Constructor for class qupath.lib.gui.logging.LogManager
LogManager.LogLevel - Enum Class in qupath.lib.gui.logging: Available log levels.
logOnce(Logger, String) - Static method in class qupath.lib.common.LogTools: Log a message once at the INFO level.
logOnce(Logger, Level, String) - Static method in class qupath.lib.common.LogTools: Log a message once at the specified level.
LogRankTest - Class in qupath.lib.analysis.stats.survival: Helper class to apply a log-rank test.
LogRankTest() - Constructor for class qupath.lib.analysis.stats.survival.LogRankTest
LogRankTest.LogRankResult - Class in qupath.lib.analysis.stats.survival: Simple structure used to manage the result of a log rank test.
logToFile(File) - Static method in class qupath.lib.gui.logging.LogManager: Request logging to the specified file.
LogTools - Class in qupath.lib.common: Helper class for logging.
LogTools() - Constructor for class qupath.lib.common.LogTools
LogViewerCommand - Class in qupath.lib.gui.commands: A viewer for log messages.
LogViewerCommand(Window) - Constructor for class qupath.lib.gui.commands.LogViewerCommand: Constructor.
longText(String) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Set the long text property of the action.
longText(ObservableValue<String>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Bind the long text property of the action to an ObservableValue, bidirectionally if possible.
longTextProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Property corresponding to CommandFinderTools.CommandEntry.getLongText()
lookupAccelerator(String) - Method in class qupath.lib.gui.QuPathGUI: Get the action or menu item associated with an accelerator.
lookupAccelerator(KeyCombination) - Method in class qupath.lib.gui.QuPathGUI: Get the action or menu item associated with an key combination.
lookupActionByText(String) - Method in class qupath.lib.gui.QuPathGUI: Search for an action based upon its text (name) property.
lookupMenuItem(String) - Method in class qupath.lib.gui.QuPathGUI: Search for a menu item based upon its path.
losslessCompression() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request the default lossless compression method.
lossyCompression() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request the default lossy compression method.
lt(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Apply a less than threshold.
lt(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Apply a less than threshold between two arrays.
LZW - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: LZW compression.

M

MAGENTA - Static variable in class qupath.lib.common.ColorTools: Packed int representing magenta.
magnification(double) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify a magnification value for the highest-resolution image.
main(String[]) - Static method in class qupath.lib.common.Timeit
main(String[]) - Static method in class qupath.lib.gui.JavadocViewer: Show javadoc stage (used for development).
main(String[]) - Static method in class qupath.lib.gui.tools.DocGenerator
main(String[]) - Static method in class qupath.QuPath: Main class to launch QuPath.
MAIN_SCENE - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType: Snapshot of the full Scene of the main QuPath Window.
MAIN_WINDOW_SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType: Screenshot of the full QuPath window as it currently appears, including any overlapping windows.
MAKE_INVERSE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
makeARGB(int, int, int, int) - Static method in class qupath.lib.scripting.QP: Make a packed int representation of an ARGB color.
makeBinaryImage(ImageProcessor, double, Roi, boolean) - Static method in class qupath.imagej.detect.dearray.TMADearrayer: Make a binary image depicting (hopefully) the TMA cores.
makeChartInteractive(Chart, NumberAxis, NumberAxis) - Static method in class qupath.lib.gui.charts.ChartTools: Make it possible to select chart regions to zoom in, and scroll to navigate around it.
makeDefaultColorDeconvolutionStains(ColorDeconvolutionStains.DefaultColorDeconvolutionStains) - Static method in class qupath.lib.color.ColorDeconvolutionStains: Create a ColorDeconvolutionStains for a default stain combination, and default max values (255 for all channels).
makeDefaultStainVector(StainVector.DefaultStains) - Static method in class qupath.lib.color.StainVector: Get a default stain vector.
makeDoubleArrayWrapper(double[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers: Create a wrapper for a double array, returning values (predictably) as doubles.
makeFileInProject(String...) - Static method in class qupath.lib.scripting.QP: Build a file path relative to the current project, and create a File object.
makeFloatArrayWrapper(float[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers: Create a wrapper for a float array, returning values as doubles.
makeFullScreenshot() - Static method in class qupath.lib.gui.tools.GuiTools: Make a BufferedImage snapshot of the full screen.
makeIntArrayWrapper(int[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers: Create a wrapper for an int array, returning values as doubles.
makeInverseAnnotation() - Static method in class qupath.lib.scripting.QP: Make an inverse annotation using the current ImageData and its current selected objects.
makeInverseAnnotation(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Make an inverse annotation for the selected objects, storing the command in the history workflow.
makeInverseAnnotation(ImageData<?>) - Static method in class qupath.lib.scripting.QP: Make an inverse annotation using the specified ImageData and current selected objects.
makeInverseAnnotation(ImageData<?>, Collection<PathObject>) - Static method in class qupath.lib.scripting.QP: Make an annotation, for which the ROI is obtained by subtracting the ROIs of the specified objects from the closest common ancestor ROI (or entire image if the closest ancestor is the root).
makeInverseAnnotation(ImageData<?>, PathObject) - Static method in class qupath.lib.scripting.QP: Make an annotation for the specified ImageData, for which the ROI is obtained by subtracting the existing ROI from the ROI of its parent object (or entire image if no suitable parent object is available).
makeInverseAnnotation(PathObject) - Static method in class qupath.lib.scripting.QP: Make an annotation for the current ImageData, for which the ROI is obtained by subtracting the existing ROI from the ROI of its parent object (or entire image if no suitable parent object is available).
makeMeasurementHistogram(Collection<PathObject>, String, int) - Static method in class qupath.lib.analysis.stats.Histogram: Create a histogram depicting values of a specific measurement extracted from a collection of PathObjects.
makeOD(double, double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Convert a single pixel value to an optical density as max(0, -log10(val/max).
makeODByLUT(float, double[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Convert a float pixel to an optical density value using a pre-computed lookup table.
makeODByLUT(int, double[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Convert an int pixel to an optical density value using a pre-computed lookup table.
makeODLUT(double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Create an optical density lookup table with 256 entries, normalizing to the specified background value.
makeODLUT(double, int) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Create an optical density lookup table, normalizing to the specified background value.
makePathInProject(String...) - Static method in class qupath.lib.scripting.QP: Build a file or directory path relative to the current project, and ensure that it exists.
makeProgressMonitor() - Method in class qupath.lib.gui.TaskRunnerFX
makeProgressMonitor() - Method in class qupath.lib.plugins.AbstractTaskRunner: Create a progress monitor to update the user on what is happening.
makeProgressMonitor() - Method in class qupath.lib.plugins.CommandLineTaskRunner
makeReplacement(URI, URI) - Method in class qupath.lib.io.UriUpdater: Add a single replacement to the replacement map.
makeRGB(int, int, int) - Static method in class qupath.lib.common.ColorTools: Deprecated.
Use ColorTools.packRGB(int, int, int) or ColorTools.packClippedRGB(int, int, int) instead.
makeRGB(int, int, int) - Static method in class qupath.lib.scripting.QP: Make a packed int representation of an RGB color.
makeRGBA(int, int, int, int) - Static method in class qupath.lib.common.ColorTools: Deprecated.
The naming and order of arguments is misleading. The output is a packed ARGB value, but arguments are provided in the order red, green, blue, alpha.
makeScaledRGB(int, double) - Static method in class qupath.lib.common.ColorTools: Scale the RGB channels for a color by a fixed amount.
makeScaledRGBwithRangeCheck(float, float, float, ColorModel) - Static method in class qupath.lib.color.ColorTransformer: Create a packed RGB pixel value by applying a ColorModel to a (possibly scaled and offset) floating point value.
makeSnapshot() - Static method in class qupath.lib.gui.tools.GuiTools: Make a BufferedImage snapshot of the current GUI.
makeSnapshot(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools: Make a snapshot (image) showing what is currently displayed in a QuPath window or the active viewer within QuPath, as determined by the SnapshotType.
makeSnapshot(QuPathGUI, QuPathViewer, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools: Make a snapshot (image) showing what is currently displayed in a QuPath window or the specified viewer, as determined by the SnapshotType.
makeSnapshotFX(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools: Make a snapshot as a JavaFX Image, using the current viewer if a viewer is required.
makeSnapshotFX(QuPathGUI, QuPathViewer, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools: Make a snapshot as a JavaFX Image.
makeTiles(ROI, int, int, boolean) - Static method in class qupath.lib.roi.RoiTools: Make fixed-size rectangular tile ROIs for a specified area.
makeUnsignedByteArrayWrapper(byte[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers: Create a wrapper for a byte array, returning values as doubles.
makeUnsignedShortArrayWrapper(short[]) - Static method in class qupath.lib.analysis.stats.ArrayWrappers: Create a wrapper for a short array, returning values as doubles.
makeViewerSnapshot() - Static method in class qupath.lib.gui.tools.GuiTools: Make a BufferedImage snapshot of the current viewer.
makeViewerSnapshot(QuPathViewer) - Static method in class qupath.lib.gui.tools.GuiTools: Make a BufferedImage snapshot of the specified viewer.
manageChildMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar: Request that a menubar is managed as a child menubar.
manageMainMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar: Request that a menubar is managed as a main menubar.
MANAGER - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
MAPS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
MARKDOWN - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for markdown
MarkdownLanguage - Class in qupath.lib.gui.scripting.languages: Class for the representation of JSON syntax in QuPath.
MarkdownLanguage() - Constructor for class qupath.lib.gui.scripting.languages.MarkdownLanguage: Constructor for JSON language.
MarkdownStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling to apply to a CodeArea, based on Markdown syntax.
markerOpacity - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
markerOpacity - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
markerOpacity - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify the marker opacity.
markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify the marker opacity.
markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify the marker opacity.
MASK_ALPHA - Static variable in class qupath.lib.common.ColorTools: Mask for use when extracting the alpha component from a packed ARGB int value.
MASK_BLUE - Static variable in class qupath.lib.common.ColorTools: Mask for use when extracting the blue component from a packed (A)RGB int value.
MASK_GREEN - Static variable in class qupath.lib.common.ColorTools: Mask for use when extracting the green component from a packed (A)RGB int value.
MASK_RED - Static variable in class qupath.lib.common.ColorTools: Mask for use when extracting the red component from a packed (A)RGB int value.
maskFunction(MaskSupplier<S, T>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Function used to lazily create a mask corresponding to the image for a specified ROI.
maskImageNames - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
maskImageNamesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request that image names are hidden within the user interface.
maskObject(ROI, PathObject) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils: Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask.
maskObjectAndSplit(ROI, PathObject) - Static method in class qupath.lib.experimental.pixels.PixelProcessorUtils: Apply a ROI mask to an object, ensuring that the child object's ROI does not extend beyond the mask, and splitting the child object's ROI to create multiple objects if it contains disjoint regions.
maskSupplier(MaskSupplier<S, T>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the mask supplier.
MaskSupplier<S,T> - Interface in qupath.lib.experimental.pixels: A functional interface for supplying a mask corresponding to an image.
MATCH_VIEWER_RESOLUTIONS - Variable in class qupath.lib.gui.actions.ViewerActions
matchByID(Collection<? extends PathObject>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Match objects according to their IDs.
matchClassName(String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
matchClassName(String...) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
matchClassName(String...) - Method in interface qupath.lib.images.servers.ImageServerBuilder: Check if this provider matches one or more specified classnames.
matchClassName(String...) - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
matchResolutions() - Method in class qupath.lib.gui.viewer.ViewerManager: Match the display resolutions (downsamples) of all viewers to match the current viewer.
matToBufferedImage(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Convert a Mat to a BufferedImage.
matToBufferedImage(Mat, ColorModel) - Static method in class qupath.opencv.tools.OpenCVTools: Convert a Mat to a BufferedImage.
matToImagePlus(String, Mat...) - Static method in class qupath.opencv.tools.OpenCVTools: Convert an OpenCV MatVector into an ImageJ ImagePlus.
matToImagePlus(Mat, String) - Static method in class qupath.opencv.tools.OpenCVTools: Convert an OpenCV Mat into an ImageJ ImagePlus.
matToImageProcessor(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Convert a single-channel OpenCV Mat into an ImageJ ImageProcessor.
matToSimpleImage(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Convert a Mat to a SimpleImage.
max() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions: Create a function to calculate the maximum value of an array.
max(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Find the maximum of all elements in a Mat, ignoring NaNs.
max(Padding) - Method in class qupath.lib.regions.Padding: Compare two paddings, and take the larger padding value on all sides.
MAX - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Maximum value
MAX_DIAMETER - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Maximum diameter; this is equivalent to the diameter of the minimum bounding circle.
maxAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
maxChannelProject() - Method in class qupath.lib.images.servers.TransformedServerBuilder: Perform a maximum projection of the channels.
maxClipboardObjects - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
maxDecimalPlaces(int) - Method in class qupath.lib.common.Timeit: Set the maximum number of decimal places when reporting timings using seconds or minutes.
maxDisplay - Variable in class qupath.lib.display.DirectServerChannelInfo
maxHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
maximum() - Static method in class qupath.opencv.ops.ImageOps.Channels: Calculate the maximum value along all channels, to give a single-channel output.
maximum(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D maximum filter.
maximum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the maximum value in an image, across all pixels (regardless of channels), ignoring NaNs.
maximum(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Get the per-element maximum value between an array and a scalar.
maximum(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Get the per-element maximum value for two arrays.
maximumFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D maximum filter (dilation) to all channels of an image.
maxMemoryGB - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
maxMemoryMBProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Get property representing the maximum memory for the Java Virtual Machine, applied after restarting the application.
maxObjectsToClipboardProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The maximum number of objects that can be copied to the system clipboard.
maxOutputChannelLimit(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Specify the maximum number of output channels allowed before QuPath will throw an exception.
maxUndoHierarchySize - Variable in class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
maxUndoHierarchySizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The requested maximum number of objects in a hierarchy for which QuPath should support undo/redo.
maxUndoLevels - Variable in class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
maxUndoLevelsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: The requested maximum number of undo levels that QuPath should support.
maxValue(Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the maximum value supported by this image.
maxValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane: The maximum value displayed on the histogram.
maxValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: Value of the maximum slider.
maxWidth(double) - Method in class qupath.lib.gui.ColorMapCanvas
maybeCellLabels(Raster, int, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Check whether a raster could be used to generate cell objects, by providing a nucleus and corresponding cell labels.
maybeCellLabels(SimpleImage, SimpleImage, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Check whether two images could be used to generate cell objects, by providing a nucleus and corresponding cell labels.
mean() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions: Create a function to calculate the mean (average) value of an array.
mean() - Static method in class qupath.opencv.ops.ImageOps.Channels: Average all channels together using the mean, to give a single-channel output.
mean(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D circular mean filter.
mean(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Calculate the mean of all elements in a Mat, ignoring NaNs.
mean(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the mean of an image, across all pixels (regardless of channels), ignoring NaNs.
mean(Scalar) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Mean values which should be subtracted from the image channels before input to the Net.
MEAN - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Arithmetic mean
MEAN_VARIANCE - Enum constant in enum class qupath.lib.classifiers.Normalization: Normalize by subtracting the mean and dividing by the standard deviation
meanFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D mean filter to all channels of an image, with symmetric boundary padding.
meanFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D mean filter to all channels of an image.
MEASURE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
MEASURE_ANNOTATIONS - Variable in class qupath.lib.gui.actions.CommonActions
MEASURE_DETECTIONS - Variable in class qupath.lib.gui.actions.CommonActions
MEASURE_GRID_ANNOTATIONS - Variable in class qupath.lib.gui.actions.CommonActions
MEASURE_GRID_TMA_CORES - Variable in class qupath.lib.gui.actions.CommonActions
MEASURE_TMA - Variable in class qupath.lib.gui.actions.CommonActions
measureHaralick(SimpleImage, SimpleImage, int, double, double, int) - Static method in class qupath.lib.analysis.features.HaralickFeatureComputer: Compute mean Haralick features from a SimpleImage, with optional masking.
measurement(PathObject, String) - Static method in class qupath.lib.scripting.QP: Extract the specified measurement from a PathObject.
Measurement - Interface in qupath.lib.measurements: Basic interface to define a measurement.
MeasurementExportCommand - Class in qupath.lib.gui.commands: Dialog box to export measurements
MeasurementExportCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.MeasurementExportCommand: Creates a simple GUI for MeasurementExporter.
MeasurementExporter - Class in qupath.lib.gui.tools: Helper class for exporting the measurements of one or more entries in a project.
MeasurementExporter() - Constructor for class qupath.lib.gui.tools.MeasurementExporter
MeasurementFactory - Class in qupath.lib.measurements: Deprecated.
MeasurementFactory() - Constructor for class qupath.lib.measurements.MeasurementFactory: Deprecated.
MeasurementList - Interface in qupath.lib.measurements: Interface defining a feature measurement list, consisting of key value pairs.
MeasurementList.MeasurementListType - Enum Class in qupath.lib.measurements: Enum representing different types of measurement list, with different priorities regarding flexibility and efficiency.
MeasurementListFactory - Class in qupath.lib.measurements: Factory for creating new measurement lists.
MeasurementMapPane - Class in qupath.lib.gui.panes: Component used for displaying measurement maps, whereby detection objects are recolored according to measurement values.
MeasurementMapPane(QuPathGUI) - Constructor for class qupath.lib.gui.panes.MeasurementMapPane: Constructor.
MeasurementMapper - Class in qupath.lib.gui.tools: Helpers class that can be used to map an object's measurement to a color (packed RGB int).
MeasurementMapper(ColorMaps.ColorMap, String, Collection<? extends PathObject>) - Constructor for class qupath.lib.gui.tools.MeasurementMapper: Constructor.
measurementMapperProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
MeasurementPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
MeasurementProcessor - Class in qupath.lib.experimental.pixels: Create PixelProcessor instances that make measurements from objects.
MeasurementProcessor() - Constructor for class qupath.lib.experimental.pixels.MeasurementProcessor
MeasurementProcessor.CustomMeasurement<S,T> - Interface in qupath.lib.experimental.pixels: Interface for calculating one custom measurement from an image, using Parameters.
MeasurementProcessor.Functions - Class in qupath.lib.experimental.pixels: Functions for calculating measurements from an array of pixels.
MeasurementProcessor.Measurements - Class in qupath.lib.experimental.pixels: Methods to create custom measurements.
measurements(Collection<? extends PathObject>, String, String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Plot two measurements against one another for the specified objects.
Measurements() - Constructor for class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements
MeasureMenuActions - Class in qupath.lib.gui.actions.menus
MeasureMenuActions.Actions - Class in qupath.lib.gui.actions.menus
median(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D median filter
median(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the median pixel value in a Mat, ignoring NaNs.
MEDIAN - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Median value
MEDIUM - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
MEDIUM - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
MEMBRANE - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments: Cell boundary, with interior removed
memoizationTimeMillis - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
MEMORY_MONITORY - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
memoryReport(CharSequence) - Static method in class qupath.opencv.tools.OpenCVTools: Create a brief report on memory use, based on JavaCPP's Pointer class.
menu() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
MenuActions - Interface in qupath.lib.gui.actions.menus: Common interface to define the contents of a menu in terms of actions.
menuPathProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Property corresponding to CommandFinderTools.CommandEntry.getMenuPath()
Menus - Class in qupath.lib.gui.actions.menus: Generate actions for installation in QuPath's main menubar.
Menus() - Constructor for class qupath.lib.gui.actions.menus.Menus
menusToMarkdown() - Static method in class qupath.lib.gui.tools.CommandFinderTools: Create a markdown representation of the menus for inclusion in the documentation, using the current QuPath instance.
menusToMarkdown(QuPathGUI, Writer) - Static method in class qupath.lib.gui.tools.CommandFinderTools: Write a markdown representation of the menus for inclusion in the documentation.
MenuTools - Class in qupath.lib.gui.tools: Static methods to help with creating and populating JavaFX menus.
MenuTools() - Constructor for class qupath.lib.gui.tools.MenuTools
merge(Collection<? extends PathObject>) - Method in class qupath.lib.objects.utils.ObjectMerger: Calculate the result of applying the merging strategy to the input objects.
MERGE_SELECTED - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
mergeAnnotations(Collection<PathObject>) - Static method in class qupath.lib.scripting.QP: Merge annotations for the current hierarchy.
mergeAnnotations(PathObjectHierarchy, Collection<PathObject>) - Static method in class qupath.lib.scripting.QP: Merge the specified annotations to create a new annotation containing the union of their ROIs.
mergeChannels(Collection<? extends Mat>, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Merge channels from a multichannel Mat.
mergeClasses(PathClass, PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Merge two classifications together.
mergeObjects(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Merge objects by calculating the union of their ROIs.
mergeObjects(Collection<? extends PathObject>, Function<? super PathObject, ? extends K>) - Static method in class qupath.lib.objects.PathObjectTools: Merge objects that share a property in common.
mergePointsForAllClasses() - Static method in class qupath.lib.scripting.QP: Merge point annotations sharing the same PathClass and ImagePlane as the selected annotations of the current hierarchy, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
mergePointsForAllClasses(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools: Merge point annotations sharing the same PathClass and ImagePlane, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
mergePointsForClass(PathObjectHierarchy, PathClass) - Static method in class qupath.lib.objects.PathObjectTools: Merge point annotations with the specified PathClass sharing the same ImagePlane, creating a single multi-point annotation for all matching points and removing the (previously-separated) annotations.
mergePointsForSelectedObjectClasses() - Static method in class qupath.lib.scripting.QP: Merge point annotations sharing the same PathClass and ImagePlane for the current hierarchy, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
mergePointsForSelectedObjectClasses(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools: Merge point annotations sharing the same PathClass and ImagePlane as the selected annotations, creating multi-point annotations for all matching points and removing the (previously-separated) annotations.
merger(ObjectMerger) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set a merger to use.
mergeSelectedAnnotations() - Static method in class qupath.lib.scripting.QP: Merge the currently-selected annotations of the current hierarchy to create a new annotation containing the union of their ROIs.
mergeSelectedAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Merge the currently-selected annotations for an image, replacing them with a single new annotation.
mergeSelectedAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Merge the currently-selected annotations to create a new annotation containing the union of their ROIs.
mergeSharedBoundaries(double) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Convenience method to set a merger that merges objects based on their shared boundary.
METADATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
MetadataStore - Interface in qupath.lib.objects: Interface that may be used to indicate that a PathObject (or other object) can store metadata.
MICROMETER - Static variable in class qupath.lib.images.servers.PixelCalibration: String to represent 'micrometer' units.
micrometerSymbol() - Static method in class qupath.lib.common.GeneralTools: Get a string to represent um (but with the proper 'mu' symbol)
microseconds() - Method in class qupath.lib.common.Timeit: Report timings in microseconds.
milliseconds() - Method in class qupath.lib.common.Timeit: Report timings in milliseconds.
MIME_TYPE_GEOJSON - Static variable in class qupath.lib.gui.commands.InteractiveObjectImporter: Mime type for GeoJson
min() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions: Create a function to calculate the minimum value of an array.
min(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Find the minimum of all elements in a Mat, ignoring NaNs.
MIN - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Minimum value
MIN_DIAMETER - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Minimum diameter.
MIN_MAX - Enum constant in enum class qupath.lib.classifiers.Normalization: Normalize into the range 0-1 using min and max values
minAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
minChannelProject() - Method in class qupath.lib.images.servers.TransformedServerBuilder: Perform a minimum projection of the channels.
minDisplay - Variable in class qupath.lib.display.DirectServerChannelInfo
minHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
MINI_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
minimum() - Static method in class qupath.opencv.ops.ImageOps.Channels: Calculate the minimum value along all channels, to give a single-channel output.
minimum(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D minimum filter.
minimum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the minimum value in an image, across all pixels (regardless of channels), ignoring NaNs.
minimum(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Get the per-element minimum value between an array and a scalar.
minimum(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Get the per-element minimum value for two arrays.
minimumFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D minimum filter (erosion) to all channels of an image.
minimumPyramidDimension - Variable in class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
MiniViewerManager(QuPathViewer, Collection<? extends ChannelDisplayInfo>) - Constructor for class qupath.lib.gui.commands.MiniViewers.MiniViewerManager: Deprecated.
use MiniViewers.createManager(QuPathViewer, Collection) instead.
MiniViewers - Class in qupath.lib.gui.commands: Command to open a small viewer window, which displays a detail from the current image depending on where the cursor is over the image.
MiniViewers() - Constructor for class qupath.lib.gui.commands.MiniViewers
MiniViewers.MiniViewerManager - Class in qupath.lib.gui.commands: A manager for one or more mini-viewers, where the 'more' means a separate viewer per channel.
minMax() - Static method in class qupath.opencv.ops.ImageOps.Normalize: Normalize the minimum and maximum values of the image to fall into the range 0 - 1.
minMax(double, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Normalize the minimum and maximum values of the image to fall into the range 'outputMin - outputMax'.
minPyramidDimensionProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Minimum image width or height before pyramidalizing (if required).
minus(Mat, Number) - Static method in class qupath.opencv.tools.GroovyCV: Subtract a constant from an array.
minus(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Subtract one array from another.
minus(Mat, Scalar) - Static method in class qupath.opencv.tools.GroovyCV: Subtract a scalar from an array.
MINUS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
minutes() - Method in class qupath.lib.common.Timeit: Report timings in minutes.
minValue(Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the minimum value supported by this image.
minValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane: The minimum value displayed on the histogram.
minValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: Value of the minimum slider.
minWidth(double) - Method in class qupath.lib.gui.ColorMapCanvas
MISSING - Enum constant in enum class qupath.lib.io.UriUpdater.UriStatus: URI refers to a file that does not appear to exist or is inaccessible.
missingValue(double) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder
mkdirs(String) - Static method in class qupath.lib.scripting.QP: Ensure directories exist for the specified path, calling file.mkdirs() if not.
ML() - Constructor for class qupath.opencv.ops.ImageOps.ML
modality(Modality) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the modality of the dialog.
modelType(OpenCVDnn.ModelType) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Set the model type, used by OpenCVDnn.buildModel().
morphologicalReconstruction(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Apply morphological operation using marker and mask images.
morphologicalReconstruction(Mat, Mat) - Static method in class qupath.opencv.tools.ProcessingCV: Compute morphological reconstruction.
morphologicalReconstruction(SimpleModifiableImage, SimpleImage) - Static method in class qupath.lib.analysis.algorithms.MorphologicalReconstruction: Apply morphological reconstruction with the specified marker and mask images.
MorphologicalReconstruction - Class in qupath.imagej.processing: Implementation of morphological reconstruction for ImageJ.
MorphologicalReconstruction - Class in qupath.lib.analysis.algorithms: Implementation of 2D morphological reconstruction, using 8-connectivity & a hybrid method.
MorphologicalReconstruction() - Constructor for class qupath.imagej.processing.MorphologicalReconstruction
MorphologicalReconstruction() - Constructor for class qupath.lib.analysis.algorithms.MorphologicalReconstruction
mouseClicked(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mouseClicked(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
mouseClicked(MouseEvent) - Method in class qupath.process.gui.WandToolEventHandler
mouseDragged(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mouseDragged(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
mouseEntered(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
mouseEntered(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mouseExited(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
mouseExited(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.process.gui.WandToolEventHandler
mouseMoved(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mouseMoved(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
mousePressed(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mousePressed(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
mouseReleased(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
mouseReleased(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
MOVE - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Move tool
MOVE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
MOVE_TOOL - Variable in class qupath.lib.gui.ToolManager
MoveToolEventHandler - Class in qupath.lib.gui.viewer.tools.handlers: The MoveTool is used for quite a lot of things, movement-related: movement around an image (panning), moving ROIs (translating) and moving individual 'handles' of ROIs (resizing/reshaping)
MoveToolEventHandler() - Constructor for class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
MoveToolEventHandler.ViewerMover - Class in qupath.lib.gui.viewer.tools.handlers: Helper class for panning a QuPathViewer (reasonably) smoothly.
multiChannel(String, List<ColorTransforms.ColorTransform>, Function<double[][], Double>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements: Create a new object measurement that requires multiple channels as input, using the main ROI of the object as a mask.
multiChannel(String, List<ColorTransforms.ColorTransform>, Function<double[][], Double>, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements: Create a new object measurement that requires multiple channels as input.
multichannelOutput(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: If true, the output image consists of multiple binary images concatenated as different channels, so that the channel number relates to a classification.
MULTICLASS_PROBABILITY - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Each channel represents a probability value, where each pixel is potentially part of multiple classes.
multiply(double...) - Static method in class qupath.opencv.ops.ImageOps.Core: Multiply all pixels by a constant.
multiply(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Multiply array elements by a constant.
multiply(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Per-element multiplication of two arrays (not matrix multiplication).
multipointToolProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Create multiple points within the same annotation when using the counting tool.
MultiscaleFeatures - Class in qupath.opencv.tools: Calculate pixel-based features in both 2D and 3D.
MultiscaleFeatures() - Constructor for class qupath.opencv.tools.MultiscaleFeatures
MultiscaleFeatures.Hessian - Interface in qupath.opencv.tools: Helper class for storing and computing pixel features from Hessian matrices.
MultiscaleFeatures.Hessian2D - Class in qupath.opencv.tools: Hessian matrix values for 2D images.
MultiscaleFeatures.Hessian3D - Class in qupath.opencv.tools: Hessian matrix values for 3D images (z-stacks).
MultiscaleFeatures.MultiscaleFeature - Enum Class in qupath.opencv.tools: Image features, dependent on Gaussian scale.
MultiscaleFeatures.MultiscaleResultsBuilder - Class in qupath.opencv.tools: Helper-class for computing pixel-features at a specified scale.
MultiscaleFeatures.MultiscaleResultsBuilder.FeatureMap - Class in qupath.opencv.tools: Helper map implementation that provides access to MultiscaleFeatures.Hessian if needed.
MultiscaleResultsBuilder() - Constructor for class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Default constructor.
MultiscaleResultsBuilder(Collection<MultiscaleFeatures.MultiscaleFeature>) - Constructor for class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Constructor prepared to calculate specified features.
multitouchActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
MultitouchActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
MULTIVIEW_ADD_COLUMN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_ADD_ROW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_CLOSE_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
MULTIVIEW_GRID_1x1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_GRID_1x2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_GRID_2x1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_GRID_2x2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_GRID_3x3 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_GRID_ACTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
MULTIVIEW_MATCH_RESOLUTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
MULTIVIEW_REMOVE_COLUMN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_REMOVE_ROW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_RESET_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
MULTIVIEW_SYNCHRONIZE_VIEWERS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
multiviewActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
MultiviewActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
MultiviewGridActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions

N

name(String) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the image name.
name(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify a series name
name(String) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: User-friendly name to use with this model.
NAME_NEGATIVE - Static variable in class qupath.lib.objects.classes.PathClass: Default name for a class representing "Negative" staining intensity
NAME_OBJECT_ID - Static variable in class qupath.lib.gui.measure.ObservableMeasurementTableData: The name used for the Object ID column
NAME_ONE_PLUS - Static variable in class qupath.lib.objects.classes.PathClass: Default name for a class representing "1+" staining intensity (i.e.
NAME_POSITIVE - Static variable in class qupath.lib.objects.classes.PathClass: Default name for a class representing "Positive" staining intensity
NAME_THREE_PLUS - Static variable in class qupath.lib.objects.classes.PathClass: Default name for a class representing "3+" staining intensity (i.e.
NAME_TWO_PLUS - Static variable in class qupath.lib.objects.classes.PathClass: Default name for a class representing "2+" staining intensity (i.e.
nameObjectsByCluster(Collection<Collection<? extends PathObject>>) - Static method in class qupath.lib.analysis.DelaunayTools: Assign object names based upon pre-computed clusters.
nameObjectsByCluster(Collection<Collection<? extends PathObject>>, Function<Integer, PathClass>) - Static method in class qupath.lib.analysis.DelaunayTools: Assign object classifications based upon pre-computed clusters.
nameProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the String property of this ViewTracker.
nameProperty() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
nameProperty() - Method in interface qupath.lib.gui.viewer.tools.PathTool: Property giving the name of the tool
nanoseconds() - Method in class qupath.lib.common.Timeit: Report timings in nanoseconds.
navigationAcceleration - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
navigationAccelerationProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Apply acceleration/deceleration effects when holding and releasing navigation key.
navigationSpeed - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
navigationSpeedProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Percentage to scale navigation speed.
nBins() - Method in class qupath.lib.analysis.stats.Histogram: Total number of histogram bins.
nCensored() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get the number of censored events.
nChannels() - Method in class qupath.lib.images.servers.AbstractImageServer
nChannels() - Method in interface qupath.lib.images.servers.ImageServer: Number of channels (3 for RGB).
nChildObjects() - Method in class qupath.lib.objects.PathObject: Total number of child objects.
nComponents() - Method in class qupath.opencv.ml.objects.features.Preprocessing.PCAProjector: Number of output components.
nCores() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
nCores() - Method in interface qupath.lib.objects.hierarchy.TMAGrid: Total number of cores in the TMA grid.
nDescendants() - Method in class qupath.lib.objects.PathObject: Total number of descendant objects.
NEAREST - Enum constant in enum class qupath.lib.gui.viewer.ImageInterpolation: Nearest neighbor interpolation.
NECROSIS - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Necrosis classification
NECROSIS - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Necrosis classification
negate() - Method in interface qupath.lib.objects.PathObjectPredicates.PathObjectPredicate
negative(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Multiply elements of an array by -1.
NEGATIVE - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

General class to represent something 'negative'
NEGATIVE - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: General class to represent something 'negative'
nEvents() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get the number of events, either observed or censored.
NEVER - Enum constant in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption: Don't use the system menubar for any windows.
NEVER - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay: Never display
newBuilder(Collection<PathObject>) - Static method in class qupath.lib.analysis.DelaunayTools: Create a new DelaunayTools.Builder to compute a triangulation using the specified objects.
newInstance() - Static method in class qupath.lib.plugins.TaskRunnerUtils: Create a new instance.
nFeatures() - Method in class qupath.lib.analysis.features.HaralickFeatures: Total number of Haralick features.
nFeatures() - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor
nFeatures() - Method in class qupath.opencv.ml.objects.features.Normalizer: The total number of features supported by this Normalizer
nFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the number of recorded frames.
nImages() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Return an estimate of the number of images if known, or -1 if unknown.
nImagesLargest() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType: Return the number of images with the largest image size, if known, or -1 if unknown.
nLevels() - Method in class qupath.lib.images.servers.ImageServerMetadata: Get the number of resolution levels.
nMissingValues() - Method in class qupath.lib.analysis.stats.Histogram: Number of NaNs in the input array.
NO - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton: Deprecated.

"No" option
nObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Number of objects in the hierarchy, excluding the root.
nObjects() - Static method in class qupath.lib.scripting.QP: Get a count of the total number of objects in the current hierarchy.
nObserved() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData: Get the number of observed (not censored) events.
NONE - Enum constant in enum class qupath.lib.classifiers.Normalization: Do not normalize features.
NONE - Enum constant in enum class qupath.lib.extension.svg.SvgTools.SvgBuilder.ImageIncludeType: Do not include images.
NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType: Don't check for any updates automatically
NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes: Do not show detections
NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting: Do not set the image type
NONE - Enum constant in enum class qupath.opencv.tools.LocalNormalization.NormalizationType: No local normalization
nonModal() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify that the dialog should be non-modal.
Normalization - Enum Class in qupath.lib.classifiers: Methods for normalizing features.
normalize(Mat, Normalizer) - Static method in class qupath.opencv.ml.objects.features.Preprocessing: Apply a Normalizer to new training data samples.
normalize(Normalization) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder: Define normalization type.
Normalize() - Constructor for class qupath.opencv.ops.ImageOps.Normalize
NORMALIZED - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode: Normalized bin counts, so that the sum of all counts is 1.0.
normalizeFeature(int, double) - Method in class qupath.opencv.ml.objects.features.Normalizer: Normalize a single feature.
normalizeFloats(boolean) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
Normalizer - Class in qupath.opencv.ml.objects.features: Class to help with simple feature normalization, by adding an offset and then multiplying by a scaling factor.
noSelection() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Returns true if no objects are selected.
nResolutions() - Method in class qupath.lib.images.servers.AbstractImageServer
nResolutions() - Method in interface qupath.lib.images.servers.ImageServer: Number of resolutions for the image.
nTimepoints() - Method in class qupath.lib.images.servers.AbstractImageServer
nTimepoints() - Method in interface qupath.lib.images.servers.ImageServer: Number of time points in a time series.
nTimepoints() - Method in class qupath.lib.images.servers.PixelCalibration: Get the number of known time points.
NUCLEI_AND_BOUNDARIES - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode: Show both cell boundaries and cell nuclei, where available.
NUCLEI_ONLY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
NUCLEI_ONLY - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode: Show only cell nuclei.
NUCLEUS - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments: Nucleus only
NUCLEUS_CELL_RATIO - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Nucleus/cell area ratio (only relevant to cell objects).
NULL_CLASS - Static variable in class qupath.lib.objects.classes.PathClass: Default PathClass that represents no classification.
numCommandThreadsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Property specifying the preferred number of threads QuPath should use for multithreaded commands.
numDimensions() - Method in class qupath.opencv.dnn.DnnShape: The total number of dimensions, i.e.
NumericParameter<S> - Class in qupath.lib.plugins.parameters: Abstract parameter to represent a numeric value.
numNaNs(double[]) - Static method in class qupath.lib.common.GeneralTools: Count the number of NaN values in an array.
NumpyTools - Class in qupath.opencv.tools: Read .npy and .npz files from NumPy.
NumpyTools() - Constructor for class qupath.opencv.tools.NumpyTools
numThreads - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
nValues() - Method in class qupath.lib.analysis.stats.Histogram: Number of values represented in the histogram (i.e.
nVertices() - Method in class qupath.lib.roi.AreaROI: Get the number of vertices used to represent this area.
nVertices() - Method in class qupath.lib.roi.PolygonROI: Get the total number of vertices in the polygon.
nZSlices() - Method in class qupath.lib.images.servers.AbstractImageServer
nZSlices() - Method in interface qupath.lib.images.servers.ImageServer: Number of slices in a z-stack.

O

OBJECT_IMPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
ObjectClassifier<T> - Interface in qupath.lib.classifiers.object: Interface defining object classifiers, which assign PathClasses to PathObjects.
ObjectClassifierCommand - Class in qupath.process.gui.commands: Command used to create and show a suitable dialog box for interactive display of OpenCV classifiers.
ObjectClassifierCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.ObjectClassifierCommand: Constructor.
ObjectClassifierLoadCommand - Class in qupath.process.gui.commands: Command to apply a pre-trained object classifier to an image.
ObjectClassifierLoadCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.ObjectClassifierLoadCommand: Constructor.
ObjectClassifiers - Class in qupath.lib.classifiers.object: Helper class for creating ObjectClassifiers.
ObjectClassifiers() - Constructor for class qupath.lib.classifiers.object.ObjectClassifiers
ObjectClassifiers.ClassifyByMeasurementBuilder<T> - Class in qupath.lib.classifiers.object: Builder to create a simple ObjectClassifier that assigns a classification based upon whether the measurement of an object is above, equal to or below a specified threshold.
ObjectClassifiers.ObjectClassifierTypeAdapterFactory - Class in qupath.lib.classifiers.object: TypeAdapterFactory to help with serializing ObjectClassifiers to and from JSON.
objectCountPostfix() - Method in class qupath.lib.objects.PathObject
ObjectDescriptionPane<T> - Class in qupath.lib.gui.panes: Wraps a pane used to display an object description, if one is available.
ObjectDetector<T> - Interface in qupath.lib.plugins: Minimal interface that may be used to plugins that perform detection within a specified ROI and using a specified ImageData with set parameters.
ObjectMeasurements - Class in qupath.lib.analysis.features: Experimental class to generate object measurements.
ObjectMeasurements() - Constructor for class qupath.lib.analysis.features.ObjectMeasurements
ObjectMeasurements.Compartments - Enum Class in qupath.lib.analysis.features: Cell compartments.
ObjectMeasurements.Measurements - Enum Class in qupath.lib.analysis.features: Requested intensity measurements.
ObjectMeasurements.ShapeFeatures - Enum Class in qupath.lib.analysis.features: Standard measurements that may be computed from shapes.
ObjectMerger - Class in qupath.lib.objects.utils: Helper class for merging objects using different criteria.
ObjectPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
ObjectsMenuActions - Class in qupath.lib.gui.actions.menus
ObjectsMenuActions.Actions - Class in qupath.lib.gui.actions.menus
ObjectsMenuActions.AnnotationActions - Class in qupath.lib.gui.actions.menus
ObjectsMenuActions.DeleteActions - Class in qupath.lib.gui.actions.menus
ObjectsMenuActions.LockActions - Class in qupath.lib.gui.actions.menus
ObjectsMenuActions.SelectActions - Class in qupath.lib.gui.actions.menus
ObjectTreeBrowser - Class in qupath.lib.gui.panes: Simple browser for exploring fields (including private fields) within an object by reflection.
ObjectTreeBrowser() - Constructor for class qupath.lib.gui.panes.ObjectTreeBrowser
ObservableMeasurementTableData - Class in qupath.lib.gui.measure: A table data model to supply observable measurements of PathObjects.
ObservableMeasurementTableData() - Constructor for class qupath.lib.gui.measure.ObservableMeasurementTableData
OD_Normalized - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: RGB values normalized to OD vector (to reduce intensity information)
of(long...) - Static method in class qupath.opencv.dnn.DnnShape: Create a new DnnShape with the specified dimension lengths.
OFF - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: Turn off logging
OMEPixelParser - Class in qupath.lib.images.servers.bioformats: This class can parse raw bytes into a BufferedImage.
OMEPixelParser.Builder - Class in qupath.lib.images.servers.bioformats: Builder for instances of OMEPixelParser.
OMEPyramidWriter - Class in qupath.lib.images.writers.ome: Write OME-TIFF files based on QuPath ImageServers.
OMEPyramidWriter.Builder - Class in qupath.lib.images.writers.ome: Builder class to define parameters when exporting an image region as OME-TIFF, possibly as an image pyramid.
OMEPyramidWriter.ChannelExportType - Enum Class in qupath.lib.images.writers.ome: Enum representing different ways in which channels may be written to a file.
OMEPyramidWriter.CompressionType - Enum Class in qupath.lib.images.writers.ome: Preferred compression type when using Bio-Formats.
OMEPyramidWriter.OMEPyramidSeries - Class in qupath.lib.images.writers.ome: Class representing a single series to write to an OME-TIFF.
OMEPyramidWriterCommand - Class in qupath.lib.images.writers.ome: OME TIFF writer command capable of exporting image pyramids based on QuPath ImageServers.
OMEPyramidWriterCommand(QuPathGUI) - Constructor for class qupath.lib.images.writers.ome.OMEPyramidWriterCommand: Constructor.
OMETiffWriter - Class in qupath.lib.images.writers.ome: ImageWriter for writing OME-TIFF images.
OMETiffWriter() - Constructor for class qupath.lib.images.writers.ome.OMETiffWriter
opacityProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions: Property representing the global opacity for overlay drawing.
OPEN_IMAGE - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
OPEN_IMAGE_OR_URL - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
opencl() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Specify OpenCL target.
opencl16() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Specify OpenCL target with 16-bit floating point.
OpenCVClassifiers - Class in qupath.opencv.ml: QuPath wrappers for OpenCV classifiers, which are instances of StatModel.
OpenCVClassifiers() - Constructor for class qupath.opencv.ml.OpenCVClassifiers
OpenCVClassifiers.BoostClassifier - Class in qupath.opencv.ml: Classifier based on Boost.
OpenCVClassifiers.DTreesClassifier - Class in qupath.opencv.ml: Classifier based on DTrees.
OpenCVClassifiers.EMClusterer - Class in qupath.opencv.ml: Clusterer based on EM.
OpenCVClassifiers.LogisticRegressionClassifier - Class in qupath.opencv.ml: Classifier based on LogisticRegression.
OpenCVClassifiers.NormalBayesClassifierCV - Class in qupath.opencv.ml: Classifier based on NormalBayesClassifier.
OpenCVClassifiers.OpenCVStatModel - Class in qupath.opencv.ml: Wrapper class for a StatModel, which standardizes how training may be performed and parameters can be set.
OpenCVClassifiers.RTreesClassifier - Class in qupath.opencv.ml: Classifier based on RTrees.
OpenCVClassifiers.SVMClassifierCV - Class in qupath.opencv.ml: Classifier based on SVM.
OpenCVClassifiers.SVMSGDClassifierCV - Class in qupath.opencv.ml: Classifier based on SVMSGD.
OpenCVDnn - Class in qupath.opencv.dnn: Wrapper for an OpenCV Net, including essential metadata about how it should be used.
OpenCVDnn() - Constructor for class qupath.opencv.dnn.OpenCVDnn
OpenCVDnn.Builder - Class in qupath.opencv.dnn: Helper class to build an OpenCVDnn.
OpenCVDnn.ModelType - Enum Class in qupath.opencv.dnn: Enum representing different classes of Model supported by OpenCV.
OpenCVDnnModelBuilder - Class in qupath.opencv.dnn: A DnnModelBuilder implementation that uses OpenCV's DNN module to build a Net.
OpenCVDnnModelBuilder() - Constructor for class qupath.opencv.dnn.OpenCVDnnModelBuilder
OpenCVMLClassifier<T> - Class in qupath.opencv.ml.objects: An ObjectClassifier that uses an OpenCVClassifiers.OpenCVStatModel for classification.
OpenCVModelObjectClassifier - Class in qupath.opencv.dnn: Initial implementation of a patch-based ObjectClassifier using an OpenCV-compatible DNN.
OpenCVModelObjectClassifier(PathObjectFilter, OpenCVDnn, List<PathClass>, int, int, double) - Constructor for class qupath.opencv.dnn.OpenCVModelObjectClassifier: Constructor.
OpenCVProcessor - Class in qupath.lib.experimental.pixels: Class to generate a PixelProcessor when using OpenCV for the primary image representation.
OpenCVProcessor() - Constructor for class qupath.lib.experimental.pixels.OpenCVProcessor
OpenCVStatModel() - Constructor for class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
OpenCVTools - Class in qupath.opencv.tools: Collection of static methods to help with using OpenCV from Java.
OpenCVTools() - Constructor for class qupath.opencv.tools.OpenCVTools
OpenCVTools.IndexedPixel - Class in qupath.opencv.tools: Class representing the indices of a pixel and its value.
OpenCVTypeAdapter() - Constructor for class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdapter
OpenCVTypeAdapters - Class in qupath.opencv.io: Helper classes for combining OpenCV's JSON serialization with Gson's.
OpenCVTypeAdapters() - Constructor for class qupath.opencv.io.OpenCVTypeAdapters
OpenCVTypeAdapters.OpenCVTypeAdapter<T> - Class in qupath.opencv.io: TypeAdapter that helps include OpenCV-based objects within a Java object being serialized to JSON.
OpenCVTypeAdapters.OpenCVTypeAdaptorFactory - Class in qupath.opencv.io: TypeAdapterFactory that helps make OpenCV's serialization methods more compatible with custom JSON/Gson serialization.
OpenCVTypeAdaptorFactory() - Constructor for class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdaptorFactory
openFile(File) - Static method in class qupath.lib.gui.tools.GuiTools: Try to open a file in the native application.
openImage(String) - Static method in class qupath.lib.images.servers.openslide.jna.OpenSlideLoader: Open an image using OpenSlide, returning an OpenSlide instance to access pixels and metadata.
openImage(QuPathViewer, String) - Method in class qupath.lib.gui.QuPathGUI
openImage(QuPathViewer, String, boolean, boolean) - Method in class qupath.lib.gui.QuPathGUI: Open a new whole slide image server, or ImageData.
openImageEntry(ProjectImageEntry<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI: Open the image represented by the specified ProjectImageEntry.
openInBrowser(String) - Static method in class qupath.lib.gui.QuPathGUI: Try to launch a browser window for a specified URL.
opening(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D morphological opening filter.
openingByReconstruction(ImageProcessor, double) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Apply opening by reconstruction, with the specified minimum filter radius.
openingFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a 2D opening filter (erosion followed by dilation) to all channels of an image.
openSavedData(QuPathViewer, File, boolean, boolean) - Method in class qupath.lib.gui.QuPathGUI: Open a saved data file within a particular viewer, optionally keeping the same ImageServer as is currently open.
OpenSlide - Class in qupath.lib.images.servers.openslide.jna: Minimal Java wrapper for OpenSlide.
openslide_close(long) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_detect_vendor(String) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_associated_image_dimensions(long, String, long[], long[]) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_associated_image_names(long) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_error(long) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_icc_profile_size(long) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_level_count(long) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_level_dimensions(long, int, long[], long[]) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_level_downsample(long, int) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_property_names(long) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_property_value(long, String) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_get_version() - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_open(String) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_read_associated_image(long, String, int[]) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_read_icc_profile(long, byte[]) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
openslide_read_region(long, int[], long, long, int, long, long) - Method in interface qupath.lib.images.servers.openslide.jna.OpenSlideJNA
OpenSlide.OpenSlideDisposedException - Exception Class in qupath.lib.images.servers.openslide.jna: Exception thrown whenever a request is made after the OpenSlide object has been closed.
OpenSlideDisposedException() - Constructor for exception class qupath.lib.images.servers.openslide.jna.OpenSlide.OpenSlideDisposedException
OpenSlideExtension - Class in qupath.ext.openslide
OpenSlideExtension() - Constructor for class qupath.ext.openslide.OpenSlideExtension
OpenslideImageServer - Class in qupath.lib.images.servers.openslide: ImageServer implementation using OpenSlide.
OpenslideImageServer(URI, String...) - Constructor for class qupath.lib.images.servers.openslide.OpenslideImageServer: Create an ImageServer using OpenSlide for the specified file.
OpenSlideJNA - Interface in qupath.lib.images.servers.openslide.jna: JNA interface for OpenSlide.
OpenSlideLoader - Class in qupath.lib.images.servers.openslide.jna: Static helper class to manage loading the OpenSlide library.
OpenSlideLoader() - Constructor for class qupath.lib.images.servers.openslide.jna.OpenSlideLoader
openslidePathProperty - Variable in class qupath.ext.openslide.OpenSlideExtension
OpenslideServerBuilder - Class in qupath.lib.images.servers.openslide: Builder for Openslide ImageServer.
OpenslideServerBuilder() - Constructor for class qupath.lib.images.servers.openslide.OpenslideServerBuilder
Optical_density_sum - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Sum of red, green and blue optical densities
opticalDensitySum(int, double[]) - Static method in class qupath.lib.color.ColorTransformer: Extract optical density sum value from a packed RGB pixel.
opticalDensitySum(int, double[], double[], double[]) - Static method in class qupath.lib.color.ColorTransformer: Extract optical density sum value from a packed RGB pixel.
options(OverlayOptions) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify the overlay options to control display.
or(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Compute the bitwise OR of two arrays.
or(PathObjectPredicates.PathObjectPredicate) - Method in interface qupath.lib.objects.PathObjectPredicates.PathObjectPredicate: Combine with another PathObjectPredicates.PathObjectPredicate through OR.
orElse(OutputHandler<S, T, U>) - Method in interface qupath.lib.experimental.pixels.OutputHandler: Append a second output handler to this one, but only call it if this one returns false.
Original - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Original image
OTHER - Enum constant in enum class qupath.lib.images.ImageData.ImageType: Other image type, not covered by any of the alternatives above.
OTHER - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Other classification
OTHER - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Other classification
OTHER - Static variable in class qupath.lib.scripting.QP: Any other image type (neither brightfield nor fluorescence)
OTHER_STRUCTURE_CHANGE - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: A more complex structural change was made than simply either adding or removing objects
output(String, long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shape as a long array for a single named output.
output(String, DnnShape) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shape for a single named output.
outputChannels(Collection<ImageChannel>) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Specify channels for output.
outputChannels(ImageChannel...) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Specify channels for output.
outputChannelType(ImageServerMetadata.ChannelType) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the channel type for the output.
outputClasses(Map<Integer, PathClass>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the classifications for the output as a map.
outputClasses(PathClass...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the classifications for the output as an array.
outputClassNames(String...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the classifications for the output as an array of classification names.
outputClassNames(Map<Integer, String>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the classifications for the output as a map with string values.
outputHandler(OutputHandler<S, T, U>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the output handler.
OutputHandler<S,T,U> - Interface in qupath.lib.experimental.pixels: A functional interface for handling the output of a Processor.
OutputHandler.ObjectOutputHandler<S,T,U> - Class in qupath.lib.experimental.pixels
OutputHandler.OutputToObjectConverter<S,T,U> - Interface in qupath.lib.experimental.pixels
outputPath(String) - Method in class qupath.lib.gui.FileCopier: Name of the output directory.
outputPath(Path) - Method in class qupath.lib.gui.FileCopier: Path representing the output directory.
outputPixelType(PixelType) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Output pixel type.
outputs(String...) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Set the layer outputs.
outputs(Map<String, DnnShape>) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shapes for one or more outputs.
outputs(Map<String, DnnShape>) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Set the layer outputs and shapes.
outputShape(long...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the shape for a single output, with the default output name.
overlap(int) - Method in class qupath.lib.images.writers.TileExporter: Define tile overlap (both x and y) in pixel units at the export resolution.
overlap(int, int) - Method in class qupath.lib.images.writers.TileExporter: Define tile overlap (x and y separately) in pixel units at the export resolution.
overlapsRequest(RegionRequest) - Method in class qupath.lib.regions.RegionRequest: Returns true if the region specified by this request overlaps with that of another request.
OverlayActions - Class in qupath.lib.gui.actions: Actions that interact with OverlayOptions.
OverlayActions(OverlayOptions) - Constructor for class qupath.lib.gui.actions.OverlayActions
overlayOpacity(double) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify the opacity for overlay layers.
OverlayOptions - Class in qupath.lib.gui.viewer: Default class for storing overlay display options.
OverlayOptions() - Constructor for class qupath.lib.gui.viewer.OverlayOptions: Constructor, using default values.
OverlayOptions(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.OverlayOptions: Constructor, initializing values based on an existing OverlayOptions object.
OverlayOptions.DetectionDisplayMode - Enum Class in qupath.lib.gui.viewer: Display modes for cells and other detections.
overrideSystemMenuBarProperty() - Static method in class qupath.lib.gui.prefs.SystemMenuBar: Property requesting that the system menubar should never be used for managed menubars.
OVERVIEW - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
owner(Window) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the dialog owner.

P

packARGB(int, int, int, int) - Static method in class qupath.lib.common.ColorTools: Make a packed ARGB value from specified input values.
packClippedARGB(int, int, int, int) - Static method in class qupath.lib.common.ColorTools: Make a packed ARGB value from specified input values, clipping to the range 0-255.
packClippedRGB(int, int, int) - Static method in class qupath.lib.common.ColorTools: Make a packed RGB value from specified input values, clipping to the range 0-255.
packRGB(int, int, int) - Static method in class qupath.lib.common.ColorTools: Make a packed RGB value from specified input values.
pad2D(int, int) - Method in class qupath.lib.regions.RegionRequest: Add symmetric padding to the x and y dimensions of a request.
pad2D(Padding) - Method in class qupath.lib.regions.RegionRequest: Add symmetric padding to the x and y dimensions of a request.
padAndApply(ImageOp, Mat) - Static method in class qupath.opencv.ops.ImageOps: Apply an op after adding symmetric (reflection) padding.
padAndApply(ImageOp, Mat, int) - Static method in class qupath.opencv.ops.ImageOps: Apply an op after adding specified padding.
PaddedOp() - Constructor for class qupath.opencv.ops.ImageOps.PaddedOp
padding(int) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the padding to use when extracting regions, using a symmetric padding.
padding(Padding) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the padding to use when extracting regions.
Padding - Class in qupath.lib.regions: Requested padding for a 2D image.
paddingXY(int) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Specify the number of pixels that the input image is padded (left, right, above, below).
paintComponent(Graphics) - Method in class qupath.lib.gui.viewer.QuPathViewer
paintConnections(PathObjectConnections, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Paint connections between objects (e.g.
paintHandles(List<Point2>, Graphics2D, double, double, Color, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Paint the handles onto a Graphics object, if we have a suitable (non-point) ROI.
paintHandles(RoiEditor, Graphics2D, double, double, Color, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Paint the handles onto a Graphics object, if we have a suitable (non-point) ROI.
paintImage(Canvas, Image) - Static method in class qupath.lib.gui.tools.GuiTools: Paint an image centered within a canvas, scaled to be as large as possible while maintaining its aspect ratio.
paintImage(Canvas, Image, double) - Static method in class qupath.lib.gui.tools.GuiTools: Paint an image centered within a canvas, scaled by the specified scale factor.
paintObject(PathObject, Graphics2D, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Paint an object (or, more precisely, its ROI).
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.GridOverlay
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in interface qupath.lib.gui.viewer.overlays.PathOverlay: Paint the overlay to a graphics object.
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.TMAGridOverlay
paintRegion(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
paintRegion(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer) - Method in interface qupath.lib.gui.images.stores.ImageRegionRenderer: Paint an image region.
paintRegionARGB(int[], long, long, int, int, int) - Method in class qupath.lib.images.servers.openslide.jna.OpenSlide
paintRegionCompletely(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, ImageObserver, ImageRenderer, long) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Similar to paintRegion, but wait until all the tiles have arrived (or abort if it is taking too long)
paintRegionCompletely(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, ImageObserver, ImageRenderer, long) - Method in interface qupath.lib.gui.images.stores.ImageRegionRenderer: Similar to ImageRegionRenderer.paintRegion(ImageServer, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer), but wait until all the tiles have arrived (or abort if it is taking too long).
paintSelectedBoundsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Specify whether the bounding box of selected objects should be painted.
paintShape(Shape, Graphics2D, Color, Stroke, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Paint the specified shape with specified stroke and fill colors.
paintSpecifiedObjects(Graphics2D, Collection<? extends PathObject>, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Paint the specified objects.
paintTileBorders - Static variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
paintTMAGrid(Graphics2D, TMAGrid, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter: Paint the specified tissue microarray grid.
paintViewer(Graphics, int, int) - Method in class qupath.lib.gui.viewer.QuPathViewer
PaneTools - Class in qupath.lib.gui.tools: Deprecated.
since v0.5.0; GridPaneUtils contains many of the features.
PaneTools() - Constructor for class qupath.lib.gui.tools.PaneTools: Deprecated.
parallelize() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Parallelize tile export, if possible.
parallelize(boolean) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify if tile export should be parallelized if possible, with the default number of threads (current 4).
parallelize(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify if tile export should be parallelized if possible, with the requested number of threads.
ParallelTileObject - Class in qupath.lib.plugins: A temporary object, used during parallel processing to represent a tile currently being used for object detection.
ParallelTileObject.Status - Enum Class in qupath.lib.plugins: Current processing status for the tile.
Parameter<S> - Interface in qupath.lib.plugins.parameters: Interface defining algorithm parameters, which need to be displayed to users somehow.
parameterChanged(ParameterList, String, boolean) - Method in class qupath.lib.gui.charts.HistogramDisplay
parameterChanged(ParameterList, String, boolean) - Method in interface qupath.lib.plugins.parameters.ParameterChangeListener: Notify listener that a parameter value has changed.
ParameterChangeListener - Interface in qupath.lib.plugins.parameters: Interface for objects that need to be notified when parameters have their values changed.
Parameterizable - Interface in qupath.lib.plugins.parameters: Interface for indicating that the implementing class takes adjustable parameters.
ParameterList - Class in qupath.lib.plugins.parameters: A collection of Parameters, which can be used for analysis & queried to construct appropriate GUIs.
ParameterList() - Constructor for class qupath.lib.plugins.parameters.ParameterList
ParameterPanelFX - Class in qupath.lib.gui.dialogs: A panel for displaying a list of parameters suitably to aid with creating JavaFX GUIs.
ParameterPanelFX(ParameterList) - Constructor for class qupath.lib.gui.dialogs.ParameterPanelFX: Create a ParameterPanelFX.
Parameters<S,T> - Class in qupath.lib.experimental.pixels: Parameters for use with a PixelProcessor.
Parameters.Builder<S,T> - Class in qupath.lib.experimental.pixels: Builder class for Parameters.
parametersInitialized - Variable in class qupath.imagej.detect.cells.WatershedCellDetection
params - Variable in class qupath.lib.plugins.AbstractInteractivePlugin
parent(Window) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Set the parent window.
parent(Window) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Set the parent window.
parent(Window) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the parent window.
parent(PathObject) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Set the parent object.
parentObjects(Collection<? extends PathObject>) - Method in class qupath.lib.images.writers.TileExporter: Specify parent objects to define tiles.
parentObjects(Predicate<PathObject>) - Method in class qupath.lib.images.writers.TileExporter: Specify a filter to extract parent objects to define tiles.
parentProxy(PathObject) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Optionally set a temporary object to use as a parent.
parse(byte[][], int, int, int, ColorModel) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser: Creates a BufferedImage from a 2-dimensional byte array.
parse(String) - Static method in class qupath.lib.common.Version: Parse a Version object representing a semantic version number from a String.
parseAnnotations(Action, AnnotatedElement) - Static method in class qupath.lib.gui.actions.ActionTools: Parse annotations relating to an action, updating the properties of the action.
parseAnnotations(Action, AnnotatedElement, String) - Static method in class qupath.lib.gui.actions.ActionTools: Parse annotations relating to an action, updating the properties of the action with an optional base menu.
parseArgStringValues(String) - Static method in class qupath.lib.common.GeneralTools: Parse the contents of a JSON String.
parseArgument(ImageData<BufferedImage>, String) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
parseArgument(ImageData<BufferedImage>, String) - Method in class qupath.imagej.gui.ImageJMacroRunner
parseArgument(ImageData<BufferedImage>, String) - Method in class qupath.opencv.CellCountsCV
parseArgument(ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractInteractivePlugin
parseArgument(ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractPlugin: Parse the input argument, returning 'true' if the argument is valid and it's possible to run the plugin.
parseColorDeconvolutionStainsArg(String) - Static method in class qupath.lib.color.ColorDeconvolutionStains: Parse color deconvolution stains from a JSON String, with keys 'Stain 1', 'Stain 2', (optionally) 'Stain 3' and 'Background'.
parseDisplaySettings(JsonElement) - Static method in class qupath.lib.display.settings.DisplaySettingUtils: Parse the JSON element into an image display settings object, if possible.
parseDisplaySettings(Path) - Static method in class qupath.lib.display.settings.DisplaySettingUtils: Parse the JSON element into an image display settings object.
parseLayers(Net, int, int, int, int) - Static method in class qupath.opencv.dnn.DnnTools: Parse the layers for a Net, which allows inspection of names and sizes.
parseNumeric(List<String>, boolean) - Static method in class qupath.lib.io.TMAScoreImporter: Parse numeric values from a list of strings.
parseObjectsFromGeoJSON(JsonElement) - Static method in class qupath.lib.io.GsonTools: Attempt to read PathObjects from a JsonElement, interpreting it as GeoJSON.
parseRegion(String, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing: Attempt to parse a RegionRequest corresponding to an image region from the file name.
parseShape(MatShapeVector) - Static method in class qupath.opencv.dnn.DnnTools: Extract Mat dimensions from a MatShapeVector.
parseStainValues(Locale, String) - Static method in class qupath.lib.color.ColorDeconvolutionStains: Parses 3 values, suitable for use as a stain vector
parseStrings(StringVector) - Static method in class qupath.opencv.dnn.DnnTools: Extract Strings from a StringVector.
parseTMALabelString(String) - Static method in class qupath.lib.objects.PathObjectTools: Parse a string input representing potential TMA core labels.
parseTransformMatrix(String) - Static method in class qupath.lib.roi.GeometryTools: Parse the matrix (String) to create and return an AffineTransformation.
paste() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
paste() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request paste from the system clipboard.
paste() - Method in class qupath.lib.gui.scripting.TextAreaControl
PASTE - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
PASTE_TO_PLANE - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
pasteAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
pasteAndEscapeAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
pasteFromClipboard(QuPathGUI, boolean) - Static method in class qupath.lib.gui.commands.Commands: Attempt to paste objects from the system clipboard to the current image, if available; otherwise, check for text on the clipboard and paste it into a new script editor tab
pasteFromClipboard(ScriptEditorControl<?>, boolean) - Static method in class qupath.lib.gui.scripting.DefaultScriptEditor
PatchClassifierParams - Class in qupath.opencv.ml: Parameters required to build a classifier that operates on an image patch.
PatchClassifierParams.Builder - Class in qupath.opencv.ml: Builder class to create PatchClassifierParams.
patchSize(int) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the requested square patch size.
patchSize(int, int) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the requested patch size.
PathAnnotationObject - Class in qupath.lib.objects: An annotation PathObject.
PathAnnotationObject() - Constructor for class qupath.lib.objects.PathAnnotationObject: Default constructor.
PathCellObject - Class in qupath.lib.objects: A subclass of a PathDetectionObject, which also supports storing an (optional) extra ROI to represent the cell nucleus.
PathCellObject() - Constructor for class qupath.lib.objects.PathCellObject: Default constructor.
PathClass - Class in qupath.lib.objects.classes: Representation of an object's classification - which can be defined using any unique string identifier (e.g.
PathClass.StandardPathClasses - Class in qupath.lib.objects.classes: Enum representing standard classifications.
PathClassFactory - Class in qupath.lib.objects.classes: Deprecated.
since v0.4.0 in favor of methods added to PathClass directly.
PathClassFactory.StandardPathClasses - Enum Class in qupath.lib.objects.classes: Deprecated.

Enum representing standard classifications.
PathClassTools - Class in qupath.lib.objects.classes: Static methods for use with PathClass objects.
PathDetectionObject - Class in qupath.lib.objects: A detection PathObject.
PathDetectionObject() - Constructor for class qupath.lib.objects.PathDetectionObject: Default constructor.
PathDetectionObject(ROI, PathClass) - Constructor for class qupath.lib.objects.PathDetectionObject: Create a new PathDetectionObject with a float measurement list.
PathHierarchyImageServer - Class in qupath.lib.gui.images.servers: A special ImageServer implementation that doesn't have a backing image, but rather constructs tiles on request from a PathObjectHierarchy and its detection objects.
PathHierarchyImageServer(ImageData<BufferedImage>, OverlayOptions) - Constructor for class qupath.lib.gui.images.servers.PathHierarchyImageServer: Constructor.
PathImage<T> - Interface in qupath.lib.images: Interface used when needing to associate pixel data with information regarding the image from which it was obtained.
PathInteractivePlugin<T> - Interface in qupath.lib.plugins: Interface to define a PathPlugin that requires a list of (user-adjustable) parameters.
PathIO - Class in qupath.lib.io: Primary class for loading/saving ImageData objects.
PathIO.GeoJsonExportOptions - Enum Class in qupath.lib.io: Options to customize the export of PathObjects as GeoJSON.
pathMemoization - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
PathObject - Class in qupath.lib.objects: Fundamental object of interest in QuPath.
PathObject() - Constructor for class qupath.lib.objects.PathObject: Default constructor.
PathObject(MeasurementList) - Constructor for class qupath.lib.objects.PathObject: Create a PathObject with a specific measurement list.
PathObjectConnectionGroup - Interface in qupath.lib.objects: Interface defining a basic structure to represent relationships between PathObjects that do not fit with the parent-child idea of the PathObjectHierarchy.
PathObjectConnections - Class in qupath.lib.objects: Data structure for storing multiple PathObjectConnectionGroups.
PathObjectConnections() - Constructor for class qupath.lib.objects.PathObjectConnections: Default constructor.
PathObjectFilter - Enum Class in qupath.lib.objects: Enumeration of filters (predicates) that can be used to select objects based on their type.
PathObjectGridView - Class in qupath.lib.gui.commands: Grid display of objects.
PathObjectGridView.GridDisplaySize - Enum Class in qupath.lib.gui.commands
PathObjectHierarchy - Class in qupath.lib.objects.hierarchy: A basic hierarchy in which to store PathObjects.
PathObjectHierarchy() - Constructor for class qupath.lib.objects.hierarchy.PathObjectHierarchy: Default constructor, creates an empty hierarchy.
PathObjectHierarchyEvent - Class in qupath.lib.objects.hierarchy.events: An event class for passing on information about modifications to a PathObjectHierarchy.
PathObjectHierarchyEvent.HierarchyEventType - Enum Class in qupath.lib.objects.hierarchy.events: Enum representing different ways in which the hierarchy may have been updated.
PathObjectHierarchyListener - Interface in qupath.lib.objects.hierarchy.events: A listener for modifications to a PathObjectHierarchy (i.e.
PathObjectHierarchyView - Class in qupath.lib.gui.panes: Component for showing a tree-based view of the object hierarchy.
PathObjectHierarchyView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.PathObjectHierarchyView: Constructor.
PathObjectHierarchyView(QuPathGUI, ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.PathObjectHierarchyView: Constructor.
PathObjectLabels - Class in qupath.lib.gui.tools: Create standardized ListCell and TreeCell instances for displaying a PathObject, or a generic pane to use elsewhere.
PathObjectLabels() - Constructor for class qupath.lib.gui.tools.PathObjectLabels
PathObjectLabels.PathObjectMiniPane - Class in qupath.lib.gui.tools: Manage a small pane that can be used to display a PathObject.
PathObjectMiniPane(Function<PathObject, String>) - Constructor for class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane: Constructor using a custom string extraction function.
PathObjectPainter - Class in qupath.lib.gui.viewer: Static methods to assist with painting PathObjects.
PathObjectPredicates - Class in qupath.lib.objects: Classes to define JSON-serializable Predicates for PathObjects.
PathObjectPredicates() - Constructor for class qupath.lib.objects.PathObjectPredicates
PathObjectPredicates.PathObjectPredicate - Interface in qupath.lib.objects: A JSON-serializable Predicate for use with PathObjects.
PathObjectReader - Interface in qupath.lib.objects: Interface for classes capable of reading PathObjects from some source.
pathObjects(Collection<? extends PathObject>) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify a collection of objects to export.
pathObjects(PathObject...) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify an array of objects to export.
PathObjects - Class in qupath.lib.objects: Helper class to create PathObject.
PathObjects() - Constructor for class qupath.lib.objects.PathObjects
PathObjectSelectionListener - Interface in qupath.lib.objects.hierarchy.events: A listener to selection changes within a PathObjectSelectionModel.
PathObjectSelectionModel - Class in qupath.lib.objects.hierarchy.events: Model for handling selection of single and multiple PathObjects.
PathObjectSelectionModel() - Constructor for class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
PathObjectTools - Class in qupath.lib.objects: A collection of static methods to help work with PathObjects.
PathObjectTools() - Constructor for class qupath.lib.objects.PathObjectTools
PathOverlay - Interface in qupath.lib.gui.viewer.overlays: Interface defining an overlay to paint on top of a viewer.
PathPlugin<T> - Interface in qupath.lib.plugins: Primary interface for defining a 'plugin' command.
PathPrefs - Class in qupath.lib.gui.prefs: Central storage of QuPath preferences.
PathPrefs() - Constructor for class qupath.lib.gui.prefs.PathPrefs
PathPrefs.AutoUpdateType - Enum Class in qupath.lib.gui.prefs: Options for automatic updating checking of QuPath and/or extensions.
PathPrefs.DetectionTreeDisplayModes - Enum Class in qupath.lib.gui.prefs: Enum for different ways that detections can be displayed in lists and trees.
PathPrefs.FontSize - Enum Class in qupath.lib.gui.prefs: Enum to control font size.
PathPrefs.ImageTypeSetting - Enum Class in qupath.lib.gui.prefs: Enum defining how setting the image type should be handled for new images.
PathROIObject - Class in qupath.lib.objects: Abstract class used for PathObjects that have ROIs associated with them.
PathRootObject - Class in qupath.lib.objects: The root object used at the base of a PathObjectHierarchy.
PathRootObject() - Constructor for class qupath.lib.objects.PathRootObject
paths(Path...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the URIs as path objects.
PathTableData<T> - Interface in qupath.lib.gui.measure: Interface defining a table model that enables measurement names to be mapped to string or numeric values (as appropriate).
PathTask - Interface in qupath.lib.plugins: Helper interface to define plugin tasks that require post-processing on a specific thread (i.e.
PathTileObject - Class in qupath.lib.objects: A subclass of PathDetectionObject, generally used to represent an image region that doesn't (in itself) correspond to any particularly interesting structure.
PathTileObject() - Constructor for class qupath.lib.objects.PathTileObject: Default constructor.
PathTileObject(ROI) - Constructor for class qupath.lib.objects.PathTileObject
PathTool - Interface in qupath.lib.gui.viewer.tools: Interface defining how a toolbar tool interacts with a viewer.
PathToolEventHandlers - Class in qupath.lib.gui.viewer.tools.handlers
PathToolEventHandlers() - Constructor for class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
PathTools - Class in qupath.lib.gui.viewer.tools: Default PathTool implementations.
PathTools() - Constructor for class qupath.lib.gui.viewer.tools.PathTools
pca(double, boolean) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder: Perform PCA to reduce features.
pearsonsCorrelation() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions: Create a function to calculate Pearson's correlation coefficient.
PENDING - Enum constant in enum class qupath.lib.plugins.ParallelTileObject.Status: Tile waiting to be processed
PERCENT - Enum constant in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType: Maps contain at least two channels.
percentile(double) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions: Create a function to calculate a percentile.
percentile(double, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Normalize the image, per channel, using low and high percentiles.
percentile(double, double, boolean, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Normalize the image using low and high percentiles.
percentiles(Mat, double...) - Static method in class qupath.opencv.tools.OpenCVTools: Get percentile values for all pixels in a Mat, ignoring NaNs.
physicalMemory() - Static method in class qupath.opencv.tools.OpenCVTools: Get a brief, one-line report on current physical memory use, based on JavaCPP's Pointer class.
pieChart() - Static method in class qupath.lib.gui.charts.Charts: Create a Charts.PieChartBuilder for generating a custom pie chart.
PIXEL - Static variable in class qupath.lib.images.servers.PixelCalibration: String to represent 'pixel' units.
PIXEL_CLASSIFICATION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
pixelCalibration(PixelCalibration, double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Set the pixel calibration, with optional x,y scaling.
PixelCalibration - Class in qupath.lib.images.servers: Class used to represent pixel sizes.
PixelCalibration.Builder - Class in qupath.lib.images.servers: Builder class for PixelCalibration objects.
pixelClassificationFilterRegionProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
PixelClassificationImageServer - Class in qupath.lib.classifiers.pixel: ImageServer that delivers pixels derived from applying a PixelClassifier to another ImageServer.
PixelClassificationImageServer(ImageData<BufferedImage>, PixelClassifier) - Constructor for class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Constructor.
PixelClassificationImageServer(ImageData<BufferedImage>, PixelClassifier, String, ColorModel) - Constructor for class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Constructor.
PixelClassificationMeasurementManager - Class in qupath.opencv.ml.pixel: Helper class to compute area-based measurements for regions of interest based on pixel classification.
PixelClassificationMeasurementManager(ImageServer<BufferedImage>) - Constructor for class qupath.opencv.ml.pixel.PixelClassificationMeasurementManager: Constructor.
PixelClassificationOverlay - Class in qupath.lib.gui.viewer.overlays: PathOverlay that gives the results of pixel classification.
PixelClassifier - Interface in qupath.lib.classifiers.pixel: Interface defining a pixel classifier.
PixelClassifierCommand - Class in qupath.process.gui.commands: Open GUI for the current viewer to train a new pixel classifier.
PixelClassifierCommand() - Constructor for class qupath.process.gui.commands.PixelClassifierCommand
PixelClassifierMetadata - Class in qupath.lib.classifiers.pixel: Metadata to control the behavior of a pixel classifier.
PixelClassifierMetadata.Builder - Class in qupath.lib.classifiers.pixel: Builder to create PixelClassifierMetadata objects.
PixelClassifierPane - Class in qupath.process.gui.commands.ml: Main user interface for interactively training a PixelClassifier.
PixelClassifierPane(QuPathGUI) - Constructor for class qupath.process.gui.commands.ml.PixelClassifierPane: Constructor.
PixelClassifiers - Class in qupath.opencv.ml.pixel: Static methods and classes for working with pixel classifiers.
PixelClassifiers() - Constructor for class qupath.opencv.ml.pixel.PixelClassifiers
PixelClassifierTools - Class in qupath.opencv.ml.pixel: Helper methods for working with pixel classification.
PixelClassifierTools() - Constructor for class qupath.opencv.ml.pixel.PixelClassifierTools
PixelClassifierTools.CreateObjectOptions - Enum Class in qupath.opencv.ml.pixel: Options when creating objects from a pixel classifier.
PixelClassifierTraining - Class in qupath.process.gui.commands.ml: Helper class for training a pixel classifier.
PixelClassifierTraining(ImageDataOp) - Constructor for class qupath.process.gui.commands.ml.PixelClassifierTraining: Create a new pixel classifier helper, to support generating training data.
PixelClassifierTraining.ClassifierTrainingData - Class in qupath.process.gui.commands.ml: Wrapper for training data.
PixelClassifierUI - Class in qupath.process.gui.commands.ml: Helper class for generating standardized UI components for pixel classification.
PixelClassifierUI() - Constructor for class qupath.process.gui.commands.ml.PixelClassifierUI
PixelImageIJ - Class in qupath.imagej.tools: Very simple wrapper that allows some non-ImageJ-oriented QuPath commands to access ImageProcessor pixel values.
PixelImageIJ(ImageProcessor) - Constructor for class qupath.imagej.tools.PixelImageIJ: Constructor.
PixelProcessor<S,T,U> - Class in qupath.lib.experimental.pixels: A class for tiled image processing.
PixelProcessor.Builder<S,T,U> - Class in qupath.lib.experimental.pixels: Builder class for a PixelProcessor
PixelProcessorUtils - Class in qupath.lib.experimental.pixels: Utility functions to help with the PixelProcessor class.
PixelProcessorUtils() - Constructor for class qupath.lib.experimental.pixels.PixelProcessorUtils
pixelSize(double) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the requested pixel size to use with requesting image regions.
pixelSize(double, double) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder: Specify the pixel width and height, used to scale x and y coordinates during conversion (default is 1.0 for both).
pixelSize(PixelCalibration) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: Requested pixel size to determine the resolution of the density map, in calibrated units.
pixelSizeCalibrated() - Method in class qupath.lib.images.servers.ImageServerMetadata: Returns true if pixel width and height calibration information is available for the image.
pixelSizeMicrons(Number, Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the pixel sizes, in microns.
pixelSizeMicrons(Number, Number) - Method in class qupath.lib.images.servers.PixelCalibration.Builder: Specify the pixel width and height in microns (the most common calibration value).
pixelSnapping - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
pixelType(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify the output PixelType as a String, e.g.
pixelType(PixelType) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
pixelType(PixelType) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the bit-depth of the image.
pixelType(PixelType) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify the output PixelType.
PixelType - Enum Class in qupath.lib.images.servers: Image bit-depths and types.
placeholderTextProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the placeholder text to show if no image is available.
PLAIN - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Plain styler (no highlighting)
PLAIN - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
PlainLanguage - Class in qupath.lib.gui.scripting.languages: Class for the representation of plain text in QuPath.
PlainLanguage() - Constructor for class qupath.lib.gui.scripting.languages.PlainLanguage: Constructor for a simple Plain Language.
PlainStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling for plain text (which really means no styling).
PLANAR - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType: Channels are stored as separate image planes ('PLANARCONFIG_SEPARATE').
PLAYBACK_PLAY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
pluginCompleted(String) - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
pluginCompleted(String) - Method in interface qupath.lib.plugins.SimpleProgressMonitor: Notify the monitor that the plugin has completed its work.
plus(Mat, Number) - Static method in class qupath.opencv.tools.GroovyCV: Add an array and a number.
plus(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Add two arrays.
plus(Mat, Scalar) - Static method in class qupath.opencv.tools.GroovyCV: Add an array and a scalar.
PngWriter - Class in qupath.lib.images.writers: ImageWriter implementation to write PNG images using ImageIO.
PngWriter() - Constructor for class qupath.lib.images.writers.PngWriter
Point - Interface in qupath.lib.geom: Simple interface defining a point.
POINT - Enum constant in enum class qupath.lib.roi.interfaces.ROI.RoiType: ROI represents points.
Point2 - Class in qupath.lib.geom: A 2D point (x & y coordinates).
Point2() - Constructor for class qupath.lib.geom.Point2: Default constructor for a point at location (0,0).
Point2(double, double) - Constructor for class qupath.lib.geom.Point2: Point constructor.
PointIO - Class in qupath.lib.io: Helper class for reading/writing point objects in terms of their x,y coordinates.
PointIO() - Constructor for class qupath.lib.io.PointIO
pointRadius - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
pointRadiusProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Radius of the circle used to draw individual points in a point annotation (in pixels).
POINTS - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Points annotation and counting tool
POINTS_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
POINTS_TOOL - Variable in class qupath.lib.gui.ToolManager
PointsROI - Class in qupath.lib.roi: ROI representing a collection of 2D points (distinct x,y coordinates).
POLYGON - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Polygon drawing tool (closed)
POLYGON_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
POLYGON_TOOL - Variable in class qupath.lib.gui.ToolManager
PolygonROI - Class in qupath.lib.roi: ROI representing an arbitrary closed polygon.
POLYLINE - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Polyline drawing tool (open)
POLYLINE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
POLYLINE_TOOL - Variable in class qupath.lib.gui.ToolManager
PolylineROI - Class in qupath.lib.roi: ROI representing an arbitrary open polyline.
populateAnnotationsMenu(QuPathGUI, ContextMenu) - Static method in class qupath.lib.gui.tools.GuiTools: Populate a ContextMenu with standard options to operate on selected annotation objects.
populateAnnotationsMenu(QuPathGUI, Menu) - Static method in class qupath.lib.gui.tools.GuiTools: Populate a Menu with standard options to operate on selected annotation objects.
positionCaret(int) - Method in interface qupath.lib.gui.scripting.EditableText: Set the caret position to the specified index
positionCaret(int) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
positionCaret(int) - Method in class qupath.lib.gui.scripting.TextAreaControl
POSITIVE - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

General class to represent something 'positive'
POSITIVE - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: General class to represent something 'positive'
PositiveCellDetection - Class in qupath.imagej.detect.cells: Alternative implementation of WatershedCellDetection that automatically applies 1 or 3 intensity thresholds to classify cells.
PositiveCellDetection() - Constructor for class qupath.imagej.detect.cells.PositiveCellDetection: Default constructor.
positiveClassification(boolean) - Static method in class qupath.lib.objects.PathObjectPredicates: Predicate that returns true of an object has a positive classification.
PositivePixelCounterIJ - Class in qupath.imagej.detect.tissue: Simple command to detect regions with positive staining.
PositivePixelCounterIJ() - Constructor for class qupath.imagej.detect.tissue.PositivePixelCounterIJ
postprocess(TaskRunner, ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin: Called immediately after running any generated tasks.
postprocess(TaskRunner, ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
postProcess(Collection<? extends PathTask>) - Method in class qupath.lib.gui.TaskRunnerFX
postProcess(Collection<? extends PathTask>) - Method in class qupath.lib.plugins.AbstractTaskRunner: Perform post-processing after a task has complete.
postprocessing(Collection<? extends ImageOp>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the postprocessing steps from a collection.
postprocessing(ImageOp...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the postprocessing steps from an array.
power(double) - Static method in class qupath.opencv.ops.ImageOps.Core: Raise every pixel element to a power.
power(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV: Raise elements of an array to a specified power.
predict(Map<String, Mat>) - Method in class qupath.opencv.dnn.AbstractDnnModel: Convenience method to convert input image patches to a blobs, apply a PredictionFunction (optionally with multiple inputs/outputs), and convert the output to a standard Mat.
predict(Map<String, Mat>) - Method in interface qupath.opencv.dnn.DnnModel: Prediction function that can take multiple inputs.
predict(Map<String, T>) - Method in interface qupath.opencv.dnn.PredictionFunction: Call a function that takes one or more inputs to produce zero or more outputs.
predict(Mat) - Method in class qupath.opencv.dnn.AbstractDnnModel: Convenience method to convert a single image patch to a blob, apply the PredictionFunction, and convert the output to a standard Mat.
predict(Mat) - Method in interface qupath.opencv.dnn.DnnModel: Prediction function that takes a single input and gives a single output.
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV: Default implementation calling
predict(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Apply classification, optionally requesting probability estimates.
predict(T) - Method in interface qupath.opencv.dnn.PredictionFunction: Call a function that takes a single input and provides a single output.
prediction(DnnModel, Padding, String...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the DNN to be used for prediction, to be applied after preprocessing and before postprocessing.
prediction(ImageOp) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the prediction image op, to be applied after preprocessing and before postprocessing.
PredictionFunction<T> - Interface in qupath.opencv.dnn: Prediction function, typically used with a deep learning framework.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier: Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier: Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer: Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier: Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV: Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV: Implement predictWithLock rather than predict to ensure predict is not called while training.
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
predictWithLock(Mat, Mat, Mat) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
PreferencePane - Class in qupath.lib.gui.panes: QuPath's preference pane, giving a means to modify many of the properties within PathPrefs.
PreferencePane() - Constructor for class qupath.lib.gui.panes.PreferencePane
PreferencePane.AppearancePreferences - Class in qupath.lib.gui.panes
PreferencePane.DrawingPreferences - Class in qupath.lib.gui.panes
PreferencePane.ExtensionPreferences - Class in qupath.lib.gui.panes
PreferencePane.GeneralPreferences - Class in qupath.lib.gui.panes
PreferencePane.InputOutputPreferences - Class in qupath.lib.gui.panes
PreferencePane.LocalePreferences - Class in qupath.lib.gui.panes
PreferencePane.MeasurementPreferences - Class in qupath.lib.gui.panes
PreferencePane.ObjectPreferences - Class in qupath.lib.gui.panes
PreferencePane.ScriptingPreferences - Class in qupath.lib.gui.panes
PreferencePane.UndoRedoPreferences - Class in qupath.lib.gui.panes
PreferencePane.ViewerPreferences - Class in qupath.lib.gui.panes
PREFERENCES - Variable in class qupath.lib.gui.actions.CommonActions
PREFERENCES - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
preferNucleus(boolean) - Method in class qupath.lib.analysis.DelaunayTools.Builder: Specify that the triangulation should be based on nucleus ROIs where possible (only affects cell objects).
preferredTileSize(int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the preferred tile height and width.
preferReturnToMove() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Returns false.
prefHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
prefHeight(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the preferred height of the dialog pane.
Prefs - Class in qupath.lib.common: Core QuPath preferences.
Prefs() - Constructor for class qupath.lib.common.Prefs
prefWidth(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the preferred width of the dialog pane.
preprocess(TaskRunner, ImageData<T>) - Method in class qupath.lib.plugins.AbstractPlugin: Called after parsing the argument String, and immediately before creating & running any generated tasks.
preprocess(TaskRunner, ImageData<T>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
preprocessing(Collection<? extends ImageOp>) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the preprocessing steps from a collection.
preprocessing(ImageOp...) - Method in class qupath.opencv.ml.PatchClassifierParams.Builder: Define the preprocessing steps from an array.
Preprocessing - Class in qupath.opencv.ml.objects.features: Helper class for preprocessing input for machine learning algorithms using OpenCV Mats.
Preprocessing() - Constructor for class qupath.opencv.ml.objects.features.Preprocessing
Preprocessing.PCAProjector - Class in qupath.opencv.ml.objects.features: Helper class to apply PCA projection.
preprocessor(FeaturePreprocessor) - Static method in class qupath.opencv.ops.ImageOps.ML: Apply a FeaturePreprocessor to pixels, considering each channel as features.
PRETTY_JSON - Enum constant in enum class qupath.lib.io.PathIO.GeoJsonExportOptions: Request pretty-printing for the JSON.
previousSelectedToolProperty() - Method in class qupath.lib.gui.ToolManager: Property storing the previous tool that was selected.
PROBABILITY - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Each channel represents a probability value, where it is assumed that there is only one true class per pixel.
process(Parameters<S, T>) - Method in interface qupath.lib.experimental.pixels.Processor: Processing method.
PROCESSING - Enum constant in enum class qupath.lib.plugins.ParallelTileObject.Status: Tile currently being processed
ProcessingCV - Class in qupath.opencv.tools: Static methods to enable existing code for watershed transforms and morphological reconstruction to be applied to OpenCV images.
ProcessingCV() - Constructor for class qupath.opencv.tools.ProcessingCV
ProcessingExtension - Class in qupath.process.gui: General-purpose processing and machine learning commands.
ProcessingExtension() - Constructor for class qupath.process.gui.ProcessingExtension
ProcessingExtension.ObjectClassificationCommands - Class in qupath.process.gui
ProcessingExtension.OpenCVCommands - Class in qupath.process.gui: Commands based on OpenCV.
ProcessingExtension.OtherCommands - Class in qupath.process.gui
ProcessingExtension.PixelClassificationCommands - Class in qupath.process.gui
processObjects(ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.lib.experimental.pixels.PixelProcessor: Process objects using the default TaskRunner.
processObjects(TaskRunner, ImageData<BufferedImage>, Collection<? extends PathObject>) - Method in class qupath.lib.experimental.pixels.PixelProcessor: Process objects using the specified TaskRunner.
processor(Processor<S, T, U>) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set the processor.
Processor<S,T,U> - Interface in qupath.lib.experimental.pixels: A generic processor designed to work with Parameters and provide an output.
project(ObjectExpression<Project<BufferedImage>>) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Current project
project(Mat, Mat) - Method in class qupath.opencv.ml.objects.features.Preprocessing.PCAProjector: Apply the projection.
Project<T> - Interface in qupath.lib.projects: Data structure to manage images and associated data in QuPath.
PROJECT_ADD_IMAGES - Variable in class qupath.lib.gui.actions.CommonActions
PROJECT_BASE_DIR - Static variable in class qupath.lib.scripting.QP: Placeholder for the path to the current project.
PROJECT_CLOSE - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
PROJECT_LOCATION - Static variable in class qupath.lib.analysis.heatmaps.DensityMaps: Default location to use when storing density maps in a project.
PROJECT_LOCATION - Static variable in interface qupath.lib.classifiers.object.ObjectClassifier: Default location to use when storing object classifiers in a project.
PROJECT_LOCATION - Static variable in interface qupath.lib.classifiers.pixel.PixelClassifier: Default location to use when storing object classifiers in a project.
PROJECT_NEW - Variable in class qupath.lib.gui.actions.CommonActions
PROJECT_NEW - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
PROJECT_OPEN - Variable in class qupath.lib.gui.actions.CommonActions
PROJECT_OPEN - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
projectActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
ProjectActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
ProjectBrowser - Class in qupath.lib.gui.panes: Component for previewing and selecting images within a project.
ProjectBrowser(QuPathGUI) - Constructor for class qupath.lib.gui.panes.ProjectBrowser: Constructor.
ProjectClassifierBindings - Class in qupath.process.gui.commands.ml: Class to help with formatting text fields for entering pixel and object classifier names.
ProjectClassifierBindings() - Constructor for class qupath.process.gui.commands.ml.ProjectClassifierBindings
ProjectCommands - Class in qupath.lib.gui.commands: Helper class implementing simple 'single-method' commands related to projects.
ProjectCommands() - Constructor for class qupath.lib.gui.commands.ProjectCommands
ProjectDialogs - Class in qupath.lib.gui.dialogs: Dialogs specifically related to managing projects.
ProjectDialogs() - Constructor for class qupath.lib.gui.dialogs.ProjectDialogs
ProjectImageEntry<T> - Interface in qupath.lib.projects: Class to represent an image entry within a project.
ProjectIO - Class in qupath.lib.projects: Read QuPath projects.
ProjectIO() - Constructor for class qupath.lib.projects.ProjectIO
projectProperty() - Method in class qupath.lib.gui.QuPathGUI: Read-only property representing the currently-open project.
Projects - Class in qupath.lib.projects: Static methods to help when working with Projects.
Projects() - Constructor for class qupath.lib.projects.Projects
PROMPT - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting: Prompt the user to specified the image type
promptForDirectory(File) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt user to select a directory.
promptForDirectory(String, File) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt user to select a directory.
promptForFile(File) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt user to select a file.
promptForFile(String...) - Static method in class qupath.lib.gui.scripting.QPEx: Prompt the user to select a file from a file chooser.
promptForFile(String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt the user for a file with some kind of file dialog.
promptForFilePathOrURL(String, String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt user to select a file or input a URL.
promptForMultipleFiles(String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt to open a list of files.
promptForParentObjects(String, ImageData<?>, boolean, Collection<Class<? extends PathObject>>) - Static method in class qupath.lib.gui.tools.GuiTools: Get the parent objects to use when running the plugin, or null if no suitable parent objects are found.
promptForSliderRange(Slider) - Static method in class qupath.lib.gui.tools.GuiTools: Prompt the user to input min/max values for a slider.
promptToAddColumnAfterSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to add a column to a TMA grid after the column containing the currently-selected object.
promptToAddColumnBeforeSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to add a column to a TMA grid before the column containing the currently-selected object.
promptToAddNoteToSelectedCores(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to type a node to associate with the selected TMA cores.
promptToAddRowAfterSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to add a row to a TMA grid after the row containing the currently-selected object.
promptToAddRowBeforeSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to add a row to a TMA grid before the row containing the currently-selected object.
promptToAddShapeFeatures(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Prompt to add shape features for selected objects.
promptToCheckURIs(Project<?>, boolean) - Static method in class qupath.lib.gui.commands.ProjectCommands: Check the URIs within a project, prompting the user to correct any broken links if required.
promptToClearAllSelectedObjects(ImageData<?>) - Static method in class qupath.lib.gui.tools.GuiTools: Prompt user to select all currently-selected objects (except TMA core objects).
promptToCopyFilesToExtensionsDirectory(Collection<File>) - Method in class qupath.lib.gui.ExtensionManager: Copy a collection of files to QuPath's extensions directory, notifying the user about what is done and prompting to create a user directory if needed.
promptToCreateObjects(ImageData<BufferedImage>, PixelClassifier, String) - Static method in class qupath.process.gui.commands.ml.PixelClassifierUI: Prompt the user to create objects directly from the pixels of an ImageServer.
promptToCreateProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Prompt the user to select an empty directory, and use this to create a new project and set it as active.
promptToCreateTMAGrid(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt the user to manually create a new TMA grid.
promptToCreateTrainingImage(Project<BufferedImage>, List<PathClass>) - Static method in class qupath.process.gui.commands.CreateTrainingImageCommand: Prompt to create a training image, based upon annotations throughout a project.
promptToDeleteObjects(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands: Prompt to delete objects of a specified type, or all objects.
promptToDeleteTMAGridColumn(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to delete a column from a TMA grid.
promptToDeleteTMAGridRow(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to delete a row from a TMA grid.
promptToEditClass(PathClass) - Static method in class qupath.lib.gui.commands.Commands: Prompt to edit the name/color of a class.
promptToEstimateStainVectors(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Prompt to estimate stain vectors for the specified image, using any current region of interest.
promptToExportImageList(Project<?>) - Static method in class qupath.lib.gui.commands.ProjectCommands: Prompt to export a text file containing a list of image paths for a project.
promptToExportImageRegion(QuPathViewer, boolean) - Static method in class qupath.lib.gui.commands.Commands: Prompt to export the current image region selected in the viewer.
promptToExportTMAData(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to export summary TMA data for a specific image to a directory.
promptToImportImages(QuPathGUI, String...) - Static method in class qupath.lib.gui.commands.ProjectCommands: Show prompt for the user to select images to import into the current project in QuPath, choosing a suitable ImageServerBuilder.
promptToImportImages(QuPathGUI, ImageServerBuilder<BufferedImage>, String...) - Static method in class qupath.lib.gui.commands.ProjectCommands: Show prompt for the user to select images to import into the current project in QuPath.
promptToImportLegacyProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.ProjectCommands: Prompt the user to select a legacy project file, and then import the images into the current project.
promptToImportObjects(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter: Import a collection of objects to an object hierarchy, prompting to confirm and asking whether to update IDs.
promptToImportObjectsFromFile(ImageData<BufferedImage>, File) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter: Prompt to import objects read from a file.
promptToImportObjectsProjectEntry(ImageData<BufferedImage>, ProjectImageEntry<?>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter: Prompt to import objects from a project entry.
promptToImportTMAData(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to import TMA data for the specified image data.
promptToOpenImageFile() - Method in class qupath.lib.gui.QuPathGUI: Show a file chooser to open a new image in the current viewer.
promptToOpenImageFileOrUri() - Method in class qupath.lib.gui.QuPathGUI: Show a dialog to open a new image in the current viewer, with support for entering a URL (rather than requiring a local file only).
promptToOpenProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Prompt the user to open an existing project and set it as active.
promptToPasteObjectsFromClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter: Prompt to paste objects from the system clipboard, if possible.
promptToRelabelTMAGrid(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands: Prompt to relabel the core names within a TMA grid.
promptToRemoveSelectedObject(PathObject, PathObjectHierarchy) - Static method in class qupath.lib.gui.tools.GuiTools: Prompt to remove a single, specified selected object.
promptToResetPreferences() - Static method in class qupath.lib.gui.commands.Commands: Reset QuPath's preferences, after confirming with the user.
promptToResolveHierarchy(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Resolve parent-child relationships within the object hierarchy.
promptToSaveFile(String, File, String, String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt user to select a file path to save.
promptToSaveFile(String, File, String, Map<String, String>) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Prompt user to select a file path to save, providing zero or more file extensions as an option.
promptToSaveImageData(QuPathGUI, ImageData<BufferedImage>, boolean) - Static method in class qupath.lib.gui.commands.Commands: Prompt to save the specified ImageData.
promptToSelectImage(String, boolean) - Method in class qupath.lib.gui.panes.ServerSelector: Prompt to select a single ImageServer.
promptToSelectImages(String) - Method in class qupath.lib.gui.panes.ServerSelector: Prompt to select multiple ImageServers.
promptToSelectObjectsByClassification(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Prompt to select objects according to their classifications.
promptToSetActiveAnnotationProperties(PathObjectHierarchy) - Static method in class qupath.lib.gui.tools.GuiTools: Prompt the user to set properties for the currently-selected annotation(s).
promptToSetFontSize() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Update the font size for the script editor and console.
promptToSetGridLineSpacing(OverlayOptions) - Static method in class qupath.lib.gui.commands.Commands: Prompt to input the spacing for the grid lines optionally displayed on viewers.
promptToSetImageType(ImageData<BufferedImage>, ImageData.ImageType) - Static method in class qupath.lib.gui.panes.ImageDetailsPane: Prompt the user to set the ImageData.ImageType for the image.
promptToSimplifySelectedAnnotations(ImageData<?>, double) - Static method in class qupath.lib.gui.commands.Commands: Show a prompt to selected annotations in a hierarchy.
promptToUpdateUris(Collection<T>, URI, URI, boolean) - Static method in class qupath.lib.gui.commands.UpdateUrisCommand: Show dialog prompting the user to update URIs for missing files.
PROP_JAVADOC_PATH - Static variable in class qupath.lib.gui.JavadocViewer: Name of the system property used to set the javadoc path.
PROPERTIES - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for Java properties files
PROPERTIES - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
PropertiesLanguage - Class in qupath.lib.gui.scripting.languages: Class for the representation of properties and config files in QuPath.
PropertiesLanguage() - Constructor for class qupath.lib.gui.scripting.languages.PropertiesLanguage: Constructor for a Java properties as a script editor language.
PropertiesStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling to apply to a CodeArea, based on Java .properties and .cfg file syntax.
PROPERTY_NAME_BACKGROUND_COLOR - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_BOUNDS_HEIGHT - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_BOUNDS_WIDTH - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_BOUNDS_X - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_BOUNDS_Y - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_COMMENT - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_MPP_X - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_MPP_Y - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_OBJECTIVE_POWER - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_QUICKHASH1 - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
PROPERTY_NAME_VENDOR - Static variable in class qupath.lib.images.servers.openslide.jna.OpenSlide
propertyChange(PropertyChangeEvent) - Method in class qupath.lib.gui.panes.ImageDetailsPane
propertyChange(PropertyChangeEvent) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
put(String, double) - Method in interface qupath.lib.measurements.MeasurementList: Put a measurement value into the list, replacing any previous measurement with the same name.
put(String, T) - Method in interface qupath.lib.projects.ResourceManager.Manager: Save a resource within the project.
put0(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Record coocurrence for a (binned) value pair without rotation
put135(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Record coocurrence for a (binned) value pair with 135 degree rotation
put45(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Record coocurrence for a (binned) value pair with 45 degree rotation
put90(int, int) - Method in class qupath.lib.analysis.features.CoocurranceMatrices: Record coocurrence for a (binned) value pair with 90 degree rotation
putActionProperty(MenuItem, Action) - Static method in class qupath.lib.gui.actions.ActionTools: Add an Action to the properties of a MenuItem, so that it may be retrieved later.
putActionProperty(Node, Action) - Static method in class qupath.lib.gui.actions.ActionTools: Add an Action to the properties of a Node, so that it may be retrieved later.
putAll(Map<String, ? extends Number>) - Method in interface qupath.lib.measurements.MeasurementList: Put all the values from the specified map into this list
putAll(MeasurementList) - Method in interface qupath.lib.measurements.MeasurementList: Put all the values from the specified list into this one
putMeasurement(String, double) - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
since v0.4.0; replaced by MeasurementList.put(String, double)
putMeasurement(Measurement) - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
since v0.4.0, since there is no real need to create a Measurement object and we don't currently use dynamic measurements
putMetadataValue(String, String) - Method in interface qupath.lib.objects.MetadataStore: Store a new metadata value.
putMetadataValue(String, String) - Method in class qupath.lib.objects.TMACoreObject
putMetadataValue(String, String) - Method in interface qupath.lib.projects.ProjectImageEntry: Store a metadata value.
putPixelsFloat(Mat, float[]) - Static method in class qupath.opencv.tools.OpenCVTools: Set pixels from a float array.
putPixelsUnsigned(Mat, byte[]) - Static method in class qupath.opencv.tools.OpenCVTools: Set pixels from a byte array.
pyramidalize(ImageServer<BufferedImage>, double...) - Static method in class qupath.lib.images.servers.ImageServers: Wrap an ImageServer to dynamically generate a pyramid.
pyramidalizeTiled(ImageServer<BufferedImage>, int, int, double...) - Static method in class qupath.lib.images.servers.ImageServers: Wrap an ImageServer to dynamically generate a pyramid, using specified tile sizes.
PYTHON - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for Python
PYTHON - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
PYTHON_IMPORTER - Static variable in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage: Pythonic import statements
PythonAutoCompletor - Class in qupath.lib.gui.scripting.completors: Auto completion support for Python.
PythonAutoCompletor(boolean) - Constructor for class qupath.lib.gui.scripting.completors.PythonAutoCompletor: Constructor.
PythonStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling to apply to a CodeArea, based on Python syntax.

Q

QP - Class in qupath.lib.scripting: Collection of static methods that are useful for scripting.
QP() - Constructor for class qupath.lib.scripting.QP
QPEx - Class in qupath.lib.gui.scripting: Alternative to QP offering static methods of use for scripting, along with some extra methods that require access of GUI features.
QPEx() - Constructor for class qupath.lib.gui.scripting.QPEx
quickShowImage(String, Roi, ImageProcessor...) - Static method in class qupath.imagej.tools.IJTools: Show an ImageProcessor (or array of similar ImageProcessors as a stack).
quickShowImage(String, ImageProcessor...) - Static method in class qupath.imagej.tools.IJTools: Show an ImageProcessor (or array of similar ImageProcessors as a stack).
QUIT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
qupath - package qupath: Package containing the main QuPath launcher.
QuPath - Class in qupath: Main QuPath launcher.
QuPath() - Constructor for class qupath.QuPath
QUPATH_AND_EXTENSIONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType: Check for QuPath and extensions on GitHub
QUPATH_ONLY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType: Check for QuPath updates only
QuPath_Send_Overlay_to_QuPath - Class in qupathj: ImageJ plugin for sending back all the ROIs on an ImageJ overlay to QuPath.
QuPath_Send_Overlay_to_QuPath() - Constructor for class qupathj.QuPath_Send_Overlay_to_QuPath
QuPath_Send_ROI_to_QuPath - Class in qupathj: ImageJ plugin for sending back the active ROI from ImageJ to QuPath.
QuPath_Send_ROI_to_QuPath() - Constructor for class qupathj.QuPath_Send_ROI_to_QuPath
QUPATH_STARTUP - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
qupath.ext.openslide - package qupath.ext.openslide
qupath.imagej.detect.cells - package qupath.imagej.detect.cells: Classes to enable cell detection, implemented with the help of ImageJ as an image processing library.
qupath.imagej.detect.dearray - package qupath.imagej.detect.dearray: Classes to help with Tissue Microarray dearraying.
qupath.imagej.detect.tissue - package qupath.imagej.detect.tissue: Classes to enable tissue detection by thresholding.
qupath.imagej.gui - package qupath.imagej.gui: User interface commands and extensions linking ImageJ and QuPath.
qupath.imagej.images.servers - package qupath.imagej.images.servers: ImageServer implementation using ImageJ as the image reading library.
qupath.imagej.images.writers - package qupath.imagej.images.writers: Image writers, using ImageJ as the writing library.
qupath.imagej.processing - package qupath.imagej.processing: Static methods that add further processing methods when working with ImageJ images.
qupath.imagej.superpixels - package qupath.imagej.superpixels: Classes to generate superpixels.
qupath.imagej.tools - package qupath.imagej.tools: Helper classes and static methods for working with ImageJ images.
qupath.lib.algorithms - package qupath.lib.algorithms: Feature calculation plugins.
qupath.lib.analysis - package qupath.lib.analysis: Classes to aid with analysis.
qupath.lib.analysis.algorithms - package qupath.lib.analysis.algorithms: Classes and static methods adding reusable processing and analysis functionality.
qupath.lib.analysis.features - package qupath.lib.analysis.features: Classes to help with calculating features.
qupath.lib.analysis.heatmaps - package qupath.lib.analysis.heatmaps: Classes and static methods associated with generating and querying heatmaps.
qupath.lib.analysis.images - package qupath.lib.analysis.images: Helper interfaces and methods to write pixel processing algorithms.
qupath.lib.analysis.stats - package qupath.lib.analysis.stats: Calculate simple statistics from arrays.
qupath.lib.analysis.stats.survival - package qupath.lib.analysis.stats.survival: Helper classes for survival analysis.
qupath.lib.awt.common - package qupath.lib.awt.common: Static classes and methods to help work with Java AWT.
qupath.lib.classifiers - package qupath.lib.classifiers: Classes and interfaces to support machine learning classifiers.
qupath.lib.classifiers.object - package qupath.lib.classifiers.object: Classes for object classification in QuPath.
qupath.lib.classifiers.pixel - package qupath.lib.classifiers.pixel: Core support for pixel classification.
qupath.lib.color - package qupath.lib.color: Classes to assist with color, including stain separation and color transforms.
qupath.lib.common - package qupath.lib.common: General-purpose helper classes.
qupath.lib.display - package qupath.lib.display: Classes to control the display of images in a QuPathViewer.
qupath.lib.display.settings - package qupath.lib.display.settings: Classes to support storing and retrieving image display settings.
qupath.lib.experimental.pixels - package qupath.lib.experimental.pixels: Experimental package to simplify pixel operations for large images.
qupath.lib.extension.svg - package qupath.lib.extension.svg: Write SVG images from QuPath using JFreeSVG (http://www.jfree.org/jfreesvg/).
qupath.lib.geom - package qupath.lib.geom: Simple, immutable classes to represent points and dimensions.
qupath.lib.gui - package qupath.lib.gui: The main QuPath user interface.
qupath.lib.gui.actions - package qupath.lib.gui.actions: Classes to manage Actions.
qupath.lib.gui.actions.annotations - package qupath.lib.gui.actions.annotations: Annotations that can be used to configure actions.
qupath.lib.gui.actions.menus - package qupath.lib.gui.actions.menus: Classes to store actions that correspond to QuPath's main menus.
qupath.lib.gui.charts - package qupath.lib.gui.charts: Classes for plotting and charting.
qupath.lib.gui.commands - package qupath.lib.gui.commands: Commands shown within the main QuPath interface.
qupath.lib.gui.commands.display - package qupath.lib.gui.commands.display: Extra package to organize the classes related to the Brightness/Contrast command.
qupath.lib.gui.commands.objects - package qupath.lib.gui.commands.objects
qupath.lib.gui.dialogs - package qupath.lib.gui.dialogs: Helper classes for creating dialogs, prompts and filt choosers within QuPath.
qupath.lib.gui.extensions - package qupath.lib.gui.extensions: Interface to define QuPath extensions.
qupath.lib.gui.images.servers - package qupath.lib.gui.images.servers: Custom ImageServers that depend upon the QuPath interface and image display settings.
qupath.lib.gui.images.stores - package qupath.lib.gui.images.stores: Classes for requesting, caching and drawing image tiles.
qupath.lib.gui.localization - package qupath.lib.gui.localization
qupath.lib.gui.logging - package qupath.lib.gui.logging: Support for logging.
qupath.lib.gui.measure - package qupath.lib.gui.measure: Classes related to extracting, calculating and displaying measurements.
qupath.lib.gui.panes - package qupath.lib.gui.panes: Panes used to display information in the QuPath interface.
qupath.lib.gui.prefs - package qupath.lib.gui.prefs: Custom preferences.
qupath.lib.gui.scripting - package qupath.lib.gui.scripting: Scripting through the QuPath interface.
qupath.lib.gui.scripting.completors - package qupath.lib.gui.scripting.completors: Classes for auto-completion in QuPath's script editor.
qupath.lib.gui.scripting.languages - package qupath.lib.gui.scripting.languages: Language and syntax definitions for QuPath scripting.
qupath.lib.gui.scripting.richtextfx - package qupath.lib.gui.scripting.richtextfx: Alternative script editor for QuPath using syntax highlighting thanks to RichTextFX (https://github.com/FXMisc/RichTextFX).
qupath.lib.gui.scripting.richtextfx.stylers - package qupath.lib.gui.scripting.richtextfx.stylers: Classes for syntax styling in QuPath's script editor.
qupath.lib.gui.scripting.syntax - package qupath.lib.gui.scripting.syntax: Classes for syntax help in QuPath's script editor.
qupath.lib.gui.tma - package qupath.lib.gui.tma: Display, summarize and query tissue microarray analysis results.
qupath.lib.gui.tools - package qupath.lib.gui.tools: Assorted helper classes for the QuPath interface.
qupath.lib.gui.viewer - package qupath.lib.gui.viewer: QuPath image viewing and display.
qupath.lib.gui.viewer.overlays - package qupath.lib.gui.viewer.overlays: Support for overlays, which may be painted on top of QuPathViewers.
qupath.lib.gui.viewer.recording - package qupath.lib.gui.viewer.recording: Record and display field of view changes made within a QuPathViewer.
qupath.lib.gui.viewer.tools - package qupath.lib.gui.viewer.tools: Drawing and navigation tools for the QuPath toolbar.
qupath.lib.gui.viewer.tools.handlers - package qupath.lib.gui.viewer.tools.handlers
qupath.lib.images - package qupath.lib.images: Defines the ImageData class to represent the key data associated with an analyzed image.
qupath.lib.images.servers - package qupath.lib.images.servers: Supports accessing pixels and metadata in QuPath.
qupath.lib.images.servers.bioformats - package qupath.lib.images.servers.bioformats: Read images using Bio-Formats (https://www.openmicroscopy.org/bio-formats/).
qupath.lib.images.servers.openslide - package qupath.lib.images.servers.openslide: Read images using OpenSlide (https://openslide.org/).
qupath.lib.images.servers.openslide.jna - package qupath.lib.images.servers.openslide.jna
qupath.lib.images.writers - package qupath.lib.images.writers: Supports for writing images of various kinds in various ways.
qupath.lib.images.writers.ome - package qupath.lib.images.writers.ome: Write OME-TIFF images.
qupath.lib.io - package qupath.lib.io: Supports reading and writing some core QuPath data structures.
qupath.lib.measurements - package qupath.lib.measurements: Provides measurement lists for use with PathObjects.
qupath.lib.objects - package qupath.lib.objects: Provides PathObjects, used to represent annotations and other image structures within QuPath.
qupath.lib.objects.classes - package qupath.lib.objects.classes: Defines classes to represent classifications for PathObjects.
qupath.lib.objects.hierarchy - package qupath.lib.objects.hierarchy: Classes to represent the object hierarchy.
qupath.lib.objects.hierarchy.events - package qupath.lib.objects.hierarchy.events: Events triggered when the hierarchy changes, such as objects being added, removed or reclassified.
qupath.lib.objects.utils - package qupath.lib.objects.utils: Helper classes for working with PathObjects.
qupath.lib.plugins - package qupath.lib.plugins: Classes to support general analysis commands.
qupath.lib.plugins.objects - package qupath.lib.plugins.objects: Plugins for manipulating objects and ROIs.
qupath.lib.plugins.parameters - package qupath.lib.plugins.parameters: Defines classes for handling parameters used in interactive dialogs or as method arguments.
qupath.lib.plugins.workflow - package qupath.lib.plugins.workflow: Classes and interfaces related to logging analysis steps to assist scripting and reproducibility.
qupath.lib.projects - package qupath.lib.projects: Classes and interfaces related to projects, which are used to manage multiple images.
qupath.lib.regions - package qupath.lib.regions: Defines immutable classes for representing image planes and regions.
qupath.lib.roi - package qupath.lib.roi: Classes that define regions of interest (ROIs).
qupath.lib.roi.interfaces - package qupath.lib.roi.interfaces: Interface that define regions of interest (ROIs).
qupath.lib.scripting - package qupath.lib.scripting: Defines helper class for running scripts.
qupath.lib.scripting.languages - package qupath.lib.scripting.languages: Base classes for defining scripting languages that QuPath can support.
qupath.opencv - package qupath.opencv: Detection plugins using OpenCV.
qupath.opencv.dnn - package qupath.opencv.dnn: QuPath classes to use OpenCV's DNN module.
qupath.opencv.features - package qupath.opencv.features: Classes for feature calculation using OpenCV.
qupath.opencv.io - package qupath.opencv.io: Support for serializing and deserializing OpenCV objects.
qupath.opencv.ml - package qupath.opencv.ml: QuPath classes to apply machine learning to pixels and objects using OpenCV.
qupath.opencv.ml.objects - package qupath.opencv.ml.objects: QuPath object classifiers using OpenCV.
qupath.opencv.ml.objects.features - package qupath.opencv.ml.objects.features: Extract object features using OpenCV.
qupath.opencv.ml.pixel - package qupath.opencv.ml.pixel: QuPath pixel classifiers using OpenCV.
qupath.opencv.ops - package qupath.opencv.ops: Image operations, implemented with OpenCV.
qupath.opencv.tools - package qupath.opencv.tools: Additional processing methods for use with OpenCV Mats.
qupath.process.gui - package qupath.process.gui: General-purpose image processing and machine learning commands.
qupath.process.gui.commands - package qupath.process.gui.commands: QuPath commands relevant for machine learning.
qupath.process.gui.commands.density - package qupath.process.gui.commands.density: UI classes to support density maps.
qupath.process.gui.commands.ml - package qupath.process.gui.commands.ml: Interfaces and helper classes for using machine learning in QuPath.
qupath.process.gui.commands.ui - package qupath.process.gui.commands.ui: Reusable UI classes to support processing commands.
QuPathApp - Class in qupath.lib.gui: Launcher application to start QuPath.
QuPathApp() - Constructor for class qupath.lib.gui.QuPathApp
QuPathExtension - Interface in qupath.lib.gui.extensions: Simple interface for QuPath extensions.
QuPathGUI - Class in qupath.lib.gui: Main GUI for QuPath, written using JavaFX.
qupathj - package qupathj: ImageJ plugins to install within QuPath's embedded ImageJ instance to enable exchanging ROIs and objects.
QuPathPenManager - Class in qupath.lib.gui.viewer.tools: Helper class for managing pressure-sensitive input.
QuPathPenManager() - Constructor for class qupath.lib.gui.viewer.tools.QuPathPenManager
QuPathPenManager.PenInputManager - Interface in qupath.lib.gui.viewer.tools: Interface defining minimal behavior for a pen input device.
QuPathResources - Class in qupath.lib.gui.localization: Load strings from the default resource bundle.
QuPathResources() - Constructor for class qupath.lib.gui.localization.QuPathResources
QuPathStyleManager - Class in qupath.lib.gui.prefs: Class to facilitate the use of different styles within QuPath.
QuPathStyleManager() - Constructor for class qupath.lib.gui.prefs.QuPathStyleManager
QuPathStyleManager.Fonts - Enum Class in qupath.lib.gui.prefs: Available font families.
QuPathStyleManager.StyleOption - Interface in qupath.lib.gui.prefs: Interface defining a style that may be applied to QuPath.
QuPathTMAViewer - Class in qupath.lib.gui.tma: Standalone viewer for looking at TMA summary results.
QuPathTMAViewer() - Constructor for class qupath.lib.gui.tma.QuPathTMAViewer
QuPathViewer - Class in qupath.lib.gui.viewer: JavaFX component for viewing a (possibly large) image, along with overlays.
QuPathViewer(DefaultImageRegionStore, OverlayOptions) - Constructor for class qupath.lib.gui.viewer.QuPathViewer: Create a new viewer.
QuPathViewerListener - Interface in qupath.lib.gui.viewer: Interface for defining a listener that needs to know whenever the data related to a QuPathViewer has changed in some way - such as by changing the underlying ImageData, or by moving the field of view.
QuPathViewerPlus - Class in qupath.lib.gui.viewer: A whole slide viewer with optional extras...
QuPathViewerPlus(DefaultImageRegionStore, OverlayOptions, ViewerPlusDisplayOptions) - Constructor for class qupath.lib.gui.viewer.QuPathViewerPlus: Create a new viewer.

R

radius(double) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: The radius of the filter used to calculate densities.
RAW - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode: Raw bin counts.
read(JsonReader) - Method in class qupath.lib.images.servers.ColorTransforms.ColorTransformTypeAdapter
read(JsonReader) - Method in class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdapter
readAllMats(String) - Static method in class qupath.opencv.tools.NumpyTools: Read a all Mats from an .npy or .npz file.
readAllMats(String, boolean) - Static method in class qupath.opencv.tools.NumpyTools: Read a all Mats from an .npy or .npz file, optionally squeezing singleton dimensions.
readAllMats(Path) - Static method in class qupath.opencv.tools.NumpyTools: Read a all Mats from an .npy or .npz path.
readAllMats(Path, boolean) - Static method in class qupath.opencv.tools.NumpyTools: Read a all Mats from an .npy or .npz path, optionally squeezing singleton dimensions This will be a single Mat for .npy but may be multiple for .npz.
readAllTiles() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Read all the tiles.
readBufferedImage(RegionRequest) - Method in interface qupath.lib.images.servers.ImageServer: Deprecated.
since v0.4.0. Implementations of ImageServer should override ImageServer.readRegion(RegionRequest) instead. This method will be removed in a future release; it exists now only to maintain compatibility with QuPath extensions that have not yet been updated to use the newer method.
readClassifier(Path) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers: Read the classifier from a file.
readClassifier(Path) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Read a standard pixel classifier from a file.
readCSV(File) - Static method in class qupath.lib.io.TMAScoreImporter: Read CSV data from a file into a map connecting column headers (keys) to lists of Strings (entries).
readCSV(String) - Static method in class qupath.lib.io.TMAScoreImporter: Read CSV data from a String into a map connecting column headers (keys) to lists of Strings (entries).
readCSV(Scanner) - Static method in class qupath.lib.io.TMAScoreImporter: Read CSV data into a map connecting column headers (keys) to lists of Strings (entries).
readExternal(ObjectInput) - Method in class qupath.lib.color.ColorDeconvolutionStains
readExternal(ObjectInput) - Method in class qupath.lib.color.StainVector
readExternal(ObjectInput) - Method in class qupath.lib.geom.Point2
readExternal(ObjectInput) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathCellObject
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathObject
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathObjectConnections
readExternal(ObjectInput) - Method in class qupath.lib.objects.PathROIObject
readExternal(ObjectInput) - Method in class qupath.lib.objects.TMACoreObject
readExternal(ObjectInput) - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
readExternal(ObjectInput) - Method in class qupath.lib.plugins.workflow.Workflow
readFile(File) - Method in class qupath.lib.gui.scripting.ScriptTab: Read the file, set the editor's text area with the content of the file and return the detected language (based on the file extension).
readFileAsString(File) - Static method in class qupath.lib.common.GeneralTools: Read the entire contents of a file into a single String.
readFileAsString(String) - Static method in class qupath.lib.common.GeneralTools: Read the entire contents of a file given by the specified path into a single String.
readHierarchy() - Method in interface qupath.lib.projects.ProjectImageEntry: Read the PathObjectHierarchy for this entry, or return an empty hierarchy if none is available.
readHierarchy(File) - Static method in class qupath.lib.io.PathIO: Read a hierarchy from a .qpdata file.
readHierarchy(InputStream) - Static method in class qupath.lib.io.PathIO: Read a PathObjectHierarchy from a saved data file (omitting all other contents).
readHierarchy(Path) - Static method in class qupath.lib.io.PathIO: Read a hierarchy from a .qpdata file.
readImageData() - Method in interface qupath.lib.projects.ProjectImageEntry: Read the ImageData associated with this entry, or create a new ImageData if none is currently present.
readImageData(File, ImageData<T>, ImageServer<T>, Class<T>) - Static method in class qupath.lib.io.PathIO: Read ImageData from a File into an existing ImageData object, or create a new one if required.
readImageData(InputStream, ImageData<T>, ImageServer<T>, Class<T>) - Static method in class qupath.lib.io.PathIO: Read ImageData from an InputStream into an existing ImageData object, or creating a new one if required.
readImageData(Path, ImageData<T>, ImageServer<T>, Class<T>) - Static method in class qupath.lib.io.PathIO: Read ImageData from a File into an existing ImageData object, or create a new one if required.
readImageJRois(File) - Static method in class qupath.imagej.tools.IJTools: Read ImageJ Rois from a .roi or a RoiSet.zip file.
readInputStreamAsString(InputStream) - Static method in class qupath.lib.common.GeneralTools: Read the entire contents of an InputStream into a single String.
readMat(InputStream, boolean) - Static method in class qupath.opencv.tools.NumpyTools: Read a single Mat from an input stream, which should follow the .npy file format specification.
readMat(String) - Static method in class qupath.opencv.tools.NumpyTools: Read a single Mat from an .npy or .npz file.
readMat(String, boolean) - Static method in class qupath.opencv.tools.NumpyTools: Read a single Mat from an .npy or .npz file, optionally squeezing singleton dimensions.
readMat(Path) - Static method in class qupath.opencv.tools.NumpyTools: Read an OpenCV Mat from a Numpy .npy file.
readMat(Path, boolean) - Static method in class qupath.opencv.tools.NumpyTools: Read an OpenCV Mat from a Numpy .npy file, optionally squeezing singleton dimensions.
readObjects(File) - Static method in class qupath.lib.io.PathIO: Read a list of PathObject from a file.
readObjects(Path) - Static method in class qupath.lib.io.PathIO: Read a list of PathObject from a file.
readObjectsFromClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter: Try to read objects from the system clipboard.
readObjectsFromGeoJSON(InputStream) - Static method in class qupath.lib.io.PathIO: Read a list of PathObject from an input stream.
readOnlyProperty() - Method in class qupath.lib.gui.QuPathGUI: Property indicating whether QuPath is in 'read-only' mode.
readPatch(ImageServer<BufferedImage>, ROI, double, int, int) - Static method in class qupath.opencv.dnn.DnnTools: Read an image patch, optionally with a fixed size and using zero-padding if required.
readPatch(ImageServer<BufferedImage>, ROI, double, int, int, int) - Static method in class qupath.opencv.dnn.DnnTools: Read an image patch, optionally with a fixed size.
readPathObjects() - Method in class qupath.imagej.images.servers.ImageJServer
readPathObjects() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
readPathObjects() - Method in interface qupath.lib.objects.PathObjectReader: Read a collection of objects from the source.
readPoints(File) - Static method in class qupath.lib.io.PointIO: Read a list of point annotations from a file.
readPoints(InputStream) - Static method in class qupath.lib.io.PointIO: Read a list of point annotations from a stream.
readPointsObjectList(File) - Static method in class qupath.lib.io.PointIO: Deprecated.
readRegion(double, int, int, int, int) - Method in interface qupath.lib.images.servers.ImageServer: Read a 2D(+C) image region from the default ImagePlane (i.e.
readRegion(double, int, int, int, int, int, int) - Method in interface qupath.lib.images.servers.ImageServer: Read a 2D(+C) image region for a specified z-plane and timepoint.
readRegion(RegionRequest) - Method in class qupath.imagej.images.servers.ImageJServer
readRegion(RegionRequest) - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.AffineTransformImageServer
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.CroppedImageServer
readRegion(RegionRequest) - Method in interface qupath.lib.images.servers.ImageServer: Read a 2D(+C) image region for a specified RegionRequest.
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.RotatedImageServer
readRegion(RegionRequest) - Method in class qupath.lib.images.servers.TransformingImageServer
readResolve() - Method in class qupath.lib.objects.classes.PathClass: Called during deserialization to ensure that only a single instance of each PathClass exists.
readSerializedServerPath(File) - Static method in class qupath.lib.io.PathIO: Deprecated.
This was useful in QuPath v0.1.2 and earlier, since all information to construct a server was stored within its path. In v0.2 and later, the server path is in general not sufficient to construct a server, and this method lingers only for backwards compatibility. It will be removed in a later version.
readTile(TileRequest) - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
readTile(TileRequest) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
readTile(TileRequest) - Method in class qupath.lib.gui.images.servers.RenderedImageServer
readTile(TileRequest) - Method in class qupath.lib.images.servers.AbstractTileableImageServer: Read a single image tile.
readTile(TileRequest) - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
readTile(TileRequest) - Method in class qupath.lib.images.servers.LabeledImageServer
readTile(TileRequest) - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
readTile(TileRequest) - Method in class qupath.lib.images.servers.SparseImageServer
readTile(TileRequest) - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
readURLAsString(URL, int) - Static method in class qupath.lib.common.GeneralTools: Read URL as String, with specified timeout in milliseconds.
rearrangeByStride(Collection<T>, T[], int) - Static method in class qupath.lib.plugins.AbstractPlugin: Test method for rearranging a collection so that entries are interleaved with a regularity given by stride.
RearrangeRGBImageServer - Class in qupath.lib.images.servers: Simple image server to swap the red and blue channels of an RGB image.
RearrangeRGBImageServer(ImageServer<BufferedImage>, String) - Constructor for class qupath.lib.images.servers.RearrangeRGBImageServer
RECENT_COMMAND_LIST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
Reclassifier - Class in qupath.lib.objects.classes: Helper class when classifying PathObjects.
Reclassifier(PathObject, PathClass, boolean) - Constructor for class qupath.lib.objects.classes.Reclassifier: Helper class to store an object prior to reclassifying it.
Reclassifier(PathObject, PathClass, boolean, double) - Constructor for class qupath.lib.objects.classes.Reclassifier: Helper class to store an object prior to reclassifying it, including a classification probability.
recomputeBounds() - Method in class qupath.lib.roi.PointsROI
recordingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Return the recording property of this ViewTracker.
RECTANGLE - Static variable in class qupath.lib.gui.viewer.tools.PathTools: Rectangle drawing tool
RECTANGLE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
RECTANGLE_TOOL - Variable in class qupath.lib.gui.ToolManager
RectangleROI - Class in qupath.lib.roi: ROI representing a square or rectangle (unrotated).
red(int) - Static method in class qupath.lib.common.ColorTools: Extract the 8-bit red value from a packed RGB value.
Red - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Red channel only
RED - Static variable in class qupath.lib.common.ColorTools: Packed int representing red.
RED - Static variable in class qupath.lib.images.servers.ImageChannel: Default red channel for RGB images.
Red_chromaticity - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Red chromaticity value, red / max(1, red + green + blue)
Red_OD - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Red channel optical densities
redChromaticity(int) - Static method in class qupath.lib.color.ColorTransformer: Extract red chromaticity value from a packed RGB pixel, red / max(1, red + green + blue)
redo() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
redo() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request redo.
redo() - Method in class qupath.lib.gui.scripting.TextAreaControl
REDO - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
redoAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
redoOnce() - Method in class qupath.lib.gui.UndoRedoManager: Request to 'redo' the last 'undone' hierarchy change for the current active viewer.
RefineAnnotationsPlugin<T> - Class in qupath.lib.plugins.objects: Plugin to create new annotations by expanding the size of existing annotations.
RefineAnnotationsPlugin() - Constructor for class qupath.lib.plugins.objects.RefineAnnotationsPlugin
refineAreas(Geometry, double, double) - Static method in class qupath.lib.roi.GeometryTools: Remove small fragments and fill small interior rings within a Geometry.
refineColorDeconvolutionStains(int[], ColorDeconvolutionStains, double, double) - Static method in class qupath.lib.color.ColorDeconvolutionHelper: Attempt to automatically refine color deconvolution stains based upon pixel values.
refineGeometryByParent(Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
refineGeometryByParent(Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
refineGeometryByParent(Geometry) - Method in class qupath.process.gui.WandToolEventHandler
refineROIByParent(ROI) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Apply clipping based on the current parent object.
refineROIByParent(ROI) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler: Apply clipping based on the current parent object.
refineROIByParent(ROI) - Method in class qupath.process.gui.WandToolEventHandler: Apply clipping based on the current parent object.
refresh() - Method in class qupath.lib.gui.commands.PathObjectGridView: Refresh the data in the grid view
refresh() - Method in class qupath.lib.gui.ExtensionClassLoader: Ensure all Jars in the extensions directory (and one subdirectory down) are available
refresh() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Refresh the current style.
REFRESH - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
REFRESH_DUPLICATE_OBJECT_IDS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
REFRESH_OBJECT_IDS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
refreshAllEditors() - Method in class qupath.lib.gui.panes.PreferencePane: Request that all the property editors are regenerated.
refreshChannelOptions() - Method in class qupath.lib.display.ImageDisplay: Refresh the channel options.
refreshCombo() - Method in class qupath.lib.gui.charts.HistogramDisplay: Refresh the available measurements.
refreshDuplicateIDs() - Static method in class qupath.lib.scripting.QP: Refresh all object IDs for the current hierarchy to ensure there are no duplicates, retaining the original IDs where possible.
refreshDuplicateIDs(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Refresh all object IDs for the current hierarchy to ensure there are no duplicates, retaining the original IDs where possible.
refreshEntries() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Refresh the measurement values.
refreshExtensions(boolean) - Method in class qupath.lib.gui.ExtensionManager: Check the extensions directory, loading any new extensions found there.
refreshFileContents() - Method in class qupath.lib.gui.scripting.ScriptTab
refreshHistogram() - Method in class qupath.lib.gui.charts.HistogramDisplay: Refresh the currently-displayed histogram (e.g.
refreshID() - Method in class qupath.lib.objects.PathObject: Regenerate a new random ID.
refreshIDs() - Static method in class qupath.lib.scripting.QP: Refresh all object IDs for the current hierarchy.
refreshIDs(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Refresh all object IDs for the current hierarchy.
refreshingExtensions() - Method in class qupath.lib.gui.ExtensionManager: Property indicating whether extensions are in the process of being refreshed.
refreshList(ListView<T>) - Static method in class qupath.lib.gui.tools.GuiTools: Refresh a ListView in the Application thread.
refreshObjectIDs(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands: Refresh object IDs to ensure uniqueness.
refreshProject() - Method in class qupath.lib.gui.panes.ProjectBrowser: Refresh the current project, updating the displayed entries.
refreshProject() - Method in class qupath.lib.gui.QuPathGUI: Refresh the project, updating the display if required.
refreshSliders() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: Refresh the sliders, to ensure they match with the current channel.
refreshTitle() - Method in class qupath.lib.gui.QuPathGUI: Refresh the title bar in the main QuPath window.
refreshTitles() - Method in class qupath.lib.gui.viewer.ViewerManager: Request that viewers refresh their titles.
region(int, int, int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Define the region to export based on a bounding box.
region(ImageRegion) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Specify the region (in terms of the full resolution image space) for export.
region(ImageRegion) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Define the region to export, including the z-slice and time point.
region(ImageRegion) - Method in class qupath.lib.images.writers.TileExporter: Define the region to be processed.
region(RegionRequest) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Specify the region to use for processing.
region(RegionRequest) - Method in class qupath.lib.images.writers.TileExporter: Define the region to be processed, including downsample.
REGION - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Region class.
REGION - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Region class.
RegionFilter - Interface in qupath.lib.gui.viewer: Define the area of an image to which pixel classification should be applied.
RegionFilter.StandardRegionFilters - Enum Class in qupath.lib.gui.viewer: Standard classification regions (hopefully all you will ever need).
RegionRequest - Class in qupath.lib.regions: Class for defining an image region that can also be used to request these region from an ImageServer.
regionToGeometry(ImageRegion) - Static method in class qupath.lib.roi.GeometryTools: Convert an ImageRegion to a rectangular Geometry.
registerAlias(Class<? extends T>, String) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory: Register an alias label for a specified subtype.
registerBuilder(DnnModelBuilder) - Static method in class qupath.opencv.dnn.DnnModels: Register a new DnnModelBuilder.
registerDataOp(Class<? extends ImageDataOp>, String) - Static method in class qupath.opencv.ops.ImageOps: Register an ImageDataOp class for JSON serialization/deserialization.
registerDnnModel(Class<T>, String) - Static method in class qupath.opencv.dnn.DnnModels: Register a new DnnModel class for JSON serialization/deserialization.
registerDnnModel(Class<T>, String) - Static method in class qupath.opencv.dnn.DnnTools: Deprecated.
since v0.4.0; use DnnModels.registerDnnModel(Class, String) instead.
registerOp(Class<? extends ImageOp>, String) - Static method in class qupath.opencv.ops.ImageOps: Register an ImageOp class for JSON serialization/deserialization.
registerRequest(TileListener<BufferedImage>, ImageServer<BufferedImage>, Shape, double, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Register a request so that the tile request queue will be populated, including potentially for nearby tiles (i.e.
registerRequest(TileListener<BufferedImage>, ImageServer<BufferedImage>, RegionRequest, double, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
registerSubtype(Class<? extends ObjectClassifier>) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers.ObjectClassifierTypeAdapterFactory: Register a new ObjectClassifier subtype for compatibility with Gson serialization.
registerSubtype(Class<? extends T>) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory: Register a subtype using the default label (the simple name of the class).
registerSubtype(Class<? extends T>, String) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory: Register a subtype using a custom label.
registerTool(QuPathViewer) - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
registerTool(QuPathViewer) - Method in interface qupath.lib.gui.viewer.tools.PathTool: Register the tool on the viewer.
RELABEL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
relabelTMAGrid(String, String, boolean) - Static method in class qupath.lib.scripting.QP: Relabel the current TMA grid.
relabelTMAGrid(PathObjectHierarchy, String, String, boolean) - Static method in class qupath.lib.scripting.QP: Relabel a TMA grid.
relabelTMAGrid(TMAGrid, String, String, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Relabel a TMA grid.
relative(URI, URI) - Method in class qupath.lib.io.UriUpdater: Identify replacements for missing URIs by relativizing URI.
relative(Path, Path) - Method in class qupath.lib.io.UriUpdater: Identify replacements for missing URIs by relativizing paths.
relativeToUserDirectory() - Method in class qupath.lib.gui.FileCopier: Specify that the copying is relative to the QuPath user directory.
RELOAD_DATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
reloadImageData(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Reload the specified image data from a previously saved version,if available.
remove(String) - Method in interface qupath.lib.measurements.MeasurementList: Remove a named measurement
remove(String) - Method in interface qupath.lib.projects.ResourceManager.Manager: Remove a resource within the project.
REMOVE_COLUMN - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
REMOVE_FRAGMENTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
REMOVE_ROW - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
removeActions - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
RemoveActions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
removeAllImages(Collection<ProjectImageEntry<T>>, boolean) - Method in interface qupath.lib.projects.Project: Remove multiple images from the project, optionally including associated data.
removeByAreas(ByteProcessor, double, double, boolean) - Static method in class qupath.imagej.processing.RoiLabeling: Remove objects containing < minPixels or > maxPixels.
removeChildObject(PathObject) - Method in class qupath.lib.objects.PathObject: Remove a single object from the child list of this object.
removeChildObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject: Remove multiple objects from the child list of this object.
removeColumn(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager: Try to remove the column containing the specified viewer, notifying the user if this isn't possible.
REMOVED - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: An object has been removed
removeEmptyParameters() - Method in class qupath.lib.plugins.parameters.ParameterList: Remove all empty parameters from this list.
removeFileDropHandler(DragDropImportListener.DropHandler<File>) - Method in class qupath.lib.gui.viewer.DragDropImportListener: Remove a File DropHandler.
removeFragments(Geometry, double) - Static method in class qupath.lib.roi.GeometryTools: Remove fragments smaller than the specified area from a Geometry, ignoring internal rings.
removeGroup(PathObjectConnectionGroup) - Method in class qupath.lib.objects.PathObjectConnections: Remove a connections group.
removeImage(ProjectImageEntry<?>, boolean) - Method in interface qupath.lib.projects.Project: Remove an image from the project, optionally including associated data.
removeInteriorRings(Geometry, double) - Static method in class qupath.lib.roi.GeometryTools: Fill all interior rings for the specified geometry that have an area < a specified threshold.
removeJsonDropHandler(DragDropImportListener.DropHandler<JsonElement>) - Method in class qupath.lib.gui.viewer.DragDropImportListener: Remove a JSON DropHandler.
removeListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Remove a hierarchy change listener.
removeMeasurements(Class<? extends PathObject>, String...) - Static method in class qupath.lib.scripting.QP: Remove measurements from objects of a specific class for the current image data.
removeMeasurements(String...) - Method in interface qupath.lib.measurements.MeasurementList: Remove all the measurements with the specified names.
removeMeasurements(PathObjectHierarchy, Class<? extends PathObject>, String...) - Static method in class qupath.lib.scripting.QP: Remove measurements from objects of a specific class for the specified hierarchy.
removeMetadataValue(String) - Method in interface qupath.lib.projects.ProjectImageEntry: Remove a metadata value.
removeNames(PathClass, String...) - Static method in class qupath.lib.objects.classes.PathClassTools: Create a PathClass with specific name elements removed (if present) from an existing classification.
removeNames(PathClass, Collection<String>) - Static method in class qupath.lib.objects.classes.PathClassTools: Create a PathClass with specific name elements removed (if present) from an existing classification.
removeObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Remove a single object from the hierarchy, firing a remove event.
removeObject(PathObject, boolean) - Static method in class qupath.lib.scripting.QP: Remove the specified object from the current PathObjectHierarchy, optionally keeping or removing descendant objects.
removeObjects(Collection<? extends PathObject>, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Remove a collection of objects, firing a single 'hierarchy changed' event afterwards to notify listeners if anything happened (i.e.
removeObjects(Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.scripting.QP: Remove the specified collection of objects from the current PathObjectHierarchy, optionally keeping or removing descendant objects.
removeObjects(PathObject[], boolean) - Static method in class qupath.lib.scripting.QP: Remove the specified array of objects from the current PathObjectHierarchy, optionally keeping or removing descendant objects.
removeObjectsOutsideImage() - Static method in class qupath.lib.scripting.QP: Remove objects that are entirely outside the current image.
removeObjectsOutsideImage(boolean) - Static method in class qupath.lib.scripting.QP: Remove objects that are entirely or partially outside the current image.
removeObjectsOutsideImage(ImageData<?>) - Static method in class qupath.lib.scripting.QP: Remove objects that are entirely or outside the specified image.
removeObjectsOutsideImage(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP: Remove objects that are entirely or partially outside the specified image.
removeObjectWithoutUpdate(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Remove a single object from the hierarchy, without firing a remove event.
removeOrClipObjectsOutsideImage() - Static method in class qupath.lib.scripting.QP: Remove objects occurring outside the current image bounds, clipping annotations where possible to retain the part that is inside the image.
removeOrClipObjectsOutsideImage(ImageData<?>) - Static method in class qupath.lib.scripting.QP: Remove objects occurring outside the specified image bounds, clipping annotations where possible to retain the part that is inside the image.
removeOverlaps(Collection<? extends PathObject>, Comparator<PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools: Resolve overlaps, discarding one and keeping the other.
removeOverlapsByLocation(Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools: Resolve overlapping object by location, retaining the object closest to the image 'origin' and discarding the object further away.
removeOverlapsBySize(Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools: Resolve overlapping objects by size, retaining the object with the larger ROI and discarding the object with the smaller ROI.
removeParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList: Remove a parameter from this list.
removeParameterChangeListener(ParameterChangeListener) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Remove a ParameterChangeListener.
removePathObject(PathObject) - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, replaced by PathObject.removeChildObject(PathObject)
removePathObjectListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Deprecated.
since v0.4.0 (the name was confusing because it wasn't intended primarily to listen to changes within individual PathObjects)
removePathObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, replaced by PathObject.removeChildObjects(Collection)
removePathObjectSelectionListener(PathObjectSelectionListener) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Remove listener for selection changes.
removeProperty(String) - Method in class qupath.lib.images.ImageData: Remove a specified property.
removePropertyChangeListener(PropertyChangeListener) - Method in class qupath.lib.images.ImageData: Remove a property change listener.
removeRow(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager: Try to remove the row containing the specified viewer, notifying the user if this isn't possible.
removeSmallAreas(ByteProcessor, double, boolean) - Static method in class qupath.imagej.processing.RoiLabeling: Remove objects having small areas, defined in terms of pixels
removeSmallPieces(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools: Remove small fragments and fill small holes of an area ROI.
removeStep(int) - Method in class qupath.lib.plugins.workflow.Workflow: Remove a single step, identified by its list index.
removeStep(WorkflowStep) - Method in class qupath.lib.plugins.workflow.Workflow: Remove a single step, firing an update event if the step was successfully removed.
removeSteps(Collection<WorkflowStep>) - Method in class qupath.lib.plugins.workflow.Workflow: Remove a collection of steps, firing an update event if the workflow was changed.
removeTextAppendableFX(TextAppendable) - Static method in class qupath.lib.gui.logging.LogManager: Deregister a TextAppendable so that it will no longer be informed of logging events.
removeTileListener(TileListener<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
removeViewerListener(QuPathViewerListener) - Method in class qupath.lib.gui.viewer.QuPathViewer: Remove a viewer listener.
removeWorkflowListener(WorkflowListener) - Method in class qupath.lib.plugins.workflow.Workflow: Remove a listener for changes to the workflow.
RenderedImageServer - Class in qupath.lib.gui.images.servers: An ImageServer that can display a rendered image, with optional overlays.
RenderedImageServer.Builder - Class in qupath.lib.gui.images.servers: Builder to create an ImageServer to display rendered images, with optional overlay layers.
renderer(ImageRenderer) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify the ImageRenderer that controls conversion to RGB.
rendererProperty() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Get the ImageRenderer property used with this overlay.
reorderRGB(String) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Rearrange the channel order of an RGB image.
repaint() - Method in class qupath.lib.gui.viewer.QuPathViewer: Request that the viewer is repainted.
repaintAllViewers() - Method in class qupath.lib.gui.viewer.ViewerManager: Request that all viewers are repainted as soon as possible.
repaintEntireImage() - Method in class qupath.lib.gui.viewer.QuPathViewer: Request that the entire image is repainted, including the thumbnail.
repaintEntireImage() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
repaintTimestamp() - Method in class qupath.lib.gui.viewer.QuPathViewer: Get the timestamp referring to the last time this viewer was repainted.
repeat(int) - Static method in class qupath.opencv.ops.ImageOps.Channels: Repeat the channels a specified number of times.
replace(double, double) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that replaces one pixel value in an image with another.
replaceClassification(String, String) - Static method in class qupath.lib.scripting.QP: Apply a new classification to all objects in the current hierarchy with a specified classification.
replaceClassification(Collection<PathObject>, PathClass, PathClass) - Static method in class qupath.lib.scripting.QP: Apply a new classification to all objects with a specified original classification in an object collection.
replaceClassification(PathClass, PathClass) - Static method in class qupath.lib.scripting.QP: Apply a new classification to all objects in the current hierarchy with a specified original classification.
replaceClassification(PathObjectHierarchy, PathClass, PathClass) - Static method in class qupath.lib.scripting.QP: Apply a new classification to all objects with a specified original classification in the provided hierarchy.
replaceCurlyQuotes(String) - Static method in class qupath.lib.common.GeneralTools: Replace different kinds of 'curly quote' in a String with straight quotes.
replaceGremlins(String, CharSequence) - Static method in class qupath.lib.common.GeneralTools: Replace non-printable characters from a String with a specified replacement (may be null).
replaceLastStep(WorkflowStep) - Method in class qupath.lib.plugins.workflow.Workflow: Replace the most recently added step with this one.
replaceNaNs(double) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that replaces NaNs with a specified value.
replaceNaNs(Mat, double) - Static method in class qupath.opencv.tools.OpenCVTools: Replace NaNs in a floating point array.
replaceSelection(String) - Method in interface qupath.lib.gui.scripting.EditableText: Insert the specified text, replacing any existing selection.
replaceSelection(String) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
replaceSelection(String) - Method in class qupath.lib.gui.scripting.TextAreaControl
replaceValues(Mat, double, double) - Static method in class qupath.opencv.tools.OpenCVTools: Replace a specific value in an array.
requestAutomaticUpdateCheck() - Method in class qupath.lib.gui.QuPathGUI: Request an automated update check in a background thread.
requestCancelDirection(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Requests that the viewer cancels either the x- or y-axis direction.
requestDecelerate() - Method in class qupath.lib.gui.viewer.QuPathViewer: Request that a viewer decelerate any existing panning smoothly.
requestedPixelSize(double) - Method in class qupath.lib.images.writers.TileExporter: Define resolution as a pixel size in calibrated units.
requestFocus() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
requestFocus() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request that the control is focused.
requestFocus() - Method in class qupath.lib.gui.scripting.TextAreaControl
requestFollowCaret() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
requestFollowCaret() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request that the X and Y scrolls are adjusted to ensure the caret is visible.
requestFullUpdateCheck() - Method in class qupath.lib.gui.QuPathGUI: Request a manual update check in a background thread.
requestHierarchyUpdate() - Method in class qupath.lib.plugins.AbstractPlugin: Optionally request a hierarchy update after the tasks have run.
requestImageTile(ImageServer<BufferedImage>, RegionRequest, Map<RegionRequest, BufferedImage>, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Request an image tile.
requestLazyInitialize() - Method in class qupath.opencv.dnn.DnnModelParams: Request that any model is loaded lazily on demand.
requestNewHandle(double, double) - Method in class qupath.lib.roi.RoiEditor: Request an updated ROI with a new handle inserted - useful e.g.
requestParallelization() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Returns true if multiple readers may be created for different threads, to enable parallel image reading.
requestParentClipping(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Query whether parent clipping should be applied.
requestParentClipping(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler: Query whether parent clipping should be applied.
requestParentClipping(MouseEvent) - Method in class qupath.process.gui.WandToolEventHandler: Query whether parent clipping should be applied.
requestPixelSnapping() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Returns true if the tool requests that pixel coordinates be snapped to integer values.
requestPixelSnapping() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler: Returns true if the tool requests that pixel coordinates be snapped to integer values.
requestPixelSnapping() - Method in class qupath.process.gui.WandToolEventHandler: Returns true if the tool requests that pixel coordinates be snapped to integer values.
requestStartMoving(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Request that the viewer start panning with a velocity determined by dx and dy.
requestStopMoving() - Method in class qupath.lib.gui.viewer.QuPathViewer: Request that the viewer stop any panning immediately.
requestUserDirectory(boolean) - Static method in class qupath.lib.gui.commands.Commands: Request the current user directory, optionally prompting the user to request a directory if none is available.
requiresTileRegion(String, ImageRegion) - Method in interface qupath.lib.gui.images.stores.TileListener: Check if the listener requires a particular tile.
requiresTileRegion(String, ImageRegion) - Method in class qupath.lib.gui.viewer.QuPathViewer
RESET_DETECTION_CLASSIFICATIONS - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
RESET_METADATA - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
RESET_PREFERENCES - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
RESET_SELECTION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
resetActiveHandle() - Method in class qupath.lib.roi.RoiEditor: Ensure that no handle is active.
resetAllSliders() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: Reset all sliders to their default values.
resetAvailablePathClasses() - Method in class qupath.lib.gui.QuPathGUI: Populate the availablePathClasses with a default list.
resetBatchProjectAndImage() - Static method in class qupath.lib.scripting.QP: Reset the Project and ImageData used for batch processing for the current thread.
resetClassifications(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Reset the PathClass for all objects of the specified type in the current hierarchy.
resetClassifications(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands: Select objects that are instances of a specified class, logging an appropriate method in the workflow.
resetClassifications(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Reset the PathClass for all objects of the specified type in the specified hierarchy.
resetConstrainingObjects() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: Reset the constraining objects.
resetConstrainingObjects() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler: Reset the constraining objects.
resetConstrainingObjects() - Method in class qupath.process.gui.WandToolEventHandler: Reset the constraining objects.
resetCustomPixelLayerOverlay() - Method in class qupath.lib.gui.viewer.QuPathViewer: Reset the custom pixel layer overlay to null.
resetDetectionClassifications() - Static method in class qupath.lib.scripting.QP: Reset the PathClass for all detection objects in the current hierarchy.
resetGridSize() - Method in class qupath.lib.gui.viewer.ViewerManager
resetImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Remove the image.
resetImageData() - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay: Reset the last image data.
resetImageData() - Method in class qupath.lib.gui.viewer.QuPathViewer: Reset the image data to null.
resetIntensityClassifications() - Static method in class qupath.lib.scripting.QP: Reset the intensity classifications for all detections in the current hierarchy.
resetIntensityClassifications(Collection<PathObject>) - Static method in class qupath.lib.scripting.QP: Reset the intensity classifications for all specified objects.
resetIntensityClassifications(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Reset the intensity classifications for all detections in the specified hierarchy.
resetMeasurementMapper() - Method in class qupath.lib.gui.viewer.OverlayOptions: Reset any MeasurementMapper, so that measurements are not used to determine object colors.
resetMinimumRepaintSpacingMillis() - Method in class qupath.lib.gui.viewer.QuPathViewer: Return to processing all repainting requests.
resetPathClass() - Method in class qupath.lib.objects.PathObject: Reset the classification (i.e.
resetPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs: Reset the preferences to their defaults.
resetSelection() - Static method in class qupath.lib.scripting.QP: Clear the selected objects for the current PathObjectHierarchy.
resetSelection(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Reset the selection for an image.
resetTMAMetadata(boolean) - Static method in class qupath.lib.scripting.QP: Remove all TMA metadata from the current TMA grid.
resetTMAMetadata(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Reset TMA metadata, if available.
resetTMAMetadata(PathObjectHierarchy, boolean) - Static method in class qupath.lib.scripting.QP: Remove all TMA metadata from the TMA grid of the specified hierarchy.
resetValue() - Method in class qupath.lib.plugins.parameters.BooleanParameter
resetValue() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
resetValue() - Method in class qupath.lib.plugins.parameters.DoubleParameter
resetValue() - Method in class qupath.lib.plugins.parameters.EmptyParameter
resetValue() - Method in class qupath.lib.plugins.parameters.IntParameter
resetValue() - Method in class qupath.lib.plugins.parameters.NumericParameter
resetValue() - Method in class qupath.lib.plugins.parameters.StringParameter
resetValue() - Method in interface qupath.lib.plugins.parameters.Parameter: Set last value to null (so default can be used).
resizable() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Make the dialog resizable (but default it is not).
resize(double, double) - Method in class qupath.lib.gui.ColorMapCanvas
resize(BufferedImage, int, int, boolean) - Static method in class qupath.lib.awt.common.BufferedImageTools: Resize the image to have the requested width/height, using area averaging and bilinear interpolation.
RESOLVE_HIERARCHY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
resolveHierarchy() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Attempt to resolve the parent-child relationships between all objects within the hierarchy.
resolveHierarchy() - Static method in class qupath.lib.scripting.QP: Resolve the location of annotations in the current hierarchy by setting parent/child relationships.
resolveHierarchy(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Resolve the location of annotations in the specified hierarchy by setting parent/child relationships.
resolveOverlaps() - Method in class qupath.lib.plugins.ParallelTileObject: Request that the tile object attempts to resolve overlaps with its neighboring tiles.
resolvePath(String) - Static method in class qupath.lib.scripting.QP: Resolve a path, replacing any placeholders.
ResourceManager - Class in qupath.lib.projects: Manage the storage and retrieval of resources with a ResourceManager.
ResourceManager() - Constructor for class qupath.lib.projects.ResourceManager
ResourceManager.Manager<T> - Interface in qupath.lib.projects: Simple manager to handle saving and retrieving resources of different kinds, for example from projects or a user directory.
resourceManagerProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane: The resource manager used to handle saving/loading.
restoreClassificationsFromMap(Map<PathObject, PathClass>) - Static method in class qupath.lib.objects.PathObjectTools: Reassign classifications to objects, as were previously obtained using PathObjectTools.createClassificationMap(Collection).
retainHessian(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Optionally retain the Hessian matrix per pixel.
retrieveMetadataKeys() - Method in class qupath.lib.objects.PathObject: Get the set of metadata keys.
retrieveMetadataValue(String) - Method in class qupath.lib.objects.PathObject: Get a metadata value.
returnToMove - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
returnToMoveModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request that the GUI returns to using the PAN tool after a ROI is drawn.
rgb(boolean) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify that the image stores pixels in (A)RGB form.
RGB - Enum constant in enum class qupath.process.gui.WandToolEventHandler.WandType: Color image (default behavior in v0.1.2 and before)
RGB_mean - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Mean of red, green and blue channels
rgbMean(int) - Static method in class qupath.lib.color.ColorTransformer: Extract mean of RGB values from a packed RGB pixel.
RichScriptEditor - Class in qupath.lib.gui.scripting.richtextfx: Rich script editor for QuPath, which can be used for handling different languages.
RichScriptEditor(QuPathGUI) - Constructor for class qupath.lib.gui.scripting.richtextfx.RichScriptEditor: Constructor.
RichScriptEditorExtension - Class in qupath.lib.gui.scripting.richtextfx: QuPath extension to add a more attractive script editor with syntax highlighting, making use of RichTextFX, Copyright (c) 2013-2014, Tomas Mikula (BSD 2-clause license).
RichScriptEditorExtension() - Constructor for class qupath.lib.gui.scripting.richtextfx.RichScriptEditorExtension
RIGID_OBJECT_EDITOR - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
ROI - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept any object that has a ROI
ROI - Interface in qupath.lib.roi.interfaces: Base interface for defining regions of interest (ROIs) within QuPath.
ROI_AREA - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept any object that has an area ROI
ROI_LINE - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept any object that has a line ROI
ROI_POINT - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept any object that has a points ROI
ROI.RoiType - Enum Class in qupath.lib.roi.interfaces: Enum representing the major different types of ROI.
roiBounds() - Method in class qupath.lib.analysis.DelaunayTools.Builder: Specify that the triangulation should be based on ROI boundary coordinates with the default densify factor.
roiBounds(double, double) - Method in class qupath.lib.analysis.DelaunayTools.Builder: Specify that the triangulation should be based on ROI boundary coordinates with a specified densify factor.
RoiEditor - Class in qupath.lib.roi: Helper class for interactively modifying existing ROIs.
RoiLabeling - Class in qupath.imagej.processing: Collection of static methods to help work with ROIs, binary & labelled images in ImageJ.
RoiLabeling() - Constructor for class qupath.imagej.processing.RoiLabeling
ROIs - Class in qupath.lib.roi: This class consists exclusively of static methods that operate on or return regions of interest (ROIs).
ROIs() - Constructor for class qupath.lib.roi.ROIs
roiToGeometry(ROI) - Method in class qupath.lib.roi.GeometryTools.GeometryConverter: Convert a QuPath ROI to a JTS Geometry.
roiToGeometry(ROI) - Static method in class qupath.lib.roi.GeometryTools: Convert to QuPath ROI to a JTS Geometry.
RoiTools - Class in qupath.lib.roi: A collection of static methods for working with ROIs.
RoiTools() - Constructor for class qupath.lib.roi.RoiTools
RoiTools.CombineOp - Enum Class in qupath.lib.roi: Methods of combining two ROIs.
rootLogLevelProperty() - Static method in class qupath.lib.gui.logging.LogManager: Property representing the current requested root log level.
rotate(RotatedImageServer.Rotation) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Rotate the image, using an increment of 90 degrees.
ROTATE_180 - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation: Rotate 180 degrees.
ROTATE_270 - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation: Rotate 270 degrees clockwise.
ROTATE_90 - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation: Rotate 90 degrees clockwise.
ROTATE_IMAGE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
ROTATE_NONE - Enum constant in enum class qupath.lib.images.servers.RotatedImageServer.Rotation: No rotation.
RotatedImageServer - Class in qupath.lib.images.servers: ImageServer that wraps another ImageServer, but intercepts region requests to effectively rotate the image by 90, 180 or 270 degrees.
RotatedImageServer(ImageServer<BufferedImage>, RotatedImageServer.Rotation) - Constructor for class qupath.lib.images.servers.RotatedImageServer: Create an image server that rotates pixel requests for a second server by a specified increment of 90 degrees.
RotatedImageServer.Rotation - Enum Class in qupath.lib.images.servers: Enum for rotations in increments of 90 degrees.
rotationProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer: Return the rotation property of this viewer.
round() - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that rounds floating point values.
round(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Round values in a floating point Mat.
ROUND - Enum constant in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap: Round cap
roundCoordinates(Geometry) - Static method in class qupath.lib.roi.GeometryTools: Round coordinates in a Geometry to integer values.
run() - Method in class qupath.lib.gui.commands.BrightnessContrastCommand
run() - Method in class qupath.lib.gui.commands.CountingDialogCommand
run() - Method in class qupath.lib.gui.commands.MeasurementExportCommand
run() - Method in class qupath.lib.gui.tma.TMAExplorer
run() - Method in class qupath.lib.gui.tools.DocGenerator
run() - Method in class qupath.lib.gui.viewer.recording.ViewTrackerControlPane
run() - Method in class qupath.lib.images.writers.ome.ConvertCommand
run() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriterCommand
run() - Method in class qupath.process.gui.commands.CellIntensityClassificationCommand
run() - Method in class qupath.process.gui.commands.CreateChannelTrainingImagesCommand
run() - Method in class qupath.process.gui.commands.CreateCompositeClassifierCommand
run() - Method in class qupath.process.gui.commands.CreateRegionAnnotationsCommand
run() - Method in class qupath.process.gui.commands.DensityMapCommand
run() - Method in class qupath.process.gui.commands.ExportTrainingRegionsCommand
run() - Method in class qupath.process.gui.commands.ObjectClassifierCommand
run() - Method in class qupath.process.gui.commands.ObjectClassifierLoadCommand
run() - Method in class qupath.process.gui.commands.PixelClassifierCommand
run() - Method in class qupath.process.gui.commands.SimpleThresholdCommand
run() - Method in class qupath.process.gui.commands.SingleMeasurementClassificationCommand
run() - Method in class qupath.process.gui.commands.SplitProjectTrainingCommand
run() - Method in class qupath.process.gui.commands.ui.LoadResourceCommand
run(String) - Method in class qupathj.QuPath_Send_Overlay_to_QuPath
run(String) - Method in class qupathj.QuPath_Send_ROI_to_QuPath
run(ImageData<?>) - Method in class qupath.lib.gui.commands.objects.SplitAnnotationsByLineCommand: Run the command for the specified image data.
runDetection(ImageData<T>, ParameterList, ROI) - Method in interface qupath.lib.plugins.ObjectDetector: Detect objects.
runGeoJsonExport(QuPathGUI) - Static method in class qupath.lib.gui.commands.ExportObjectsCommand: Run the path object GeoJSON export command.
runGeoJsonObjectExport(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Show a dialog to export object(s) to a GeoJSON file.
RunningStatistics - Class in qupath.lib.analysis.stats: Helper class for computing basic statistics from values as they are added.
RunningStatistics() - Constructor for class qupath.lib.analysis.stats.RunningStatistics: Default constructor.
runObjectClassifier(String...) - Static method in class qupath.lib.scripting.QP: Apply an object classifier to the current ImageData.
runObjectClassifier(ImageData, String...) - Static method in class qupath.lib.scripting.QP: Apply an object classifier to the specified ImageData.
runObjectImport(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Show a dialog to import object(s) from a file.
runPlugin(String, String) - Static method in class qupath.lib.gui.scripting.QPEx
runPlugin(String, String) - Static method in class qupath.lib.scripting.QP: Run the specified plugin on the current ImageData.
runPlugin(String, Map<String, ?>) - Static method in class qupath.lib.scripting.QP: Run the specified plugin on the current ImageData, using a map for arguments.
runPlugin(String, ImageData<?>, String) - Static method in class qupath.lib.gui.scripting.QPEx
runPlugin(String, ImageData<?>, String) - Static method in class qupath.lib.scripting.QP: Run the specified plugin on the specified ImageData.
runPlugin(String, ImageData<?>, Map<String, ?>) - Static method in class qupath.lib.scripting.QP: Run the specified plugin on the specified ImageData, using a map for arguments.
runPlugin(Map<String, ?>, String) - Static method in class qupath.lib.scripting.QP: Run the specified plugin on the current ImageData, with Groovy keyword argument support.
runPlugin(Map<String, ?>, String, ImageData<?>) - Static method in class qupath.lib.scripting.QP: Run the specified plugin on the specified ImageData, with Groovy keyword argument support.
runPlugin(PathPlugin<BufferedImage>, String, boolean) - Method in class qupath.lib.gui.QuPathGUI: Run a plugin, interactively (i.e.
runPlugin(TaskRunner, ImageData<BufferedImage>, String) - Method in class qupath.imagej.detect.cells.SubcellularDetection
runPlugin(TaskRunner, ImageData<BufferedImage>, String) - Method in class qupath.imagej.gui.ImageJMacroRunner
runPlugin(TaskRunner, ImageData<BufferedImage>, String) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
runPlugin(TaskRunner, ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractPlugin
runPlugin(TaskRunner, ImageData<T>, String) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
runPlugin(TaskRunner, ImageData<T>, String) - Method in interface qupath.lib.plugins.PathPlugin: Run the plugin.
runProjectScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
runProjectScriptNoSaveAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
RunSavedClassifierWorkflowStep - Class in qupath.lib.plugins.workflow: WorkflowStep for running a saved PathObjectClassifier.
RunSavedClassifierWorkflowStep(String) - Constructor for class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep: Constructor, taking the path to the serialized classifier.
RunSavedClassifierWorkflowStep(String, String) - Constructor for class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep: Create a workflow step to run a classifier.
runScript(File, String) - Method in class qupath.lib.gui.QuPathGUI: Convenience method to execute a script.
runScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
runSelectedAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
runTasks(Collection<? extends Runnable>) - Method in class qupath.lib.gui.TaskRunnerFX
runTasks(Collection<? extends Runnable>) - Method in class qupath.lib.plugins.AbstractTaskRunner
runTasks(Collection<? extends Runnable>) - Method in interface qupath.lib.plugins.TaskRunner: Pass a collection of parallelizable tasks to run.

S

sameClassificationPredicate() - Static method in class qupath.lib.analysis.DelaunayTools: BiPredicate that returns true for objects that share the same classification.
samplesPerPixel(int[]) - Method in class qupath.lib.images.servers.bioformats.OMEPixelParser.Builder
SANS_SERIF - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts: Preferred sans-serif font.
saturation(int) - Static method in class qupath.lib.color.ColorTransformer: Extract saturation value from RGB-to-HSB transform.
Saturation - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Saturation value (from RGB-HSB transform)
saturationPercentProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer: Get the percentage of any non-8-bit image that should be saturated when applying auto contrast settings.
SAVE_DATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
SAVE_DATA_AS - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
saveAnnotationMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save annotation measurements for the current image.
saveAnnotationMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save annotation measurements for the specified image.
saveChannelColorProperties() - Method in class qupath.lib.display.ImageDisplay: Save color channels in the ImageData properties.
saveDetectionMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save detection measurements for the current image.
saveDetectionMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save detection measurements for the specified image.
savedName(StringProperty) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Property to store the saved name; this is useful if the name is required externally
saveImageData(ImageData<T>) - Method in interface qupath.lib.projects.ProjectImageEntry: Save the ImageData for this entry using the default storage location for the project.
saveImageMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save whole image measurements for the current image.
saveImageMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save whole image measurements for the specified image.
saveMeasurements(Class<? extends PathObject>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save measurements for the current image for objects of a fixed type.
saveMeasurements(ImageData<?>, Class<? extends PathObject>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save measurements for the specified image for objects of a fixed type.
savePreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs: Save the preferences.
SaveResourcePaneBuilder<T> - Class in qupath.process.gui.commands.ui: Small JavaFX pane to support saving object/pixel classifiers and density maps within a project in a standardized way.
SaveResourcePaneBuilder(Class<T>, ObjectExpression<? extends T>) - Constructor for class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Constructor.
saveSnapshot(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.commands.Commands: Save an image snapshot, prompting the user to select the output file.
saveTableModel(PathTableData<?>, File, Collection<String>) - Static method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand: Save the data from a table to a text file, using the default delimiter from PathPrefs.
saveTMAMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save TMA measurements for the current image.
saveTMAMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx: Save TMA measurements for the specified image.
scalarMat(double, int) - Static method in class qupath.opencv.tools.OpenCVTools: Create a 1x1 single-channel Mat with a specific value.
scalarMatWithType(double, int) - Static method in class qupath.opencv.tools.OpenCVTools: Create a 1x1 Mat with a specific value, with 1 or more channels.
scale - Variable in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType: Smoothing scale for Gaussian subtraction.
scale(double) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Scale values, by which channels should be multiplied (after mean subtraction) before input to the Net.
scale(double, double) - Method in interface qupath.lib.roi.interfaces.ROI: Create a scaled version of this ROI.
scale(double, double, double, double) - Method in class qupath.lib.roi.AreaROI
scale(double, double, double, double) - Method in class qupath.lib.roi.EllipseROI
scale(double, double, double, double) - Method in class qupath.lib.roi.GeometryROI
scale(double, double, double, double) - Method in interface qupath.lib.roi.interfaces.ROI: Create a scaled version of this ROI.
scale(double, double, double, double) - Method in class qupath.lib.roi.LineROI
scale(double, double, double, double) - Method in class qupath.lib.roi.PointsROI
scale(double, double, double, double) - Method in class qupath.lib.roi.PolygonROI
scale(double, double, double, double) - Method in class qupath.lib.roi.PolylineROI
scale(double, double, double, double) - Method in class qupath.lib.roi.RectangleROI
scaleAllObjects(double) - Static method in class qupath.lib.scripting.QP: Resize the ROIs of all objects in the current object hierarchy.
scaleAllObjects(PathObjectHierarchy, double) - Static method in class qupath.lib.scripting.QP: Resize the ROIs of all objects in the specified object hierarchy.
scalebarFontSize - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
scalebarFontSizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Preferred font size for the scalebar in the viewer.
scalebarFontWeight - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
scalebarFontWeightProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Preferred font weight in the viewer.
scalebarLineWidth - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
scalebarLineWidthProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Preferred line width for the scalebar.
scaleColor(Color, double) - Static method in class qupath.lib.color.ColorToolsAwt: Get a scaled version of the specified color, where the RGB values are independently scaled by a specified factor.
scaledDownsampling(double) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Downsample by specific increasing factor each time (e.g.
scaledDownsampling(double, double) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Downsample by specific increasing factor each time, with a specified initial downsample value (e.g.
scaleVariance - Variable in class qupath.opencv.tools.LocalNormalization.LocalNormalizationType: Smoothing scale for Gaussian-weighted standard deviation estimate.
scatterChart() - Static method in class qupath.lib.gui.charts.Charts: Create a Charts.ScatterChartBuilder for generating a custom scatter plot.
SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
SCRIPT_EDITOR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
SCRIPT_EDITOR - Variable in class qupath.lib.gui.actions.AutomateActions
SCRIPT_EDITOR - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
SCRIPT_INTERPRETER - Variable in class qupath.lib.gui.actions.AutomateActions
SCRIPT_INTERPRETER - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
ScriptableWorkflowStep - Interface in qupath.lib.plugins.workflow: A WorkflowStep that can also return some Javascript that, if run, would perform the step.
ScriptAttributes - Class in qupath.lib.scripting: Default attributes that can be set when running scripts.
ScriptAttributes() - Constructor for class qupath.lib.scripting.ScriptAttributes
ScriptAutoCompletor - Interface in qupath.lib.scripting.languages: Interface for classes that implement auto-completion (e.g.
ScriptEditor - Interface in qupath.lib.gui.scripting: Minimal interface for a script editor that the GUI can call.
ScriptEditorControl<T> - Interface in qupath.lib.gui.scripting: Basic script editor control using JavaFX.
ScriptingPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ScriptingPreferences
ScriptLanguage - Class in qupath.lib.scripting.languages: Abstract class to represent languages supported by the script editor.
ScriptLanguage(String, String) - Constructor for class qupath.lib.scripting.languages.ScriptLanguage: Default constructor for a ScriptLanguage.
ScriptLanguage(String, Collection<String>) - Constructor for class qupath.lib.scripting.languages.ScriptLanguage: Default constructor for a ScriptLanguage.
ScriptLanguageProvider - Class in qupath.lib.gui.scripting.languages: Class with static methods to fetch all the available ScriptLanguages.
ScriptLanguageProvider() - Constructor for class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
ScriptParameters - Class in qupath.lib.scripting: Class that stores key information that is useful for running scripts.
ScriptParameters.Builder - Class in qupath.lib.scripting: Builder class for ScriptParameters.
scriptRunning() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Observable value indicating whether a script is currently running or not.
scriptsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager: Read only property representing the shared scripts directory.
scriptsPath - Variable in class qupath.lib.gui.panes.PreferencePane.ExtensionPreferences
scriptsPath - Variable in class qupath.lib.gui.panes.PreferencePane.ScriptingPreferences
scriptsPathProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Path to a directory containing scripts for quick-access through the user interface.
ScriptStyler - Interface in qupath.lib.gui.scripting.richtextfx.stylers: Interface for classes that apply some styling to a RichTextFX's CodeArea.
ScriptStylerProvider - Class in qupath.lib.gui.scripting.richtextfx.stylers: Class with static methods to fetch all the available ScriptStylers.
ScriptStylerProvider() - Constructor for class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider
ScriptSyntax - Interface in qupath.lib.gui.scripting.syntax: Interface for classes that apply some syntax formatting to an EditableText.
ScriptSyntaxProvider - Class in qupath.lib.gui.scripting.syntax: Class with static methods to fetch all the available ScriptSyntaxes.
ScriptSyntaxProvider() - Constructor for class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
ScriptTab - Class in qupath.lib.gui.scripting: Class representing a script tab (e.g.
scrollSpeed - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
scrollSpeedProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Percentage to scale scroll speed for zooming etc.
searchDepth(int) - Method in class qupath.lib.io.UriUpdater: Maximum search depth when using UriUpdater.searchDepth(int) to match filenames in directories and subdirectories.
searchPath(Path) - Method in class qupath.lib.io.UriUpdater: Search for filenames that match missing URIs, recursively up to the depth specified by UriUpdater.searchDepth(int).
seconds() - Method in class qupath.lib.common.Timeit: Report timings in seconds.
segment(SegmentationModel, Mat, Mat) - Static method in class qupath.opencv.dnn.DnnTools: Apply a segmentation model to an image region.
segment(SegmentationModel, ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.opencv.dnn.DnnTools: Apply a segmentation model to an image region.
segmentation() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Set the model type to be OpenCVDnn.ModelType.SEGMENTATION.
SEGMENTATION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Refers to SegmentationModel.
SELECT_ALL_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
SELECT_ALL_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SELECT_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SELECT_BY_CLASSIFICATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SELECT_BY_PLANE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SELECT_CELLS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SELECT_NEW - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions: Set the new objects to be selected
SELECT_TILES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SELECT_TMA_CORES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
selectable(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Sets the selectable property of the action.
SelectableItem<T> - Class in qupath.lib.gui: Helper class for managing items when only one of them may be selected.
SelectableItem(ObjectProperty<T>, T) - Constructor for class qupath.lib.gui.SelectableItem: Constructor.
selectActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
SelectActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
selectAllObjects() - Static method in class qupath.lib.scripting.QP: Select all objects in the current hierarchy, excluding the root object.
selectAllObjects(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Select all objects (excluding the root object) in the imageData.
selectAllObjects(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Select all objects in the specified hierarchy, excluding the root object.
selectAllObjects(PathObjectHierarchy, boolean) - Static method in class qupath.lib.scripting.QP: Set selected objects to contain all objects.
selectAnnotations() - Static method in class qupath.lib.scripting.QP: Select all annotation objects in the current hierarchy.
selectAnnotations(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Select all annotation objects in the specified hierarchy.
selectCells() - Static method in class qupath.lib.scripting.QP: Select all cell objects in the current hierarchy.
selectCells(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Select all cell objects in the specified hierarchy.
selectDetections() - Static method in class qupath.lib.scripting.QP: Select all detection objects in the current hierarchy.
selectDetections(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Select all detection objects in the specified hierarchy.
selected(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Set the selected property of the action.
selected(ObservableValue<Boolean>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Bind the selected property of the action to an ObservableValue, bidirectionally if possible.
selectedChannelProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane: The channel to which the sliders are applied.
selectedChannels() - Method in class qupath.lib.display.ImageDisplay: ObservableList containing the channels currently selected for display.
selectedColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
SelectedMeasurementTableView - Class in qupath.lib.gui.panes: Component to show measurements for a currently-selected object.
SelectedMeasurementTableView(ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.SelectedMeasurementTableView: Constructor.
selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.UndoRedoManager
selectedObjectChanged(QuPathViewer, PathObject) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener: Called when the primary selected object has changed in a viewer.
selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.viewer.ViewerManager
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.AnnotationPane
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.QuPathViewer
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in interface qupath.lib.objects.hierarchy.events.PathObjectSelectionListener: Fired when the selected objects have changed.
selectedProperty() - Method in class qupath.lib.gui.SelectableItem: Property representing the item that has been selected (which may or may not be the same as SelectableItem.getItem()).
selectedStyleProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Get the current selected style.
selectedTextProperty() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
selectedTextProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Text currently selected in the editor control.
selectedTextProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
selectedTool() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
selectedToolProperty() - Method in class qupath.lib.gui.ToolManager: Property containing the currently-selected PathTool.
SELECTION_MODE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
SELECTION_MODE - Variable in class qupath.lib.gui.ToolManager
selectionModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Convert drawing tools to select objects, rather than creating new objects.
selectObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Ensure the specified objects are selected.
selectObjects(Collection<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Set all objects in a collection to be selected, without any being chosen as the main object.
selectObjects(Collection<? extends PathObject>, PathObject) - Static method in class qupath.lib.scripting.QP: Set all objects in a collection to be selected, including a specified main selected object.
selectObjects(Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP: Set selected objects to contain (only) all objects in the current hierarchy according to a specified predicate.
selectObjects(PathObjectHierarchy, Predicate<PathObject>) - Static method in class qupath.lib.scripting.QP: Set selected objects to contain (only) all objects in the specified hierarchy according to a specified predicate.
selectObjects(PathObjectHierarchy, PathObject...) - Static method in class qupath.lib.scripting.QP: Set one or more objects to be selected within the specified hierarchy.
selectObjects(PathObject...) - Static method in class qupath.lib.scripting.QP: Set one or more objects to be selected within the current hierarchy.
selectObjectsByClass(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Set objects that are a subclass of a specified class.
selectObjectsByClass(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands: Select objects that are instances of a specified class, logging an appropriate method in the workflow.
selectObjectsByClass(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP: Set objects that are a subclass of a specified class.
selectObjectsByClassification(String...) - Static method in class qupath.lib.scripting.QP: Select objects for the current hierarchy that have one of the specified classifications.
selectObjectsByClassification(ImageData<?>, PathClass...) - Static method in class qupath.lib.gui.commands.Commands: Select objects by classification, logging the step (if performed) in the history workflow.
selectObjectsByClassification(PathObjectHierarchy, String...) - Static method in class qupath.lib.scripting.QP: Select objects for the specified hierarchy that have one of the specified classifications.
selectObjectsByMeasurement(ImageData<?>, String) - Static method in class qupath.lib.scripting.QP: Deprecated.
selectObjectsByPathClass(PathClass...) - Static method in class qupath.lib.scripting.QP: Select objects for the current hierarchy that have one of the specified PathClass classifications assigned.
selectObjectsByPathClass(PathObjectHierarchy, PathClass...) - Static method in class qupath.lib.scripting.QP: Select objects for the specified hierarchy that have one of the specified PathClass classifications assigned.
selectObjectsByPlane(int, int) - Static method in class qupath.lib.scripting.QP: Selected objects in the current hierarchy occurring on the specified z-slice and timepoint.
selectObjectsByPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP: Selected objects in the specified hierarchy occurring on the specified plane (z-slice and timepoint).
selectObjectsByPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP: Selected objects in the current hierarchy occurring on the specified plane (z-slice and timepoint).
selectObjectsOnCurrentPlane(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands: Select all the objects on the current plane of the viewer.
selectRange(int, int) - Method in interface qupath.lib.gui.scripting.EditableText: Set the range of the selected text.
selectRange(int, int) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
selectRange(int, int) - Method in class qupath.lib.gui.scripting.TextAreaControl
selectTiles() - Static method in class qupath.lib.scripting.QP: Select all tile objects in the current hierarchy.
selectTiles(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Select all tile objects in the specified hierarchy.
selectTMACores() - Static method in class qupath.lib.scripting.QP: Select all TMA core objects in the current hierarchy, excluding missing cores.
selectTMACores(boolean) - Static method in class qupath.lib.scripting.QP: Select all TMA core objects in the current hierarchy, optionally including missing cores.
selectTMACores(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Select all TMA core objects in the specified hierarchy, excluding missing cores.
selectTMACores(PathObjectHierarchy, boolean) - Static method in class qupath.lib.scripting.QP: Select all TMA core objects in the specified hierarchy, optionally including missing cores.
sendLogToConsoleProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Boolean property indicating whether the console should display the log, rather than directly-printed information.
sendQuitRequest() - Method in class qupath.lib.gui.QuPathGUI: Request to quit QuPath.
SEP - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
SEP - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
SEP_0 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
SEP_0 - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
SEP_0 - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
SEP_0 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
SEP_0 - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
SEP_0 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_00 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
SEP_00 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
SEP_00 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
SEP_01 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
SEP_01 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
SEP_02 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
SEP_02 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
SEP_1 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_2 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
SEP_2 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
SEP_2 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
SEP_2 - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
SEP_2 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SEP_2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_22 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
SEP_2B - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
SEP_3 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
SEP_3 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
SEP_3 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
SEP_3 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
SEP_3 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
SEP_3 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
SEP_4 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
SEP_4 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
SEP_4 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
SEP_4 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
SEP_4 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_5 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
SEP_5 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
SEP_5 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_6 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
SEP_6 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
SEP_6 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_7 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
SEP_7 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
SEP_7 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_8 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
SEP_8 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
SEP_8 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SEP_9 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
separator(String) - Method in class qupath.lib.gui.tools.MeasurementExporter: Specify the separator used between measurement values.
sepFilter2D(Mat, Mat, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a separable filter to an image, with symmetric boundary padding.
sepFilter2D(Mat, Mat, Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a separable filter to an image.
sequential(Collection<? extends ImageOp>) - Static method in class qupath.opencv.ops.ImageOps.Core: Apply a collection of ops sequentially, chaining the output of one op as the input for the next.
sequential(ImageOp...) - Static method in class qupath.opencv.ops.ImageOps.Core: Apply an array of ops sequentially, chaining the output of one op as the input for the next.
series(String, double[], double[]) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Create a scatterplot using arrays of numeric values.
series(String, double[], double[], List<T>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Create a scatterplot using collections of numeric values, with an associated custom object.
series(String, double[], double[], T[]) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Create a scatterplot using collections of numeric values, with an associated custom object.
series(String, String[], double[]) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Create a bar chart using arrays of String values and associated numeric values.
series(String, String[], double[], List<T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Create a bar chart using collections of String values and associated numeric values, with an associated custom object.
series(String, String[], double[], T[]) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Create a bar chart using collections String values and associated numeric values, with an associated custom object.
series(String, Collection<? extends Number>, Collection<? extends Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Create a scatterplot using collections of numeric values.
series(String, Collection<? extends String>, Collection<T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Create a bar chart using collections of numeric values.
series(String, Collection<? extends T>, Function<T, Number>, Function<T, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Plot values extracted from objects within a specified collection.
series(String, Collection<? extends T>, Function<T, PathClass>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Plot values extracted from objects within a specified collection.
series(String, Collection<XYChart.Data<Number, Number>>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Create a scatterplot from existing data plots.
series(String, Collection<XYChart.Data<String, Number>>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Create a bar chart from existing data plots.
series(String, Map<String, T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Create a bar chart using a map of String values and associated numeric values.
SERIF - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts: Preferred serif font.
server(ImageServer<BufferedImage>) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Set the server.
serverRegion(ImageRegion, double, ImageServer<BufferedImage>) - Method in class qupath.lib.images.servers.SparseImageServer.Builder: Add a region based on an existing ImageServer.
ServerSelector - Class in qupath.lib.gui.panes: Helper class for selecting one image server out of a collection.
ServerTools - Class in qupath.lib.images.servers: Static methods helpful when dealing with ImageServers.
ServerTools() - Constructor for class qupath.lib.images.servers.ServerTools
setAccelerator(String, String) - Method in class qupath.lib.gui.QuPathGUI: Set an accelerator for the specified menu command.
setAccelerator(MenuItem, KeyCombination) - Method in class qupath.lib.gui.QuPathGUI: Set the accelerator for the specified menu item.
setAccelerator(Action, KeyCombination) - Method in class qupath.lib.gui.QuPathGUI: Set the accelerator for the specified action.
setActiveHandlePosition(double, double, double, boolean) - Method in class qupath.lib.roi.RoiEditor: If a handle has been grabbed, update its displacement.
setActiveTool(PathTool) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the active PathTool for input to this viewer.
setActiveViewer(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager: Sets the value of the activeViewer property.
setAll() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level to LogLevel.ALL.
setAlphaComposite(Graphics2D) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
setArgs(String[]) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set optional string args to pass to the script.
setBatchIndex(int) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the current image index for batch processing (default is 0).
setBatchProjectAndImage(Project<BufferedImage>, ImageData<BufferedImage>) - Static method in class qupath.lib.scripting.QP: Set the Project and ImageData to use for batch processing for the current thread.
setBatchSaveResult(boolean) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Specify whether the script that is running should save results or not.
setBatchSize(int) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the batch size for batch processing (default is 1).
setBioformatsEnabled(boolean) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Set whether Bio-Formats should be enabled or disabled (in favor of other readers).
setBorderColor(Color) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the border color for this viewer.
setBoundaryLabel(String, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Set the classification and label to use for boundaries for classified areas.
setBoundaryLabel(String, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Set the classification and label to use for boundaries for classified areas.
setBoundaryLabel(PathClass, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Set the classification and label to use for boundaries for classified areas.
setBoundaryLabel(PathClass, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Set the classification and label to use for boundaries for classified areas.
setBoundaryStrategy(BoundaryStrategy) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Set the strategy for handling the boundaries of area annotations.
setCache(Map<RegionRequest, T>, Class<T>) - Static method in class qupath.lib.images.servers.ImageServerProvider: Set the cache to be used for image tiles of a specific type.
setCaseID(String) - Method in class qupath.lib.objects.TMACoreObject: Set the case ID metadata value.
setCellIntensityClassifications(String, double...) - Static method in class qupath.lib.scripting.QP: Set the intensity classifications for cells in the current hierarchy.
setCellIntensityClassifications(PathObjectHierarchy, String, double...) - Static method in class qupath.lib.scripting.QP
setCenterPixelLocation(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the image pixel to display in the center of the viewer (using image pixel coordinates at the full-resolution)
setChanged(boolean) - Method in class qupath.lib.images.ImageData: Set ImageData.isChanged() status.
setChannelColors(Integer...) - Static method in class qupath.lib.scripting.QP: Set the channel colors for the current ImageData.
setChannelColors(ImageData<?>, Integer...) - Static method in class qupath.lib.scripting.QP: Set the channel colors for the specified ImageData.
setChannelDisplayRange(int, double, double) - Static method in class qupath.lib.gui.scripting.QPEx: Set the minimum and maximum display range for the current ImageData for a channel identified by number.
setChannelDisplayRange(String, double, double) - Static method in class qupath.lib.gui.scripting.QPEx: Set the minimum and maximum display range for the current ImageData for a channel identified by name.
setChannelDisplayRange(ImageData<BufferedImage>, int, double, double) - Static method in class qupath.lib.gui.scripting.QPEx: Set the minimum and maximum display range for the specified ImageData for a channel identified by number.
setChannelDisplayRange(ImageData<BufferedImage>, String, double, double) - Static method in class qupath.lib.gui.scripting.QPEx: Set the minimum and maximum display range for the specified ImageData for a channel identified by name.
setChannelNames(String...) - Static method in class qupath.lib.scripting.QP: Set the channel names for the current ImageData.
setChannelNames(ImageData<?>, String...) - Static method in class qupath.lib.scripting.QP: Set the channel names for the specified ImageData.
setChannels(ImageData<?>, ImageChannel...) - Static method in class qupath.lib.scripting.QP: Set the channels for the specified ImageData.
setChannels(ImageChannel...) - Static method in class qupath.lib.scripting.QP: Set the channels for the current ImageData.
setChannelSelected(ChannelDisplayInfo, boolean) - Method in class qupath.lib.display.ImageDisplay: Set the selection of a channel on or off.
setChannelType(ImageServerMetadata.ChannelType) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder: Specify the output channel type.
setClassifications(Collection<String>) - Method in class qupath.lib.objects.PathObject: Set the PathClass from a collection of names according to the rules: If the collection is empty, reset the PathClass If the collection has one element, set it to be the name of the PathClass If the collection has multiple element, create and set a derived PathClass with each unique element the name of a PathClass component The uniqueness is equivalent to copying the elements into a set; if a set is provided as input then a defensive copy will be made..
setColor(int, int, int) - Method in class qupath.lib.objects.classes.PathClass: Set the color as 8-bit RGB values
setColor(int, int, int) - Method in class qupath.lib.objects.PathObject: Set the display color as 8-bit RGB values
setColor(Integer) - Method in class qupath.lib.objects.classes.PathClass: Set the color that should be used to display objects with this classification.
setColor(Integer) - Method in class qupath.lib.objects.PathObject: Set the display color as a packed (A)RGB integer (alpha may not be used by viewing code).
setColorDeconvolutionStains(String) - Static method in class qupath.lib.scripting.QP: Set the color deconvolution stains for hte current image data using a (JSON) String representation
setColorDeconvolutionStains(ColorDeconvolutionStains) - Method in class qupath.lib.images.ImageData: Set the color deconvolution stain vectors for the current image type.
setColorMap(ColorMaps.ColorMap) - Method in class qupath.lib.gui.ColorMapCanvas: Set the ColorMaps.ColorMap to display to the one with the specified list index.
setColorMapper(ColorMaps.ColorMap) - Method in class qupath.lib.gui.tools.MeasurementMapper: Set a new color mapper.
setColorModel(ColorModel) - Method in class qupath.lib.gui.images.stores.ColorModelRenderer: Set the color model to use.
setColorModel(ColorModel) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay: Optionally set a custom ColorModel.
setColorRGB(Integer) - Method in class qupath.lib.objects.PathObject: Deprecated.
since v0.4.0, use PathObject.setColor(Integer) instead.
setComplete(boolean) - Method in class qupath.lib.plugins.ParallelTileObject: Notify the tile that its processing is done.
setContextMenu(ContextMenu) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
setContextMenu(ContextMenu) - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Set the context menu for the control.
setContextMenu(ContextMenu) - Method in class qupath.lib.gui.scripting.TextAreaControl
setCountsTransform(HistogramChart.CountsTransformMode) - Method in class qupath.lib.gui.charts.HistogramChart: Set the current counts transform.
setCreateFunction(IntFunction<TaskRunner>) - Method in class qupath.lib.plugins.TaskRunnerUtils: Set the function used to generate new headless TaskRunner instances.
setCreateHeadlessFunction(IntFunction<TaskRunner>) - Method in class qupath.lib.plugins.TaskRunnerUtils: Set the function used to generate new TaskRunner instances.
setCursor(Cursor) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the requested cursor to display in this viewer
setCustomPixelLayerOverlay(PathOverlay) - Method in class qupath.lib.gui.viewer.QuPathViewer: Optionally set a custom overlay to use for the pixel layer.
setDebug() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level to DEBUG.
setDebugMode(boolean) - Static method in class qupath.imagej.detect.cells.WatershedCellDetection: Set whether to use debug mode.
setDefaultColorMap(ColorMaps.ColorMap) - Static method in class qupath.lib.color.ColorMaps: Set the default ColorMaps.ColorMap.
setDefaultImageData(ImageData<BufferedImage>) - Static method in class qupath.lib.scripting.QP: Set the default image data, which will be returned by QP.getCurrentImageData() if it would otherwise return null (i.e.
setDefaultImports(Collection<Class<?>>) - Method in class qupath.lib.scripting.ScriptParameters.Builder
setDefaultProject(Project<BufferedImage>) - Static method in class qupath.lib.scripting.QP: Set the default project, which will be returned by QP.getProject() if it would otherwise return null (i.e.
setDefaultStaticImports(Collection<Class<?>>) - Method in class qupath.lib.scripting.ScriptParameters.Builder
setDescription(String) - Method in class qupath.lib.objects.PathAnnotationObject: Set a free text description for this annotation.
setDescription(String) - Method in interface qupath.lib.projects.ProjectImageEntry: Set the description.
setDetectionDisplayMode(OverlayOptions.DetectionDisplayMode) - Method in class qupath.lib.gui.viewer.OverlayOptions: Set the current OverlayOptions.DetectionDisplayMode.
setDetectionIntensityClassifications(String, double...) - Static method in class qupath.lib.scripting.QP: Set the intensity classifications for detections in the current hierarchy.
setDetectionIntensityClassifications(PathObjectHierarchy, String, double...) - Static method in class qupath.lib.scripting.QP: Set the intensity classifications for detections in the specified hierarchy.
setDisplayMaxValue(double) - Method in class qupath.lib.gui.tools.MeasurementMapper: Set the measurement value that maps to the last color in the color mapper.
setDisplayMinValue(double) - Method in class qupath.lib.gui.tools.MeasurementMapper: Set the measurement value that maps to the first color in the color mapper.
setDisplayMode(HistogramChart.DisplayMode) - Method in class qupath.lib.gui.charts.HistogramChart: Set the histogram display mode.
setDoFasterRepaint(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set flag to indicate that repaints should prefer speed over accuracy.
setDoubleLastValue(double) - Method in class qupath.lib.plugins.parameters.DoubleParameter
setDoubleLastValue(double) - Method in class qupath.lib.plugins.parameters.IntParameter
setDoubleLastValue(double) - Method in class qupath.lib.plugins.parameters.NumericParameter: A class for setting the numeric value as a double (subclasses should convert this as needed).
setDownsample(double) - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager: Set the downsample to use within the mini viewers.
setDownsampleFactor(double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the downsample factor for this viewer.
setDownsampleFactor(double, double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set downsample factor, so that the specified coordinate in the image space is not shifted in the viewer afterwards.
setDownsampleFactor(double, double, double, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set downsample factor, so that the specified coordinate in the image space is not shifted in the viewer afterwards.
setError() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level to LogLevel.ERROR.
setErrorWriter(Writer) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the main error writer.
setExcludeOutsideRange(boolean) - Method in class qupath.lib.gui.tools.MeasurementMapper: Specify whether out-of-range values should be excluded.
setExpandToWindow(boolean) - Method in class qupath.lib.gui.panes.SimpleImageViewer: Control whether the image should be allowed to expand beyond its preferred width and height to fill the window.
setFeatureOp(ImageDataOp) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Set the ImageDataOp used to calculate features.
setFile(File) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Set the file for this ViewTracker.
setFile(File) - Method in class qupath.lib.scripting.ScriptParameters.Builder
setFilesOnly(boolean) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Set whether Bio-Formats should support only local files (rather than any URL).
setFillAnnotations(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show annotation objects 'filled' in viewers.
setFillDetections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show detection objects 'filled' in viewers.
setFillHeight(Boolean, Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the GridPane.setFillHeight(Node, Boolean) property for specified nodes.
setFillWidth(Boolean, Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the GridPane.setFillWidth(Node, Boolean) property for specified nodes.
setFontSize(float) - Method in class qupath.lib.gui.viewer.OverlayOptions: Set the requested font size for the 'Show names' option
setGamma(double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the gamma value for this viewer.
setGridLines(GridLines) - Method in class qupath.lib.gui.viewer.OverlayOptions: Set the GridLines object that defines how a counting grid may be show in viewers
setGridSize(int, int) - Method in class qupath.lib.gui.viewer.ViewerManager: Set the grid to have a specific number of rows and columns.
setHGrowPriority(Priority, Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the GridPane.setHgrow(Node, Priority) property for specified nodes.
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.BooleanParameter
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.ChoiceParameter
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.DoubleParameter
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.EmptyParameter
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.IntParameter
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.NumericParameter
setHidden(boolean) - Method in class qupath.lib.plugins.parameters.StringParameter
setHidden(boolean) - Method in interface qupath.lib.plugins.parameters.Parameter: Mark that a parameter should not be displayed to a user.
setHiddenParameters(boolean, String...) - Method in class qupath.lib.plugins.parameters.ParameterList: Set the 'hidden' flag for parameters with the specified keys.
setHideChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Request that the specified channel is hidden.
setHideIfEmpty(boolean) - Method in class qupath.lib.gui.charts.HistogramChart: Request that the chart is automatically hidden (visibility set to false) when there is no data.
setHierarchy(PathObjectHierarchy) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Set the contents of this hierarchy to be the same as that of another hierarchy.
setID(UUID) - Method in class qupath.lib.objects.PathObject: Set the ID for this object.
setImageData(ImageData<?>) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the current image data for the script.
setImageData(ImageData<?>, Collection<? extends PathObject>) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Set the ImageData and a collection of objects to measure.
setImageData(ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the current image for this viewer.
setImageData(ImageData<BufferedImage>, boolean) - Method in class qupath.lib.display.ImageDisplay: Set the ImageData to a new value
setImageJPath(String) - Static method in class qupath.imagej.gui.IJExtension: Set the path for a local ImageJ installation, if required.
setImageName(String) - Method in interface qupath.lib.projects.ProjectImageEntry: Set the image name for this project entry.
setImageName(ImageServer<?>, String) - Static method in class qupath.lib.images.servers.ServerTools: Set the name property of the metadata for an ImageServer.
setImageType - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
setImageType(String) - Static method in class qupath.lib.scripting.QP: Set the image type for the current image data, using a String to represent the enum ImageData.ImageType
setImageType(ImageData.ImageType) - Method in class qupath.lib.images.ImageData: Set the image type.
setImageType(ImageData.ImageType) - Static method in class qupath.lib.scripting.QP: Set the image type for the current image data
setInfo() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level to DEBUG.
setInputFile(File) - Method in class qupath.lib.gui.tma.TMASummaryViewer: Deprecated.

Set the input file for the summary viewer.
setIntensityClassification(PathObject, String, double...) - Static method in class qupath.lib.objects.PathObjectTools: Assign cell classifications as positive or negative based upon a specified measurement, using up to 3 intensity bins.
setIntensityClassifications(Class<? extends PathObject>, String, double...) - Static method in class qupath.lib.scripting.QP: Set the intensity classifications for objects of the specified class in the current hierarchy.
setIntensityClassifications(Collection<? extends PathObject>, String, double...) - Static method in class qupath.lib.objects.PathObjectTools: Set the intensity classifications for the specified objects.
setIntensityClassifications(Collection<? extends PathObject>, String, double...) - Static method in class qupath.lib.scripting.QP: Set the intensity classifications for the specified objects.
setIntensityClassifications(PathObjectHierarchy, Class<? extends PathObject>, String, double...) - Static method in class qupath.lib.scripting.QP: Set the intensity classifications for objects of the specified class in the specified hierarchy.
setIntensityClassificationsForSelected(PathObjectHierarchy, String, double...) - Static method in class qupath.lib.scripting.QP: Set intensity classifications for all selected (detection) objects in the specified hierarchy.
setInterpolation(Graphics2D) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
setInterpolation(ImageInterpolation) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay: Set the preferred method of interpolation to use for display.
setIsInteractive(boolean) - Method in class qupath.lib.gui.charts.ChartThresholdPane: Sets the value of ChartThresholdPane.isInteractiveProperty().
setLastSavedPath(String, boolean) - Method in class qupath.lib.images.ImageData: Set the last path used to save this object;
setLineChartLegendLines(Chart, double) - Static method in class qupath.lib.gui.charts.ChartTools: Charts tend to show their legends with circular/square markers...
setLineWidth(double) - Method in class qupath.lib.gui.charts.ChartThresholdPane: Set the threshold line width.
setLivePrediction(boolean) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Turn on or off live prediction.
setLocationStringFunction(AbstractOverlay.LocationStringFunction) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay: Set a custom function to calculate a location string for the overlay.
setLocked(boolean) - Method in class qupath.lib.objects.PathObject: Set locked status, if possible.
setLocked(boolean) - Method in class qupath.lib.objects.PathROIObject: Set locked flag, indicating that the object ROI should not be modified.
setLUTColor(int, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo: Set the 'maximum' color, which defines the lookup table to use.
setMagnification(double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the downsample factor based upon magnification values.
setMaskImageNames(boolean) - Method in interface qupath.lib.projects.Project: Request that entries return masked image names, rather than the 'true' image names.
setMaxDisplay(float) - Method in class qupath.lib.display.DirectServerChannelInfo
setMaxDisplay(float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo: Set the max display value for this channel.
setMaxHeight(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the max height property for the specified regions.
setMaxThreads(int) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Set the maximum number of threads that may be used during live prediction.
setMaxWidth(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the max width property for the specified regions.
setMeasurementMapper(MeasurementMapper) - Method in class qupath.lib.gui.viewer.OverlayOptions: Set the MeasurementMapper that defines how detections should be color coded according to their measurement values in viewers
setMemoizationTimeMillis(int) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Set the number of milliseconds that must elapse when opening an image before a memoization file is generated.
setMemoryThreshold(double) - Static method in class qupath.imagej.tools.IJTools
setMetadata(ImageServerMetadata) - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer: Not allowed - throws an UnsupportedOperationException.
setMetadata(ImageServerMetadata) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer: Throws an exception - metadata should not be set for a hierarchy image server directly.
setMetadata(ImageServerMetadata) - Method in class qupath.lib.images.servers.AbstractImageServer
setMetadata(ImageServerMetadata) - Method in interface qupath.lib.images.servers.ImageServer: Set the metadata to use, e.g.
setMetadata(ImageServerMetadata) - Method in class qupath.lib.images.servers.LabeledImageServer: Throws an exception - metadata should not be set for a hierarchy image server directly.
setMinDisplay(float) - Method in class qupath.lib.display.DirectServerChannelInfo
setMinDisplay(float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo: Set the min display value for this channel.
setMinHeight(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the min height property for the specified regions.
setMinimumRepaintSpacingMillis(long) - Method in class qupath.lib.gui.viewer.QuPathViewer: Prevent frequent repaints (temporarily) by setting a minimum time that must have elapsed after the previous repaint for a new one to be triggered.
setMinMaxAllowed(float, float) - Method in class qupath.lib.display.DirectServerChannelInfo
setMinMaxAllowed(float, float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo: Set the maximum permissible range for the image display.
setMinMaxDisplay(ChannelDisplayInfo, float, float) - Method in class qupath.lib.display.ImageDisplay: Set the min/max display values for a specified ChannelDisplayInfo.
setMinWidth(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the min width property for the specified regions.
setMissing(boolean) - Method in class qupath.lib.objects.TMACoreObject: Set the missing flag for this core, for example because insufficient tissue is present.
setName(String) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Set the name of this ViewTracker.
setName(String) - Method in class qupath.lib.objects.PathObject: Set the stored object name.
setNumBins(int) - Method in class qupath.lib.gui.charts.HistogramDisplay: Set the number of bins for the histogram.
setNumericParameterValue(String, Number) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Set a numeric parameter value (either int or double).
setNumericParameterValueRange(String, double, double) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Set the minimum and maximum value for a numeric parameter.
setNumThreads(int) - Static method in class qupath.lib.common.Prefs: Set the requested number of threads.
setOff() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level to LogLevel.OFF.
setOpacity(double) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay: Set opacity between 0 (completely transparent) and 1 (completely opaque).
setOpacity(float) - Method in class qupath.lib.gui.viewer.OverlayOptions: Set global opacity for overlay drawing.
setOptionalParameters(boolean, boolean, boolean, boolean) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Set optional parameters for this ViewTracker.
setOverrideSystemMenuBar(boolean) - Static method in class qupath.lib.gui.prefs.SystemMenuBar: Set the current value of the override property, which optionally specifies whether the system menubar should not be used by any window - no matter what the value of SystemMenuBar.systemMenubarProperty().
setParallelism(int) - Static method in class qupath.lib.common.ThreadTools: Set the requested level of parallelism.
setParameterEnabled(String, boolean) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Set the enabled status of a parameter by key, to determine if it can be edited.
setParameterEnabled(Parameter<?>, boolean) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX: Set the enabled status of a parameter, to determine if it can be edited.
setPathClass(PathClass) - Method in class qupath.lib.objects.PathObject: Set the classification of the object, without specifying any classification probability.
setPathClass(PathClass, double) - Method in class qupath.lib.objects.PathObject: Set the classification of the object, specifying a classification probability.
setPathClass(PathClass, double) - Method in class qupath.lib.objects.PathROIObject
setPathClass(PathClass, double) - Method in class qupath.lib.objects.PathRootObject
setPathClasses(Collection<? extends PathClass>) - Method in interface qupath.lib.projects.Project: Update the available PathClasses.
setPathClassHidden(PathClass, boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Request that objects with a particular PathClass not be displayed.
setPathMemoization(String) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Set the directory where memoization files should be written.
setPathObject(PathObject) - Method in class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane: Set the PathObject to display (may be null).
setPenManager(QuPathPenManager.PenInputManager) - Static method in class qupath.lib.gui.viewer.tools.QuPathPenManager: Set the PenInputManager.
setPieChartData(PieChart, Map<T, ? extends Number>, Function<T, String>, Function<T, Color>, boolean, boolean) - Static method in class qupath.lib.gui.charts.ChartTools: Set pie chart data from a count map.
setPixelClassificationRegionFilter(RegionFilter) - Method in class qupath.lib.gui.viewer.OverlayOptions: Control where pixel classifications should be calculated during live prediction
setPixelLayer(ImageData<BufferedImage>, ImageServer<BufferedImage>) - Static method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Set an ImageServer as a property in the ImageData.
setPixelSizeMicrons(Number, Number) - Static method in class qupath.lib.scripting.QP: Set the metadata for the current ImageData to have the required pixel sizes.
setPixelSizeMicrons(Number, Number, Number) - Static method in class qupath.lib.scripting.QP: Set the metadata for the current ImageData to have the required pixel sizes and z-spacing.
setPixelSizeMicrons(ImageData<?>, Number, Number, Number) - Static method in class qupath.lib.scripting.QP: Set the metadata for an ImageServer to have the required pixel sizes and z-spacing.
setPlaceholderText(String) - Method in class qupath.lib.gui.panes.SimpleImageViewer: Set the placeholder text to show if no image is available.
setPredicate(Predicate<? super PathObject>) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Set a predicate used to filter the rows of the table.
setPreferredOverlayColor(Color) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay: Set a preferred overlay color, which the overlay may or may not make use of.
setProject(Project<?>) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the current project for the script.
setProject(Project<BufferedImage>) - Method in class qupath.lib.gui.panes.ProjectBrowser: Set the project.
setProject(Project<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI: Set the active project, triggering any necessary GUI updates.
setProperty(String, Object) - Method in class qupath.lib.images.ImageData: Set a property.
setRange(double, double) - Method in class qupath.lib.plugins.parameters.NumericParameter: Set the upper and lower bounds.
setReaderOptions(Map<String, String>) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Set additional arguments that should be passed to readers.
setReadOnly(boolean) - Method in class qupath.lib.gui.QuPathGUI: Specify whether QuPath should be in 'read-only' mode.
setRecording(boolean) - Method in class qupath.lib.gui.viewer.recording.ViewTracker: Set the recording property of this ViewTracker.
setRenderer(ImageRenderer) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Set the ImageRenderer to be used with this overlay.
setRequestedDataFileVersion(int) - Static method in class qupath.lib.io.PathIO: Set the requested version for .qpdata files.
setRequestParallelization(boolean) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions: Optionally enable or disable parallelization when reading images.
setResolution(PixelCalibration) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining: Set the resolution at which the training should occur.
setROI(ROI) - Method in class qupath.lib.objects.PathROIObject: Set the ROI for this object.
setROI(ROI) - Method in class qupath.lib.roi.RoiEditor: Set the active ROI, stopping any ROI translation currently in progress.
setROI(ROI, boolean) - Method in class qupath.lib.roi.RoiEditor: Set the active ROI, optionally stopping any ROI translation currently in progress.
setRootLogLevel(LogManager.LogLevel) - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level.
setRotation(double) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the rotation; angle in radians.
setSaturationPercent(double) - Method in class qupath.lib.gui.panes.SimpleImageViewer: Set the percentage of pixels to use when applying auto contrast settings to a non-8-bit image.
setScript(String) - Method in class qupath.lib.scripting.ScriptParameters.Builder
setScriptEditor(ScriptEditor) - Method in class qupath.lib.gui.QuPathGUI: Set a new ScriptEditor, which will be used from now on.
setSelectable(Action, boolean) - Static method in class qupath.lib.gui.actions.ActionTools: Set the selectable property for an action.
setSelected(boolean) - Method in class qupath.lib.gui.SelectableItem: Set the item to be selected.
setSelectedObject(PathObject) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set selected object in the current hierarchy, without centering the viewer.
setSelectedObject(PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Set the specified object to be selected, deselecting all others.
setSelectedObject(PathObject) - Static method in class qupath.lib.scripting.QP: Set the selected object for the current PathObjectHierarchy.
setSelectedObject(PathObject, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set selected object in the current hierarchy, without centering the viewer.
setSelectedObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Select the specified object to be the primary selected object, optionally retaining the existing selected objects.
setSelectedObjects(Collection<? extends PathObject>, PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Specify a collection of objects to be selected, and which among them should be the primary.
setSelectedTool(PathTool) - Method in class qupath.lib.gui.ToolManager: Programmatically select the active PathTool.
setServiceLoader(ServiceLoader<ImageServerBuilder>) - Static method in class qupath.lib.images.servers.ImageServerProvider: Replace the default service loader with another.
setShowAnnotations(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show the annotations on the image.
setShowChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Request that the specified channel is shown.
setShowConnections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show connections between objects, if available.
setShowDetections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show the objects as an overlay on the image.
setShowGrid(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Set whether a counting grid should be shown in viewers
setShowLocation(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Set the value of ViewerPlusDisplayOptions.showLocationProperty().
setShowNames(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show the object names on the image.
setShowOverview(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Set the value of ViewerPlusDisplayOptions.showOverviewProperty().
setShowPixelClassification(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show pixel classification overlays.
setShowScalebar(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Set the value of ViewerPlusDisplayOptions.showScalebarProperty().
setShowTickLabels(boolean) - Method in class qupath.lib.gui.charts.HistogramChart: Request that tick labels are visible or not for both x and y axis.
setShowTMACoreLabels(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show TMA core names on top of the image.
setShowTMAGrid(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions: Show the TMA grid on the image, if present.
setSlidersPosition(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewerPlus: Sets the Z and T sliders' position to allow space for command bar
setSpaceDown(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer: Notify this viewer that the isSpaceDown status should be changed.
setSpaceX(double) - Method in class qupath.lib.gui.viewer.GridLines: Set the horizontal spacing between lines for any counting grid.
setSpaceY(double) - Method in class qupath.lib.gui.viewer.GridLines: Set the vertical spacing between lines for any counting grid.
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.BooleanParameter
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.ChoiceParameter: This will only work for string choices...
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.EmptyParameter
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.NumericParameter
setStringLastValue(Locale, String) - Method in interface qupath.lib.plugins.parameters.Parameter: Set last value using a string; implementing classes may need to parse this
setStringLastValue(Locale, String) - Method in class qupath.lib.plugins.parameters.StringParameter
setStyle() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption: Set the style for the QuPath application.
setSwitchToGrayscaleChannel(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay: Set the value of ImageDisplay.switchToGrayscaleChannelProperty().
setSynchronizeViewers(boolean) - Method in class qupath.lib.gui.viewer.ViewerManager: Sets the value of the synchronizeViewers property.
setSystemWriters() - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the output and error writers to use System.out and System.err.
setText(String) - Method in interface qupath.lib.gui.scripting.EditableText: Set all the text in the editor.
setText(String) - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl: Sets the value of the text property.
setText(String) - Method in class qupath.lib.gui.scripting.TextAreaControl: Sets the value of the text property.
setTextFieldFromNumber(TextField, Number, String) - Static method in class qupath.lib.gui.dialogs.ParameterPanelFX
setThickness(BoundaryStrategy, double) - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy: Create a boundary strategy with the specified thickness.
setThresholdColor(ObservableNumberValue, Color) - Method in class qupath.lib.gui.charts.ChartThresholdPane: Set the color of a specified threshold line.
setThresholds(Color, double...) - Method in class qupath.lib.gui.charts.ChartThresholdPane: Set thresholds, which are visualized as vertical lines.
setThumbnail(T) - Method in interface qupath.lib.projects.ProjectImageEntry: Set a thumbnail for the image.
settings(ImageDisplaySettings) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify the ImageDisplaySettings that control conversion to RGB.
settingsCompatibleWithDisplay(ImageDisplay, ImageDisplaySettings) - Static method in class qupath.lib.display.settings.DisplaySettingUtils: Check if the settings are compatible with the display.
setTitleFromObject(PathImage<ImagePlus>, PathObject) - Static method in class qupath.imagej.tools.IJTools: Set the name of an image based on a PathObject.
setTMAEntriesFromImageData(ImageData<BufferedImage>) - Method in class qupath.lib.gui.tma.TMASummaryViewer: Deprecated.

Set the TMA entries from the TMACoreObjects of a specific ImageData.
setTMAGrid(TMAGrid) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Set the tma grid for this hierarchy.
setToExpandGridPaneHeight(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set constraints and max width values (where possible) so that the specified nodes fill all available vertical space in a GridPane.
setToExpandGridPaneWidth(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set constraints and max width values (where possible) so that the specified nodes fill all available horizontal space in a GridPane.
setToolSwitchingEnabled(boolean) - Method in class qupath.lib.gui.ToolManager: Toggle whether the user is permitted to switch to a new active PathTool.
setTooltipFunction(Function<Double, String>) - Method in class qupath.lib.gui.ColorMapCanvas: Set the function that will take a value between 0 and 255 (from the color map) and output a displayable string
setTPosition(int) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the requested time point to be visible.
setTrace() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level to LogLevel.TRACE.
setupTarget(Node) - Method in class qupath.lib.gui.viewer.DragDropImportListener: Prepare a target node to accept drag and drop events.
setupTarget(Scene) - Method in class qupath.lib.gui.viewer.DragDropImportListener: Prepare a target scene to accept drag and drop events.
setUseCuda(boolean) - Static method in class qupath.opencv.dnn.DnnTools: Request that CUDA is used.
setUseGrayscaleLuts(boolean) - Method in class qupath.lib.display.ImageDisplay: Set the value of ImageDisplay.useGrayscaleLutProperty()
setUseInvertedBackground(boolean) - Method in class qupath.lib.display.ImageDisplay: Set the value of ImageDisplay.useInvertedBackgroundProperty()
setUseMicrons(boolean) - Method in class qupath.lib.gui.viewer.GridLines: Specify whether to use calibrated units when calculating coordinates for any counting grid.
setUserPath(Path) - Method in class qupath.lib.gui.UserDirectoryManager: Set the user path where additional files may be stored.
setValue(int, int, float) - Method in class qupath.imagej.tools.PixelImageIJ
setValue(int, int, float) - Method in interface qupath.lib.analysis.images.SimpleModifiableImage: Set the value of a single pixel.
setValue(Double) - Method in class qupath.lib.plugins.parameters.DoubleParameter: Set the last value; this will apply a range check using clipping.
setValue(Integer) - Method in class qupath.lib.plugins.parameters.IntParameter: Set the last value; this will apply a range check using clipping.
setValue(Boolean) - Method in class qupath.lib.plugins.parameters.BooleanParameter
setValue(S) - Method in class qupath.lib.plugins.parameters.ChoiceParameter
setValue(String) - Method in class qupath.lib.plugins.parameters.EmptyParameter
setValue(S) - Method in class qupath.lib.plugins.parameters.NumericParameter
setValue(String) - Method in class qupath.lib.plugins.parameters.StringParameter
setValue(S) - Method in interface qupath.lib.plugins.parameters.Parameter: Set the Parameter to have a specified value.
setValues(DataBuffer, double) - Static method in class qupath.lib.awt.common.BufferedImageTools: Set all values in a DataBuffer.
setValueWithBoundsCheck(Double) - Method in class qupath.lib.plugins.parameters.DoubleParameter
setValueWithBoundsCheck(Integer) - Method in class qupath.lib.plugins.parameters.IntParameter
setValueWithBoundsCheck(S) - Method in class qupath.lib.plugins.parameters.NumericParameter: Set the value of this parameter, constraining it to be within any lower and upper bounds if necessary.
setVGrowPriority(Priority, Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Set the GridPane.setVgrow(Node, Priority) property for specified nodes.
setViewerDownsample(QuPathViewer, double) - Static method in class qupath.lib.gui.commands.Commands: Set the downsample factor for the specified viewer.
setWandSensitivity(double) - Static method in class qupath.process.gui.WandToolEventHandler: Set the wand sensitivity value, which influences how similar local intensity values must be for the wand region growing.
setWandSigmaPixels(double) - Static method in class qupath.process.gui.WandToolEventHandler: Set the Gaussian sigma value used to smooth the image when applying the wand.
setWandUseOverlays(boolean) - Static method in class qupath.process.gui.WandToolEventHandler: Set whether the wand tool should be influenced by pixel values painted on image overlays.
setWarn() - Static method in class qupath.lib.gui.logging.LogManager: Set the root log level to LogLevel.WARN.
setWriter(Writer) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the main output writer.
setZPosition(int) - Method in class qupath.lib.gui.viewer.QuPathViewer: Set the requested z-slice to be visible.
shape(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Get the shape of a multidimensional Mat.
SHAPE_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
ShapeFeaturesPlugin<T> - Class in qupath.lib.plugins.objects: Add shape measurements
ShapeFeaturesPlugin() - Constructor for class qupath.lib.plugins.objects.ShapeFeaturesPlugin: Constructor.
ShapeSimplifier - Class in qupath.lib.roi: Helper methods for simplifying shapes, such removing polygon points while retaining the a similar overall shape at a coarser level.
ShapeSimplifier() - Constructor for class qupath.lib.roi.ShapeSimplifier
shapeToGeometry(Shape) - Static method in class qupath.lib.roi.GeometryTools: Convert a java.awt.Shape to a JTS Geometry.
SharedThreadPoolManager - Class in qupath.lib.gui: Manager to simplify submitting short tasks in background threads using a shared ExecutorService.
show() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Add the chart to a stage, and show it in the Application thread.
show() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Add the chart to a stage, and show it in the Application thread.
show() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Add the chart to a stage, and show it in the Application thread.
show() - Method in class qupath.lib.gui.commands.LogViewerCommand
show() - Method in class qupath.lib.gui.commands.PathObjectGridView: Create the stage and show the grid view.
show() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Show the dialog.
SHOW_ANALYSIS_PANE - Variable in class qupath.lib.gui.actions.CommonActions
SHOW_ANALYSIS_PANEL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_ANNOTATIONS - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_CELL_BOUNDARIES - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
SHOW_CELL_BOUNDARIES - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_CELL_BOUNDARIES_AND_NUCLEI - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
SHOW_CELL_BOUNDARIES_AND_NUCLEI - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_CELL_CENTROIDS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
SHOW_CELL_CENTROIDS - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_CELL_NUCLEI - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
SHOW_CELL_NUCLEI - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_CONNECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_CONNECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_DETECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_GRID - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_LOCATION - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_LOCATION - Variable in class qupath.lib.gui.actions.ViewerActions
SHOW_LOG - Variable in class qupath.lib.gui.actions.CommonActions
SHOW_LOG - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_NAMES - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
SHOW_NAMES - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_NAMES - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_OBJECT_DESCRIPTIONS - Variable in class qupath.lib.gui.actions.CommonActions
SHOW_OBJECT_DESCRIPTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
SHOW_OVERVIEW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_OVERVIEW - Variable in class qupath.lib.gui.actions.ViewerActions
SHOW_PIXEL_CLASSIFICATION - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_PIXEL_CLASSIFICATION - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_POINTS_DIALOG - Variable in class qupath.lib.gui.actions.CommonActions
SHOW_SCALEBAR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
SHOW_SCALEBAR - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_SCALEBAR - Variable in class qupath.lib.gui.actions.ViewerActions
SHOW_TMA_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_TMA_GRID - Variable in class qupath.lib.gui.actions.OverlayActions
SHOW_TMA_GRID_LABELS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SHOW_TMA_GRID_LABELS - Variable in class qupath.lib.gui.actions.OverlayActions
showAnalysisPaneProperty() - Method in class qupath.lib.gui.QuPathGUI
showAndWait() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Show the dialog.
showAnnotationGridView(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Show a grid view for annotation objects.
showAnnotationMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Show a measurement table for all annotation objects.
showAnnotationsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showCellMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Show a measurement table for all cell objects.
showChannelViewer(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands: Show a channel viewer window associated with a specific viewer.
showChoiceDialog(String, String, Collection<T>, T) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a choice dialog with a collection of choices (selection from ComboBox or similar).
showChoiceDialog(String, String, T[], T) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a choice dialog with an array of choices (selection from ComboBox or similar).
showConfirmDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a confirm dialog (OK/Cancel).
showConfirmDialog(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a confirm dialog (OK/Cancel).
showConnectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showDeprecatedCommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
showDetectionMeasurementManager(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Show a simple dialog for viewing (and optionally removing) detection measurements.
showDetectionMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Show a measurement table for all detection objects.
showDetectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
showEditor() - Method in interface qupath.lib.gui.scripting.ScriptEditor: Show the script editor.
showErrorMessage(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an error message.
showErrorMessage(String, Throwable) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an error message, displaying the localized message of a Throwable.
showErrorMessage(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an error message, with the content defined within a Node.
showErrorNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an error notification.
showErrorNotification(String, Throwable) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an error notification, displaying the localized message of a Throwable.
showExperimentalCommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
showExperimentalOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Flag to indicate that menu items marked 'experimental' should be shown to the user.
showGridProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showHistogram(String) - Method in class qupath.lib.gui.charts.HistogramDisplay: Show the histogram for a specified data column.
showImageNameInTitle - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
showImageNameInTitleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Property specifying if QuPath should show the image title in the main window title.
showInfoNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an info notification.
showingProperty() - Method in class qupath.lib.gui.panes.SlideLabelView: Property indicating whether the label is showing on screen or not.
showInputDialog(String, String, Double) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an input dialog requesting a numeric value.
showInputDialog(String, String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an input dialog requesting a String input.
showInputDisplayProperty() - Method in class qupath.lib.gui.QuPathGUI: Property to indicate whether the input display is currently showing
showInstalledExtensions(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Show a dialog displaying the extensions installed for a specified QuPath instance.
showLegacyOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Flag to indicate that the legacy options should be shown to the user - normally not desirable.
showLocationProperty() - Method in class qupath.lib.gui.viewer.ViewerManager: Show the cursor location.
showLocationProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Show the cursor location.
showMeasurementTableObjectIDs - Variable in class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
showMeasurementTableObjectIDsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Specify whether measurement tables should show object IDs by default or not.
showMeasurementTableThumbnails - Variable in class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
showMeasurementTableThumbnailsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Specify whether measurement tables should show thumbnail images by default or not.
showMessageDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a standard message dialog.
showMessageDialog(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a message dialog (OK button only), with the content contained within a Node.
showMiniViewer(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands: Show a mini viewer window associated with a specific viewer.
showNamesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showNoImageError(String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an error message that no image is available.
showNoImageError(String) - Static method in class qupath.lib.gui.tools.GuiTools: Show an error message that no image is available.
showNoProjectError(String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show an error message that no project is available.
showNoProjectError(String) - Static method in class qupath.lib.gui.tools.GuiTools: Show an error message that no project is available.
showOverviewProperty() - Method in class qupath.lib.gui.viewer.ViewerManager: Show the overview image.
showOverviewProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Show the overview image.
showParameterDialog(String, ParameterList) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a (modal) dialog for a specified ParameterList.
showParameterDialog(String, ParameterList) - Static method in class qupath.lib.gui.tools.GuiTools: Show a (modal) dialog for a specified ParameterList.
showPixelClassificationProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showPlainMessage(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a plain message.
showPlainNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a plain notification.
showPointHullsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Show the convex hull for point annotations within the viewer.
showProjectMetadataEditor(Project<?>) - Static method in class qupath.lib.gui.commands.ProjectCommands: Show the metadata editor for the specified project.
showScalebarProperty() - Method in class qupath.lib.gui.viewer.ViewerManager: Show the scalebar.
showScalebarProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions: Show the scalebar.
showScript(File) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
showScript(File) - Method in interface qupath.lib.gui.scripting.ScriptEditor: Show the script editor, opening an existing script file.
showScript(String, String) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
showScript(String, String) - Method in interface qupath.lib.gui.scripting.ScriptEditor: Show the script editor, including a new script with the specified name.
showScript(ScriptEditor, Workflow) - Static method in class qupath.lib.gui.panes.WorkflowCommandLogView: Show a script in the script editor based on the specified workflow.
showScriptEditor(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Show the script editor, or bring the window to the front if it is already open.
showScriptInterpreter(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Show a script interpreter window for a Qupath instance.
showSelection(boolean) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Request whether selected objects are displayed.
showStartupMessageProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Show a startup message when QuPath is launched.
showTable(ImageData<BufferedImage>, Class<? extends PathObject>) - Method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand: Show a measurement table for the specified image data.
showTextWindow(Window, String, String, Modality, boolean) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a window containing plain text, with the specified properties.
showTMACommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
showTMACoreGridView(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Show a grid view for TMA core objects.
showTMACoreLabelsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showTMAGridProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
showTMAMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands: Show a measurement table for all TMA core objects.
showTMAOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Flag to indicate that the TMA menu should be shown to the user - only relevant when working with Tissue Microarrays.
showToolBarBadgesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Show badges on the toolbar, e.g.
showViewTracker(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Show a dialog to track the viewed region of an image.
showWarningNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a warning notification.
showWithScreenSizeConstraints(Stage, double) - Static method in class qupath.lib.gui.tools.GuiTools: Show a stage, while ensuring that it cannot be larger than the screen size.
showWithSizeConstraints(Stage, double, double) - Static method in class qupath.lib.gui.tools.GuiTools: Show a stage, while ensuring that it cannot be larger the maximum dimensions provided This effectively sets the maximum dimensions of the stage, shows it, and then restores the previous maximum dimensions.
showWorkflowScript(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands: Show the QuPath script editor with a script corresponding to the command history of a specified image.
showYesNoCancelDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a Yes/No/Cancel dialog.
showYesNoDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs: Deprecated.

Show a Yes/No dialog.
shrinkLabels(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Shrink labels to a single point.
shuffleInstanceLabels(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Optionally request that instance labels are shuffled.
sigmaX(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Set all Gaussian sigma values for the horizontal filter.
sigmaXY(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Set all Gaussian sigma values (x, y) to the same value.
sigmaY(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Set all Gaussian sigma values for the vertical filter.
sigmaZ(double) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Set all Gaussian sigma values for the z-dimension filter.
sigmoid() - Static method in class qupath.opencv.ops.ImageOps.Normalize: Replace Mat values by 1.0/(1.0 + Math.exp(-value))
SIGNED_DISTANCE_TO_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
SimpleImage - Interface in qupath.lib.analysis.images: A minimal interface for accessing pixel values in a single-channel image.
SimpleImages - Class in qupath.lib.analysis.images: Create SimpleImage instances for basic pixel processing.
SimpleImages() - Constructor for class qupath.lib.analysis.images.SimpleImages
SimpleImageViewer - Class in qupath.lib.gui.panes: A simple viewer for a single image, with options to save or copy.
SimpleImageViewer() - Constructor for class qupath.lib.gui.panes.SimpleImageViewer: Create a new simple image viewer.
SimpleModifiableImage - Interface in qupath.lib.analysis.images: A minimal interface to define a means to provide access to pixel values from a 2D, 1-channel image.
SimplePluginWorkflowStep - Class in qupath.lib.plugins.workflow: Updated version of DefaultPluginWorkflowStep, adapted to use Externalizable and to avoid storing the plugin class as a class object (preferring a String instead).
SimplePluginWorkflowStep() - Constructor for class qupath.lib.plugins.workflow.SimplePluginWorkflowStep: Default public constructor, required for Externalizable.
SimplePluginWorkflowStep(String, Class<? extends PathPlugin<?>>, String) - Constructor for class qupath.lib.plugins.workflow.SimplePluginWorkflowStep: Constructor for a workflow step that calls a plugin.
SimplePluginWorkflowStep(String, Class<? extends PathPlugin<?>>, String, String, String) - Constructor for class qupath.lib.plugins.workflow.SimplePluginWorkflowStep: Constructor for a workflow step that calls a plugin, which optionally should include additional scripting lines before or afterwards.
SimpleProgressMonitor - Interface in qupath.lib.plugins: Class for monitoring the process of a plugin and displaying feedback to the user.
SimpleThresholdCommand - Class in qupath.process.gui.commands: Apply simple thresholding to an image via the pixel classification framework to support thresholding at any resolution, optionally with visual feedback via an overlay.
SimpleThresholdCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.SimpleThresholdCommand: Constructor.
SimpleThresholding - Class in qupath.imagej.processing: Collection of static methods to threshold images, either with single global thresholds or using the pixel values of a second image.
SimpleThresholding() - Constructor for class qupath.imagej.processing.SimpleThresholding
SimpleTissueDetection2 - Class in qupath.imagej.detect.tissue: Very basic global thresholding command to identify tissue regions.
SimpleTissueDetection2() - Constructor for class qupath.imagej.detect.tissue.SimpleTissueDetection2: Constructor.
SIMPLIFY_SHAPE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
simplifyPath(Path2D, double) - Static method in class qupath.lib.roi.ShapeSimplifier: Create a simplified path (fewer coordinates) using method based on Visvalingam's Algorithm.
simplifyPolygon(PolygonROI, double) - Static method in class qupath.lib.roi.ShapeSimplifier: Create a simplified polygon (fewer coordinates) using method based on Visvalingam's Algorithm.
simplifyPolygonPoints(List<Point2>, double) - Static method in class qupath.lib.roi.ShapeSimplifier: Create a simplified polygon (fewer coordinates) using method based on Visvalingam's Algorithm.
simplifyShape(ROI, double) - Static method in class qupath.lib.roi.ShapeSimplifier: Create a simplified shape (fewer coordinates) using method based on Visvalingam's Algorithm.
simplifyTitledPane(TitledPane, boolean) - Static method in class qupath.lib.gui.tools.PaneTools: Deprecated.

Simplify the appearance of a TitledPane using CSS.
singleChannel(String, ColorTransforms.ColorTransform, Function<double[], Double>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements: Create a new object measurement that requires one channel as input, using the main ROI of the object as a mask.
singleChannel(String, ColorTransforms.ColorTransform, Function<double[], Double>, Function<PathObject, ROI>) - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Measurements: Create a new object measurement that requires one channel as input.
SingleChannelDisplayInfo - Interface in qupath.lib.display: ChannelDisplayInfo that determines colors based upon a single value for each pixel.
SingleMeasurementClassificationCommand - Class in qupath.process.gui.commands: Command to (sub)classify objects based on a single measurement.
SingleMeasurementClassificationCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.SingleMeasurementClassificationCommand: Constructor.
singleSelection() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel: Returns true if only one object has been selected, accessible by getSelectedObject();
size - Variable in class qupath.lib.analysis.stats.RunningStatistics
size() - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper: Number of entries in the array.
size() - Method in class qupath.lib.analysis.stats.RunningStatistics: Get count of the number of non-NaN values added.
size() - Method in interface qupath.lib.measurements.MeasurementList: Returns the number of measurements in the list.
size() - Method in class qupath.lib.plugins.workflow.Workflow: Total number of steps in the workflow.
size() - Method in class qupath.opencv.dnn.DnnShape: Total number of elements in a blob with this shape This is the product of the lengths returned by DnnShape.getShape() or DnnShape.UNKNOWN_SHAPE.
size(double, double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Set the preferred size of the chart.
size(double, double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Set the preferred size of the chart.
size(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the preferred size of the chart.
size(double, double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the dialog height.
size(int, int) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Export image size.
size(int, int) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Input width and height.
size(Size) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Input width and height.
sizeT(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the number of time points.
sizeZ(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the number of z-slices.
skipExtensions - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
skipMissingCores - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
skipMissingCoresProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Skip ('jump over') missing cores when navigating through TMA grids.
SLICSuperpixelsPlugin - Class in qupath.imagej.superpixels: An implementation of SLIC superpixels, as described at http://ivrl.epfl.ch/research/superpixels
SLICSuperpixelsPlugin() - Constructor for class qupath.imagej.superpixels.SLICSuperpixelsPlugin
SLIDE_LABEL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
SlideLabelView - Class in qupath.lib.gui.panes: A simple viewer for a slide label, tied to the current viewer.
SlideLabelView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.SlideLabelView: Constructor.
SMALL - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
SMALL - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
smartEditing - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
smartEditingAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
smartStringComparator() - Static method in class qupath.lib.common.GeneralTools: Comparator for smart String sorting.
smartStringSort(Collection<T>) - Static method in class qupath.lib.common.GeneralTools: Smart-sort a collection using the Object.toString() method applied to each element.
smartStringSort(Collection<T>, Function<T, String>) - Static method in class qupath.lib.common.GeneralTools: Smart-sort a collection after extracting a String representation of each element.
SMOOTHED_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
SmoothFeaturesPlugin<T> - Class in qupath.lib.plugins.objects: Plugin to supplement the measurements for detection objects with the weighted sum of measurements from nearby objects, using weights derived from a 2D Gaussian function.
SmoothFeaturesPlugin() - Constructor for class qupath.lib.plugins.objects.SmoothFeaturesPlugin: Default constructor.
smoothImage(BufferedImage) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors: Smooth out compression artefacts by running 3x3 filter twice (roughly approximates a small Gaussian filter).
smoothMeasurements(List<PathObject>, List<String>, double, String, boolean, boolean) - Static method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin: Using the centroids of the ROIs within PathObjects, 'smooth' measurements by summing up the corresponding measurements of nearby objects, weighted by centroid distance.
smoothPoints(List<Point2>) - Static method in class qupath.lib.roi.ShapeSimplifier: Apply a simple 3-point moving average to a list of points.
SNAPSHOT_VIEWER_CONTENT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
SNAPSHOT_WINDOW - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
SNAPSHOT_WINDOW_CONTENT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
SOLIDITY - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Ratio of the area to the convex area.
sortNames(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Create a PathClass with name elements sorted alphabetically.
sortNames(PathClass, Comparator<String>) - Static method in class qupath.lib.objects.classes.PathClassTools: Create a PathClass with name elements sorted using an arbitrary Comparator.
SOURCE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
SparseImageServer - Class in qupath.lib.images.servers: An ImageServer that combines regions from multiple separate ImageServers, repositioning these as necessary to generate one larger field of view.
SparseImageServer.Builder - Class in qupath.lib.images.servers: Builder to create a new SparseImageServer.
SparseImageServer.SparseImageServerManager - Class in qupath.lib.images.servers: Helper class for SparseImageServers, capable of returning the appropriate ImageServer for different ImageRegions and different resolutions.
SparseImageServerManager() - Constructor for class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager
spearmansCorrelation() - Static method in class qupath.lib.experimental.pixels.MeasurementProcessor.Functions: Create a function to calculate Spearman's correlation coefficient.
SPECIFY_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
SPLIT - Enum constant in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions: Split connected components
SPLIT_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
SPLIT_ANNOTATIONS_BY_LINES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
splitAdd(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by adding corresponding values.
splitAllAnnotationAreasByLines() - Static method in class qupath.lib.scripting.QP: Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitAllAnnotationAreasByLines(double, boolean) - Static method in class qupath.lib.scripting.QP: Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitAllAnnotationAreasByLines(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitAllAnnotationAreasByLines(PathObjectHierarchy, double, boolean) - Static method in class qupath.lib.scripting.QP: Split annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
SplitAnnotationsByLineCommand - Class in qupath.lib.gui.commands.objects: Command to split annotations using lines.
SplitAnnotationsByLineCommand() - Constructor for class qupath.lib.gui.commands.objects.SplitAnnotationsByLineCommand
SplitAnnotationsPlugin<T> - Class in qupath.lib.plugins.objects: Plugin to create new annotations by expanding the size of existing annotations.
SplitAnnotationsPlugin() - Constructor for class qupath.lib.plugins.objects.SplitAnnotationsPlugin
splitAreasByBufferedLines(Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools: Given a collection of objects, split the objects with area ROIs using dividing lines extracted from the objects with line ROIs, after 'buffering' the lines to increase their thickness.
splitAreasByBufferedLines(Collection<? extends PathObject>, Collection<? extends PathObject>, double) - Static method in class qupath.lib.objects.PathObjectTools: Split the objects with area ROIs using dividing lines extracted from the objects with line ROIs, after 'buffering' the lines to increase their thickness.
splitAreasByLines(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Given a collection of objects, split the objects with area ROIs using dividing lines extracted from the objects with line ROIs.
splitAreasByLines(Collection<? extends PathObject>, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Given a collection of objects with area ROIs, split these using dividing lines extracted from objects with line ROIs.
splitAreaToPolygons(Area, int, int, int) - Static method in class qupath.lib.roi.RoiTools: Split Area into PolygonROIs for the exterior and the holes.
splitChannels(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Split channels of an array.
splitChannels(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Split channels from a Mat.
splitConnectedRegions(SparseImageServer, double, boolean) - Static method in class qupath.lib.images.servers.SparseImageServer: Split a SparseImageServer into multiple servers, whereby each split server represents one connected region.
splitDivide(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by dividing corresponding values.
splitGeometryByLineStrings(Geometry, Collection<? extends Geometry>) - Static method in class qupath.lib.roi.GeometryTools: Split an input polygonal geometry using a collection of split lines.
splitLines(String) - Static method in class qupath.lib.common.GeneralTools: Split new lines (in a cross-platform way...
splitMerge(Collection<? extends ImageOp>) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that applies all the specified ops to the input Mat, concatenating the results as channels of the output.
splitMerge(ImageOp...) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that applies all the specified ops to the input Mat, concatenating the results as channels of the output.
splitMultiply(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by multiplying corresponding values.
splitNames(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Get a list containing the names of all constituent parts of a PathClass.
SplitProjectTrainingCommand - Class in qupath.process.gui.commands: Divide a project into training, validation and test sets but flagging individual image entries.
SplitProjectTrainingCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.SplitProjectTrainingCommand: Constructor.
splitROI(ROI) - Static method in class qupath.lib.roi.RoiTools: Split a multi-part ROI into separate pieces.
splitSelectedAnnotationAreasByLines() - Static method in class qupath.lib.scripting.QP: Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitSelectedAnnotationAreasByLines(double, boolean) - Static method in class qupath.lib.scripting.QP: Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitSelectedAnnotationAreasByLines(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP: Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, then remove the lines from the object hierarchy.
splitSelectedAnnotationAreasByLines(PathObjectHierarchy, double, boolean) - Static method in class qupath.lib.scripting.QP: Split selected annotation objects with area ROIs using dividing lines extracted from annotations objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitSpecifiedAreasByLines(PathObjectHierarchy, Collection<? extends PathObject>, double, boolean) - Static method in class qupath.lib.scripting.QP: Split the specified objects with area ROIs using dividing lines extracted from specified objects with line ROIs, with an optional line thickness and optionally removing the dividing lines.
splitSubtract(ImageOp, ImageOp) - Static method in class qupath.opencv.ops.ImageOps.Core: Create an op that duplicates a Mat, applies different operations to each duplicate, and combines the result by subtracting corresponding values.
splitViewer(QuPathViewer, boolean) - Method in class qupath.lib.gui.viewer.ViewerManager
sqrt() - Static method in class qupath.opencv.ops.ImageOps.Core: Calculate the square root of all pixel values.
SQUARE - Enum constant in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap: Square cap
Stain_1 - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: First stain after color deconvolution
Stain_2 - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Second stain after color deconvolution
Stain_3 - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Third stain after color deconvolution
StainVector - Class in qupath.lib.color: Representation of a color deconvolution stain vector, defined in terms of RGB optical densities.
StainVector() - Constructor for class qupath.lib.color.StainVector: Default constructor, required for Externalizable interface.
StainVector.DefaultStains - Enum Class in qupath.lib.color: Enum representing default stains.
standardizeClassifications(Collection<PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Standardize the classifications for a collection of objects.
standardizeClassifications(Collection<PathObject>, Comparator<String>) - Static method in class qupath.lib.objects.PathObjectTools: Standardize the classifications for a collection of objects.
StandardPathClasses() - Constructor for class qupath.lib.objects.classes.PathClass.StandardPathClasses
start() - Method in class qupath.lib.common.Timeit: Start the Timeit and create a checkpoint with the default name.
start(String) - Method in class qupath.lib.common.Timeit: Start the Timeit and create a checkpoint with the specified name.
start(Stage) - Method in class qupath.lib.gui.QuPathApp
start(Stage) - Method in class qupath.lib.gui.tma.QuPathTMAViewer
startMonitoring(String, int, boolean) - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
startMonitoring(String, int, boolean) - Method in interface qupath.lib.plugins.SimpleProgressMonitor: Set the plugin to monitor, and begin monitoring.
startMoving(double, double, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover: Start moving, with initial velocity given by dx and dy.
startTranslation(double, double, boolean) - Method in class qupath.lib.roi.RoiEditor: Returns true if the current ROI is translatable, and at the end of this call the translation has started.
startupMessage - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
startupScriptPath - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
startupScriptProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Path to a startup script that should be run immediately after QuPath's launch.
StatisticsHelper - Class in qupath.lib.analysis.stats: Static methods for computing statistics from images, with or without a corresponding labeled image.
StatisticsHelper() - Constructor for class qupath.lib.analysis.stats.StatisticsHelper
statModel(OpenCVClassifiers.OpenCVStatModel, boolean) - Static method in class qupath.opencv.ops.ImageOps.ML: Apply a StatModel to pixels to generate a prediction.
std(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Calculate the standard deviation of all elements in a Mat, ignoring NaNs.
STD_DEV - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Standard deviation value
stdDev(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D circular standard deviation filter.
stdDev(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the standard deviation of an image, across all pixels (regardless of channels), ignoring NaNs.
stdDevFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D local standard deviation filter to all channels of an image, with symmetric boundary padding.
stdDevFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D local standard deviation filter to all channels of an image.
stop() - Method in class qupath.lib.common.Timeit: Stop the Timeit.
stop() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay: Stop the overlap, halting any pending tile requests.
stopMoving() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover: Stop moving immediately.
stopWaiting(RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
store(DefaultImageRegionStore) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder: Specify the region store used to paint the underlying image.
storeMetadataValue(String, String) - Method in class qupath.lib.objects.PathObject: Store a metadata value.
StringParameter - Class in qupath.lib.plugins.parameters: Parameter to represent a String value.
stripExtension(String) - Static method in class qupath.lib.common.GeneralTools: Strip the extension from a file name or path, leaving the rest of the string unchanged.
stripInvalidFilenameChars(String) - Static method in class qupath.lib.common.GeneralTools: Strip characters that would make a String invalid as a filename.
STROMA - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Stroma classification
STROMA - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Stroma classification
STRUCTURE_TENSOR_COHERENCE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Coherence, defined as ((l1 - l2)/(l1 + l2))^2 where l1 and l2 are the largest and second largest eigenvalues of the structure tensor respectively.
STRUCTURE_TENSOR_EIGENVALUE_MAX - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Maximum eigenvalue of the 2x2 or 3x3 structure tensor, calculated per pixel (by value, not absolute value)
STRUCTURE_TENSOR_EIGENVALUE_MIDDLE - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Middle eigenvalue of the 3x3 structure tensor, calculated per pixel (by value, not absolute value)
STRUCTURE_TENSOR_EIGENVALUE_MIN - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Minimum eigenvalue of the 2x2 or 3x3 structure tensor, calculated per pixel (by value, not absolute value)
structureTensorEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate the eigenvalues of the structure tensor (not yet implemented!).
SubcellularDetection - Class in qupath.imagej.detect.cells: Experimental plugin to help with the quantification of subcellular structures.
SubcellularDetection() - Constructor for class qupath.imagej.detect.cells.SubcellularDetection
Subcommand - Interface in qupath.lib.gui.extensions: A subcommand for the command line interface.
submitShortTask(Runnable) - Method in class qupath.lib.gui.QuPathGUI: Deprecated.
since v0.5.0; use QuPathGUI.getThreadPoolManager()
submitShortTask(Runnable) - Method in class qupath.lib.gui.SharedThreadPoolManager: Submit a short task to a shared thread pool
subsample(int[], int) - Static method in class qupath.lib.analysis.algorithms.EstimateStainVectors: Subsample an array so that it contains no more than maxEntries.
SUBSTRING_TOKENIZER - Static variable in class qupath.lib.scripting.languages.AutoCompletions: A completion tokenizer that simply takes the first part of the text up to the caret position.
subtract(double...) - Static method in class qupath.opencv.ops.ImageOps.Core: Subtract a constant from all pixels.
subtract(Padding) - Method in class qupath.lib.regions.Padding: Add another padding from this one.
subtract(ROI, Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools: Subtract a collection of ROIs from another ROI.
subtract(ROI, ROI...) - Static method in class qupath.lib.roi.RoiTools: Subtract one or more ROIs from another ROI.
SUBTRACT - Enum constant in enum class qupath.lib.roi.RoiTools.CombineOp: Subtract from first ROI.
suggestNeighbor(ParallelTileObject) - Method in class qupath.lib.plugins.ParallelTileObject: Register a neighboring tile, if it intersects with the bounds of this one
sum() - Static method in class qupath.opencv.ops.ImageOps.Channels: Add all channels together, to give a single-channel output.
sum(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D circular sum filter.
sum(long[]) - Static method in class qupath.lib.common.GeneralTools: Compute the sum of elements in a long array (possibly representing a histogram).
sum(Mat) - Static method in class qupath.opencv.tools.GroovyCV: Calculate the sum of all elements in a Mat, ignoring NaNs.
sum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Get the sum of an image, across all pixels (regardless of channels), ignoring NaNs.
SUM - Enum constant in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType: No normalization; maps provide raw object counts in a defined radius.
sumFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D sum filter to all channels of an image, with symmetric boundary padding.
sumFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D sum filter to all channels of an image.
summarize(Net, int, int, int) - Static method in class qupath.opencv.dnn.DnnTools: Create a (multiline) summary String for a Net, given the specified image input dimensions.
summarizeCheckpoints() - Method in class qupath.lib.common.Timeit: Request that checkpoints are summarized in the Timeit.toString() method.
summarizeCheckpoints(boolean) - Method in class qupath.lib.common.Timeit: Optionally request that checkpoints are summarized in the Timeit.toString() method.
SummaryMeasurementTableCommand - Class in qupath.lib.gui.commands: Show a summary table for an object of a particular type (annotation, detection, TMA core...)
SummaryMeasurementTableCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.SummaryMeasurementTableCommand: Command to show a summary measurement table, for PathObjects of a specified type (e.g.
supports2D() - Method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Returns true if the feature can be computed for 2D images.
supports3D() - Method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Returns true if the feature can be computed for 3D images (z-stacks).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier: Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier: Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer: Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier: Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV: Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier: Returns true (the default value).
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Classifier can be trained interactively (i.e.
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
supportsAutoUpdate() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
supportsDynamicMeasurements() - Method in interface qupath.lib.measurements.MeasurementList: Deprecated.
since v0.4.0; the initial implementation of dynamic measurements was never used
supportsFile(File) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor: Query whether a file represents a supported script.
supportsFile(File) - Method in interface qupath.lib.gui.scripting.ScriptEditor: Check if the script editor supports a particular file.
supportsImage(ImageData<BufferedImage>) - Method in interface qupath.lib.classifiers.pixel.PixelClassifier: Query whether the classifier supports a particular image.
supportsImage(ImageData<BufferedImage>) - Method in interface qupath.opencv.ops.ImageDataOp: Query whether this transform can be applied to the specified image.
supportsImage(ImageServer<?>) - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Returns true if the compression type supports a specific image server, or false if it is incompatible.
supportsImage(ImageServer<BufferedImage>) - Method in interface qupath.lib.images.servers.ColorTransforms.ColorTransform: Query whether this transform can be applied to the specified image.
supportsImage(PixelType, int, boolean) - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Returns true if the compression type supports a specific PixelType output with the given number of channels - and (optionally) RGB status.
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.imagej.images.writers.TiffWriterIJ
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.imagej.images.writers.ZipWriterIJ
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.JpegWriter
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
supportsImageType(ImageServer<BufferedImage>) - Method in class qupath.lib.images.writers.PngWriter
supportsImageType(ImageServer<T>) - Method in interface qupath.lib.images.writers.ImageWriter: Test whether images provided by a specified ImageServer can be successfully written.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV: Tree classifiers in OpenCV support missing values, others do not.
supportsMissingValues() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Classifier can handle missing (NaN) values
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV: Returns false (the default value).
supportsMulticlass() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Classifier is able to handle more than one outputs for a single sample.
supportsPixelSize() - Method in class qupath.imagej.images.writers.TiffWriterIJ
supportsPixelSize() - Method in class qupath.imagej.images.writers.ZipWriterIJ
supportsPixelSize() - Method in class qupath.lib.images.writers.JpegWriter
supportsPixelSize() - Method in class qupath.lib.images.writers.PngWriter
supportsPixelSize() - Method in interface qupath.lib.images.writers.ImageWriter: Returns true if the writer is capable of storing pixel size information.
supportsPixelSize() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
supportsProbabilities() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Classifier can output a prediction confidence (expressed between 0 and 1), so may be interpreted as a probability...
supportsPyramidal() - Method in class qupath.imagej.images.writers.TiffWriterIJ
supportsPyramidal() - Method in class qupath.imagej.images.writers.ZipWriterIJ
supportsPyramidal() - Method in class qupath.lib.images.writers.JpegWriter
supportsPyramidal() - Method in class qupath.lib.images.writers.PngWriter
supportsPyramidal() - Method in interface qupath.lib.images.writers.ImageWriter: Returns true if the writer is capable of writing pyramidal images.
supportsPyramidal() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
supportsRGB() - Method in class qupath.imagej.images.writers.TiffWriterIJ
supportsRGB() - Method in class qupath.imagej.images.writers.ZipWriterIJ
supportsRGB() - Method in class qupath.lib.images.writers.JpegWriter
supportsRGB() - Method in class qupath.lib.images.writers.PngWriter
supportsRGB() - Method in interface qupath.lib.images.writers.ImageWriter: Check if writer can handle RGB (it probably can...).
supportsRGB() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
supportsT() - Method in class qupath.imagej.images.writers.TiffWriterIJ
supportsT() - Method in class qupath.imagej.images.writers.ZipWriterIJ
supportsT() - Method in class qupath.lib.images.writers.JpegWriter
supportsT() - Method in class qupath.lib.images.writers.PngWriter
supportsT() - Method in interface qupath.lib.images.writers.ImageWriter: Check if writer can handle multiple timepoints.
supportsT() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
supportsZ() - Method in class qupath.imagej.images.writers.TiffWriterIJ
supportsZ() - Method in class qupath.imagej.images.writers.ZipWriterIJ
supportsZ() - Method in class qupath.lib.images.writers.JpegWriter
supportsZ() - Method in class qupath.lib.images.writers.PngWriter
supportsZ() - Method in interface qupath.lib.images.writers.ImageWriter: Check if writer can handle multiple z-slices.
supportsZ() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
SvgBuilder() - Constructor for class qupath.lib.extension.svg.SvgTools.SvgBuilder: Create a new builder, which will later be customized.
SvgBuilder(QuPathViewer) - Constructor for class qupath.lib.extension.svg.SvgTools.SvgBuilder: Create a builder initialized according to the current viewer.
SvgExtension - Class in qupath.lib.extension.svg: Extension for SVG image export.
SvgExtension() - Constructor for class qupath.lib.extension.svg.SvgExtension
SvgExtension.SvgActions - Class in qupath.lib.extension.svg
SvgTools - Class in qupath.lib.extension.svg: Helper class for writing SVG images, in particular rendered PathObjects to create high-quality figures.
SvgTools() - Constructor for class qupath.lib.extension.svg.SvgTools
SvgTools.SvgBuilder - Class in qupath.lib.extension.svg: Builder class to enable the export of rendered QuPath objects as SVG images.
SvgTools.SvgBuilder.ImageIncludeType - Enum Class in qupath.lib.extension.svg: Enum defining ways in which raster images may be included in the SVG file.
swapNameAndClass(PathObject, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Swap the name and PathClass of an object.
swapRGBOrder(BufferedImage, String) - Static method in class qupath.lib.awt.common.BufferedImageTools: Swap the order of pixels in an RGB image.
switchToGrayscaleChannelProperty() - Method in class qupath.lib.display.ImageDisplay: Property indicating which channel should be used if ImageDisplay.useGrayscaleLutProperty() is turned on.
SYMBOL_MICROMETER - Static variable in class qupath.lib.common.GeneralTools: String to represent um (but with the proper 'mu' symbol)
SYMBOL_MU - Static variable in class qupath.lib.common.GeneralTools: Small Greek mu (useful for micrometers)
SYMBOL_SIGMA - Static variable in class qupath.lib.common.GeneralTools: Small Greek sigma (useful for Gaussian filter sizes, standard deviations)
symDifference(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools: Compute the symmetric difference between two ROIs (XOR).
symmetric(int) - Static method in class qupath.lib.regions.Padding: Get a padding object with 'pad' pixels on all sides.
syncChanges() - Method in interface qupath.lib.projects.Project: Save the project.
synchronizeViewersProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
syncProject(Project<?>) - Static method in class qupath.lib.gui.panes.ProjectBrowser: Try to save a project, showing an error message if this fails.
systemMenubar - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
SystemMenuBar - Class in qupath.lib.gui.prefs: Helper class for managing MenuBar.useSystemMenuBarProperty() values based upon a property value.
SystemMenuBar() - Constructor for class qupath.lib.gui.prefs.SystemMenuBar
SystemMenuBar.SystemMenuBarOption - Enum Class in qupath.lib.gui.prefs: Enum specifying when and where the system menubar should be used.
systemMenubarProperty() - Static method in class qupath.lib.gui.prefs.SystemMenuBar: Property used to specify whether the system menubar should be used for the main QuPath stage.

T

TABLE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
tableDelimiterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Delimiter to use when exporting tables.
target(int) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Specify the target, e.g.
taskComplete(boolean) - Method in interface qupath.lib.plugins.PathTask: Perform optional post-processing after a task has completed.
TaskRunner - Interface in qupath.lib.plugins: A minimal interface for a class capable of running tasks in parallel, giving feedback to the user.
TaskRunnerFX - Class in qupath.lib.gui: Plugin runner that takes care of showing progress (in the appropriate thread) using JavaFX components.
TaskRunnerFX(QuPathGUI) - Constructor for class qupath.lib.gui.TaskRunnerFX: Constructor.
TaskRunnerFX(QuPathGUI, int) - Constructor for class qupath.lib.gui.TaskRunnerFX: Constructor specifying the number of threads.
TaskRunnerUtils - Class in qupath.lib.plugins: A utility class to help with the creation of TaskRunner instances.
TemporaryObject - Interface in qupath.lib.objects: Marker interface used to indicate that child objects shouldn't be added to any cache for display.
test(ImageData<?>, RegionRequest) - Method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
test(PathObject) - Method in enum class qupath.lib.objects.PathObjectFilter
text(String) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Set the text property of the action.
text(ObservableValue<String>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder: Bind the text property of the action to an ObservableValue, bidirectionally if possible.
TEXT_DETECTION_DB - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Refers to TextDetectionModel_DB.
TEXT_DETECTION_EAST - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Refers to TextDetectionModel_EAST.
TEXT_RECOGNITION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Refers to TextRecognitionModel.
TextAppendable - Interface in qupath.lib.gui.logging: Interface to indicate anything for which text can be appended.
TextAreaControl - Class in qupath.lib.gui.scripting: Simple text area control (JavaFX) with basic operations and no styling support.
TextAreaControl(boolean) - Constructor for class qupath.lib.gui.scripting.TextAreaControl: Constructor to create a new text area and wrap it in a TextAreaControl.
TextAreaControl(TextArea, boolean) - Constructor for class qupath.lib.gui.scripting.TextAreaControl: Constructor to wrap an existing text area and wrap it in a TextAreaControl.
textFieldPrompt(String) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Prompt to include beside the resource name text field
textProperty() - Method in class qupath.lib.gui.actions.InfoMessage: Read only property containing the message text.
textProperty() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
textProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Text currently in the editor control.
textProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
textProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry: Property corresponding to CommandFinderTools.CommandEntry.getText()
theme - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
thin(Mat) - Static method in class qupath.opencv.tools.Thinning: Thin the binary image in Mat.
Thinning - Class in qupath.opencv.tools: Implementation of the 3D binary thinning algorithm of Lee et al.
Thinning() - Constructor for class qupath.opencv.tools.Thinning
ThreadTools - Class in qupath.lib.common: Create a thread factory that supports adding a prefix to the name and setting daemon status.
ThreadTools() - Constructor for class qupath.lib.common.ThreadTools
threshold(double) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the threshold value used for the classification.
threshold(double...) - Static method in class qupath.opencv.ops.ImageOps.Threshold: Apply a fixed threshold.
threshold(PathObjectHierarchy, ImageServer<BufferedImage>, int, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps: Threshold a single channel of a density map to generate new annotations.
threshold(PathObjectHierarchy, ImageServer<BufferedImage>, Map<Integer, ? extends Number>, String, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps: Threshold one or more channels of a density map to generate new annotations.
Threshold() - Constructor for class qupath.opencv.ops.ImageOps.Threshold
thresholdAbove(ImageProcessor, float) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by thresholding pixels to find where ip1 > threshold
thresholdAboveEquals(ImageProcessor, float) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by thresholding pixels to find where ip1 >= threshold
thresholdBelow(ImageProcessor, float) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by thresholding pixels to find where ip1 < threshold
thresholdBelowEquals(ImageProcessor, float) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by thresholding pixels to find where ip1 <= threshold
thresholdBetween(ImageProcessor, float, float) - Static method in class qupath.imagej.processing.SimpleThresholding: Created a binary image by thresholding pixels to find where ip >= lowThreshold and ip <= highThreshold
thresholdMeanStd(double...) - Static method in class qupath.opencv.ops.ImageOps.Threshold: Threshold each channel based upon the channel mean and standard deviation.
thresholdMedianAbsDev(double...) - Static method in class qupath.opencv.ops.ImageOps.Threshold: Threshold each channel based upon the channel median and median absolute deviation.
thresholdToROI(ImageProcessor, RegionRequest) - Static method in class qupath.imagej.processing.SimpleThresholding: Generate a QuPath ROI from an ImageProcessor.
thresholdToROI(BufferedImage, double, double, int, RegionRequest) - Static method in class qupath.imagej.processing.SimpleThresholding: Generate a QuPath ROI by thresholding an image channel image.
thresholdToROI(Raster, double, double, int, TileRequest) - Static method in class qupath.imagej.processing.SimpleThresholding: Generate a QuPath ROI by thresholding an image channel image, deriving coordinates from a TileRequest.
thumbnailCache - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
TiffWriterIJ - Class in qupath.imagej.images.writers: ImageWriter implementation to write TIFF images using ImageJ.
TiffWriterIJ() - Constructor for class qupath.imagej.images.writers.TiffWriterIJ
tile(int, int) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set a default tiler to use, with a specified tile size.
tile(TileRequest) - Method in class qupath.lib.experimental.pixels.Parameters.Builder: Specify the tile relevant for processing.
tileAvailable(String, ImageRegion, BufferedImage) - Method in class qupath.lib.gui.viewer.QuPathViewer
tileAvailable(String, ImageRegion, T) - Method in interface qupath.lib.gui.images.stores.TileListener: Notify a listener that an image tile has been received read & is available.
tileBrush - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
tileCache - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
tileCachePercentageProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Requested percentage of available memory to use for tile caching.
TileClassificationsToAnnotationsPlugin<T> - Class in qupath.lib.plugins.objects: Plugin to merge classified tiles into annotation objects.
TileClassificationsToAnnotationsPlugin() - Constructor for class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
TileExporter - Class in qupath.lib.images.writers: Helper class for exporting image tiles, typically for further analysis elsewhere or for training up an AI algorithm.
TileExporter(ImageData<BufferedImage>) - Constructor for class qupath.lib.images.writers.TileExporter: Create a builder to export tiles.
tileHeight(int) - Method in class qupath.lib.objects.utils.Tiler.Builder: Change the height of output tiles
TileListener<T> - Interface in qupath.lib.gui.images.stores: Interface for anything that needs to know when image tiles become available.
tileListeners - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
tiler(Tiler) - Method in class qupath.lib.experimental.pixels.PixelProcessor.Builder: Set a tiler to use.
Tiler - Class in qupath.lib.objects.utils: A class used to split ROI or Geometry objects into rectangular tiles.
Tiler.Builder - Class in qupath.lib.objects.utils
Tiler.TileAlignment - Enum Class in qupath.lib.objects.utils: Enum representing the possible alignments for tiles.
TileRequest - Class in qupath.lib.images.servers: A wrapper for a RegionRequest, useful to precisely specify image tiles at a particular resolution.
TileRequestManager - Interface in qupath.lib.images.servers: Helper class to manage tile requests from an ImageServer.
TilerPlugin<T> - Class in qupath.lib.algorithms: Simple plugin to create square tiles, which may later have measurements added.
TilerPlugin() - Constructor for class qupath.lib.algorithms.TilerPlugin: Default constructor.
tiles() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder: Set the filter to accept tile objects only.
TILES - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept tiles
tileSize(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Set tile width and height (square tiles).
tileSize(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Define the requested tile size (width == height).
tileSize(int) - Method in class qupath.lib.images.writers.TileExporter: Define the tile size in pixel units at the export resolution.
tileSize(int, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Set tile width and height.
tileSize(int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Define the requested tile width and height.
tileSize(int, int) - Method in class qupath.lib.images.writers.TileExporter: Define the horizontal and vertical tile size in pixel units at the export resolution.
tileWidth(int) - Method in class qupath.lib.objects.utils.Tiler.Builder: Change the width of output tiles
Timeit - Class in qupath.lib.common: Helper class to time code execution.
Timeit() - Constructor for class qupath.lib.common.Timeit
Timeit.Checkpoint - Class in qupath.lib.common: Class representing a named checkpoint with a timestamp in nanoseconds.
timePoint(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify a single timepoint to be written from a time series.
timepoints(TimeUnit, double...) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the time unit and individual time points.
timepoints(TimeUnit, double...) - Method in class qupath.lib.images.servers.PixelCalibration.Builder: Specify timepoints and units.
timePoints(int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify a range of timepoints to be written from a time series.
timestamp - Variable in class qupath.lib.gui.images.stores.AbstractImageRenderer: Timestamp variable; this should be updated by implementing classes.
TINY - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
TINY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
title - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
title - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
title - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
title(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify the chart title.
title(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify the chart title.
title(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify the chart title.
title(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the dialog title.
title(String) - Method in class qupath.lib.gui.FileCopier: Title for any dialog.
title(String) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Title to display in any dialogs
TMA - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
TMA_ADD_NOTE - Variable in class qupath.lib.gui.actions.CommonActions
TMA_CORES - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept TMA cores
TMA_DEARRAYING_DATA_EXTENSION - Static variable in class qupath.lib.gui.tma.TMADataIO
TMA_EXPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
TMA_GRID - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
TMA_IMPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
TMA_VIEWER - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
tmaActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
TmaActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
tmaColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
TMACommands - Class in qupath.lib.gui.commands: Helper class implementing simple 'single-method' commands related to tissue microarrays for easy inclusion in the GUI.
TMACommands() - Constructor for class qupath.lib.gui.commands.TMACommands
TMACoreObject - Class in qupath.lib.objects: A special PathObject used exclusively to represent TMA cores.
TMACoreObject() - Constructor for class qupath.lib.objects.TMACoreObject: Default constructor.
TMADataIO - Class in qupath.lib.gui.tma: Static methods for exporting TMA data, optionally with small images.
TMADataIO() - Constructor for class qupath.lib.gui.tma.TMADataIO
TMADearrayer - Class in qupath.imagej.detect.dearray: Static methods used by the TMA dearrayer plugin.
TMADearrayer() - Constructor for class qupath.imagej.detect.dearray.TMADearrayer
TMADearrayerPluginIJ - Class in qupath.imagej.detect.dearray: Plugin for automatically dearraying tissue microarrays (TMAs).
TMADearrayerPluginIJ() - Constructor for class qupath.imagej.detect.dearray.TMADearrayerPluginIJ: Default constructor.
TMAExplorer - Class in qupath.lib.gui.tma: The aim of this is to enable the exploration of TMA data from multiple images in a project.
TMAExplorer(QuPathGUI) - Constructor for class qupath.lib.gui.tma.TMAExplorer: Constructor.
tmaExportDownsample - Variable in class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
tmaExportDownsampleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Default downsample factor to use when exporting TMA cores.
TMAGrid - Interface in qupath.lib.objects.hierarchy: Interface defining a (rectangular) TMA grid.
TMAGridOverlay - Class in qupath.lib.gui.viewer.overlays: An overlay capable of painting a TMA Grid.
TMAGridOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.TMAGridOverlay: Constructor.
TMAMenuActions - Class in qupath.lib.gui.actions.menus
TMAMenuActions.Actions - Class in qupath.lib.gui.actions.menus
TMAMenuActions.Actions.AddActions - Class in qupath.lib.gui.actions.menus
TMAMenuActions.Actions.RemoveActions - Class in qupath.lib.gui.actions.menus
tmaMissingColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
TMAScoreImporter - Class in qupath.lib.io: Helper class for importing data in connection with TMA slides.
TMAScoreImporter() - Constructor for class qupath.lib.io.TMAScoreImporter
TMASummaryViewer - Class in qupath.lib.gui.tma: Deprecated.
since v0.4.0
TMASummaryViewer(Stage) - Constructor for class qupath.lib.gui.tma.TMASummaryViewer: Deprecated.

Constructor.
toBlob(Mat...) - Method in interface qupath.opencv.dnn.BlobFunction: Convert one or more mats to a blob.
toEncodedURI(String) - Static method in class qupath.lib.common.GeneralTools: Try to convert a path to an encoded URI.
toFriendlyString() - Method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Get a friendlier string representation
TOGGLE_SELECTED_OBJECTS_LOCKED - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
TOGGLE_SYNCHRONIZE_VIEWERS - Variable in class qupath.lib.gui.actions.ViewerActions
toggleObjectsLocked(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Toggle the 'locked' status of specified objects.
toggleSelectedObjectsLocked(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools: Toggle the 'locked' status of selected objects, firing an update event if the status of any object is changed.
toggleShowHideChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Toggle the visibility of the specified channel.
toJSON(boolean) - Method in class qupath.lib.display.ImageDisplay: Create a JSON representation of the main components of the current display.
toJTS(AffineTransform) - Static method in class qupath.lib.awt.common.AffineTransforms: Create a Java Topology Suite affine transformation from a Java affine transform.
TOOLBAR_ICON_SIZE - Static variable in class qupath.lib.gui.QuPathGUI: Icon size to use in the main QuPath toolbar
ToolManager - Class in qupath.lib.gui: Manage (drawing) tool selection in a QuPath UI.
tooltip(ObservableValue<String>) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder: Text to include in any tooltip.
tooltips(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Request tooltips to be shown when the cursor hovers over the pie chart.
TOP_CENTER - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
TOP_LEFT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
TOP_RIGHT - Enum constant in enum class qupath.lib.objects.utils.Tiler.TileAlignment
toPath(URI) - Static method in class qupath.lib.common.GeneralTools: Try to identify a Path from a URI, dropping any query or fragment elements.
toSet() - Method in class qupath.lib.objects.classes.PathClass: Return a view of this path class as an unmodifiable set, with each element representing the name of a path class component names.
toStage() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Add the chart to a stage, but do not show it.
toStage() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Add the chart to a stage, but do not show it.
toStage() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Add the chart to a stage, but do not show it.
toString() - Method in class qupath.lib.analysis.features.HaralickFeatures
toString() - Method in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
toString() - Method in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType
toString() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
toString() - Method in class qupath.lib.analysis.stats.Histogram
toString() - Method in class qupath.lib.analysis.stats.RunningStatistics
toString() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent
toString() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
toString() - Method in enum class qupath.lib.classifiers.Normalization
toString() - Method in class qupath.lib.color.ColorDeconvMatrix3x3
toString() - Method in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains
toString() - Method in class qupath.lib.color.ColorDeconvolutionStains
toString() - Method in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
toString() - Method in enum class qupath.lib.color.StainVector.DefaultStains
toString() - Method in class qupath.lib.color.StainVector
toString() - Method in class qupath.lib.common.Timeit.Checkpoint
toString() - Method in class qupath.lib.common.Timeit: Returns a snapshot string representation of the Timeit's status.
toString() - Method in class qupath.lib.common.Version
toString() - Method in class qupath.lib.display.DirectServerChannelInfo
toString() - Method in enum class qupath.lib.extension.svg.SvgTools.SvgBuilder.ImageIncludeType
toString() - Method in class qupath.lib.geom.Point2
toString() - Method in class qupath.lib.gui.BuildInfo
toString() - Method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
toString() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
toString() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
toString() - Method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
toString() - Method in class qupath.lib.gui.scripting.ScriptTab
toString() - Method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
toString() - Method in enum class qupath.lib.gui.viewer.ImageInterpolation
toString() - Method in class qupath.lib.gui.viewer.QuPathViewer
toString() - Method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
toString() - Method in enum class qupath.lib.images.ImageData.ImageType
toString() - Method in class qupath.lib.images.ImageData
toString() - Method in class qupath.lib.images.servers.AbstractImageServer
toString() - Method in class qupath.lib.images.servers.ImageChannel
toString() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
toString() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
toString() - Method in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
toString() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
toString() - Method in class qupath.lib.images.servers.ImageServerMetadata
toString() - Method in class qupath.lib.images.servers.PixelCalibration
toString() - Method in enum class qupath.lib.images.servers.RotatedImageServer.Rotation
toString() - Method in class qupath.lib.images.servers.TileRequest
toString() - Method in class qupath.lib.io.UriUpdater.SingleUriItem
toString() - Method in class qupath.lib.objects.classes.PathClass
toString() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
toString() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
toString() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
toString() - Method in class qupath.lib.objects.PathObject
toString() - Method in enum class qupath.lib.objects.PathObjectFilter
toString() - Method in class qupath.lib.objects.PathRootObject
toString() - Method in class qupath.lib.objects.TMACoreObject
toString() - Method in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap
toString() - Method in class qupath.lib.plugins.parameters.BooleanParameter
toString() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
toString() - Method in class qupath.lib.plugins.parameters.DoubleParameter
toString() - Method in class qupath.lib.plugins.parameters.IntParameter
toString() - Method in class qupath.lib.plugins.parameters.NumericParameter
toString() - Method in class qupath.lib.plugins.parameters.StringParameter
toString() - Method in class qupath.lib.plugins.parameters.EmptyParameter
toString() - Method in class qupath.lib.plugins.workflow.DefaultScriptableWorkflowStep
toString() - Method in class qupath.lib.plugins.workflow.RunSavedClassifierWorkflowStep
toString() - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
toString() - Method in class qupath.lib.regions.ImagePlane
toString() - Method in class qupath.lib.regions.ImageRegion
toString() - Method in class qupath.lib.regions.Padding
toString() - Method in class qupath.lib.regions.RegionRequest
toString() - Method in class qupath.lib.roi.AreaROI
toString() - Method in class qupath.lib.roi.EllipseROI
toString() - Method in class qupath.lib.roi.GeometryROI
toString() - Method in class qupath.lib.roi.LineROI
toString() - Method in class qupath.lib.roi.PolygonROI
toString() - Method in class qupath.lib.roi.PolylineROI
toString() - Method in class qupath.lib.roi.RectangleROI
toString() - Method in class qupath.lib.roi.PointsROI
toString() - Method in class qupath.lib.scripting.languages.ScriptLanguage
toString() - Method in class qupath.opencv.dnn.DnnShape
toString() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer
toString() - Method in class qupath.opencv.ml.FeaturePreprocessor
toString() - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
toString() - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel
toString() - Method in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions
toString() - Method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
toString() - Method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature
toString() - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
toString() - Method in class qupath.process.gui.commands.ml.ClassificationResolution
toString(String) - Method in class qupath.lib.objects.classes.PathClass: Create a string representation, using the specified delimiter between elements of derived PathClasses.
totalBytes() - Method in class qupath.lib.gui.UndoRedoManager: The total number of bytes used for all viewers.
toURI(String) - Static method in class qupath.lib.common.GeneralTools: Try to convert a path to a URI.
tPositionProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer: Current t-position for the timepoint currently visible in the viewer.
TRACE - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: Trace logging (an awful lot of messages)
traceGeometries(ImageServer<BufferedImage>, RegionRequest, Geometry, ContourTracing.ChannelThreshold...) - Static method in class qupath.lib.analysis.images.ContourTracing: Trace one or more geometries in an image.
traceGeometry(ImageServer<BufferedImage>, RegionRequest, Geometry, int, double, double) - Static method in class qupath.lib.analysis.images.ContourTracing: Trace a geometry from a single channel of a single image.
trackedMemory() - Static method in class qupath.opencv.tools.OpenCVTools: Get a brief, one-line report on tracked memory use, based on JavaCPP's Pointer class.
TRACKING_RECORD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
TRACKING_REWIND - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
TRACKING_STOP - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.OpenCVStatModel: Train the classifier using data in an appropriate format.
train(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
TRAIN_VALIDATION_TEST_METADATA_KEY - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand: Metadata key for the flag indicating the image type (Train, Validation, Test or None).
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.BoostClassifier: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.DTreesClassifier: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.EMClusterer: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.LogisticRegressionClassifier: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.NormalBayesClassifierCV: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMClassifierCV: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
trainWithLock(TrainData) - Method in class qupath.opencv.ml.OpenCVClassifiers.SVMSGDClassifierCV: Implement trainWithLock rather than train directly to ensure a lock is set when training, which can be used to prevent prediction occurring simultaneously.
tRange(int, int) - Method in class qupath.lib.images.writers.TileExporter: Define the range of timepoints to process.
TRANSFER_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
transform(AffineTransform) - Method in class qupath.lib.images.servers.TransformedServerBuilder: Apply an AffineTransform to the server.
transformAllObjects(AffineTransform) - Static method in class qupath.lib.scripting.QP: Apply an affine transform to all selected objects in the current hierarchy.
transformAllObjects(PathObjectHierarchy, AffineTransform) - Static method in class qupath.lib.scripting.QP: Apply an affine transform to all selected objects in the specified hierarchy.
TransformedServerBuilder - Class in qupath.lib.images.servers: Helper class for creating an ImageServer that applies one or more transforms to another (wrapped) ImageServer.
TransformedServerBuilder(ImageServer<BufferedImage>) - Constructor for class qupath.lib.images.servers.TransformedServerBuilder: Create a transformed ImageServer.
TransformingImageServer<T> - Class in qupath.lib.images.servers: An ImageServer implementation used to apply transforms to another ImageServer.
TransformingImageServer(ImageServer<T>) - Constructor for class qupath.lib.images.servers.TransformingImageServer
transformObject(PathObject, AffineTransform, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Create a transformed version of a PathObject with a new ID.
transformObject(PathObject, AffineTransform, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Create a transformed version of a PathObject, optionally with a new ID.
transformObjectRecursive(PathObject, AffineTransform, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Create (optionally) transformed versions of the PathObject and all its descendants, recursively.
transformObjectRecursive(PathObject, AffineTransform, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Create (optionally) transformed versions of the PathObject and all its descendants, recursively, optionally assigning new IDs to the created objects.
transformPadded(Mat) - Method in class qupath.opencv.ops.ImageOps.PaddedOp: Apply the op, but ignoring padding.
transformRGB(int[], int[], ColorTransformer.ColorTransformMethod, float, float, boolean) - Static method in class qupath.lib.color.ColorTransformer: Apply a specified color transform to a packed (A)RGB array and output another (A)RGB array.
transformROI(ROI, AffineTransform) - Static method in class qupath.lib.roi.RoiTools: Apply an affine transform to a ROI, returning the result.
transformSelectedObjects(AffineTransform) - Static method in class qupath.lib.scripting.QP: Apply an affine transform to all objects in the current hierarchy, retaining parent-child relationships between objects.
transformSelectedObjects(PathObjectHierarchy, AffineTransform) - Static method in class qupath.lib.scripting.QP: Apply an affine transform to all objects in the specified hierarchy, retaining parent-child relationships between objects.
transformsToOp(Collection<? extends BioimageIoSpec.Processing>) - Static method in class qupath.opencv.ml.BioimageIoTools: Create an ImageOp that applies the specified transforms sequentially.
transformToOp(BioimageIoSpec.Processing) - Static method in class qupath.opencv.ml.BioimageIoTools: Create an ImageOp that applies the specified transforms, if possible.
translate(double, double) - Method in class qupath.lib.roi.AreaROI
translate(double, double) - Method in class qupath.lib.roi.EllipseROI
translate(double, double) - Method in class qupath.lib.roi.GeometryROI
translate(double, double) - Method in interface qupath.lib.roi.interfaces.ROI: Create a translated version of this ROI.
translate(double, double) - Method in class qupath.lib.roi.LineROI
translate(double, double) - Method in class qupath.lib.roi.PointsROI
translate(double, double) - Method in class qupath.lib.roi.PolygonROI
translate(double, double) - Method in class qupath.lib.roi.PolylineROI
translate(double, double) - Method in class qupath.lib.roi.RectangleROI
translate(int, int) - Method in class qupath.lib.regions.RegionRequest: Create a RegionRequest equivalent to this one with the x and y coordinates updated by translation.
translateAllObjects(double, double) - Static method in class qupath.lib.scripting.QP: Translate (move) the ROIs of all objects in the current object hierarchy.
translateAllObjects(PathObjectHierarchy, double, double) - Static method in class qupath.lib.scripting.QP: Translate (move) the ROIs of all objects in the specified object hierarchy.
TRANSLUCENT_BLACK - Static variable in class qupath.lib.color.ColorToolsAwt: Black, with 50% opacity.
TRANSLUCENT_BLACK_FX - Static variable in class qupath.lib.gui.tools.ColorToolsFX: Black with opacity at 50%.
TRANSLUCENT_WHITE - Static variable in class qupath.lib.color.ColorToolsAwt: White, with 50% opacity.
TRANSLUCENT_WHITE_FX - Static variable in class qupath.lib.gui.tools.ColorToolsFX: White with opacity at 50%.
TRANSPARENT - Static variable in class qupath.lib.images.servers.ImageChannel: Special color indicating pixel values for a channel indicate levels of transparency.
tryToClassify(List<? extends PathObject>, ImageServer<BufferedImage>, double, IntFunction<PathClass>) - Method in class qupath.opencv.dnn.DnnObjectClassifier: Try to classify a batch of objects.
tryToClassify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, IntFunction<PathClass>) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
tryToClassify(PathObject, ImageServer<BufferedImage>, double, IntFunction<PathClass>) - Method in class qupath.opencv.dnn.DnnObjectClassifier
tryToFixPolygon(Polygon) - Static method in class qupath.lib.roi.GeometryTools: Test a polygon for validity, attempting to fix TopologyValidationErrors if possible.
tryToInterpretMessage(Throwable, int, boolean) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
tryToLoad(String...) - Static method in class qupath.lib.images.servers.openslide.jna.OpenSlideLoader: Try to load OpenSlide.
tryToLoadQuietly(String...) - Static method in class qupath.lib.images.servers.openslide.jna.OpenSlideLoader: Try to load OpenSlide, but don't throw an exception if it fails.
tryToParseMicrons(double, String) - Static method in class qupath.imagej.tools.IJTools: Based on a value and its units, try to get something suitable in microns.
TUMOR - Enum constant in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Tumor classification
TUMOR - Static variable in class qupath.lib.objects.classes.PathClass.StandardPathClasses: Tumor classification
type(DensityMaps.DensityMapType) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder: The type of the density map, which determines any associated normalization.
typeToChannels(int) - Static method in class qupath.opencv.tools.OpenCVTools: Determine the number of channels from a specified Mat type (which also encodes depth).
typeToDepth(int) - Static method in class qupath.opencv.tools.OpenCVTools: Determine the depth from a specified Mat type (which may also encode the number of channels).

U

uiBlocked() - Method in class qupath.lib.gui.QuPathGUI: Observable value indicating that the user interface is/should be blocked.
UINT16 - Enum constant in enum class qupath.lib.images.servers.PixelType: 16-bit unsigned integer
UINT32 - Enum constant in enum class qupath.lib.images.servers.PixelType: 32-bit unsigned integer (not supported by BufferedImage)
UINT8 - Enum constant in enum class qupath.lib.images.servers.PixelType: 8-bit unsigned integer
uncompressed() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Request no compression.
UNCOMPRESSED - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: No compression (faster to write, no loss of information, but large file sizes).
undo() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
undo() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request undo.
undo() - Method in class qupath.lib.gui.scripting.TextAreaControl
UNDO - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
undoAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
undoOnce() - Method in class qupath.lib.gui.UndoRedoManager: Request to 'undo' the last observed hierarchy change for the current active viewer.
UndoRedoManager - Class in qupath.lib.gui: Helper class to add undo/redo support to QuPath.
UndoRedoPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
union(Collection<? extends Geometry>) - Static method in class qupath.lib.roi.GeometryTools: Calculate the union of multiple Geometry objects.
union(Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools: Create union of multiple ROIs from a collection.
union(ROI...) - Static method in class qupath.lib.roi.RoiTools: Create union of multiple ROIs.
uniqueNames(PathClass) - Static method in class qupath.lib.objects.classes.PathClassTools: Remove duplicate names from a derived PathClass.
unitsMatch2D() - Method in class qupath.lib.images.servers.PixelCalibration: Returns true if the units for pixel width and height are the same.
unitsMatch3D() - Method in class qupath.lib.images.servers.PixelCalibration: Returns true if the units for pixel width, height and z-spacing are the same.
UNKNOWN - Enum constant in enum class qupath.lib.io.UriUpdater.UriStatus: URI status is unclear, e.g.
UNKNOWN - Static variable in class qupath.lib.common.Version: Constant representing any unknown version.
UNKNOWN_LENGTH - Static variable in class qupath.opencv.dnn.DnnShape: Constant to represent an unknown dimension length.
UNKNOWN_SHAPE - Static variable in class qupath.opencv.dnn.DnnShape: Constant to represent an unknown shape.
UNKNOWN_SIZE - Static variable in class qupath.opencv.dnn.DnnShape: Constant to represent an unknown size (i.e.
unlimitedDatapoints() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Show all datapoints, without subsampling, even when this may cause performance issues.
UNLOCK_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
UNLOCKED - Enum constant in enum class qupath.lib.objects.PathObjectFilter: Accept any object that is 'unlocked'
unlockObjects(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools: Set specified objects to be 'unlocked'.
unlockSelectedObjects(PathObjectHierarchy) - Static method in class qupath.lib.objects.PathObjectTools: Set selected objects to be 'unlocked', firing an update event if the status of any object is changed.
unmanageMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar: Do not manage the system menubar status for the given menubar.
unpackARGB(int) - Static method in class qupath.lib.common.ColorTools: Unpack a packed ARGB int into red, green and blue values, returning the result as a 4-element int array.
unpackARGB(int, int[]) - Static method in class qupath.lib.common.ColorTools: Unpack a packed ARGB int into red, green and blue values, into a 4-element int array.
unpackRGB(int) - Static method in class qupath.lib.common.ColorTools: Unpack a packed (A)RGB int into red, green and blue values, returning the result as a 3-element int array.
unpackRGB(int, int[]) - Static method in class qupath.lib.common.ColorTools: Unpack a packed (A)RGB int into red, green and blue values, into a 3-element int array.
UNSET - Enum constant in enum class qupath.lib.images.ImageData.ImageType: Image type has not been set.
unzippedExtensions(Path, String...) - Static method in class qupath.lib.io.PathIO: Get the extension of a file, or of all entries within a zip file.
UPDATE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
updateAffineTransform() - Method in class qupath.lib.gui.viewer.QuPathViewer
updateAffineTransform() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
updateAvailableStyles() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager: Request that the list of available styles is updated.
updateBounds(double, double) - Method in class qupath.lib.roi.PointsROI
updateChart(BarChart<String, Number>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
updateChart(PieChart) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
updateChart(ScatterChart<Number, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
UpdateChecker - Class in qupath.lib.gui.extensions: Helper class to query for updates using GitHub's web API.
UpdateChecker() - Constructor for class qupath.lib.gui.extensions.UpdateChecker
UpdateChecker.ReleaseVersion - Class in qupath.lib.gui.extensions: Class to represent a release version.
updateCooccurrenceMatrices(CoocurranceMatrices, SimpleImage, SimpleImage, int, double, double, int) - Static method in class qupath.lib.analysis.features.HaralickFeatureComputer: Update existing CoocurranceMatrices with the values in a SimpleImage.
updateCursor() - Method in class qupath.lib.gui.viewer.QuPathViewer
updateDefaults(ImageData<BufferedImage>) - Method in class qupath.process.gui.commands.density.DensityMapDialog: Update default parameters with a specified ImageData.
updateDownsample(double) - Method in class qupath.lib.regions.RegionRequest: Create a RegionRequest equivalent to this one with the updated downsample value.
updateFromDisplay(ImageDisplay) - Method in class qupath.lib.display.ImageDisplay: Update the current display based upon a different display.
updateHistogram(ImageDisplay, ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane: Update the histogram to show the data for the given channel.
updateImage(String, BufferedImage) - Method in class qupath.lib.gui.panes.SimpleImageViewer: Update the image using a buffered image.
updateImage(String, Image) - Method in class qupath.lib.gui.panes.SimpleImageViewer: Update the image using a JavaFX image.
updateMeasurementList() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData: Update the entire measurement list for the current objects.
updateMeasurements() - Method in class qupath.lib.gui.panes.MeasurementMapPane: Update the measurements according to the current image
updateObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy: Update an object that is already in the hierarchy (e.g.
updateParameterList(ParameterList, Map<String, String>, Locale) - Static method in class qupath.lib.plugins.parameters.ParameterList: Update a ParameterList with the values specified in a map.
updatePath(String) - Method in class qupath.lib.regions.RegionRequest: Create a RegionRequest equivalent to this one with the updated path.
updatePlane(PathObject, ImagePlane, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Update the ROI plane for a single object.
updatePlane(ImagePlane) - Method in class qupath.lib.roi.AreaROI
updatePlane(ImagePlane) - Method in class qupath.lib.roi.EllipseROI
updatePlane(ImagePlane) - Method in class qupath.lib.roi.GeometryROI
updatePlane(ImagePlane) - Method in interface qupath.lib.roi.interfaces.ROI: Create a new ROI defining the same region on a different ImagePlane.
updatePlane(ImagePlane) - Method in class qupath.lib.roi.LineROI
updatePlane(ImagePlane) - Method in class qupath.lib.roi.PointsROI
updatePlane(ImagePlane) - Method in class qupath.lib.roi.PolygonROI
updatePlane(ImagePlane) - Method in class qupath.lib.roi.PolylineROI
updatePlane(ImagePlane) - Method in class qupath.lib.roi.RectangleROI
updatePlaneRecursive(PathObject, ImagePlane) - Static method in class qupath.lib.objects.PathObjectTools: Update the ROI plane for a single object and any descendant objects, creating new object IDs and ignoring any additional measurements.
updatePlaneRecursive(PathObject, ImagePlane, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools: Update the ROI plane for a single object, and any descendant objects.
updateProgress(int, String, ImageRegion) - Method in class qupath.lib.plugins.CommandLineTaskRunner.CommandLineProgressMonitor
updateProgress(int, String, ImageRegion) - Method in interface qupath.lib.plugins.SimpleProgressMonitor: Update the displayed progress, and optionally inform the PluginRunner that data related to a specified image region has been updated.
updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo: Update an array of existing pixels (packed RGB) additively using the colors to display a specified image.
updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo: Update an existing pixel (packed RGB) additively using the color used to display a specified one
updateRunningStatistics(RunningStatistics, SimpleImage) - Static method in class qupath.lib.analysis.stats.StatisticsHelper: Add all pixels from a SimpleImage to an existing RunningStatistics object.
updateServerMetadata(ImageServerMetadata) - Method in class qupath.lib.images.ImageData: Update the ImageServer metadata.
updateServerURIs(Map<URI, URI>) - Method in interface qupath.lib.projects.ProjectImageEntry: Deprecated.
use instead UriResource.updateURIs(Map)
updateStatus(ParallelTileObject.Status) - Method in class qupath.lib.plugins.ParallelTileObject: Notify the object if it is currently being processed.
updateT(int) - Method in class qupath.lib.regions.RegionRequest: Create a RegionRequest equivalent to this one with the updated t value.
updateTable() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane: Ensure the table is up-to-date.
updateTranslation(double, double, ImageRegion) - Method in class qupath.lib.roi.RoiEditor: Update a ROI by translation, optionally constraining its movement within a specified boundary.
updateUris(Map<URI, URI>) - Method in interface qupath.lib.io.UriResource
updateURIs(Map<URI, URI>) - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
updateURIs(Map<URI, URI>) - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder: Update the URIs required by this builder.
updateURIs(Map<URI, URI>) - Method in interface qupath.lib.io.UriResource: Update the specified URIs.
updateURIs(Map<URI, URI>) - Method in class qupath.opencv.dnn.DnnObjectClassifier
updateURIs(Map<URI, URI>) - Method in class qupath.opencv.dnn.OpenCVDnn
updateURIs(Map<URI, URI>) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
updateURIs(Map<URI, URI>) - Method in interface qupath.opencv.ops.ImageOp: Default implementation makes no changes; classes should override this if necessary.
UpdateUrisCommand<T> - Class in qupath.lib.gui.commands: Fix broken URIs by using relative paths or prompting the user to select files.
updateZ(int) - Method in class qupath.lib.regions.RegionRequest: Create a RegionRequest equivalent to this one with the updated z value.
updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler: New annotations can be constrained while they are being drawn, to avoid overlaps with existing annotations or to ensure they are drawn within a parent annotation.
updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler: New annotations can be constrained while they are being drawn, to avoid overlaps with existing annotations or to ensure they are drawn within a parent annotation.
updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.process.gui.WandToolEventHandler: New annotations can be constrained while they are being drawn, to avoid overlaps with existing annotations or to ensure they are drawn within a parent annotation.
UriResource - Interface in qupath.lib.io: Interface for objects that depend upon URIs.
URIs(URI...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the URIs.
URIs(Collection<URI>) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the URIs as a collection.
UriUpdater<T> - Class in qupath.lib.io: Helper class for updating URIs, for example whenever files have moved or projects have been transferred between computers.
UriUpdater.SingleUriItem - Class in qupath.lib.io: Wrapper for a URI, providing access to a Path if available.
UriUpdater.UriStatus - Enum Class in qupath.lib.io: Enum representing the status of a URI, i.e.
Urls - Class in qupath.lib.gui: Class to return core QuPath URLs centrally.
Urls() - Constructor for class qupath.lib.gui.Urls
useAnnotations() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Use annotations for labels.
useCalibratedLocationStringProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Show the cursor location on a viewer in calibrated units, rather than pixels.
useCellNuclei() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Use cells rather than annotations for labels, requesting the nucleus ROI where available.
useCells() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Use cells rather than annotations for labels.
useColorLUTs() - Method in class qupath.lib.display.ImageDisplay: The opposite of ImageDisplay.useGrayscaleLuts()
useCompiled() - Method in class qupath.lib.scripting.ScriptParameters: Request that any script should be compiled before being evaluated, and previously compiled versions reused when possible.
useCompiled(boolean) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Request that the script is compiled before being evaluated, or a previously compiled version is used where available.
useCuda() - Static method in class qupath.opencv.dnn.DnnTools: Returns true if CUDA is available and requested.
useDetections() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Use detections rather than annotations for labels.
useExtensions - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
useFilter(Predicate<PathObject>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Use a custom method of selecting objects for inclusion.
useGrayscaleLutProperty() - Method in class qupath.lib.display.ImageDisplay: Property that specifies whether grayscale lookup tables should be preferred to color lookup tables
useGrayscaleLuts() - Method in class qupath.lib.display.ImageDisplay: Get the value of ImageDisplay.useGrayscaleLutProperty()
useInstanceLabels() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Request that unique labels are used for all objects, rather than classifications.
useInstanceLabels(boolean) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Optionally request that unique labels are used for all objects, rather than classifications.
useInvertedBackground() - Method in class qupath.lib.display.ImageDisplay: Get the value of ImageDisplay.useInvertedBackgroundProperty()
useInvertedBackgroundProperty() - Method in class qupath.lib.display.ImageDisplay: Property that specifies whether the background should be inverted (i.e.
useLogWriters() - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the output and error writers to append to the default logger.
useLogWriters(Logger) - Method in class qupath.lib.scripting.ScriptParameters.Builder: Set the output and error writers to append to the specified logger.
useMicrons() - Method in class qupath.lib.gui.viewer.GridLines: Query whether to use calibrated units when calculating coordinates for any counting grid.
useMultipoint - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
useOverlays - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
useParallelization - Variable in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension.BioFormatsPreferences
usePixelSnappingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: If true, pixels should be snapped to integer coordinates when using the drawing tools.
UserDirectoryManager - Class in qupath.lib.gui: Helper class for managing a user directory, and associated subdirectories.
userDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager: Property representing the user directory.
useROIBounds(boolean) - Method in class qupath.lib.images.writers.TileExporter: Optionally use the full ROI for parent objects, rather than TileExporter.tileSize(int, int).
useRotateGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
useRotateGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Support rotate gestures for touchscreens and trackpads.
userPathProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: A path where additional files may be stored, such as extensions and log files.
useScrollGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Support scroll gestures for touchscreens and trackpads.
useSelectedColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
useSelectedColorProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Use a specified color for highlighting selected objects in the viewer.
useSystemMenubarProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Deprecated.
useTileBrushProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request that the brush tool automatically uses any available tiles, rather than creating 'circles' as normal.
useUniqueLabels() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder: Deprecated.
in favor of LabeledImageServer.Builder.useInstanceLabels()
useZoomGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
useZoomGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Support zoom gestures for touchscreens and trackpads.

V

validateMarkerMask(ImageProcessor, ImageProcessor) - Static method in class qupath.imagej.processing.MorphologicalReconstruction: Check that marker and mask images have the same size, and ensure that marker pixels are <= mask pixels, making this if necessary.
value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionAccelerator: String form of an accelerator, compatible with KeyCombination.valueOf(String).
value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig: Key to external properties file.
value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionIcon: Icon to associate with the action's graphic property.
value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionMenu: Menu path, in the form "Menu>Submenu>Command name".
VALUE_NONE - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand: Metadata value for unassigned images.
VALUE_TEST - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand: Metadata value for test images.
VALUE_TRAINING - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand: Metadata value for training images.
VALUE_VALIDATION - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand: Metadata value for validation images.
valueOf(String) - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.classifiers.Normalization: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.color.StainVector.DefaultStains: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.display.ChannelDisplayMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.extension.svg.SvgTools.SvgBuilder.ImageIncludeType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.actions.InfoMessage.MessageType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton: Deprecated.

Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.logging.LogManager.LogLevel: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.tools.GuiTools.SnapshotType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.tools.IconFactory.PathIcons: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.viewer.ImageInterpolation: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.ImageData.ImageType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.servers.PixelType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.servers.RotatedImageServer.Rotation: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.io.PathIO.GeoJsonExportOptions: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.io.UriUpdater.UriStatus: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.measurements.MeasurementList.MeasurementListType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.PathObjectFilter: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.objects.utils.Tiler.TileAlignment: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.plugins.ParallelTileObject.Status: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.roi.interfaces.ROI.RoiType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.roi.RoiTools.CombineOp: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.tools.LocalNormalization.NormalizationType: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.process.gui.WandToolEventHandler.WandType: Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Compartments: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.classifiers.Normalization: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.color.ColorDeconvolutionStains.DefaultColorDeconvolutionStains: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.color.StainVector.DefaultStains: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.display.ChannelDisplayMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.extension.svg.SvgTools.SvgBuilder.ImageIncludeType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.actions.InfoMessage.MessageType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton: Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.logging.LogManager.LogLevel: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.tools.GuiTools.SnapshotType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.tools.IconFactory.PathIcons: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.viewer.ImageInterpolation: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.ImageData.ImageType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.servers.PixelType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.servers.RotatedImageServer.Rotation: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.ChannelExportType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.io.PathIO.GeoJsonExportOptions: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.io.UriUpdater.UriStatus: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.measurements.MeasurementList.MeasurementListType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Method in interface qupath.lib.measurements.MeasurementList: Get all measurement values as a double array
values() - Static method in enum class qupath.lib.objects.classes.PathClassFactory.StandardPathClasses: Deprecated.

Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.objects.PathObjectFilter: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.objects.utils.Tiler.TileAlignment: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.plugins.objects.DilateAnnotationPlugin.LineCap: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.plugins.ParallelTileObject.Status: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.roi.interfaces.ROI.RoiType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.roi.RoiTools.CombineOp: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.dnn.OpenCVDnn.ModelType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.ml.pixel.PixelClassifierTools.CreateObjectOptions: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.tools.LocalNormalization.NormalizationType: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.process.gui.WandToolEventHandler.WandType: Returns an array containing the constants of this enum class, in the order they are declared.
variance(int) - Static method in class qupath.opencv.ops.ImageOps.Filters: Apply a 2D circular variance filter.
VARIANCE - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.Measurements: Variance value
varianceFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D local variance filter to all channels of an image, with symmetric boundary padding.
varianceFilter(Mat, int, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a circular 2D local variance filter to all channels of an image.
vConcat(Collection<? extends Mat>, Mat) - Static method in class qupath.opencv.tools.OpenCVTools: Vertical concatenation for a Mat.
Version - Class in qupath.lib.common: Helper class for working with semantic versioning.
VERSION - Static variable in class qupath.lib.scripting.QP: The current QuPath version, parsed according to semantic versioning.
VIEW_TRACKER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
viewer - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
viewer - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
viewer - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify a viewer.
viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Specify a viewer.
viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify a viewer.
VIEWER - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType: Snapshot of the current viewer content.
VIEWER_GRID_1x1 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
VIEWER_GRID_1x1 - Variable in class qupath.lib.gui.actions.ViewerActions
VIEWER_GRID_1x2 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
VIEWER_GRID_1x2 - Variable in class qupath.lib.gui.actions.ViewerActions
VIEWER_GRID_2x1 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
VIEWER_GRID_2x1 - Variable in class qupath.lib.gui.actions.ViewerActions
VIEWER_GRID_2x2 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
VIEWER_GRID_2x2 - Variable in class qupath.lib.gui.actions.ViewerActions
VIEWER_GRID_3x3 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
VIEWER_GRID_3x3 - Variable in class qupath.lib.gui.actions.ViewerActions
ViewerActions - Class in qupath.lib.gui.actions: Actions that interact with one or more viewers.
ViewerActions(ViewerManager) - Constructor for class qupath.lib.gui.actions.ViewerActions
viewerBackgroundColorProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Color to paint behind any image.
viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.UndoRedoManager
viewerClosed(QuPathViewer) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener: Called when a viewer is closed.
viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
viewerGammaProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Requested gamma value applied to the image in each viewer (for display only).
viewerInterpolateBilinearProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request that images are displayed in viewers using bilinear interpolation.
ViewerManager - Class in qupath.lib.gui.viewer: Class to manage multiple QuPathViewer instances in a UI region.
ViewerMover(QuPathViewer) - Constructor for class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover: Constructor.
ViewerPlusDisplayOptions - Class in qupath.lib.gui.viewer: A group of properties determining what should be displayed for each viewer.
ViewerPlusDisplayOptions() - Constructor for class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
ViewerPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
viewerProperty() - Method in class qupath.lib.gui.QuPathGUI: Property representing the viewer currently active.
ViewMenuActions - Class in qupath.lib.gui.actions.menus
ViewMenuActions.Actions - Class in qupath.lib.gui.actions.menus
ViewMenuActions.CellDisplayActions - Class in qupath.lib.gui.actions.menus
ViewMenuActions.MultitouchActions - Class in qupath.lib.gui.actions.menus
ViewMenuActions.MultiviewActions - Class in qupath.lib.gui.actions.menus
ViewMenuActions.MultiviewGridActions - Class in qupath.lib.gui.actions.menus
ViewMenuActions.ZoomActions - Class in qupath.lib.gui.actions.menus
ViewTracker - Class in qupath.lib.gui.viewer.recording: Default ViewTracker implementation.
ViewTrackerControlPane - Class in qupath.lib.gui.viewer.recording: Panel for viewing ViewTracker controls.
ViewTrackerControlPane(QuPathGUI) - Constructor for class qupath.lib.gui.viewer.recording.ViewTrackerControlPane: Create a ViewTrackerControlPane.
ViewTrackerDataMap - Class in qupath.lib.gui.viewer.recording: Class for storing the values of a data map as well as generating a proper BufferedImage with the appropriate pixel type.
visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.UndoRedoManager
visibleRegionChanged(QuPathViewer, Shape) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener: Called when the visible region has changed in a viewer.
visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.viewer.ViewerManager

W

WAND_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
WandPreferences() - Constructor for class qupath.process.gui.WandToolEventHandler.WandPreferences
wandSensitivity - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
wandSensitivityProperty() - Static method in class qupath.process.gui.WandToolEventHandler: Property representing the wand sensitivity value, which influences how similar local intensity values must be for the wand region growing.
wandSigma - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
wandSigmaPixelsProperty() - Static method in class qupath.process.gui.WandToolEventHandler: Property representing the Gaussian sigma value used to smooth the image when applying the wand.
WandToolEventHandler - Class in qupath.process.gui: Wand tool, which acts rather like the brush - except that it expands regions (sometimes rather too eagerly?) based upon local pixel values.
WandToolEventHandler(QuPathGUI) - Constructor for class qupath.process.gui.WandToolEventHandler: Constructor.
WandToolEventHandler.WandPreferences - Class in qupath.process.gui
WandToolEventHandler.WandType - Enum Class in qupath.process.gui: Enum reflecting different color images that may be used by the Wand tool.
wandToRoi(Wand) - Static method in class qupath.imagej.processing.RoiLabeling: Convert a traced outline from the ImageJ Wand into a PolygonRoi.
wandType - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
wandTypeProperty() - Static method in class qupath.process.gui.WandToolEventHandler: Property specifying whether the wand tool should be influenced by pixel values painted on image overlays.
wandUseOverlaysProperty() - Static method in class qupath.process.gui.WandToolEventHandler: Property specifying whether the wand tool should be influenced by pixel values painted on image overlays.
WARN - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType: Warning.
WARN - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: Warn logging (only if something is moderately important)
warning() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Create a warning alert dialog.
warning(String) - Static method in class qupath.lib.gui.actions.InfoMessage: Create a warning message with static text.
warning(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage: Create a warning message with static text and a count.
warning(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage: Create a warning message to show a count of warnings.
warning(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage: Create a warning message.
warning(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage: Create a warning message with a count.
WARNING - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
warnOnce(Logger, String) - Static method in class qupath.lib.common.LogTools: Log a message once at the WARN level.
Watershed - Class in qupath.imagej.processing: Implementation of 2D watershed transform for ImageJ.
Watershed - Class in qupath.lib.analysis.algorithms: Implementation of 2D watershed transform.
Watershed() - Constructor for class qupath.imagej.processing.Watershed
Watershed() - Constructor for class qupath.lib.analysis.algorithms.Watershed
WatershedCellDetection - Class in qupath.imagej.detect.cells: Default command for cell detection within QuPath, assuming either a nuclear or cytoplasmic staining.
WatershedCellDetection() - Constructor for class qupath.imagej.detect.cells.WatershedCellDetection
WatershedCellMembraneDetection - Class in qupath.imagej.detect.cells: Cell detection that takes into consideration membrane staining.
WatershedCellMembraneDetection() - Constructor for class qupath.imagej.detect.cells.WatershedCellMembraneDetection: Default constructor.
watershedExpandLabels(ImageProcessor, double, boolean) - Static method in class qupath.imagej.processing.Watershed: Expand non-zero regions in a labeled image up to a maximum distance, using a watershed transform to prevent region merging.
watershedIntensitySplit(Mat, Mat, double, int) - Static method in class qupath.opencv.tools.OpenCVTools: Apply a watershed transform to refine a binary image, guided either by a distance transform or a supplied intensity image.
WatershedNucleiCV - Class in qupath.opencv: Alternative (incomplete) attempt at nucleus segmentation.
WatershedNucleiCV() - Constructor for class qupath.opencv.WatershedNucleiCV
WebViews - Class in qupath.lib.gui.tools: Helper class for creating a WebView in a standardized way.
WebViews() - Constructor for class qupath.lib.gui.tools.WebViews
WEIGHTED_STD_DEV - Enum constant in enum class qupath.opencv.tools.MultiscaleFeatures.MultiscaleFeature: Weighted standard deviation
weightedStdDev(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder: Calculate a Gaussian-weighted standard deviation.
WelcomeStage - Class in qupath.lib.gui: Welcome page when launching QuPath.
WelcomeStage() - Constructor for class qupath.lib.gui.WelcomeStage
White - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod: All pixels white
WHITE - Static variable in class qupath.lib.common.ColorTools: Packed int representing white.
width - Variable in class qupath.lib.geom.ImmutableDimension: Width of the ImmutableDimension.
width - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
width - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
width - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
width(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Set the preferred width of the chart.
width(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Set the preferred width of the chart.
width(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the preferred width of the chart.
width(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Deprecated.

Specify the dialog width.
width(int) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Export image width.
width(int) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the full-resolution image width.
windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Title to use for the window, if the chart is shown.
windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder: Title to use for the window, if the chart is shown.
windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Title to use for the window, if the chart is shown.
WITH_ICONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes: Show detections with ROI icons
WITHOUT_ICONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes: Show detections without ROI icons
workerComplete(TileWorker<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore: Every TileWorker should call this when the task is done!
Workflow - Class in qupath.lib.plugins.workflow: A collection of steps that relate to how an image has been - or should be - processed.
Workflow() - Constructor for class qupath.lib.plugins.workflow.Workflow
WorkflowCommandLogView - Class in qupath.lib.gui.panes: Show logged commands, and optionally generate a script.
WorkflowCommandLogView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.WorkflowCommandLogView: Construct a view to display the workflow for the currently-active ImageData within a running QuPath instance.
WorkflowCommandLogView(QuPathGUI, Workflow) - Constructor for class qupath.lib.gui.panes.WorkflowCommandLogView: Construct a view displaying a static workflow (i.e.
WorkflowListener - Interface in qupath.lib.plugins.workflow: Interface for listening to changes in Workflows, e.g.
WorkflowStep - Interface in qupath.lib.plugins.workflow: Basic interface for a loggable workflow step.
workflowUpdated(Workflow) - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
workflowUpdated(Workflow) - Method in class qupath.lib.images.ImageData
workflowUpdated(Workflow) - Method in interface qupath.lib.plugins.workflow.WorkflowListener: Called whenever a Workflow has been updated in some way, such as a new step added.
wrap(URI...) - Static method in class qupath.lib.io.UriUpdater: Wrap one or more URIs in a UriResource so they can be updated together.
wrap(Collection<? extends PathObject>) - Static method in class qupath.lib.io.FeatureCollection: Wrap a collection of PathObjects as a FeatureCollection, ignoring nested (child) objects.
wrap(Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.io.FeatureCollection: Wrap a collection of PathObjects as a FeatureCollection.
wrap(Collection<URI>) - Static method in class qupath.lib.io.UriUpdater: Wrap one or more URIs in a UriResource so they can be updated together.
wrapInPointerScope(Processor<S, T, U>) - Static method in class qupath.lib.experimental.pixels.OpenCVProcessor: Wrap a processor in a second processor that uses a PointerScope to ensure that pointers are released (except for any output).
WrappedBufferedImageServer - Class in qupath.lib.images.servers: Implementation of an ImageServer that simply wraps an existing BufferedImage.
WrappedBufferedImageServer(String, BufferedImage) - Constructor for class qupath.lib.images.servers.WrappedBufferedImageServer: Create an ImageServer<BufferedImage> using an image that has been provided directly.
WrappedBufferedImageServer(String, BufferedImage, List<ImageChannel>) - Constructor for class qupath.lib.images.servers.WrappedBufferedImageServer: Create an ImageServer<BufferedImage> using an image that has been provided directly.
wrapStatModel(StatModel) - Static method in class qupath.opencv.ml.OpenCVClassifiers: Create an OpenCVClassifiers.OpenCVStatModel by wrapping an existing StatModel.
wrapTextProperty() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
wrapTextProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl: Request wordwrap.
wrapTextProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
write(JsonWriter, ColorTransforms.ColorTransform) - Method in class qupath.lib.images.servers.ColorTransforms.ColorTransformTypeAdapter
write(JsonWriter, T) - Method in class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdapter
writeClassifier(ObjectClassifier<T>, Path) - Static method in class qupath.lib.classifiers.object.ObjectClassifiers: Write the classifier to a file.
writeClassifier(PixelClassifier, Path) - Static method in class qupath.opencv.ml.pixel.PixelClassifiers: Write a pixel classifier to a file.
writeDensityMapImage(String, String) - Static method in class qupath.lib.scripting.QP: Write the output of applying a density map to the current image image.
writeDensityMapImage(ImageData<BufferedImage>, DensityMaps.DensityMapBuilder, String) - Static method in class qupath.lib.scripting.QP: Write the output of applying a density map to an image.
writeExternal(ObjectOutput) - Method in class qupath.lib.color.ColorDeconvolutionStains
writeExternal(ObjectOutput) - Method in class qupath.lib.color.StainVector
writeExternal(ObjectOutput) - Method in class qupath.lib.geom.Point2
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathCellObject
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathObject
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathObjectConnections
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.PathROIObject
writeExternal(ObjectOutput) - Method in class qupath.lib.objects.TMACoreObject
writeExternal(ObjectOutput) - Method in class qupath.lib.plugins.workflow.SimplePluginWorkflowStep
writeExternal(ObjectOutput) - Method in class qupath.lib.plugins.workflow.Workflow
writeImage(ImagePlus, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(ImagePlus, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(ImagePlus, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(ImagePlus, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(BufferedImage, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(BufferedImage, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(BufferedImage, OutputStream) - Method in class qupath.lib.images.writers.JpegWriter
writeImage(BufferedImage, OutputStream) - Method in class qupath.lib.images.writers.PngWriter
writeImage(BufferedImage, OutputStream) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
writeImage(BufferedImage, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(BufferedImage, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(BufferedImage, String) - Static method in class qupath.lib.images.writers.ImageWriterTools: Write a 2D image using the default writer based on the file path.
writeImage(BufferedImage, String) - Method in class qupath.lib.images.writers.JpegWriter
writeImage(BufferedImage, String) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
writeImage(BufferedImage, String) - Method in class qupath.lib.images.writers.PngWriter
writeImage(BufferedImage, String) - Static method in class qupath.lib.scripting.QP: Write an image to the specified path.
writeImage(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter: Write an image consisting of one or more series to the specified path.
writeImage(Image, String) - Static method in class qupath.lib.gui.scripting.QPEx: Write a JavaFX image to the specified path.
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.lib.images.writers.JpegWriter
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.lib.images.writers.PngWriter
writeImage(ImageServer<BufferedImage>, OutputStream) - Method in class qupath.lib.images.writers.ome.OMETiffWriter: Write OME-TIFF image to an output stream.
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.lib.images.writers.JpegWriter
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.lib.images.writers.PngWriter
writeImage(ImageServer<BufferedImage>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools: Write a (possibly multidimensional) image region using the default writer based on the file path.
writeImage(ImageServer<BufferedImage>, String) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter: Static helper method to write an image using Bio-Formats.
writeImage(ImageServer<BufferedImage>, String) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
writeImage(ImageServer<BufferedImage>, String) - Static method in class qupath.lib.scripting.QP: Write a full image to the specified path.
writeImage(ImageServer<BufferedImage>, String, OMEPyramidWriter.CompressionType) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter: Static helper method to write an image using Bio-Formats with the specified compression.
writeImage(ImageServer<BufferedImage>, String, OMEPyramidWriter.CompressionType, ImageRegion) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter: Static helper method to write an image region using Bio-Formats with the specified compression.
writeImage(ImageServer<BufferedImage>, String, OMEPyramidWriter.CompressionType, ImageRegion, boolean, boolean) - Static method in class qupath.lib.images.writers.ome.OMEPyramidWriter: Static helper method to write an image using Bio-Formats for a defined region with the specified compression, optionally including all z-slices or timepoints.
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.lib.images.writers.JpegWriter
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.lib.images.writers.PngWriter
writeImage(ImageServer<BufferedImage>, RegionRequest, OutputStream) - Method in class qupath.lib.images.writers.ome.OMETiffWriter: Write OME-TIFF image to an output stream.
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.imagej.images.writers.TiffWriterIJ
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.imagej.images.writers.ZipWriterIJ
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.lib.images.writers.JpegWriter
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.lib.images.writers.PngWriter
writeImage(ImageServer<BufferedImage>, RegionRequest, String) - Method in class qupath.lib.images.writers.ome.OMETiffWriter
writeImage(ImageServer<T>, OutputStream) - Method in interface qupath.lib.images.writers.ImageWriter: Write a full image to a specified output stream.
writeImage(ImageServer<T>, String) - Method in interface qupath.lib.images.writers.ImageWriter: Write a full image to a specified path.
writeImage(ImageServer<T>, RegionRequest, OutputStream) - Method in interface qupath.lib.images.writers.ImageWriter: Write an image region to a specified output stream.
writeImage(ImageServer<T>, RegionRequest, String) - Method in interface qupath.lib.images.writers.ImageWriter: Write an image region to a specified path.
writeImage(T, OutputStream) - Method in interface qupath.lib.images.writers.ImageWriter: Write a full image to a specified output stream.
writeImage(T, String) - Method in interface qupath.lib.images.writers.ImageWriter: Write a full image to a specified path.
writeImageData(File, ImageData<?>) - Static method in class qupath.lib.io.PathIO: Write (binary) file containing ImageData for later use.
writeImageData(OutputStream, ImageData<?>) - Static method in class qupath.lib.io.PathIO: Serialize an ImageData object to an output stream.
writeImageData(Path, ImageData<?>) - Static method in class qupath.lib.io.PathIO: Write (binary) file containing ImageData for later use.
writeImageRegion(ImageServer<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.images.writers.ImageWriterTools: Write a 2D image region using the default writer based on the file path.
writeImageRegion(ImageServer<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.scripting.QP: Write an image region image to the specified path.
writePoints(File, Collection<? extends PathObject>) - Static method in class qupath.lib.io.PointIO: Write a list of point annotations to a file.
writePoints(OutputStream, Collection<? extends PathObject>) - Static method in class qupath.lib.io.PointIO: Write a list of point annotations to a stream.
writePredictionImage(String, String) - Static method in class qupath.lib.scripting.QP: Write the output of applying a pixel classifier to the current image image.
writePredictionImage(ImageData<BufferedImage>, PixelClassifier, String) - Static method in class qupath.lib.scripting.QP: Write the output of applying a pixel classifier to an image.
writePyramid(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries: Deprecated.
use OMEPyramidWriter.OMEPyramidSeries.writeSeries(String) instead
writePyramid(PyramidOMETiffWriter, IMetadata, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries: Deprecated.
use OMEPyramidWriter.OMEPyramidSeries.writeSeries(IFormatWriter, IMetadata, int) instead
writeRenderedImage(QuPathViewer, String) - Static method in class qupath.lib.gui.scripting.QPEx: Write a rendered image for the current viewer to the specified path.
writeRenderedImage(ImageData<BufferedImage>, String) - Static method in class qupath.lib.gui.scripting.QPEx: Write a rendered image to the specified path.
writeRenderedImageRegion(QuPathViewer, RegionRequest, String) - Static method in class qupath.lib.gui.scripting.QPEx: Write a rendered image region for the current viewer to the specified path.
writeRenderedImageRegion(ImageData<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.gui.scripting.QPEx: Write a rendered image region to the specified path.
writeSeries(String) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries: Write an image to the given file.
writeSeries(IFormatWriter, IMetadata, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.OMEPyramidSeries: Append an image as a specific series.
writeSVG(File) - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder: Write the SVG image to a file, including any references images if required.
writeTiles(String) - Method in class qupath.lib.images.writers.TileExporter: Export the image tiles to the specified directory.
writeTMAData(File, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.tma.TMADataIO: Write TMA summary data, without any image export.
writeTMAData(File, ImageData<BufferedImage>, OverlayOptions, double) - Static method in class qupath.lib.gui.tma.TMADataIO: Write TMA data in a human-readable (and viewable) way, with JPEGs and TXT/CSV files.
writeViewerSnapshot(QuPathViewer, File) - Static method in class qupath.lib.extension.svg.SvgTools: Write an SVG image representing the contents of the specified viewer.

X

x - Variable in class qupath.lib.roi.EllipseROI
x - Variable in class qupath.lib.roi.RectangleROI
x2 - Variable in class qupath.lib.roi.EllipseROI
x2 - Variable in class qupath.lib.roi.RectangleROI
xAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the upper bound for the x-axis.
xAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the lower bound for the x-axis.
xAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the lower and upper bounds for the x-axis.
xLabel - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
xLabel - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
xLabel(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify the x-axis label.
xLabel(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify the x-axis label.
XML - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for XML
XML - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
XmlLanguage - Class in qupath.lib.gui.scripting.languages: Class for representing XML in QuPath.
XmlLanguage() - Constructor for class qupath.lib.gui.scripting.languages.XmlLanguage: Constructor for XML Language.
XmlStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling to apply to a CodeArea for XML.
xor(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV: Compute the bitwise XOR of two arrays.

Y

y - Variable in class qupath.lib.roi.EllipseROI
y - Variable in class qupath.lib.roi.RectangleROI
y2 - Variable in class qupath.lib.roi.EllipseROI
y2 - Variable in class qupath.lib.roi.RectangleROI
YAML - Static variable in class qupath.lib.gui.scripting.richtextfx.stylers.ScriptStylerProvider: Styler for YAML
YAML - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
YamlLanguage - Class in qupath.lib.gui.scripting.languages: Class for the representation of YAML syntax in QuPath.
YamlLanguage() - Constructor for class qupath.lib.gui.scripting.languages.YamlLanguage: Constructor for YAML language.
YamlStyler - Class in qupath.lib.gui.scripting.richtextfx.stylers: Styling to apply to a CodeArea, based on YAML syntax.
yAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Set the upper bound for the y-axis.
yAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the upper bound for the y-axis.
yAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Set the lower bound for the y-axis.
yAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the lower bound for the y-axis.
yAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Set the lower and upper bounds for the y-axis.
yAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Set the lower and upper bounds for the y-axis.
YELLOW - Static variable in class qupath.lib.common.ColorTools: Packed int representing yellow.
YES - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton: Deprecated.

"Yes" option
yLabel - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
yLabel - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
yLabel(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder: Specify the y-axis label.
yLabel(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder: Specify the y-axis label.

Z

Z_SLICE - Static variable in class qupath.lib.images.servers.PixelCalibration: String to represent 'z-slice' units.
zapGremlins(String) - Static method in class qupath.lib.common.GeneralTools: Remove non-printable characters from a String.
zeroMeanUnitVariance(boolean) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Normalize a Mat by subtracting the mean value and dividing by the standard deviation.
zeroMeanUnitVariance(boolean, double) - Static method in class qupath.opencv.ops.ImageOps.Normalize: Normalize a Mat by subtracting the mean value and dividing by the standard deviation + eps.
ZipWriterIJ - Class in qupath.imagej.images.writers: ImageWriter implementation to write zipped TIFF images using ImageJ.
ZipWriterIJ() - Constructor for class qupath.imagej.images.writers.ZipWriterIJ
ZLIB - Enum constant in enum class qupath.lib.images.writers.ome.OMEPyramidWriter.CompressionType: ZLIB compression.
ZOOM_1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
ZOOM_10 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
ZOOM_100 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
ZOOM_400 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
ZOOM_IN - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ZOOM_IN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
ZOOM_OUT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ZOOM_OUT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
ZOOM_TO_FIT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
ZOOM_TO_FIT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
ZOOM_TO_FIT - Variable in class qupath.lib.gui.actions.ViewerActions
zoomActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
zoomIn() - Method in class qupath.lib.gui.viewer.QuPathViewer: Zoom in by one step.
zoomIn(int) - Method in class qupath.lib.gui.viewer.QuPathViewer: Zoom in by a specified number of steps, where one 'step' indicates a minimal zoom increment.
zoomOut() - Method in class qupath.lib.gui.viewer.QuPathViewer: Zoom out by one step.
zoomOut(int) - Method in class qupath.lib.gui.viewer.QuPathViewer: Zoom out by a specified number of steps, where one 'step' indicates a minimal zoom increment.
zoomToFit() - Method in class qupath.lib.gui.viewer.QuPathViewer: Request that the downsample is set to contain the entire image, and the image is centered in the viewer.
zPositionProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer: Current z-position for the z-slice currently visible in the viewer.
zRange(int, int) - Method in class qupath.lib.images.writers.TileExporter: Define the range of Z-slices to process.
zSlice(int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify the z-slice to export.
zSlices(int, int) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder: Specify the start (inclusive) and end (exclusive) z-slices.
zSpacingCalibrated() - Method in class qupath.lib.images.servers.ImageServerMetadata: Returns true if z-spacing calibration information is available for the image.
zSpacingMicrons(Number) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder: Specify the spacing between z-slices, in microns.
zSpacingMicrons(Number) - Method in class qupath.lib.images.servers.PixelCalibration.Builder: Specify spacing between z-slices, in microns.

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