Index (QuPath 0.4.0)

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
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
AbstractPluginRunner<T> - Class in qupath.lib.plugins: Abstract PluginRunner to help with the creation of plugin runners for specific circumstances, e.g.
AbstractPluginRunner() - Constructor for class qupath.lib.plugins.AbstractPluginRunner
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.ActionTools.ActionBuilder: Bind the accelerator property of the action to an ObservableValue, bidirectionally if possible.
accelerator(KeyCombination) - Method in class qupath.lib.gui.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()
actionBuilder() - Static method in class qupath.lib.gui.ActionTools: Create an ActionTools.ActionBuilder with no properties set.
actionBuilder(String, Consumer<ActionEvent>) - Static method in class qupath.lib.gui.ActionTools: Create an ActionTools.ActionBuilder with the specified text and event handler.
actionBuilder(Consumer<ActionEvent>) - Static method in class qupath.lib.gui.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
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
actionExtractRegion - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
actionFastCellCounts - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands: Deprecated.
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
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
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
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: Helper methods for generating and configuring Actions and UI elements.
ActionTools() - Constructor for class qupath.lib.gui.ActionTools
ActionTools.ActionAccelerator - Annotation Interface in qupath.lib.gui: Annotation used to specify a preferred accelerator for an an action.
ActionTools.ActionBuilder - Class in qupath.lib.gui: Builder class for custom Action objects.
ActionTools.ActionDescription - Annotation Interface in qupath.lib.gui: Description of an action.
ActionTools.ActionIcon - Annotation Interface in qupath.lib.gui: Default icon for an action.
ActionTools.ActionMenu - Annotation Interface in qupath.lib.gui: Annotation indicating the menu path where an action should be installed.
ActionTools.ActionMethod - Annotation Interface in qupath.lib.gui: Annotation indicating that a method should be converted to an Action if possible.
actionTrainingImage - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
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.
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).
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: Add a new choice preference, to select from a list of possibilities.
addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String, boolean) - Method in class qupath.lib.gui.panes.PreferencePane: Add a new choice preference, to select from an optionally searchable list of possibilities.
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: Add a new color preference based on a specified IntegerProperty (storing a packed RGBA value).
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: Add a new directory preference based on a specified StrongProperty.
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.
addExtensionJar(File) - Method in class qupath.lib.gui.QuPathGUI: Request that a specified Jar file be added to the extension classpath.
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: 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.
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>, 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: Add a new preference based on a specified Property.
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.HistogramPanelFX.ThresholdedChartWrapper: Add a threshold value.
addThreshold(double, Color) - Method in class qupath.lib.gui.charts.HistogramPanelFX.ThresholdedChartWrapper: Add a threshold value with its display color.
addThreshold(ObservableNumberValue) - Method in class qupath.lib.gui.charts.HistogramPanelFX.ThresholdedChartWrapper: 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: Create a dialog styled as a specified alert type.
ALL - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel: All log messages
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
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.
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.
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.
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_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
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+.
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 class qupath.lib.gui.commands.LogViewerCommand
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.
applyReplacements() - Method in class qupath.lib.io.UriUpdater: Apply all current replacements, updating the UriResource objects.
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.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.
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.
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.
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
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.AbstractPluginRunner: 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(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.
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.
batchConvertAndPredict(Mat...) - Method in interface qupath.opencv.dnn.DnnModel: Convenience method to convert one or more image patches to a blob, apply the PredictionFunction, and convert the output to standard Mats.
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.
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.
bindSliderAndTextField(Slider, TextField, boolean) - Static method in class qupath.lib.gui.tools.GuiTools: Bind the value of a slider and contents of a text field with a default number of decimal places, so that both may be used to set a numeric (double) value.
bindSliderAndTextField(Slider, TextField, boolean, int) - Static method in class qupath.lib.gui.tools.GuiTools: Bind the value of a slider and contents of a text field, so that both may be used to set a numeric (double) value.
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
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.
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.QuPathGUI.DefaultActions: Show the brightness/contrast dialog.
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.
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.QuPathGUI.DefaultActions: Brush tool action
brushCreateNewObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Create new objects by default when drawing with the Brush tool.
brushDiameterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Default brush tool diameter, in pixels.
brushScaleByMagProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Optionally scale the default brush tool diameter by the viewer magnification (downsample value).
BrushTool - Class in qupath.lib.gui.viewer.tools: Tool for drawing (and subtract from) freehand regions, optionally adapting brush size to magnification.
BrushTool() - Constructor for class qupath.lib.gui.viewer.tools.BrushTool
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.
BufferedImageTools - Class in qupath.lib.awt.common: Static methods for working with BufferedImages and QuPath objects.
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.gui.ActionTools.ActionBuilder: Create an Action with this builder.
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: 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.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.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.gui.dialogs.Dialogs: 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(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(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(PathObjectPredicates.PathObjectPredicate) - Static method in class qupath.lib.analysis.heatmaps.DensityMaps: Create a new DensityMaps.DensityMapBuilder to generate a customized density map.
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.gui.dialogs.Dialogs.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.
buttons(String...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Specify the buttons to display in the dialog.
buttons(ButtonType...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Specify the buttons to display in the dialog.

C

cache - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
calculatePadding() - Method in class qupath.opencv.ops.ImageOps.PaddedOp: Calculate the required padding.
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.
call(PropertySheet.Item) - Method in class qupath.lib.gui.panes.PreferencePane.PropertyEditorFactory
callOnApplicationThread(Callable<T>) - Static method in class qupath.lib.gui.tools.GuiTools: Return a result after executing a Callable on the JavaFX Platform thread.
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: "Cancel" option
cancelDirection(boolean) - Method in class qupath.lib.gui.viewer.tools.MoveTool.ViewerMover: Cancel either the x- or y-axis direction of the movement.
cancelled() - Method in class qupath.lib.plugins.CommandLinePluginRunner.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
category(String) - Method in class qupath.lib.gui.panes.PreferencePane.PropertyItem: Support fluent interface to define a category.
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
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
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 QuPathViewerPlus>, QuPathViewerPlus, QuPathViewerPlus) - Method in class qupath.lib.gui.UndoRedoManager
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.BrightnessContrastCommand
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.CountingPanelCommand
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).
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
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.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.
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
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.
CircularSlider - Class in qupath.lib.gui: A custom JavaFX circular-slider control.
CircularSlider() - Constructor for class qupath.lib.gui.CircularSlider: Create a circular slider
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.
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.
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.
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.HistogramPanelFX.ThresholdedChartWrapper: 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.
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.images.servers.PathHierarchyImageServer
close() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
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.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
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)
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.
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
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.
CommandLinePluginRunner<T> - Class in qupath.lib.plugins: A PluginRunner that simply logs progress and output.
CommandLinePluginRunner(ImageData<T>) - Constructor for class qupath.lib.plugins.CommandLinePluginRunner: Constructor for a PluginRunner that send progress to a log.
CommandLinePluginRunner.CommandLineProgressMonitor - Class in qupath.lib.plugins: A SimpleProgressMonitor that sends progress to a log.
CommandLineProgressMonitor() - Constructor for class qupath.lib.plugins.CommandLinePluginRunner.CommandLineProgressMonitor
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
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.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.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: 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.
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.
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: Specify a Node to display within the dialog.
contentText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: Specify the dialog content text.
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
convertAndPredict(Map<String, Mat>) - Method in interface qupath.opencv.dnn.DnnModel: 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.
convertAndPredict(Mat) - Method in interface qupath.opencv.dnn.DnnModel: Convenience method to convert a single image patch to a blob, apply the PredictionFunction, and convert the output to a standard Mat.
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.
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_POINTS - Variable in class qupath.lib.gui.QuPathGUI.DefaultActions: Display the convex hull of point ROIs.
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
copyAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
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.
COUNTING_PANEL - Variable in class qupath.lib.gui.QuPathGUI.DefaultActions: Show the counting tool dialog.
CountingPanelCommand - Class in qupath.lib.gui.commands: Command to open up a counting panel to aid with creating Point annotations.
CountingPanelCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.CountingPanelCommand: 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.
countReplacements() - Method in class qupath.lib.io.UriUpdater: Get a count of the number of replacements for missing items.
cpu() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder: Request CPU backend and target, if available.
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, 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(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(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.
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.ActionTools: Create an action whose event handler calls a runnable.
createAction(Runnable, String) - Static method in class qupath.lib.gui.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.
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).
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.
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.
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.
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.
createButton(Action, boolean) - Static method in class qupath.lib.gui.ActionTools: Create a button from an action.
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).
createCellObject(ROI, ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects: Create a cell object.
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.ActionTools: Create a checkbox from an action.
createCheckMenuItem(Action) - Static method in class qupath.lib.gui.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.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: Create a GridPane containing columns that resize similarly to Swing's GridLayout().
createColumnGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: Create a GridPane containing columns that resize similarly to Swing's GridLayout().
createColumnGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: 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.
createCustomListCell(Function<T, String>) - Static method in class qupath.lib.gui.tools.GuiTools: Create a ListCell with custom methods to derive text for a specific object.
createCustomListCell(Function<T, String>, Function<T, Node>) - Static method in class qupath.lib.gui.tools.GuiTools: Create a ListCell with custom methods to derive text and a graphic for a specific object.
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
createDefaultSkin() - Method in class qupath.lib.gui.CircularSlider
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.
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.
createDynamicStepSpinner(double, double, double, double, int) - Static method in class qupath.lib.gui.tools.GuiTools: Create a new Spinner for double values with a step size that adapts according to the absolute value of the current spinner value.
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.
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).
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.
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.
createHistogramData(Histogram, boolean, Integer) - Static method in class qupath.lib.gui.charts.HistogramPanelFX: Create a HistogramData object to wrap a histogram & some info about its display.
createHistogramData(Histogram, boolean, Color) - Static method in class qupath.lib.gui.charts.HistogramPanelFX: Create a HistogramData object to wrap a histogram & some info about its display.
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.
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(long) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreFactory: Create an ImageRegionStore.
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.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(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.
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.
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.
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.
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.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.
createNewChart() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
createNewChart() - Method in class qupath.lib.gui.charts.Charts.ScatterchartBuilder
createNewChart(Axis<Number>, Axis<Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterchartBuilder
createNewImageData(ImageServer<BufferedImage>, boolean) - Method in class qupath.lib.gui.QuPathGUI: Create a new ImageData, optionally estimating the image type.
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.BrushTool
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.EllipseTool
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.LineTool
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.PolygonTool
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.PolylineTool
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.RectangleTool
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.
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.
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.
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.
createPersistentJsonPreference(String, T, Class<T>) - Static method in class qupath.lib.gui.prefs.PathPrefs: Create a persistent property representing any JSON-serializable object, which will be saved to/reloaded from the user preferences.
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, 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.
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.
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.
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.
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: Create a default PropertySheet.Item for a generic property.
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.
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.
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.
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: Create a GridPane containing rows that resize similarly to Swing's GridLayout().
createRowGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools: 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>, String) - Static method in class qupath.lib.gui.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.ActionTools: Create an action with its Action.selectedProperty() bound to a specified property, with optional graphic and accelerator.
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.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.BrushTool: 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.WandToolCV
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.
createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.QuPathGUI: Create a completion service that uses a shared threadpool for the application.
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.
createSingleThreadExecutor(Object) - Method in class qupath.lib.gui.QuPathGUI: Create an executor using a single thread.
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.
createStepBinding(ObservableValue<Double>, double, int) - Static method in class qupath.lib.gui.tools.GuiTools: Create a binding that may be used with a Spinner to adjust the step size dynamically based upon the absolute value of the input.
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.
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, MeasurementList) - Static method in class qupath.lib.objects.PathObjects: Create a tile object.
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, boolean) - Static method in class qupath.lib.gui.ActionTools: Create a toggle button from an action.
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.
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.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.
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.
cross3(double[], double[]) - Static method in class qupath.lib.color.StainVector: Compute the cross product of two vectors.
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.
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.MoveTool.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.
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
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.
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 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.
description(String) - Method in class qupath.lib.gui.panes.PreferencePane.PropertyItem: Support fluent interface to set the description.
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.
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_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.
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.
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: Collection of static methods to help with showing information to a user, as well as requesting some basic input.
Dialogs() - Constructor for class qupath.lib.gui.dialogs.Dialogs
Dialogs.Builder - Class in qupath.lib.gui.dialogs: Builder class to create a custom Dialog.
Dialogs.DialogButton - Enum Class in qupath.lib.gui.dialogs: 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
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.ActionTools.ActionBuilder: Set the disabled property of the action.
disabled(ObservableValue<Boolean>) - Method in class qupath.lib.gui.ActionTools.ActionBuilder: Bind the disabled property of the action to an ObservableValue, bidirectionally if possible.
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()
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.
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<T> - Interface in qupath.opencv.dnn: Wrapper for a deep learning model in a pipeline using OpenCV.
DnnModelBuilder<T> - 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<T> - Class in qupath.opencv.dnn: Initial implementation of a patch-based ObjectClassifier using an OpenCV-compatible DNN.
DnnObjectClassifier(PathObjectFilter, DnnModel<T>, 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.
doCreateLogFilesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs: Request a log file to be generated.
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
DONE - Enum constant in enum class qupath.lib.plugins.ParallelTileObject.Status: Tile processing complete
doNormalizeCounts() - Method in class qupath.lib.gui.charts.HistogramPanelFX.HistogramData: Returns true if the counts are normalized for display.
DOUBLE - Enum constant in enum class qupath.lib.measurements.MeasurementList.MeasurementListType: A list backed by an array of doubles.
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.
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.
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.
dumpPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs: Dump the current preferences to an XML string.
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.
editSelectedAnnotation(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands: Prompt to edit the selected annotation by translation and rotation.
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.QuPathGUI.DefaultActions: Ellipse tool action
EllipseROI - Class in qupath.lib.roi: ROI implementing a circle, or (unrotated) ellipse.
EllipseTool - Class in qupath.lib.gui.viewer.tools: PathTool for drawing ellipses.
EllipseTool() - Constructor for class qupath.lib.gui.viewer.tools.EllipseTool
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.
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.
ensureDuplicatableGlyph(Glyph) - Static method in class qupath.lib.gui.tools.GuiTools: Ensure that a Glyph is 'duplicatable', without losing its key properties.
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: Create an error alert dialog.
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.
expandableContent(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder: 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.
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.
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.
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.
ExtensionClassLoader - Class in qupath.lib.gui: ClassLoader for loading QuPath extensions and other jars from the user directory.
ExtensionClassLoader() - Constructor for class qupath.lib.gui.ExtensionClassLoader: Constructor.
EXTENSIONS_ONLY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType: Check for extensions on GitHub only (not new QuPath releases)
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.
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.
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.
files(File...) - Method in class qupath.opencv.dnn.DnnModelParams.Builder: Specify the URIs as files.
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.QuPathGUI.DefaultActions: Display annotations filled in.
FILL_DETECTIONS - Variable in class qupath.lib.gui.QuPathGUI.DefaultActions: Display detections filled in.
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.
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.
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.
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.

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.
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.
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.
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.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.ActionTools: Retrieve an Action stored within the properties of a node, or null if no action is found.
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
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).
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.ActionTools: Actions can be parsed from the accessible (usually public) fields of any object, as well as methods annotated with ActionTools.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.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.
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.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
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.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.
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: Create a default list model for storing 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.QuPathGUI: Get a list of the current available tools.
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 interface qupath.opencv.dnn.DnnModel: 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 interface qupath.opencv.dnn.DnnModel: 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.
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.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.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.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.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.BrushTool
getBrushDiameter() - Method in class qupath.process.gui.WandToolCV: Don't actually need the diameter for calculations here, but it's helpful for setting the cursor
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.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.
getCachedRegion(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
getCachedStroke(double) - Static method in class qupath.lib.gui.viewer.PathHierarchyPaintingHelper: 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 property caretPosition.
getCaretPosition() - Method in class qupath.lib.gui.scripting.TextAreaControl: Gets the value of the property caretPosition.
getCaseID() - Method in class qupath.lib.objects.TMACoreObject: Get the case ID metadata value.
getCategory() - Method in class qupath.lib.gui.panes.PreferencePane.PropertyItem
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.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.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.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.
getChart() - Method in class qupath.lib.gui.charts.HistogramPanelFX: Get the AreaChart depicting the histogram.
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: 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.
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.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.
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.
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: 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: 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.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.
getCountsForBin(int) - Method in class qupath.lib.analysis.stats.Histogram: Get the histogram counts for the specified bin.
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.
getCssStylesPath() - Static method in class qupath.lib.gui.prefs.PathPrefs: 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 property currentLanguage.
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 property currentSyntax.
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.
getDefaultActions() - Method in class qupath.lib.gui.QuPathGUI: Get the default actions associated with this QuPath instance.
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.
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.
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.
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.ChoiceParameter
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.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.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 class qupath.lib.gui.panes.PreferencePane.PropertyItem
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.
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.
getDisplayText() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion: Get the text that should be displayed for this completion.
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.
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.
getExtensionClassLoader() - Static method in class qupath.lib.gui.QuPathGUI: Get the ClassLoader used to load extensions.
getExtensionDirectory() - Static method in class qupath.lib.gui.QuPathGUI: Directory containing 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.
getExtensionsPath() - Static method in class qupath.lib.gui.prefs.PathPrefs: 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
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.HistogramPanelFX.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.
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.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.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.BrushTool
getGreen() - Method in class qupath.lib.color.StainVector: Get the green component of the (normalized) stain vector.
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.ChoiceParameter
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.
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.
getHierarchy(PluginRunner<T>) - Method in class qupath.lib.plugins.AbstractPlugin: Get the hierarchy from a PluginRunner, or null if no hierarchy is available.
getHistogram() - Method in class qupath.lib.gui.charts.HistogramPanelFX.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.HistogramPanelFX: 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.
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 interface qupath.lib.images.PathImage: Get the pixel data (image).
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 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.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.plugins.AbstractPluginRunner
getImageData() - Method in class qupath.lib.plugins.CommandLinePluginRunner
getImageData() - Method