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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
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
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.
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
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.
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
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() - 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
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
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
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
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
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
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
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
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
convertTransform(AffineTransformation) - Static method in class qupath.lib.roi.GeometryTools
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(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
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
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
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.
createSelectAllObject(boolean, int, int) - Static method in class qupath.lib.scripting.QP
Deprecated.
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
displayMode() - Method in class qupath.lib.display.ImageDisplay
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
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
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
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
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
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