Index
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 drawingBufferedImage
s. - AbstractImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
- AbstractImageRenderer - Class in qupath.lib.gui.images.stores
-
Abstract
ImageRenderer
, which adds a timestamp variable. - AbstractImageRenderer() - Constructor for class qupath.lib.gui.images.stores.AbstractImageRenderer
- AbstractImageServer<T> - Class in qupath.lib.images.servers
-
Abstract implementation of ImageServer providing some common functionality.
- AbstractImageServer(Class<T>) - Constructor for class qupath.lib.images.servers.AbstractImageServer
- AbstractInteractivePlugin<T> - Class in qupath.lib.plugins
-
Abstract class to help with implementing an interactive plugin.
- AbstractInteractivePlugin() - Constructor for class qupath.lib.plugins.AbstractInteractivePlugin
- AbstractObjectClassifier<T> - Class in qupath.lib.classifiers.object
-
Abstract class to help with the creation of object classifiers.
- AbstractObjectClassifier(PathObjectFilter) - Constructor for class qupath.lib.classifiers.object.AbstractObjectClassifier
- AbstractOverlay - Class in qupath.lib.gui.viewer.overlays
-
Abstract class to help with implementing PathOverlays.
- AbstractOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.AbstractOverlay
- AbstractOverlay.LocationStringFunction - Interface in qupath.lib.gui.viewer.overlays
-
Define a function to perform the task of
PathOverlay.getLocationString(ImageData, double, double, int, int)
- AbstractPlugin<T> - Class in qupath.lib.plugins
-
General abstract plugin implementation, which defines some methods to facilitate creating plugins that do parallel processing.
- AbstractPlugin() - Constructor for class qupath.lib.plugins.AbstractPlugin
- AbstractPluginRunner<T> - Class in qupath.lib.plugins
-
Abstract PluginRunner to help with the creation of plugin runners for specific circumstances, e.g.
- AbstractPluginRunner() - Constructor for class qupath.lib.plugins.AbstractPluginRunner
- AbstractTileableDetectionPlugin<T> - Class in qupath.lib.plugins
-
Abstract plugin used for detection tasks that support breaking large regions into smaller ones, and analyzing these in parallel - optionally with overlaps.
- AbstractTileableDetectionPlugin() - Constructor for class qupath.lib.plugins.AbstractTileableDetectionPlugin
- AbstractTileableImageServer - Class in qupath.lib.images.servers
-
Abstract
ImageServer
for BufferedImages that internally breaks up requests into constituent tiles. - AbstractTileableImageServer() - Constructor for class qupath.lib.images.servers.AbstractTileableImageServer
- accelerator(ObservableValue<KeyCombination>) - Method in class qupath.lib.gui.ActionTools.ActionBuilder
-
Bind the accelerator property of the action to an
ObservableValue
, bidirectionally if possible. - accelerator(KeyCombination) - Method in class qupath.lib.gui.ActionTools.ActionBuilder
-
Set the accelerator property of the action.
- acceleratorTextProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Property corresponding to
CommandFinderTools.CommandEntry.getAcceleratorText()
- actionBuilder() - Static method in class qupath.lib.gui.ActionTools
-
Create an
ActionTools.ActionBuilder
with no properties set. - actionBuilder(String, Consumer<ActionEvent>) - Static method in class qupath.lib.gui.ActionTools
-
Create an
ActionTools.ActionBuilder
with the specified text and event handler. - actionBuilder(Consumer<ActionEvent>) - Static method in class qupath.lib.gui.ActionTools
-
Create an
ActionTools.ActionBuilder
with the specified event handler. - actionCellDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionCellMembraneDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
-
Deprecated.
- actionChannelTraining - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
- actionComposite - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
- actionCreateRegions - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
- actionDelaunay - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands
- actionDensityMap - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands
- actionDensityMapLoad - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands
- actionDoG - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionExtractRegion - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionFastCellCounts - Variable in class qupath.process.gui.ProcessingExtension.OpenCVCommands
-
Deprecated.
- actionImportROIs - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionIntensity - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
- actionLoadObjectClassifier - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
- actionLoadPixelClassifier - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
- actionMacroRunner - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionMeasurement - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
- actionObjectClassifier - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
- actionPixelClassifier - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
- actionPixelCount - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
-
Deprecated.
- actionPlugins - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionPositiveCellDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionSimpleThreshold - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
- actionSimpleTissueDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
-
Deprecated.
- actionSLIC - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionSnapshot - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- actionSplitProject - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
- actionSubcellularDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
-
Deprecated.
- actionTiles - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
- ActionTools - Class in qupath.lib.gui
-
Helper methods for generating and configuring Actions and UI elements.
- ActionTools() - Constructor for class qupath.lib.gui.ActionTools
- ActionTools.ActionAccelerator - Annotation Interface in qupath.lib.gui
-
Annotation used to specify a preferred accelerator for an an action.
- ActionTools.ActionBuilder - Class in qupath.lib.gui
-
Builder class for custom
Action
objects. - ActionTools.ActionDescription - Annotation Interface in qupath.lib.gui
-
Description of an action.
- ActionTools.ActionIcon - Annotation Interface in qupath.lib.gui
-
Default icon for an action.
- ActionTools.ActionMenu - Annotation Interface in qupath.lib.gui
-
Annotation indicating the menu path where an action should be installed.
- ActionTools.ActionMethod - Annotation Interface in qupath.lib.gui
-
Annotation indicating that a method should be converted to an
Action
if possible. - actionTrainingImage - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
- ACTIVE_SERVER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- activeToolProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the activeTool property of this tracker.
- add(double...) - Static method in class qupath.opencv.ops.ImageOps.Core
-
Add a constant to all pixels.
- add(Padding) - Method in class qupath.lib.regions.Padding
-
Add this padding to another.
- ADD - Enum constant in enum class qupath.lib.roi.RoiTools.CombineOp
-
Add ROIs (union).
- addAllRegions(ImageServer<BufferedImage>, int) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Add all regions for a specific level of an
ImageServer
. - addBooleanParameter(String, String, boolean) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a boolean parameter.
- addBooleanParameter(String, String, boolean, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a boolean parameter, with help text.
- addChartExportMenu(XYChart<Number, Number>, ContextMenu) - Static method in class qupath.lib.gui.charts.ChartTools
-
Add a menu item to a context menu for displaying a chart for export.
- addChildObject(PathObject) - Method in class qupath.lib.objects.PathObject
-
Add an object to the child list of this object.
- addChildObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.PathObject
-
Add a collection of objects to the child list of this object.
- addChoiceParameter(String, String, S, List<S>) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a choice parameter, with an list of choices.
- addChoiceParameter(String, String, S, List<S>, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a choice parameter, with an list of choices and help text.
- addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Add a new choice preference, to select from a list of possibilities.
- addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String, boolean) - Method in class qupath.lib.gui.panes.PreferencePane
-
Add a new choice preference, to select from an optionally searchable list of possibilities.
- addClusterMeasurements() - Method in class qupath.opencv.features.DelaunayTriangulation
-
Compute mean measurements from clustering all connected objects.
- addColorPropertyPreference(IntegerProperty, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Add a new color preference based on a specified IntegerProperty (storing a packed RGBA value).
- addCompletion(AutoCompletions.Completion) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- addCompletions(Collection<? extends AutoCompletions.Completion>) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- addCompletions(AutoCompletions.Completion...) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- addDensities(String, PathObjectPredicates.PathObjectPredicate) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
-
Add a filter for computing densities.
- addDirectoryPropertyPreference(Property<String>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Add a new directory preference based on a specified StrongProperty.
- addDoubleParameter(String, String, double) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a double parameter to this list.
- addDoubleParameter(String, String, double, String, double, double, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a bounded double parameter to this list.
- addDoubleParameter(String, String, double, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a double parameter to this list, optionally including a unit and help text.
- addDuplicate(ProjectImageEntry<T>, boolean) - Method in interface qupath.lib.projects.Project
-
Add an image by duplicating an existing entry.
- ADDED - Enum constant in enum class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent.HierarchyEventType
-
An object has been added
- addEmptyParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add an 'empty' parameter, that is one that does not take any values.
- addEvent(double, boolean) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
-
Insert a new event.
- addEvents(Collection<KaplanMeierData.KaplanMeierEvent>) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
-
Add a collection of events.
- addExtensionJar(File) - Method in class qupath.lib.gui.QuPathGUI
-
Request that a specified Jar file be added to the extension classpath.
- addFileDropHandler(DragDropImportListener.DropHandler<File>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
-
Add a new File DropHandler.
- addFullResolutionLevel() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
-
Add the full-resolution image as a level of the pyramid.
- addGridRow(GridPane, int, int, String, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Add a row of nodes.
- addGroup(PathObjectConnectionGroup) - Method in class qupath.lib.objects.PathObjectConnections
-
Add a new connections group.
- addImage(ImageServerBuilder.ServerBuilder<T>) - Method in interface qupath.lib.projects.Project
-
Add an image for a particular ImageServer.
- addIntensityMeasurements(ImageServer<BufferedImage>, PathObject, double, Collection<ObjectMeasurements.Measurements>, Collection<ObjectMeasurements.Compartments>) - Static method in class qupath.lib.analysis.features.ObjectMeasurements
-
Measure all channels of an image for one individual object or cell.
- addIntParameter(String, String, int) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add an int parameter.
- addIntParameter(String, String, int, String, double, double, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a bounded int parameter, with optional unit and help text.
- addIntParameter(String, String, int, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add an int parameter, with optional unit and help text.
- addLabel(String, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
- addLabel(String, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add a single label by classname, where the label represents the integer label used for annotations with the given classname.
- addLabel(PathClass, int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add a single label by
PathClass
, where the label represents the integer label used for annotations with the given classification. - addLabel(PathClass, int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add a single label by
PathClass
, where the label represents the integer label used for annotations with the given classification. - addLabels(Map<PathClass, Integer>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add multiple labels by PathClass, where the key represents a PathClass and the value represents the integer label that should be used for annotations of the given class.
- addLabelsByName(Map<String, Integer>) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add multiple labels by classname, where the key represents a classname and the value represents the integer label that should be used for annotations of the given class.
- addLevel(double, int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
-
Add a new level by providing a downsample value, width and height.
- addLevel(int, int) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
-
Add a new level based on level dimensions, estimating the corresponding downsample value as required.
- addLevel(ImageServerMetadata.ImageResolutionLevel) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
-
Add a new level directly.
- addLevelByDownsample(double) - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
-
Add a new level, calculating dimensions using a downsample factor applied to the full-resolution image.
- addListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Add a hierarchy change listener.
- addMeasurement(String, double) - Method in interface qupath.lib.measurements.MeasurementList
-
Deprecated.
- addMeasurements(Collection<? extends PathObject>, PixelClassificationMeasurementManager, String) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Add measurements to specified objects from a
PixelClassificationMeasurementManager
. - addMeasurementsToSelectedObjects(ImageData<BufferedImage>, PixelClassifier, String) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Add measurements to selected objects based upon the output of a
PixelClassifier
. - addMenuItems(List<MenuItem>, Object...) - Static method in class qupath.lib.gui.tools.MenuTools
-
Add menu items to the specified list.
- addMenuItems(Menu, Object...) - Static method in class qupath.lib.gui.tools.MenuTools
-
Add menu items to an existing menu.
- addNewScript(String, ScriptLanguage, boolean) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
-
Create a new script in the specified language.
- addNodeMeasurements() - Method in class qupath.opencv.features.DelaunayTriangulation
-
Add Delaunay measurements to each pathObject.
- addNoise(Mat, double, double) - Static method in class qupath.opencv.tools.OpenCVTools
-
Add Gaussian noise with specified mean and standard deviation to all channels of a Mat.
- addObject(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Add an object to the hierarchy, firing an event.
- addObject(PathObject) - Static method in class qupath.lib.scripting.QP
-
Add the specified object to the current
PathObjectHierarchy
. - addObject(PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Add an object to the hierarchy, optionally firing an event.
- addObjectBelowParent(PathObject, PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Add path object as descendant of the requested parent.
- addObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Add multiple objects to the hierarchy.
- addObjects(Collection<PathObject>) - Static method in class qupath.lib.scripting.QP
-
Add the specified collection of objects to the current
PathObjectHierarchy
. - addObjects(PathObject[]) - Static method in class qupath.lib.scripting.QP
-
Add the specified array of objects to the current
PathObjectHierarchy
. - addParameterChangeListener(ParameterChangeListener) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
-
Add a
ParameterChangeListener
to be notified as parameters are modified by the user. - addPathObject(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Deprecated.since v0.4.0; use
PathObjectHierarchy.addObject(PathObject)
instead (for naming consistency) - addPathObject(PathObject) - Method in class qupath.lib.objects.PathObject
-
Deprecated.since v0.4.0, replaced by
PathObject.addChildObject(PathObject)
- addPathObjectBelowParent(PathObject, PathObject, boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Deprecated.
- addPathObjectListener(PathObjectHierarchyListener) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Deprecated.since v0.4.0 (the name was confusing because it wasn't intended primarily to listen to changes within individual PathObjects)
- addPathObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Deprecated.since v0.4.0; use
PathObjectHierarchy.addObjects(Collection)
instead - addPathObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.PathObject
-
Deprecated.since v0.4.0, replaced by
PathObject.addChildObjects(Collection)
- addPathObjectSelectionListener(PathObjectSelectionListener) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
-
Add listener for selection changes.
- addPathObjectWithoutUpdate(PathObject) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Deprecated.since v0.4.0, use
PathObjectHierarchy.addObject(PathObject, boolean)
instead (for naming consistency) - addPixelClassifierMeasurements(String, String) - Static method in class qupath.lib.scripting.QP
-
Add measurements from pixel classification to the selected objects.
- addPixelClassifierMeasurements(PixelClassifier, String) - Static method in class qupath.lib.scripting.QP
-
Add measurements from pixel classification to the selected objects.
- addPropertyChangeListener(PropertyChangeListener) - Method in class qupath.lib.images.ImageData
-
Add a new property change listener.
- addPropertyPreference(Property<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
-
Add a new preference based on a specified Property.
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.cells.SubcellularDetection
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.gui.ImageJMacroRunner
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
- addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.opencv.DetectCytokeratinCV
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.algorithms.TilerPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.AbstractPlugin
-
For a specified parent object, generate a task to run.
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin
-
Intercepts the 'standard' addRunnableTasks to (if necessary) insert ParallelTileObjects along the way, thereby breaking an excessively-large parentObject into more manageable pieces.
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
- addRunnableTasks(ImageData<T>, PathObject, List<Runnable>) - Method in class qupath.opencv.features.DelaunayClusteringPlugin
- addShapeMeasurements(String...) - Static method in class qupath.lib.scripting.QP
-
Add the specified shape measurements to the current selected objects of the current image.
- addShapeMeasurements(Collection<? extends PathObject>, PixelCalibration, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.analysis.features.ObjectMeasurements
-
Add shape measurements for multiple objects.
- addShapeMeasurements(ImageData<?>, Collection<? extends PathObject>, String, String...) - Static method in class qupath.lib.scripting.QP
-
Add shape measurements to the specified objects.
- addShapeMeasurements(ImageData<?>, Collection<? extends PathObject>, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.scripting.QP
-
Add shape measurements to the specified objects.
- addShapeMeasurements(PathObject, PixelCalibration, ObjectMeasurements.ShapeFeatures...) - Static method in class qupath.lib.analysis.features.ObjectMeasurements
-
Add shape measurements for one object.
- addSingleImageToProject(Project<BufferedImage>, ImageServer<BufferedImage>, ImageData.ImageType) - Static method in class qupath.lib.gui.commands.ProjectCommands
-
Add a single image to a project.
- addSlice(Object, Number) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Add a slice to the pie.
- addStep(WorkflowStep) - Method in class qupath.lib.plugins.workflow.Workflow
-
Append a new step to the end of the workflow, firing an update event.
- addSteps(Collection<WorkflowStep>) - Method in class qupath.lib.plugins.workflow.Workflow
-
Append multiple steps to the end of the workflow, firing a single update event.
- addStringParameter(String, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a String parameter.
- addStringParameter(String, String, String, String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a String parameter, with help text.
- addTextAppendableFX(TextAppendable) - Static method in class qupath.lib.gui.logging.LogManager
-
Register a
TextAppendable
that will be accept logging events and be updated on the JavaFX Application thread. - addThreshold(double) - Method in class qupath.lib.gui.charts.HistogramPanelFX.ThresholdedChartWrapper
-
Add a threshold value.
- addThreshold(double, Color) - Method in class qupath.lib.gui.charts.HistogramPanelFX.ThresholdedChartWrapper
-
Add a threshold value with its display color.
- addThreshold(ObservableNumberValue) - Method in class qupath.lib.gui.charts.HistogramPanelFX.ThresholdedChartWrapper
-
Add a threshold value.
- addTileListener(TileListener<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- addTitleParameter(String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Add a title parameter.
- addTMAGrid(ImageData<?>, String, String, boolean, double) - Static method in class qupath.lib.objects.PathObjectTools
-
Create a new regular
TMAGrid
and set it as active on the hierarchy for an image. - addUnclassifiedLabel(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
- addUnclassifiedLabel(int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Add a single label for objects that are unclassified, where the label represents the integer label used for annotations that have no classification set.
- addValue(double) - Method in class qupath.lib.analysis.stats.RunningStatistics
-
Add another value; NaN values are counted but do not contribute to the statistics.
- addViewerListener(QuPathViewerListener) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Add a viewer listener.
- addWorkflowListener(WorkflowListener) - Method in class qupath.lib.plugins.workflow.Workflow
-
Add a listener for changes to the workflow.
- addWorkflowStep(ImageData<BufferedImage>, String) - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
- addWorkflowStep(ImageData<T>, String) - Method in class qupath.lib.plugins.AbstractPlugin
-
Add a workflow step to the ImageData indicating the argument that this plugin was run with.
- AffineTransformImageServer - Class in qupath.lib.images.servers
-
ImageServer that dynamically applies an AffineTransform to an existing ImageServer.
- AffineTransformImageServer(ImageServer<BufferedImage>, AffineTransform) - Constructor for class qupath.lib.images.servers.AffineTransformImageServer
- AffineTransforms - Class in qupath.lib.awt.common
-
Helper class for working with affine transforms.
- AffineTransforms() - Constructor for class qupath.lib.awt.common.AffineTransforms
- alertType(Alert.AlertType) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Create a dialog styled as a specified alert type.
- ALL - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
-
All log messages
- ALLOW_MEMOIZATION_PROPERTY - Static variable in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
-
System property controlling whether memoization is allowed or not.
- allowMemoization() - Static method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
-
Check whether memoization should be allowed or not.
- allowSmoothInterpolation() - Method in class qupath.lib.images.servers.AbstractTileableImageServer
-
Returns true if this server is permitted to use smooth interpolation when resizing.
- allredMinPercentagePositiveProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The minimum positive percentage of cells for Allred proportion score to be non-zero.
- allTimePoints() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Request that all timepoints of a time series will be written.
- allZSlices() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Request that all z-slices are exported.
- almostTheSame(double, double, double) - Static method in class qupath.lib.common.GeneralTools
-
Test if two doubles are approximately equal, within a specified tolerance.
- alpha(int) - Static method in class qupath.lib.common.ColorTools
-
Extract the 8-bit alpha value from a packed ARGB value.
- ALWAYS - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
-
Always display
- alwaysPaintSelectedObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Always paint selected objects in the viewer, even if the opacity setting is 0.
- alwaysPromptForObjects() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
- alwaysPromptForObjects() - Method in class qupath.lib.plugins.AbstractInteractivePlugin
- alwaysPromptForObjects() - Method in interface qupath.lib.plugins.PathInteractivePlugin
-
If this returns true, then a prompt is requested every time the command is run - even if there are valid parent objects already selected.
- and(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
-
Compute the bitwise AND of two arrays.
- and(PathObjectPredicates.PathObjectPredicate) - Method in interface qupath.lib.objects.PathObjectPredicates.PathObjectPredicate
-
Combine with another
PathObjectPredicates.PathObjectPredicate
through AND. - annotatedCentroidTilesOnly(boolean) - Method in class qupath.lib.images.writers.TileExporter
-
Specify whether tiles without any annotations over the tile centroid should be included.
- annotatedTilesOnly(boolean) - Method in class qupath.lib.images.writers.TileExporter
-
Specify whether tiles that do not overlap with any annotations should be included.
- AnnotationPane - Class in qupath.lib.gui.panes
-
Component for displaying annotations within the active image.
- AnnotationPane(QuPathGUI) - Constructor for class qupath.lib.gui.panes.AnnotationPane
-
Constructor.
- AnnotationPane(QuPathGUI, ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.AnnotationPane
-
Constructor.
- ANNOTATIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- ANNOTATIONS - Enum constant in enum class qupath.lib.objects.PathObjectFilter
-
Accept annotation objects
- ANNOTATIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- annotationStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred stroke thickness to use when drawing annotation ROIs.
- ANY_ANNOTATIONS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the ROIs of any annotations
- ANY_ANNOTATIONS_BOUNDS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the bounding box of any annotations
- ANY_CLASS - Static variable in class qupath.process.gui.commands.density.DensityMapUI
-
Ignore classification (accept all objects).
- ANY_OBJECTS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the ROIs of any objects
- ANY_OBJECTS_BOUNDS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
-
Regions overlapping the bounding box of any objects
- ANY_POSITIVE_CLASS - Static variable in class qupath.process.gui.commands.density.DensityMapUI
-
Accept any positive classification, including 1+, 2+, 3+.
- appendFrame(ViewRecordingFrame) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Append frame to the collection of frames.
- appendOps(ImageOp...) - Method in interface qupath.opencv.ops.ImageDataOp
-
Append one or more additional
ImageOp
s 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
- applyTransforms(BufferedImage, BufferedImage) - Method in class qupath.lib.display.ImageDisplay
-
Apply the required transforms to a BufferedImage to get the appropriate display.
- applyTransforms(BufferedImage, BufferedImage) - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
- applyTransforms(BufferedImage, BufferedImage) - Method in interface qupath.lib.gui.images.stores.ImageRenderer
-
Apply the required transforms to a BufferedImage to get the appropriate display.
- applyTransforms(BufferedImage, BufferedImage, List<? extends ChannelDisplayInfo>, boolean) - Static method in class qupath.lib.display.ImageDisplay
-
Deprecated.
- 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
- asType(ImageProcessor, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
-
Helper method to convert an
ImageProcessor
to aMat
using Groovy's 'as' syntax. - asType(BufferedImage, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
-
Helper method to convert a
BufferedImage
to aMat
,ImageProcessor
orImagePlus
using Groovy's 'as' syntax. - asType(Number, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
- asType(Mat, Class<T>) - Static method in class qupath.opencv.tools.GroovyCV
-
Helper method to convert a
Mat
to aBufferedImage
,ImagePlus
,ImageProcessor
, double or float array using Groovy's 'as' syntax. - attemptOperation(Geometry, Function<Geometry, Geometry>) - Static method in class qupath.lib.roi.GeometryTools
-
Attempt to apply a function to a geometry, returning the input unchanged if there was an exception.
- AUTO_ESTIMATE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
-
Automatically estimate the image type
- autoBrightnessContrastSaturationPercentProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Controls percentage of saturated pixels to apply when automatically setting brightness/contrast.
- AutoCompletions - Class in qupath.lib.scripting.languages
-
Class to deal with script auto-completions.
- AutoCompletions() - Constructor for class qupath.lib.scripting.languages.AutoCompletions
- AutoCompletions.Completion - Interface in qupath.lib.scripting.languages
-
A single completion.
- AutoCompletions.CompletionTokenizer - Interface in qupath.lib.scripting.languages
-
Functional interface to extract a token from a string needed to determine a completion.
- autoSetAnnotationClassProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Classification that should automatically be applied to all new annotations.
- autoSetDisplayRange(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
-
Automatically set the display range for a channel, using the default saturation defined in
PathPrefs.autoBrightnessContrastSaturationPercentProperty()
. - autoSetDisplayRange(ChannelDisplayInfo, double) - Method in class qupath.lib.display.ImageDisplay
-
Automatically set the display range for a channel.
- autoUnits() - Method in class qupath.lib.common.Timeit
- autoUpdateCheckProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Check for updates when launching QuPath, if possible.
- availableChannels() - Method in class qupath.lib.display.ImageDisplay
-
ObservableList
containing the channels currently available for display. - availableFontsProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Get a list of available fonts.
- availableStylesProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
-
Get the current available styles as an observable list.
- averageChannelProject() - Method in class qupath.lib.images.servers.TransformedServerBuilder
-
Perform an average (mean) projection of the channels.
- awaitCompletion() - Method in class qupath.lib.plugins.AbstractPluginRunner
-
Await the completion of currently-running tasks, notifying any listener if necessary.
- AwtTools - Class in qupath.lib.awt.common
-
A collection of static methods useful when working with AWT shapes and
ImageRegions
.
B
- backend(int) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
-
Specify the backend, e.g.
- backgroundColor(int, boolean) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify a base color.
- backgroundColor(Color) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Specify a base color.
- backgroundLabel(int) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Specify the background label (0 by default).
- backgroundLabel(int, Integer) - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Specify the background label (0 by default) and color.
- baseClassification(PathClass...) - Static method in class qupath.lib.objects.PathObjectPredicates
-
Predicate that returns true if an object has any of the specified base classifications, regardless of any subclassification.
- BATCH_INDEX - Static variable in class qupath.lib.scripting.ScriptAttributes
-
Index of the current run when batch processing (starting at 0).
- BATCH_LAST - Static variable in class qupath.lib.scripting.ScriptAttributes
-
Boolean flag to indicate if the current script is the last in a batch.
- BATCH_SAVE - Static variable in class qupath.lib.scripting.ScriptAttributes
-
Boolean flag to indicate whether changes to the image data should automatically be saved.
- BATCH_SIZE - Static variable in class qupath.lib.scripting.ScriptAttributes
-
Size of the current batch processing batch.
- batchConvertAndPredict(Mat...) - Method in interface qupath.opencv.dnn.DnnModel
-
Convenience method to convert one or more image patches to a blob, apply the
PredictionFunction
, and convert the output to standard Mats. - beautify(String) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Beautifies the specified text, according to the syntax.
- beautifySourceAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- below(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
-
Set the classification (by name) for objects for which the specified measurement has a value below the threshold.
- below(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
-
Set the classification for objects for which the specified measurement has a value below the threshold.
- belowEquals(String) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
-
Set the classification (by name) for objects for which the specified measurement has a value below or equal to the threshold.
- belowEquals(PathClass) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
-
Set the classification for objects for which the specified measurement has a value below or equal to the threshold.
- bigTiff() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Request that the image is written in BigTIFF format.
- bigTiff(boolean) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Specify whether the image should be written in BigTIFF format.
- BILINEAR - Enum constant in enum class qupath.lib.gui.viewer.ImageInterpolation
-
Bilinear interpolation.
- binaryReconstruction(ByteProcessor, ByteProcessor, boolean) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
-
Alternative morphological reconstruction (based on ImageJ's FloodFiller) suitable for binary images only.
- bindObjectClassifierNameInput(TextField, ObjectExpression<Project<BufferedImage>>) - Static method in class qupath.process.gui.commands.ml.ProjectClassifierBindings
-
Set styling for a text field to use object classifier names for the current project.
- bindPixelClassifierNameInput(TextField, ObjectExpression<Project<BufferedImage>>) - Static method in class qupath.process.gui.commands.ml.ProjectClassifierBindings
-
Set styling for a text field to use pixel classifier names for the current project.
- bindSliderAndTextField(Slider, TextField, boolean) - Static method in class qupath.lib.gui.tools.GuiTools
-
Bind the value of a slider and contents of a text field with a default number of decimal places, so that both may be used to set a numeric (double) value.
- bindSliderAndTextField(Slider, TextField, boolean, int) - Static method in class qupath.lib.gui.tools.GuiTools
-
Bind the value of a slider and contents of a text field, so that both may be used to set a numeric (double) value.
- bindUserStylesheetToStyle(WebEngine) - Static method in class qupath.lib.gui.tools.WebViews
-
Bind the
WebEngine.userStyleSheetLocationProperty()
to a stylesheet determined based on QuPath's current style (e.g. - bioformatsEnabled() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
-
Returns true if Bio-Formats is enabled and may be used to read images.
- BioFormatsImageServer - Class in qupath.lib.images.servers.bioformats
-
QuPath ImageServer that uses the Bio-Formats library to read image data.
- BioFormatsImageServer(URI, String...) - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsImageServer
-
Create an ImageServer using the Bio-Formats library.
- BioFormatsOptionsExtension - Class in qupath.lib.images.servers.bioformats
-
A QuPath extension that adds options relating to the BioFormatsImageServer to the main QuPath preference pane.
- BioFormatsOptionsExtension() - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
- BioFormatsServerBuilder - Class in qupath.lib.images.servers.bioformats
-
Builder for ImageServers that make use of the Bio-Formats library.
- BioFormatsServerBuilder() - Constructor for class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
- BioFormatsServerOptions - Class in qupath.lib.images.servers.bioformats
-
Container for various options that can customize the behavior of the
BioFormatsImageServer
. - BioimageIoTools - Class in qupath.opencv.ml
-
Helper class for working with Bioimage Model Zoo model specs, and attempting to replicating the processing within QuPath.
- BioimageIoTools() - Constructor for class qupath.opencv.ml.BioimageIoTools
- bitwiseNegate(Mat) - Static method in class qupath.opencv.tools.GroovyCV
-
Compute the bitwise NOT of an array.
- Black - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
-
All pixels black
- BLACK - Static variable in class qupath.lib.common.ColorTools
-
Packed int representing black.
- blankString(String, boolean) - Static method in class qupath.lib.common.GeneralTools
-
Check if a string is blank, i.e.
- blobFromImage(Mat) - Static method in class qupath.opencv.dnn.DnnTools
-
Create an OpenCV blob from a single mat.
- blobFromImages(Collection<Mat>, double, Size, Scalar, boolean, boolean) - Static method in class qupath.opencv.dnn.DnnTools
-
Create an OpenCV blob from a batch of Mats with optional scaling, resizing and cropping.
- blobFromImages(Mat...) - Static method in class qupath.opencv.dnn.DnnTools
-
Create an OpenCV blob from one or more mats.
- blobFromImages(Mat, double, Size, Scalar, boolean, boolean) - Static method in class qupath.opencv.dnn.DnnTools
-
Create an OpenCV blob from a Mat with optional scaling, resizing and cropping.
- BlobFunction<T> - Interface in qupath.opencv.dnn
-
Convert OpenCV Mats into blobs (tensors) for use with a deep learning framework.
- blue(int) - Static method in class qupath.lib.common.ColorTools
-
Extract the 8-bit blue value from a packed RGB value.
- Blue - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
-
Blue channel only
- BLUE - Static variable in class qupath.lib.common.ColorTools
-
Packed int representing blue.
- BLUE - Static variable in class qupath.lib.images.servers.ImageChannel
-
Default blue channel for RGB images.
- Blue_chromaticity - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
-
Blue chromaticity value,
blue / max(1, red + green + blue)
- Blue_OD - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
-
Blue channel optical densities
- blueChromaticity(int) - Static method in class qupath.lib.color.ColorTransformer
-
Extract blue chromaticity value from a packed RGB pixel,
blue / max(1, red + green + blue)
- BooleanParameter - Class in qupath.lib.plugins.parameters
-
Parameter that can take on true of false value - or null.
- BOUNDARIES_ONLY - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
-
Show only cell boundaries.
- boundaryDistancePredicate(double, boolean) - Static method in class qupath.lib.analysis.DelaunayTools
-
BiPredicate that returns true for objects with ROI boundaries within a specified distance.
- BoundaryStrategy - Class in qupath.process.gui.commands.ml
-
Helper class for handling the boundaries of training annotations when creating a pixel classifier.
- BRIGHTFIELD_H_DAB - Enum constant in enum class qupath.lib.images.ImageData.ImageType
-
Brightfield image with hematoxylin and DAB stains.
- BRIGHTFIELD_H_DAB - Static variable in class qupath.lib.scripting.QP
-
Brightfield image type with hematoxylin and DAB staining
- BRIGHTFIELD_H_E - Enum constant in enum class qupath.lib.images.ImageData.ImageType
-
Brightfield image with hematoxylin and eosin stains.
- BRIGHTFIELD_H_E - Static variable in class qupath.lib.scripting.QP
-
Brightfield image type with hematoxylin and eosin staining
- BRIGHTFIELD_OTHER - Enum constant in enum class qupath.lib.images.ImageData.ImageType
-
Brightfield image with any stains.
- BRIGHTFIELD_OTHER - Static variable in class qupath.lib.scripting.QP
-
Brightfield image type
- brightness(int) - Static method in class qupath.lib.color.ColorTransformer
-
Extract brightness value from RGB-to-HSB transform.
- Brightness - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
-
Brightness value (from RGB-HSB transform)
- BRIGHTNESS_CONTRAST - Variable in class qupath.lib.gui.QuPathGUI.DefaultActions
-
Show the brightness/contrast dialog.
- BrightnessContrastCommand - Class in qupath.lib.gui.commands
-
Command to show a Brightness/Contrast dialog to adjust the image display.
- BrightnessContrastCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.BrightnessContrastCommand
-
Constructor.
- brown(int) - Static method in class qupath.lib.color.ColorTransformer
-
Extract brown value,
(blue - (red + green)*0.3f)
- Brown - Enum constant in enum class qupath.lib.color.ColorTransformer.ColorTransformMethod
-
Brown value,
(blue - (red + green)*0.3f)
- browseDirectory(File) - Static method in class qupath.lib.gui.tools.GuiTools
-
Open the directory containing a file for browsing.
- browseURI(URI) - Static method in class qupath.lib.gui.tools.GuiTools
-
Try to open a URI in a web browser.
- BRUSH - Static variable in class qupath.lib.gui.viewer.tools.PathTools
-
Brush drawing tool
- BRUSH_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- BRUSH_TOOL - Variable in class qupath.lib.gui.QuPathGUI.DefaultActions
-
Brush tool action
- brushCreateNewObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Create new objects by default when drawing with the Brush tool.
- brushDiameterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Default brush tool diameter, in pixels.
- brushScaleByMagProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Optionally scale the default brush tool diameter by the viewer magnification (downsample value).
- BrushTool - Class in qupath.lib.gui.viewer.tools
-
Tool for drawing (and subtract from) freehand regions, optionally adapting brush size to magnification.
- BrushTool() - Constructor for class qupath.lib.gui.viewer.tools.BrushTool
- buffer(ROI, double) - Static method in class qupath.lib.roi.RoiTools
-
Buffer the specified ROI, dilating (or eroding) by the specified distance.
- BufferedImageOverlay - Class in qupath.lib.gui.viewer.overlays
-
An overlay used to display one or more
BufferedImage
objects on top of a primary image shown in a viewer. - BufferedImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an empty overlay without any images to display.
- BufferedImageOverlay(OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to display multiple image regions.
- BufferedImageOverlay(OverlayOptions, ImageRegion, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to display one specified image region.
- BufferedImageOverlay(QuPathViewer, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
- BufferedImageOverlay(QuPathViewer, Map<ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
- BufferedImageOverlay(QuPathViewer, OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
-
Create an overlay to display multiple image regions.
- BufferedImageTools - Class in qupath.lib.awt.common
-
Static methods for working with BufferedImages and QuPath objects.
- build() - Method in class qupath.lib.analysis.DelaunayTools.Builder
-
Build the
DelaunayTools.Subdivision
with the current parameters. - build() - Method in interface qupath.lib.analysis.heatmaps.ColorModels.ColorModelBuilder
-
Build a
ColorModel
. - build() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
-
Build the classifier defined by the parameters of this builder.
- build() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
-
Build a new PixelClassifierMetadata object.
- build() - Method in interface qupath.lib.color.ColorModels.ColorModelBuilder
-
Build a
ColorModel
. - build() - Method in class qupath.lib.gui.ActionTools.ActionBuilder
-
Create an
Action
with this builder. - build() - Method in class qupath.lib.gui.charts.Charts.ScatterchartBuilder
-
Build a chart according to the specified parameters.
- build() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Build the dialog.
- build() - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Create the rendered image server.
- build() - Method in class qupath.lib.images.servers.ImageServerBuilder.AbstractServerBuilder
- build() - Method in interface qupath.lib.images.servers.ImageServerBuilder.ServerBuilder
-
Build a new ImageServer instance.
- build() - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
-
Build an
ImageServerMetadata
. - build() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel.Builder
-
Build a list of ImageResolutionLevels, which can be used with an
ImageServerMetadata
object. - build() - Method in class qupath.lib.images.servers.LabeledImageServer.Builder
-
Build the
ImageServer
with the requested parameters. - build() - Method in class qupath.lib.images.servers.PixelCalibration.Builder
-
Build
PixelCalibration
object. - build() - Method in class qupath.lib.images.servers.SparseImageServer.Builder
-
Build a new SparseImageServer.
- build() - Method in class qupath.lib.images.servers.TransformedServerBuilder
-
Get the
ImageServer
that applies all the requested transforms. - build() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Create an
OMEPyramidWriter.OMEPyramidSeries
to write the OME-TIFF. - build() - Method in class qupath.lib.roi.GeometryTools.GeometryConverter.Builder
-
Build a new converter with the specified parameters.
- build() - Method in class qupath.lib.scripting.ScriptParameters.Builder
-
Build the
ScriptParameters
with the current options. - build() - Method in class qupath.opencv.dnn.DnnModelParams.Builder
-
Build the params.
- build() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
-
Build a new
OpenCVDnn
. - build() - Method in class qupath.opencv.ml.PatchClassifierParams.Builder
-
Build the patch classifier parameters.
- build() - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
-
Build the pane
- build(List<Mat>) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
-
Calculate results as a list of maps connecting features and Mats for all slices of a z-stack.
- build(List<Mat>, int) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
-
Calculate results for a map of features and Mats for one slice of a z-stack.
- build(Mat) - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder
-
Calculate results for a single Mat.
- build(Mat, boolean) - Method in class qupath.opencv.ml.FeaturePreprocessor.Builder
-
Build a
FeaturePreprocessor
. - buildClassifier(ImageData<BufferedImage>) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
-
Build a
PixelClassifier
for a density map using the current parameters and the specifiedImageData
. - buildDnnModel(BioimageIoSpec.BioimageIoModel) - Static method in class qupath.opencv.ml.BioimageIoTools
-
Attempt to build a
DnnModel
that follows this spec as closely as possible. - builder() - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Create a new builder to generate a custom dialog.
- builder() - Static method in class qupath.lib.scripting.ScriptParameters
-
Create a new builder for
ScriptParameters
. - builder() - Static method in class qupath.opencv.dnn.DnnModelParams
-
Create a new params builder, with default values.
- builder() - Static method in class qupath.opencv.ml.FeaturePreprocessor
-
Create a
FeaturePreprocessor.Builder
to build a customFeaturePreprocessor
. - 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 specifiedImageData
. - 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, useQP.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 classBufferedImage
. - 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 classBufferedImage
. - 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
- buildServer(ImageData<BufferedImage>, ImageDataOp, PixelCalibration, int, int) - Static method in class qupath.opencv.ops.ImageOps
- 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
- 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
- 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
andChannelDisplayInfo
. - ChannelDisplayTransformServer - Class in qupath.lib.gui.images.servers
-
ImageServer that applies a color transform to an image.
- channelMaximum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
-
Get the minimum of an image channel, ignoring NaNs.
- channelMean(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
-
Get the mean of an image channel, ignoring NaNs.
- channelMinimum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
-
Get the minimum of an image channel, ignoring NaNs.
- channels(int...) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Override default of writing all channels in their original order to be able to specify which channels are output, and in which order.
- channels(int...) - Method in class qupath.lib.images.writers.TileExporter
-
Export only specified channels.
- channels(String...) - Method in class qupath.lib.images.writers.TileExporter
-
Export only specified channels, identified by name.
- channels(Collection<ImageChannel>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
-
Specify the image channels.
- Channels() - Constructor for class qupath.opencv.ops.ImageOps.Channels
- channelsImages() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Request that channels are written as separate images.
- channelsInterleaved() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Request that channels are written interleaved within a single image plane.
- channelSoftmax(double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
-
Apply softmax, with the specified output maxValue.
- channelsPlanar() - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Request that channels are written as separate image planes.
- channelStdDev(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
-
Get the standard deviation of image channels, ignoring NaNs.
- channelSum(double) - Static method in class qupath.opencv.ops.ImageOps.Normalize
-
Normalize channels so that they sum to the specified value.
- channelSum(Mat) - Static method in class qupath.opencv.tools.OpenCVTools
-
Get the sum of image channels, ignoring NaNs.
- ChannelTransformFeatureServer - Class in qupath.lib.images.servers
-
A
TransformingImageServer
that applies color transforms to generate channels. - channelType(ImageServerMetadata.ChannelType) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
-
Specify the interpretation of channels.
- Charts - Class in qupath.lib.gui.charts
-
Helper class for generating interactive charts.
- Charts() - Constructor for class qupath.lib.gui.charts.Charts
- Charts.PieChartBuilder - Class in qupath.lib.gui.charts
-
Builder for creating pie charts.
- Charts.ScatterchartBuilder - Class in qupath.lib.gui.charts
-
Builder for creating scatter charts.
- ChartTools - Class in qupath.lib.gui.charts
-
Collection of static methods to help when working with JavaFX charts, and adapting these for QuPath's purposes.
- ChartTools() - Constructor for class qupath.lib.gui.charts.ChartTools
- checkExtensions(String, String...) - Static method in class qupath.lib.common.GeneralTools
-
Check whether a path ends with one of a number of specified extensions (case insensitive).
- checkForUpdate() - Static method in class qupath.lib.gui.extensions.UpdateChecker
-
Query the most recent QuPath release on GitHub.
- checkForUpdate(GitHubProject.GitHubRepo) - Static method in class qupath.lib.gui.extensions.UpdateChecker
-
Query the latest release from a GitHub repo.
- checkImageSupport(URI, String...) - Method in class qupath.imagej.images.servers.ImageJServerBuilder
- checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
- checkImageSupport(URI, String...) - Method in interface qupath.lib.images.servers.ImageServerBuilder
-
Check whether a URI is supported by this builder.
- checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.JsonImageServerBuilder
- checkImageSupport(URI, String...) - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
- checkMinVersion(String) - Static method in class qupath.lib.scripting.QP
-
Check whether the current QuPath version is ≥ the specified version.
- checkpoint() - Method in class qupath.lib.common.Timeit
-
Create a new checkpoint with a default name.
- checkpoint(String) - Method in class qupath.lib.common.Timeit
-
Create a new checkpoint with the specified name.
- checkpointAndRun(Runnable) - Method in class qupath.lib.common.Timeit
-
Create a checkpoint with the default name and immediately run the provided runnable.
- checkpointAndRun(String, Runnable) - Method in class qupath.lib.common.Timeit
-
Create a checkpoint and immediately run the provided Runnable.
- checkpointAndRun(String, Runnable, int) - Method in class qupath.lib.common.Timeit
-
Create a checkpoint and immediately run the provided Runnable nIterations times.
- checkType(URI) - Static method in class qupath.lib.images.servers.FileFormatInfo
-
Check the type of an image for a specified URI.
- checkVersionRange(String, String) - Static method in class qupath.lib.scripting.QP
-
Check whether the current QuPath version is ≥ the specified minimum version, and < the specified maximum.
- ChoiceParameter<S> - Class in qupath.lib.plugins.parameters
-
Parameter that supports a list of choices.
- choices - Variable in class qupath.lib.plugins.parameters.ChoiceParameter
- CIRCULARITY - Enum constant in enum class qupath.lib.analysis.features.ObjectMeasurements.ShapeFeatures
-
Circularity.
- CircularSlider - Class in qupath.lib.gui
-
A custom JavaFX circular-slider control.
- CircularSlider() - Constructor for class qupath.lib.gui.CircularSlider
-
Create a circular slider
- classification() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
-
Set the model type to be
OpenCVDnn.ModelType.CLASSIFICATION
. - CLASSIFICATION - Enum constant in enum class qupath.lib.images.servers.ImageServerMetadata.ChannelType
-
Each channel represents a classification, such as in a labelled image.
- CLASSIFICATION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
-
Refers to
ClassificationModel
. - classificationLabels(Map<Integer, PathClass>) - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata.Builder
-
Specify classification labels.
- classificationLabels(Map<Integer, PathClass>) - Method in class qupath.lib.images.servers.ImageServerMetadata.Builder
-
Specify the interpretation of classification labels.
- classificationLabelsToChannels(Map<Integer, PathClass>, boolean) - Static method in class qupath.lib.images.servers.ServerTools
-
Create a list of channels from classification labels.
- ClassificationResolution - Class in qupath.process.gui.commands.ml
-
Wrapper for a
PixelCalibration
to be used to define classifier resolution. - classify(ClassificationModel, PathObject, Mat, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools
-
Apply a classification model to an existing image patch to classify an object.
- classify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, int, int, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools
-
Apply a classification model to an image patch to classify an object.
- classify(ClassificationModel, PathObject, ImageServer<BufferedImage>, double, IntFunction<PathClass>, String) - Static method in class qupath.opencv.dnn.DnnTools
-
Apply a classification model to an image patch to classify an object.
- ClassifyByMeasurementBuilder(String) - Constructor for class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
-
Constructor.
- classifyCellsByCentroid(ImageData<BufferedImage>, PixelClassifier, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Classify cells according to the prediction of the pixel corresponding to the cell centroid using a
PixelClassifier
. - classifyDetectionsByCentroid(String) - Static method in class qupath.lib.scripting.QP
-
Classify detections according to the prediction of the pixel corresponding to the detection centroid using a
PixelClassifier
. - classifyDetectionsByCentroid(PixelClassifier) - Static method in class qupath.lib.scripting.QP
-
Classify detections according to the prediction of the pixel corresponding to the detection centroid using a
PixelClassifier
. - classifyDetectionsByCentroid(ImageData<BufferedImage>, PixelClassifier) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Classify detections according to the prediction of the pixel corresponding to the detection centroid using a
PixelClassifier
. - classifyObjects(ImageData<BufferedImage>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.dnn.DnnObjectClassifier
- classifyObjects(ImageData<BufferedImage>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.dnn.OpenCVModelObjectClassifier
- classifyObjects(ImageData<T>, boolean) - Method in class qupath.lib.classifiers.object.AbstractObjectClassifier
- classifyObjects(ImageData<T>, boolean) - Method in interface qupath.lib.classifiers.object.ObjectClassifier
-
Classify all compatible objects from an
ImageData
. - classifyObjects(ImageData<T>, Collection<? extends PathObject>, boolean) - Method in interface qupath.lib.classifiers.object.ObjectClassifier
-
Classify the objects in the specified collection.
- classifyObjects(ImageData<T>, Collection<? extends PathObject>, boolean) - Method in class qupath.opencv.ml.objects.OpenCVMLClassifier
- classifyObjectsByCentroid(ImageData<BufferedImage>, PixelClassifier, Collection<PathObject>, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Classify objects according to the prediction of the pixel corresponding to the object's ROI centroid using a
PixelClassifier
. - classifyObjectsByCentroid(ImageServer<BufferedImage>, Collection<PathObject>, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Apply classification from a server to a collection of objects.
- classifyObjectsByCluster(Collection<Collection<? extends PathObject>>) - Static method in class qupath.lib.analysis.DelaunayTools
-
Assign object classifications based upon pre-computed clusters.
- classifyObjectsByCluster(Collection<Collection<? extends PathObject>>, Function<Integer, PathClass>) - Static method in class qupath.lib.analysis.DelaunayTools
-
Assign object classifications based upon pre-computed clusters.
- classifySelected(String) - Static method in class qupath.lib.scripting.QP
-
Set the classification of the selected objects in the current hierarchy.
- classifySelected(PathObjectHierarchy, String) - Static method in class qupath.lib.scripting.QP
-
Set the classification of the selected objects.
- clear() - Method in interface qupath.lib.gui.scripting.EditableText
-
Request clear the contents of the control.
- clear() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
- clear() - Method in class qupath.lib.gui.scripting.TextAreaControl
- clear() - Method in class qupath.lib.gui.UndoRedoManager
-
Clear all undo/redo stacks (useful when memory is low).
- clear() - Method in interface qupath.lib.measurements.MeasurementList
-
Remove all the measurements from the list.
- clear() - Method in class qupath.lib.objects.PathObjectConnections
-
Clear all existing connections.
- clear() - Method in class qupath.lib.plugins.workflow.Workflow
-
Remove all steps, firing an update event if the workflow was not previously empty.
- clearAll() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Remove all objects from the hierarchy.
- clearAllObjects() - Static method in class qupath.lib.scripting.QP
-
Remove all the objects in the current
PathObjectHierarchy
, and clear the selection. - clearAllObjects(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
-
Remove all the objects of a specified Java class.
- clearAnnotationMeasurements() - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all annotations in the current hierarchy.
- clearAnnotationMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all annotations in a hierarchy.
- clearAnnotations() - Static method in class qupath.lib.scripting.QP
-
Remove all the annotation objects from the current
PathObjectHierarchy
. - clearBoundary(ByteProcessor, Roi, double) - Static method in class qupath.imagej.processing.RoiLabeling
-
Starting from all white pixels (value = 255) on a ROI's boundary, fill the pixels with black
- clearCache() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Clear the cache, including thumbnails, and cancel any pending requests.
- clearCache() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Clear any cached tiles.
- clearCache(boolean, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Clear the cache, optionally including thumbnails and stopping any pending requests.
- clearCachedOverlay() - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
-
Clear previously-cached tiles for this overlay.
- clearCachedOverlayForRegion(ImageRegion) - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
-
Clear previously-cached tiles for a specified region of this overlay.
- clearCacheForRequestOverlap(RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- clearCacheForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- clearCellMeasurements() - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all cells in the current hierarchy.
- clearCellMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all cells in a hierarchy.
- clearChildObjects() - Method in class qupath.lib.objects.PathObject
-
Remove all child objects.
- clearDetectionMeasurements() - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all detections in the current hierarchy.
- clearDetectionMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all detections in a hierarchy (including sub-classes of detections).
- clearDetections() - Static method in class qupath.lib.scripting.QP
-
Remove all the detection objects from the current
PathObjectHierarchy
. - clearMeasurements() - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all detections in the current hierarchy.
- clearMeasurements(Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for objects of a specific class in the current hierarchy (subclasses are not included!).
- clearMeasurements(PathObjectHierarchy, Class<? extends PathObject>) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for objects of a specific class in a hierarchy (subclasses are not included!).
- clearMeasurements(PathObjectHierarchy, Collection<PathObject>) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for specified objects within a hierarchy.
- clearMeasurements(PathObjectHierarchy, PathObject...) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for specified objects within a hierarchy.
- clearMetadata() - Method in class qupath.lib.objects.TMACoreObject
-
Clear all associated metadata.
- clearMetadata() - Method in interface qupath.lib.projects.ProjectImageEntry
-
Remove all metadata.
- clearMetadataMap() - Method in class qupath.lib.objects.PathObject
-
Remove all stored metadata values.
- clearOutside(ImageProcessor, Roi) - Static method in class qupath.imagej.processing.RoiLabeling
-
Clear (i.e.
- clearPathObjects() - Method in class qupath.lib.objects.PathObject
-
Deprecated.since v0.4.0, replaced by
PathObject.clearChildObjects()
- clearReaderOptions() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
-
Clear all reader options, returning these to their defaults.
- clearRootMeasurements() - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for the root object.
- clearRootMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for the root object.
- clearSelectedObjects() - Static method in class qupath.lib.scripting.QP
-
Clear selected objects, but keep child (descendant) objects.
- clearSelectedObjects(boolean) - Static method in class qupath.lib.scripting.QP
-
Delete the selected objects from the current hierarchy, optionally keeping their child (descendant) objects.
- clearSelection() - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
-
Clear selection so that no objects are selected.
- clearThresholds() - Method in class qupath.lib.gui.charts.HistogramPanelFX.ThresholdedChartWrapper
-
Clear all thresholds.
- clearTileMeasurements() - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all tiles in the current hierarchy.
- clearTileMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all tiles in a hierarchy.
- clearTMACoreMeasurements() - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all TMA core objects in the current hierarchy.
- clearTMACoreMeasurements(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
-
Clear the measurement lists for all TMA core objects in a hierarchy.
- clearTMAGrid() - Static method in class qupath.lib.scripting.QP
-
Remove the TMA grid from the current
PathObjectHierarchy
. - clip(double, double) - Static method in class qupath.opencv.ops.ImageOps.Core
-
Create an op that clips Mat values to the specified minimum and maximum.
- clip(Mat, double, double) - Static method in class qupath.opencv.tools.GroovyCV
-
Clip values of a Mat to be within a specified minimum and maximum.
- clip255(double) - Static method in class qupath.lib.common.ColorTools
-
Convert a double value to an int, flooring and clipping to the range 0-255.
- clipROIsForHierarchyProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Request ROIs to be clipped and inserted as the right place in the hierarchy when drawing (to prevent overlapping ROIs being created accidentally).
- clipToAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
- clipToROI(ROI, Collection<? extends ROI>) - Static method in class qupath.lib.roi.RoiTools
-
Intersect a collection of ROIs with a single parent ROI, returning all results that are valid.
- clipValue(double, double, double) - Static method in class qupath.lib.common.GeneralTools
-
Clip a value to be within a specific range.
- clipValue(int, int, int) - Static method in class qupath.lib.common.GeneralTools
-
Clip a value to be within a specific range.
- close() - Method in class qupath.imagej.images.servers.ImageJServer
- close() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
- close() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- close() - Method in class qupath.lib.images.servers.AbstractImageServer
- close() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
- close() - Method in class qupath.lib.images.servers.LabeledImageServer
- close() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
- close() - Method in class qupath.lib.images.servers.SparseImageServer
- close() - Method in class qupath.lib.images.servers.SparseImageServer.SparseImageServerManager
- close() - Method in interface qupath.lib.measurements.MeasurementList
-
Close the list.
- close() - Method in interface qupath.opencv.dnn.DnnModel
-
Close this model if it will not be needed again.
- close() - Method in class qupath.opencv.dnn.OpenCVDnn
- close() - Method in class qupath.opencv.ml.objects.features.Preprocessing.PCAProjector
- close() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
- close() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
- closeProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Close the current project open in the
QuPathGUI
. - closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Request that this viewer is closed.
- closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
- closing(int) - Static method in class qupath.opencv.ops.ImageOps.Filters
-
Apply a 2D morphological closing filter.
- closingByReconstruction(ImageProcessor, double) - Static method in class qupath.imagej.processing.MorphologicalReconstruction
-
Apply a morphological closing by reconstruction.
- closingFilter(Mat, int) - Static method in class qupath.opencv.tools.OpenCVTools
-
Apply a 2D closing filter (dilation followed by erosion) to all channels of an image.
- CM_GRAYSCALE - Static variable in class qupath.lib.display.DirectServerChannelInfo
- CM_GRAYSCALE_INVERTED - Static variable in class qupath.lib.display.DirectServerChannelInfo
- CodeAreaControl - Class in qupath.lib.gui.scripting.richtextfx
-
Code area control using RichTextFX.
- COG - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- CoherenceFeaturePlugin - Class in qupath.lib.algorithms
-
Plugin to calculate coherence features for image tiles.
- CoherenceFeaturePlugin() - Constructor for class qupath.lib.algorithms.CoherenceFeaturePlugin
-
Default constructor.
- COLOR - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
-
Show using default color LUT (may be composite)
- ColorDeconvMatrix3x3 - Class in qupath.lib.color
-
Simple class for representing - and inverting a 3x3 matrix.
- ColorDeconvMatrix3x3(double[][]) - Constructor for class qupath.lib.color.ColorDeconvMatrix3x3
-
Constructor for a 3x3 matrix.
- ColorDeconvolutionHelper - Class in qupath.lib.color
-
Static methods to assist with color deconvolution.
- ColorDeconvolutionHelper() - Constructor for class qupath.lib.color.ColorDeconvolutionHelper
- ColorDeconvolutionStains - Class in qupath.lib.color
-
Helper class for storing stain vectors and maximum channel values to be used for color deconvolution.
- ColorDeconvolutionStains() - Constructor for class qupath.lib.color.ColorDeconvolutionStains
-
Default constructor, for Externalizable.
- ColorDeconvolutionStains(String, StainVector, StainVector, double, double, double) - Constructor for class qupath.lib.color.ColorDeconvolutionStains
-
Constructor for ColorDeconvolutionStains with two stain vectors.
- ColorDeconvolutionStains(String, StainVector, StainVector, StainVector, double, double, double) - Constructor for class qupath.lib.color.ColorDeconvolutionStains
-
Constructor for ColorDeconvolutionStains with three stain vectors.
- ColorDeconvolutionStains.DefaultColorDeconvolutionStains - Enum Class in qupath.lib.color
-
Enum for common stain defaults.
- colorDeconvolve(ColorProcessor, ColorDeconvolutionStains) - Static method in class qupath.imagej.tools.IJTools
-
Apply color deconvolution, outputting 3 'stain' images in the same order as the stain vectors.
- colorDeconvolveReconvolveRGBArray(int[], ColorDeconvolutionStains, ColorDeconvolutionStains, boolean, int[]) - Static method in class qupath.lib.color.ColorTransformer
-
Deconvolve RGB array with one set of stain vectors, and reconvolve with another.
- colorDeconvolveReconvolveRGBArray(int[], ColorDeconvolutionStains, ColorDeconvolutionStains, boolean, int[], float, float) - Static method in class qupath.lib.color.ColorTransformer
-
Deconvolve RGB array with one set of stain vectors, and reconvolve with another - with optional scaling.
- colorDeconvolveRGBPixel(int, ColorDeconvolutionStains, int) - Static method in class qupath.lib.color.ColorTransformer
-
Calculate the color deconvolved value for a single pixel, stored as a packed (A)RGB int.
- colorDefaultObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display objects of any type, where a default has not otherwise been specified.
- ColorMapCanvas - Class in qupath.lib.gui
-
Canvas to show the range of a ColorMap (i.e.
- ColorMapCanvas(double, ColorMaps.ColorMap) - Constructor for class qupath.lib.gui.ColorMapCanvas
- ColorMapCanvas(double, ColorMaps.ColorMap, Function<Double, String>) - Constructor for class qupath.lib.gui.ColorMapCanvas
-
Create a canvas that displays the range of the specified
ColorMaps.ColorMap
with key tooltips. - colorMapProperty() - Method in class qupath.lib.gui.ColorMapCanvas
-
Return the ColorMap property of this canvas.
- ColorMaps - Class in qupath.lib.color
-
Helper class to manage colormaps, which are rather like lookup tables but easily support interpolation.
- ColorMaps() - Constructor for class qupath.lib.color.ColorMaps
- ColorMaps.ColorMap - Interface in qupath.lib.color
-
colormap, which acts as an interpolating lookup table with an arbitrary range.
- colorModel(ColorModels.ColorModelBuilder) - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapBuilder
-
Set a
ColorModels.ColorModelBuilder
that can be used in conjunction withDensityMaps.DensityMapBuilder.buildServer(ImageData)
. - ColorModelFactory - Class in qupath.lib.color
-
Factory methods to help create ColorModels for use with BufferedImages.
- ColorModelRenderer - Class in qupath.lib.gui.images.stores
-
An
ImageRenderer
that uses aColorModel
. - ColorModelRenderer(ColorModel) - Constructor for class qupath.lib.gui.images.stores.ColorModelRenderer
-
Constructor.
- ColorModels - Class in qupath.lib.analysis.heatmaps
-
Helper class for creating a JSON-serializable way to generate a
ColorModel
. - ColorModels - Class in qupath.lib.color
-
Helper class for creating a JSON-serializable way to generate a
ColorModel
. - ColorModels() - Constructor for class qupath.lib.analysis.heatmaps.ColorModels
- ColorModels() - Constructor for class qupath.lib.color.ColorModels
- ColorModels.ColorModelBuilder - Interface in qupath.lib.analysis.heatmaps
-
Simple builder to create a
ColorModel
. - ColorModels.ColorModelBuilder - Interface in qupath.lib.color
-
Simple builder to create a
ColorModel
. - ColorModels.DisplayBand - Class in qupath.lib.analysis.heatmaps
-
Helper class to the display of a single channel (band) in a
ColorModel
. - ColorModels.DisplayBand - Class in qupath.lib.color
-
Helper class to the display of a single channel (band) in a
ColorModel
. - colorSelectedObjectProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display selected objects.
- colorTileProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display tile objects.
- colorTMAMissingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display missing TMA core objects.
- colorTMAProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
The default color used to display TMA core objects.
- ColorTools - Class in qupath.lib.common
-
Static functions to help work with RGB(A) colors using packed ints.
- ColorToolsAwt - Class in qupath.lib.color
-
Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
- ColorToolsAwt() - Constructor for class qupath.lib.color.ColorToolsAwt
- ColorToolsFX - Class in qupath.lib.gui.tools
-
Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
- ColorToolsFX() - Constructor for class qupath.lib.gui.tools.ColorToolsFX
- ColorTransformer - Class in qupath.lib.color
-
Static methods for computing a range of color transforms for packed RGB values.
- ColorTransformer() - Constructor for class qupath.lib.color.ColorTransformer
- ColorTransformer.ColorTransformMethod - Enum Class in qupath.lib.color
-
Enum consisting of color transforms that may be applied to RGB images.
- ColorTransforms - Class in qupath.lib.images.servers
-
Color transforms that may be used to extract single-channel images from BufferedImages.
- ColorTransforms() - Constructor for class qupath.lib.images.servers.ColorTransforms
- ColorTransforms.ColorTransform - Interface in qupath.lib.images.servers
-
Interface defining a color transform that can extract a float values from a BufferedImage.
- ColorTransforms.ColorTransformTypeAdapter - Class in qupath.lib.images.servers
-
TypeAdapter
to support serializing aColorTransforms.ColorTransform
. - ColorTransformTypeAdapter() - Constructor for class qupath.lib.images.servers.ColorTransforms.ColorTransformTypeAdapter
- combineROIs(ROI, ROI, RoiTools.CombineOp) - Static method in class qupath.lib.roi.RoiTools
-
Combine two shape ROIs together.
- combineSelectedAnnotations(ImageData<?>, RoiTools.CombineOp) - Static method in class qupath.lib.gui.commands.Commands
-
Combine the selected annotations for the specified hierarchy.
- comboPasteEscape - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- commandBarDisplayProperty() - Static method in class qupath.lib.gui.tools.CommandFinderTools
-
Property specifying where the command bar should be displayed relative to the main viewer window.
- CommandFinderTools - Class in qupath.lib.gui.tools
-
Helper tools for creating components that enable fast access to menu commands via a filtered list.
- CommandFinderTools() - Constructor for class qupath.lib.gui.tools.CommandFinderTools
- CommandFinderTools.CommandBarDisplay - Enum Class in qupath.lib.gui.tools
-
Available modes for displaying the command bar.
- CommandFinderTools.CommandEntry - Class in qupath.lib.gui.tools
-
Helper class to wrap summary data for a command to display in the list.
- CommandLinePluginRunner<T> - Class in qupath.lib.plugins
-
A PluginRunner that simply logs progress and output.
- CommandLinePluginRunner(ImageData<T>) - Constructor for class qupath.lib.plugins.CommandLinePluginRunner
-
Constructor for a PluginRunner that send progress to a log.
- CommandLinePluginRunner.CommandLineProgressMonitor - Class in qupath.lib.plugins
-
A
SimpleProgressMonitor
that sends progress to a log. - CommandLineProgressMonitor() - Constructor for class qupath.lib.plugins.CommandLinePluginRunner.CommandLineProgressMonitor
- Commands - Class in qupath.lib.gui.commands
-
Helper class implementing simple 'single-method' commands for easy inclusion in the GUI.
- Commands() - Constructor for class qupath.lib.gui.commands.Commands
- COMPARATOR_FULL - Static variable in class qupath.lib.common.Version
-
Compare full version, including any suffixes.
- COMPARATOR_MAJOR - Static variable in class qupath.lib.common.Version
-
Compare major versions only.
- COMPARATOR_MAJOR_MINOR - Static variable in class qupath.lib.common.Version
-
Compare major then minor versions.
- COMPARATOR_MAJOR_MINOR_PATCH - Static variable in class qupath.lib.common.Version
-
Compare major then minor then patch versions (ignoring suffixes).
- compare(PathObject, PathObject) - Method in class qupath.lib.objects.DefaultPathObjectComparator
- compare(ROI, ROI) - Method in class qupath.lib.roi.DefaultROIComparator
- compareTo(KaplanMeierData.KaplanMeierEvent) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData.KaplanMeierEvent
- compareTo(Version) - Method in class qupath.lib.common.Version
- compareTo(PathClass) - Method in class qupath.lib.objects.classes.PathClass
-
This is now equivalent to
this.toString().compareTo(o.toString())
. - compareTo(ImagePlane) - Method in class qupath.lib.regions.ImagePlane
-
Compare with another ImagePlane, in the order t, z, c.
- completionCodeCombination - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- componentContains(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
- componentPointToImagePoint(double, double, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Convert x and y coordinates from the component space to the image space.
- componentPointToImagePoint(Point2D, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Convert a coordinate from the viewer into the corresponding pixel coordinate in the full-resolution image - optionally constraining it to any server bounds.
- compress(String) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
-
Compresses the specified text by removing extra space, according to the syntax.
- compression(OMEPyramidWriter.CompressionType) - Method in class qupath.lib.images.writers.ome.OMEPyramidWriter.Builder
-
Request the output compression type.
- compressSourceAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- computeAboveThresholdCounts(WritableRaster, int, double, WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Count the number of above-threshold pixels in a specified band of a raster, with optional mask.
- computeAboveThresholdCounts(WritableRaster, int, double, WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Count the number of above-threshold pixels in a specified band of a raster, with optional mask and/or bounding rectangle.
- computeAngle(StainVector, StainVector) - Static method in class qupath.lib.color.StainVector
-
Calculate the angle between two stain vectors, in degrees.
- computeArgMaxHistogram(WritableRaster, long[], WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Create a histogram that identifies the channels (bands) of an image with the maximum values according to the argmax criterion.
- computeArgMaxHistogram(WritableRaster, long[], WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Create a histogram that identifies the channels (bands) of an image with the maximum values according to the argmax criterion, with an optional bounding rectangle.
- computeConsoleStyles(String, boolean) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.GroovyStyler
- computeConsoleStyles(String, boolean) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PythonStyler
- computeConsoleStyles(String, boolean) - Method in interface qupath.lib.gui.scripting.richtextfx.stylers.ScriptStyler
-
Compute styling for the specified
text
, considering it will be used in the console. - computeCoordinateDistance(Coordinate, Collection<Coordinate>) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the shortest distance from a coordinate to one of a collection of target coordinates.
- computeCoordinateDistance(Coordinate, STRtree) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the distance to the nearest coordinate stored within an
STRtree
. - computeDistance(Coordinate, Geometry, PointOnGeometryLocator) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the (unsigned) shortest distance from a coordinate to a target geometry, or zero if the coordinate occurs within
- computeDistance(Coordinate, Geometry, PointOnGeometryLocator, boolean) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the shortest distance from a coordinate to a target geometry.
- computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.GroovyStyler
- computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.JsonStyler
- computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.MarkdownStyler
- computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PlainStyler
- computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.PythonStyler
- computeEditorStyles(String) - Method in interface qupath.lib.gui.scripting.richtextfx.stylers.ScriptStyler
-
Compute styling for the specified
text
, considering it will be used in the main editor. - computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.XmlStyler
- computeEditorStyles(String) - Method in class qupath.lib.gui.scripting.richtextfx.stylers.YamlStyler
- computeFeatures() - Method in class qupath.lib.analysis.features.CoocurranceMatrices
-
Compute features.
- computeLocalBinaryPatterns16(SimpleImage, double) - Static method in class qupath.lib.analysis.features.LocalBinaryPatterns
-
Compute local binary pattern descriptor for a SimpleImage.
- computeLogRankTest(KaplanMeierData, KaplanMeierData) - Static method in class qupath.lib.analysis.stats.survival.LogRankTest
-
Compare KaplanMeier objects using log-rank test.
- computeRunningStatistics(double[]) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
-
Create a RunningStatistics object using all the values from a specified array.
- computeRunningStatistics(SimpleImage) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
-
Compute running statistics using all pixels from a SimpleImage.
- computeRunningStatistics(SimpleImage, SimpleImage, List<RunningStatistics>) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
-
Calculate RunningStatistics for each label > 0 in an image, up to a maximum of
statsList.size()
. - computeTiledROIs(ROI, ImmutableDimension, ImmutableDimension, boolean, int) - Static method in class qupath.lib.roi.RoiTools
-
Create a collection of tiled ROIs corresponding to a specified parentROI if it is larger than sizeMax, with optional overlaps.
- computeUnsignedIntHistogram(WritableRaster, long[], WritableRaster) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Compute the full histogram for a raster containing 8-bit or 16-bit unsigned integer values.
- computeUnsignedIntHistogram(WritableRaster, long[], WritableRaster, Rectangle) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Compute the full histogram for a raster containing 8-bit or 16-bit unsigned integer values, optionally restricted to a bounding rectangle.
- concatChannels(Collection<ImageServer<BufferedImage>>) - Method in class qupath.lib.images.servers.TransformedServerBuilder
-
Concatenate a collection of additional servers along the 'channels' dimension (iteration order is used).
- concatChannels(ImageServer<BufferedImage>...) - Method in class qupath.lib.images.servers.TransformedServerBuilder
-
Concatenate additional servers along the 'channels' dimension.
- config(String) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
-
Path to config file (if required).
- config(URI) - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
-
Path to config file (if required).
- confirmation() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Create an confirmation alert dialog.
- constrainCellByNucleusDistance(PathCellObject, double, boolean) - Static method in class qupath.lib.objects.CellTools
-
Constrain a cell boundary to fall within a maximum region, determined by buffering the convex hull of the nucleus ROI by a fixed distance.
- constrainCellByScaledNucleus(PathCellObject, double, boolean) - Static method in class qupath.lib.objects.CellTools
-
Constrain a cell boundary to fall within a maximum region, determined by scaling the nucleus ROI by a fixed scale factor about its centroid.
- constrainCellOverlaps(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.CellTools
-
Adjust cell boundary ROIs to be non-overlapping, by assigning overlaps to the cell with the closest nucleus.
- constrainToBounds(Geometry, double, double, double, double) - Static method in class qupath.lib.roi.GeometryTools
-
Compute the intersection of a Geometry and a specified bounding box.
- contains(double, double) - Method in class qupath.lib.roi.AreaROI
- contains(double, double) - Method in class qupath.lib.roi.EllipseROI
- contains(double, double) - Method in class qupath.lib.roi.GeometryROI
- contains(double, double) - Method in interface qupath.lib.roi.interfaces.ROI
-
Test is the ROI contains specified x, y coordinates.
- contains(double, double) - Method in class qupath.lib.roi.LineROI
- contains(double, double) - Method in class qupath.lib.roi.PointsROI
- contains(double, double) - Method in class qupath.lib.roi.PolygonROI
- contains(double, double) - Method in class qupath.lib.roi.PolylineROI
- contains(double, double) - Method in class qupath.lib.roi.RectangleROI
- contains(int, int, int, int) - Method in class qupath.lib.regions.ImageRegion
-
Check if this region contains a specified coordinate.
- contains(String) - Method in interface qupath.lib.projects.ResourceManager.Manager
-
Returns true if the manager knows a resource with the specified name exists.
- containsClassification(String...) - Static method in class qupath.lib.objects.PathObjectPredicates
-
Predicate that returns true if any component of its classification has any of the specified names.
- containsImageJRois(File) - Static method in class qupath.imagej.tools.IJTools
-
Check whether a file is likely to contain an ImageJ ROI, based upon its extension or .zip file contents.
- containsKey(Object) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Returns true if a parameter exists in this list with a specified key.
- containsKey(String) - Method in interface qupath.lib.measurements.MeasurementList
-
Returns true if this list contains a measurement with the specified name.
- containsMetadata(String) - Method in interface qupath.lib.projects.ProjectImageEntry
-
Check if a metadata value is present for a specified key.
- containsName(PathClass, String) - Static method in class qupath.lib.objects.classes.PathClassTools
-
Query whether a
PathClass
or any of its ancestor classes contains a specified name. - containsNamedMeasurement(String) - Method in interface qupath.lib.measurements.MeasurementList
-
Deprecated.since v0.4.0; replaced by
MeasurementList.containsKey(String)
- containsObject(PathObject) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
- containsObject(PathObject) - Method in interface qupath.lib.objects.PathObjectConnectionGroup
-
Returns true if the specified PathObject is contained within this group.
- containsObject(PathObject) - Method in class qupath.opencv.features.DelaunayTriangulation
- containsObject(PathObject, PathObject) - Static method in class qupath.lib.objects.PathObjectTools
-
Deprecated.
- containsROI(ROI, ROI) - Static method in class qupath.lib.objects.PathObjectTools
-
Deprecated.
- content(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Specify a
Node
to display within the dialog. - contentText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
-
Specify the dialog content text.
- ContourTracing - Class in qupath.lib.analysis.images
-
Class to convert labelled images to Geometry objects, ROIs and PathObjects.
- ContourTracing() - Constructor for class qupath.lib.analysis.images.ContourTracing
- ContourTracing.ChannelThreshold - Class in qupath.lib.analysis.images
-
Helper class defining global thresholds to apply to a single image channel.
- CONTRAST - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- convertAndPredict(Map<String, Mat>) - Method in interface qupath.opencv.dnn.DnnModel
-
Convenience method to convert input image patches to a blobs, apply a
PredictionFunction
(optionally with multiple inputs/outputs), and convert the output to a standardMat
. - 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 standardMat
. - ConvertCommand - Class in qupath.lib.images.writers.ome
-
Allows command line option to convert an input image to OME-TIFF
- ConvertCommand() - Constructor for class qupath.lib.images.writers.ome.ConvertCommand
- convertDetectionsToPoints(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Convert detection objects to point annotations based upon their ROI centroids.
- convertLabelsToCells(ImageProcessor, ImageProcessor, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Convert integer labeled images into cell objects.
- convertLabelsToCells(ImageProcessor, ImageProcessor, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Convert integer labeled images into cell objects.
- convertPixelsToOpticalDensities(float[], double, boolean) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
-
For originally-8-bit images, optical densities can usually be computed faster by preallocating a LUT with the 0-255 required values.
- convertToAnnotation(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Create an annotation object for a specific ImageJ Roi, using an
ImagePlus
to help set properties. - convertToAnnotation(Roi, double, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
-
Create an annotation object for a specific ImageJ Roi.
- convertToAnnotation(ImagePlus, ImageServer<?>, Roi, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Deprecated.
- convertToBufferedImage(ImagePlus, int, int, ColorModel) - Static method in class qupath.imagej.images.servers.ImageJServer
-
Convert an ImagePlus to a BufferedImage, for a specific z-slice and timepoint.
- convertToDetection(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Create a detection object for a specific ImageJ Roi, using an
ImagePlus
to help set properties. - convertToDetection(Roi, double, ImagePlus) - Static method in class qupath.imagej.tools.IJTools
-
Create a detection object for a specific ImageJ Roi.
- convertToDetection(ImagePlus, ImageServer<?>, Roi, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Deprecated.
- convertToFloatProcessor(SimpleImage) - Static method in class qupath.imagej.tools.IJTools
-
Convert a
SimpleImage
to anImageProcessor
. - 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 aPathImage<ImagePlus>
. - convertToImagePlus(ImageServer<BufferedImage>, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
-
Read a region from an
ImageServer<BufferedImage
as aPathImage<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 anImagePlus
to help set properties. - convertToPathObject(ImagePlus, ImageServer<?>, Roi, double, Function<ROI, PathObject>, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Deprecated.
- convertToPercentages(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
-
Request that pie chart values are converted to percentages for tooltips.
- convertToPoints(Collection<PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools
-
Convert a collection of PathObjects to Point annotations, based on ROI centroids.
- convertToPoints(PathObjectHierarchy, Collection<PathObject>, boolean, boolean) - Static method in class qupath.lib.objects.PathObjectTools
-
Convert a collection of PathObjects to Point annotations, based on ROI centroids, and add the points to the hierarchy.
- convertToPolygonROI(PolygonRoi, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Convert an ImageJ PolygonRoi to a QuPath PolygonROI.
- convertToROI(Roi, double, double, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Create a ROI from an ImageJ Roi.
- convertToROI(Roi, Calibration, double, ImagePlane) - Static method in class qupath.imagej.tools.IJTools
-
Create a ROI from an ImageJ Roi, using the Calibration object of an ImagePlus.
- convertToROI(Roi, T) - Static method in class qupath.imagej.tools.IJTools
-
Create a ROI from an ImageJ Roi.
- convertToUncalibratedImagePlus(String, BufferedImage) - Static method in class qupath.imagej.tools.IJTools
-
Convert a BufferedImage to an ImagePlus, without pixel size information or other calibration.
- convertTransform(AffineTransform) - Static method in class qupath.lib.roi.GeometryTools
-
Convert an
AffineTransform
to anAffineTransformation
. - convertTransform(AffineTransformation) - Static method in class qupath.lib.roi.GeometryTools
-
Convert an
AffineTransformation
to anAffineTransform
. - CONVEX_POINTS - Variable in class qupath.lib.gui.QuPathGUI.DefaultActions
-
Display the convex hull of point ROIs.
- ConvexHull - Class in qupath.lib.roi
-
Helper method for calculating the convex hull from a list of points.
- ConvexHull() - Constructor for class qupath.lib.roi.ConvexHull
- CoocurranceMatrices - Class in qupath.lib.analysis.features
-
Data structure to hold cooccurrence matrices for computation of Haralick features.
- CoocurranceMatrices(int) - Constructor for class qupath.lib.analysis.features.CoocurranceMatrices
-
Initialize coocurrence matrices.
- coordinateExtractor(Function<PathObject, Collection<Coordinate>>) - Method in class qupath.lib.analysis.DelaunayTools.Builder
-
Specify a default method of extracting coordinates for triangulation from an object, rather than centroids or the ROI boundary.
- copy() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
- copy() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Request copy the current selection.
- copy() - Method in class qupath.lib.gui.scripting.TextAreaControl
- copyAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
- copyAnnotationsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Attempt to annotation objects to the system clipboard, if available
- copySelectedAnnotationsToCurrentPlane(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
-
Copy the selected objects and add them to the plane currently active in the viewer.
- copySelectedAnnotationsToPlane(int, int) - Static method in class qupath.lib.scripting.QP
-
Copy the selected annotations in the current hierarchy to the specified z-slice and timepoint.
- copySelectedAnnotationsToPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP
-
Copy the selected annotations in the specified hierarchy to the specified image plane.
- copySelectedAnnotationsToPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP
-
Copy the selected annotations in the current hierarchy to the specified image plane.
- copySelectedObjectsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
-
Attempt to copy selected objects to the system clipboard, if available
- copySelectedObjectsToPlane(int, int) - Static method in class qupath.lib.scripting.QP
-
Copy the selected objects in the current hierarchy to the specified z-slice and timepoint.
- copySelectedObjectsToPlane(PathObjectHierarchy, ImagePlane) - Static method in class qupath.lib.scripting.QP
-
Copy the selected objects in the specified hierarchy to the specified image plane.
- copySelectedObjectsToPlane(ImagePlane) - Static method in class qupath.lib.scripting.QP
-
Copy the selected objects in the current hierarchy to the specified image plane.
- copyTableContentsToClipboard(PathTableData<?>, Collection<String>) - Static method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand
-
Get a single String representing the data in a table and copy it to the clipboard.
- copyToClipboard(Object) - Static method in class qupath.lib.gui.scripting.QPEx
-
Try to copy an object to the clipboard.
- Core() - Constructor for class qupath.opencv.ops.ImageOps.Core
- countDescendants(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
-
Count the descendants of a PathObject recursively.
- COUNTING_PANEL - Variable in class qupath.lib.gui.QuPathGUI.DefaultActions
-
Show the counting tool dialog.
- CountingPanelCommand - Class in qupath.lib.gui.commands
-
Command to open up a counting panel to aid with creating Point annotations.
- CountingPanelCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.CountingPanelCommand
-
Constructor.
- countMissing() - Method in class qupath.lib.io.UriUpdater
-
Get a count of the items flagged as missing.
- countObjectsWithClass(Collection<? extends PathObject>, PathClass, boolean) - Static method in class qupath.lib.objects.PathObjectTools
-
Count the number of PathObjects in a collection with a specified class or base class.
- countReplacements() - Method in class qupath.lib.io.UriUpdater
-
Get a count of the number of replacements for missing items.
- cpu() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
-
Request CPU backend and target, if available.
- create(boolean) - Static method in class qupath.lib.gui.tools.WebViews
-
Create a new
WebView
. - create(int) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
-
Create a simple channel threshold.
- create(int, double, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
-
Create a threshold to select values between a minimum and maximum (inclusive).
- create(Gson, TypeToken<R>) - Method in class qupath.lib.io.GsonTools.SubTypeAdapterFactory
- create(Gson, TypeToken<T>) - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ObjectClassifierTypeAdapterFactory
- create(Gson, TypeToken<T>) - Method in class qupath.opencv.io.OpenCVTypeAdapters.OpenCVTypeAdaptorFactory
- create(String, String, String) - Static method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
-
Create a new
GitHubProject
. - create(String, Version, URI) - Static method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
-
Create a new
UpdateChecker.ReleaseVersion
. - create(Collection<? extends ImageServer<BufferedImage>>) - Static method in class qupath.lib.gui.panes.ServerSelector
- create(Collection<T>) - Static method in class qupath.lib.io.UriUpdater
-
Create a new UriUpdater to support updating URIs for one or more
UriResource
objects. - create(Collection<T>, Collection<UriUpdater.SingleUriItem>, Map<UriUpdater.SingleUriItem, UriUpdater.SingleUriItem>) - Static method in class qupath.lib.io.UriUpdater
-
Create a new UriUpdater using the specified collections.
- create(List<TMACoreObject>, int) - Static method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
-
Create a new TMAGrid based on a list of cores and grid width.
- create(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display a live image that can be created from an existing
ImageData
. - create(OverlayOptions, Map<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display a live image that can be created from an existing
ImageData
. - create(OverlayOptions, PixelClassifier) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display the live application of a
PixelClassifier
to an image, using the default number of parallel threads for classification. - create(OverlayOptions, PixelClassifier, int) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Create an overlay to display the live application of a
PixelClassifier
to an image. - create(OpenCVClassifiers.OpenCVStatModel, PathObjectFilter, FeatureExtractor<T>, List<PathClass>) - Static method in class qupath.opencv.ml.objects.OpenCVMLClassifier
-
Create a new
ObjectClassifier
that uses anOpenCVClassifiers.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 theScriptParameters
. - createCoordinateCache(Collection<Coordinate>) - Static method in class qupath.lib.analysis.DistanceTools
-
Create an
STRtree
to enable nearest neighbor searching for a collection of coordinates. - createCustomListCell(Function<T, String>) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a
ListCell
with custom methods to derive text for a specific object. - createCustomListCell(Function<T, String>, Function<T, Node>) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a
ListCell
with custom methods to derive text and a graphic for a specific object. - createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
- createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- createDefaultRGBImage(int, int) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
-
Create the default (blank) RGB image for this server.
- createDefaultRGBImage(int, int) - Method in class qupath.lib.images.servers.LabeledImageServer
- createDefaultSkin() - Method in class qupath.lib.gui.CircularSlider
- createDetectionObject(ROI) - Static method in class qupath.lib.objects.PathObjects
-
Create an unclassified detection object.
- createDetectionObject(ROI, PathClass) - Static method in class qupath.lib.objects.PathObjects
-
Create a classified detection object.
- createDetectionObject(ROI, PathClass, MeasurementList) - Static method in class qupath.lib.objects.PathObjects
-
Create a classified detection object with a specified measurement list.
- createDetections(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
-
Create detection objects by tracing contours in a labelled image.
- createDetections(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
-
Create detection objects from a labelled image.
- createDetectionsFromPixelClassifier(String, double, double, String...) - Static method in class qupath.lib.scripting.QP
-
Create detection objects based upon the output of a pixel classifier, applied to selected objects.
- createDetectionsFromPixelClassifier(PixelClassifier, double, double, String...) - Static method in class qupath.lib.scripting.QP
-
Create detection objects based upon the output of a pixel classifier, applied to selected objects.
- createDetectionsFromPixelClassifier(ImageData<BufferedImage>, PixelClassifier, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Create detection objects based upon the output of a pixel classifier, applied to selected objects.
- createDetectionsFromPixelClassifier(PathObjectHierarchy, ImageServer<BufferedImage>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Create detection objects based upon an
ImageServer
that provides classification or probability output, applied to selected objects. - createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.PositiveCellDetection
-
Wrap the detector to apply any required classification.
- createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellDetection
- createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
- createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
- createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
- createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.CellCountsCV
- createDetector(ImageData<BufferedImage>, ParameterList) - Method in class qupath.opencv.WatershedNucleiCV
- createDetector(ImageData<T>, ParameterList) - Method in class qupath.lib.plugins.AbstractTileableDetectionPlugin
-
Create a new ObjectDetector, compatible with the specified ImageData and ParameterList.
- createDisk(int, boolean) - Static method in class qupath.opencv.tools.OpenCVTools
-
Create a disk filter.
- createDocument() - Method in class qupath.lib.extension.svg.SvgTools.SvgBuilder
-
Create a String representation of the SVG document.
- createDynamicStepSpinner(double, double, double, double, int) - Static method in class qupath.lib.gui.tools.GuiTools
-
Create a new
Spinner
for double values with a step size that adapts according to the absolute value of the current spinner value. - createEllipseROI(double, double, double, double, ImagePlane) - Static method in class qupath.lib.roi.ROIs
-
Create an ellipse ROI defined by its bounding box.
- createEmptyMeasurementList() - Method in class qupath.lib.objects.PathDetectionObject
-
Default to a simple, float measurement list.
- createEmptyMeasurementList() - Method in class qupath.lib.objects.PathObject
-
Create a new MeasurementList of the preferred type for this object.
- createEmptyROI() - Static method in class qupath.lib.roi.ROIs
-
Create an 'empty' ROI with no length or area.
- createExactly(int, double) - Static method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
-
Create a threshold to select values that are exactly equal to a specified threshold.
- createFeatureDisplayOverlay(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
-
Deprecated.
- 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 anImageData
. - 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 aColorMaps.ColorMap
. - createIndexedColorModel8bit(ColorMaps.ColorMap, int) - Static method in class qupath.lib.color.ColorModelFactory
-
Create an 8-bit
IndexColorModel
from aColorMaps.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
ROI
s. - 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 aJsonElement
. - 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
- createListCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
ListCell
for displaying aPathObject
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
- 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 anImageServer
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 aContextMenu
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 defaultObjectInputFilter
for core QuPath-related and Java classes only. - createObjectRemovedEvent(Object, PathObjectHierarchy, PathObject, PathObject) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
-
Create a hierarchy event indicating objects were removed.
- createObjects(Raster, int, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing
-
Create objects from one band of a raster containing integer labels.
- createObjects(Mat, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.opencv.tools.OpenCVTools
-
Create objects by tracing contours in a labelled image.
- createObjects(SimpleImage, RegionRequest, int, int, BiFunction<ROI, Number, PathObject>) - Static method in class qupath.lib.analysis.images.ContourTracing
-
Create objects from a labelled image.
- createObjectsChangedEvent(Object, PathObjectHierarchy, PathObjectHierarchyEvent.HierarchyEventType, Collection<? extends PathObject>, boolean) - Static method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
-
Create a hierarchy event indicating objects have changed in a way consistent with the specified event type.
- createObjectsFromPixelClassifier(ImageServer<BufferedImage>, Map<Integer, PathClass>, ROI, Function<ROI, ? extends PathObject>, double, double, boolean) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Create objects based upon an
ImageServer
that provides classification or probability output. - createObjectsFromPredictions(ImageServer<BufferedImage>, PathObjectHierarchy, Collection<PathObject>, Function<ROI, ? extends PathObject>, double, double, PixelClassifierTools.CreateObjectOptions...) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Create objects from an image (usually created with a pixel classifier) where values represent classifications or predictions.
- createObjectsFromROIs(ImagePlus, Collection<? extends Roi>, double, boolean, boolean, ImagePlane) - Static method in class qupathj.QuPath_Send_Overlay_to_QuPath
-
Turn an array of ImageJ ROIs into a list of QuPath PathObjects, optionally adding measurements as well.
- createObjectTreeBrowser(String, Object) - Static method in class qupath.lib.gui.panes.ObjectTreeBrowser
-
Create a
TreeTableView
showing the names and values of object fields, accessed via reflection. - createPane() - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
- createPane() - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
PathObjectLabels.PathObjectMiniPane
using the defaultPathObject.toString()
method. - createPane(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
PathObjectLabels.PathObjectMiniPane
using a custom method to create a string representation of the object. - createPane(ObservableValue<ImageData<T>>) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
- createPane(ObservableValue<ImageData<T>>, boolean) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
- createPathImage(ImageServer<BufferedImage>, ImagePlus, RegionRequest) - Static method in class qupath.imagej.tools.IJTools
-
Create a
PathImage
from an ImagePlus and region. - createPathObjectIcon(PathObject, int, int) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create an icon depicting a PathObject.
- createPathObjectsFromROIs(ImagePlus, Roi[], ImageServer<?>, double, boolean, boolean, ImagePlane) - Static method in class qupathj.QuPath_Send_Overlay_to_QuPath
- 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 aPixelClassifier
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 aPixelClassifier
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 aProject
. - 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 specifiedImageRenderer
. - createROIIcon(ROI, int, int, Color) - Static method in class qupath.lib.gui.tools.IconFactory
-
Create an icon depicting a ROI.
- createROIMask(int, int, ROI, double, double, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Create a grayscale BufferedImage representing a mask for a specified ROI.
- createROIMask(int, int, ROI, RegionRequest) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Create a grayscale BufferedImage representing a mask for a specified ROI.
- createROIMask(Shape, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Create a Shape mask using the minimal bounding box for the Shape.
- createROIMask(ROI, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Create a ROI mask using the minimal bounding box for the ROI.
- createROIs(Raster, int, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
-
Create ROIs from one band of a raster containing integer label values.
- createROIs(Mat, RegionRequest, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
-
Convert integer labels into ROIs.
- createROIs(SimpleImage, RegionRequest, int, int) - Static method in class qupath.lib.analysis.images.ContourTracing
-
Create ROIs from a labelled image containing integer labels.
- createRotateImageDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a dialog for rotating the image in the current viewer (for display only).
- createRowGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Create a GridPane containing rows that resize similarly to Swing's GridLayout().
- createRowGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
-
Create a GridPane containing columns that resize similarly to Swing's GridLayout(), while also resizing contained objects to have the corresponding widths.
- createRunnableTask(ObjectDetector<T>, ParameterList, ImageData<T>, PathObject) - Static method in class qupath.lib.plugins.DetectionPluginTools
-
Create a task that applies an object detector to a parent object.
- createRunningStatisticsList(int) - Static method in class qupath.lib.analysis.stats.StatisticsHelper
-
Create a list of n (empty) RunningStatistics objects.
- createSaveDensityMapPane(ObjectExpression<Project<BufferedImage>>, ObjectExpression<DensityMaps.DensityMapBuilder>, StringProperty) - Static method in class qupath.process.gui.commands.density.DensityMapUI
-
Create a pane that can be used to save a
DensityMaps.DensityMapBuilder
, with standardized display and prompts. - createSavePixelClassifierPane(ObjectExpression<Project<BufferedImage>>, ObjectExpression<PixelClassifier>, StringProperty) - Static method in class qupath.process.gui.commands.ml.PixelClassifierUI
-
Create a pane that contains a text field and save button to allow a pixel classifier to be saved in a project.
- createScaledInstance(double, double) - Method in class qupath.lib.images.servers.PixelCalibration
-
Get a scaled instance of this PixelCalibration, multiplying pixel sizes for x and y by the specified scale values.
- createScaledInstance(double, double, double) - Method in class qupath.lib.images.servers.PixelCalibration
-
Get a scaled instance of this PixelCalibration, multiplying pixel sizes for x, y and z by the specified scale values.
- createScript() - Method in class qupath.lib.plugins.workflow.Workflow
-
Generate a script from the current workflow steps.
- createSelectableAction(ObservableValue<Boolean>, String) - Static method in class qupath.lib.gui.ActionTools
-
Create an action with its
Action.selectedProperty()
bound to a specified property. - createSelectableAction(ObservableValue<Boolean>, String, Node, KeyCombination) - Static method in class qupath.lib.gui.ActionTools
-
Create an action with its
Action.selectedProperty()
bound to a specified property, with optional graphic and accelerator. - createSelectAllObject(boolean) - Static method in class qupath.lib.scripting.QP
-
Deprecated.v0.4.0 use
QP.createFullImageAnnotation(boolean)
instead - createSelectAllObject(boolean, int, int) - Static method in class qupath.lib.scripting.QP
-
Deprecated.v0.4.0 use
QP.createFullImageAnnotation(boolean, int, int)
instead - createSeparator() - Static method in class qupath.lib.gui.ActionTools
-
Create an action indicating that a separator should be added (e.g.
- createServerBuilder() - Method in class qupath.imagej.images.servers.ImageJServer
- createServerBuilder() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
-
Returns null (does not support ServerBuilders).
- createServerBuilder() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
-
Returns null (does not support ServerBuilders).
- createServerBuilder() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
-
Returns null (does not support ServerBuilders).
- createServerBuilder() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
- createServerBuilder() - Method in class qupath.lib.images.servers.AbstractImageServer
-
Create a ServerBuilder, which can be used to construct an identical ImageServer.
- createServerBuilder() - Method in class qupath.lib.images.servers.AffineTransformImageServer
- createServerBuilder() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
-
Returns a builder capable of creating a server like this one.
- createServerBuilder() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
-
Returns null (does not support ServerBuilders).
- createServerBuilder() - Method in class qupath.lib.images.servers.CroppedImageServer
- createServerBuilder() - Method in class qupath.lib.images.servers.LabeledImageServer
-
Returns null (does not support ServerBuilders).
- createServerBuilder() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
- createServerBuilder() - Method in class qupath.lib.images.servers.RearrangeRGBImageServer
- createServerBuilder() - Method in class qupath.lib.images.servers.RotatedImageServer
- createServerBuilder() - Method in class qupath.lib.images.servers.SparseImageServer
- createServerBuilder() - Method in class qupath.lib.images.servers.WrappedBufferedImageServer
-
Returns null (does not support ServerBuilders).
- createShape(MouseEvent, double, double, boolean, Geometry) - Method in class qupath.lib.gui.viewer.tools.BrushTool
-
Create a new Geometry using the specified tool, assuming a user click/drag at the provided x & y coordinates.
- createShape(MouseEvent, double, double, boolean, Geometry) - Method in class qupath.process.gui.WandToolCV
- createShapeMask(int, int, Shape, double, double, double) - Static method in class qupath.lib.awt.common.BufferedImageTools
-
Create a grayscale BufferedImage representing a mask for a specified ROI.
- createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.QuPathGUI
-
Create a completion service that uses a shared threadpool for the application.
- createShowSystemInfoDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a window summarizing key system information relevant for QuPath.
- createSingleStageAction(Supplier<Stage>) - Static method in class qupath.lib.gui.commands.Commands
-
Create a command that generates a persistent single dialog on demand.
- createSingleThreadExecutor(Object) - Method in class qupath.lib.gui.QuPathGUI
-
Create an executor using a single thread.
- createSpecifyAnnotationDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
-
Create a stage to prompt the user to specify an annotation to add.
- createStainVector(String, double, double, double) - Static method in class qupath.lib.color.StainVector
-
Create a stain vector.
- createStatModel(Class<? extends StatModel>) - Static method in class qupath.opencv.ml.OpenCVClassifiers
-
Create an
OpenCVClassifiers.OpenCVStatModel
for a specific class ofStatModel
. - 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
- createTreeCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
-
Create a
TreeCell
for displaying aPathObject
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
forLocale.Category.DISPLAY
. - defaultLocaleFormatProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get a property for setting the default
Locale
forLocale.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 aScriptEngine
. - 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 aScriptEngineFactory
. - 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 forDensityMaps.DensityMapParameters
. - DensityMaps.DensityMapParameters - Class in qupath.lib.analysis.heatmaps
-
Class for storing parameters to build a
ImageServer
representing a density map. - DensityMaps.DensityMapType - Enum Class in qupath.lib.analysis.heatmaps
-
Density map types.
- DensityMapUI - Class in qupath.process.gui.commands.density
-
UI elements associated with density maps.
- DensityMapUI() - Constructor for class qupath.process.gui.commands.density.DensityMapUI
- deregister() - Method in class qupath.process.gui.commands.density.DensityMapDialog
-
Deregister listeners.
- deregisterTool(QuPathViewer) - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Deregister the tool from the viewer.
- describe(Class<?>) - Static method in class qupath.lib.scripting.QP
-
List the fields and methods of a specified class.
- describe(Object) - Static method in class qupath.lib.scripting.QP
-
List the fields and methods of a specified object.
- description(String) - Method in class qupath.lib.gui.panes.PreferencePane.PropertyItem
-
Support fluent interface to set the description.
- deselect() - Method in interface qupath.lib.gui.scripting.EditableText
-
Deselect any currently-selected text.
- deselect() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
- deselect() - Method in class qupath.lib.gui.scripting.TextAreaControl
- deselectAll() - Static method in class qupath.lib.scripting.QP
-
Clear the selection for the current hierarchy, so that no objects of any kind are selected.
- deselectAll(PathObjectHierarchy) - Static method in class qupath.lib.scripting.QP
-
Clear the selection, so that no objects of any kind are selected.
- deselectObject(PathObject) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
-
Ensure that the specified object is removed from the selection.
- deselectObjects(Collection<? extends PathObject>) - Method in class qupath.lib.objects.hierarchy.events.PathObjectSelectionModel
-
Ensure the specified objects are deselected.
- detect(DetectionModel, Mat, RegionRequest, IntFunction<PathClass>, Function<ROI, PathObject>) - Static method in class qupath.opencv.dnn.DnnTools
-
Apply a detection model to generate rectangles surrounding distinct structures.
- detect(DetectionModel, ImageServer<BufferedImage>, RegionRequest, IntFunction<PathClass>, Function<ROI, PathObject>) - Static method in class qupath.opencv.dnn.DnnTools
-
Apply a detection model to generate rectangles surrounding distinct structures.
- DetectCytokeratinCV - Class in qupath.opencv
-
Simple command to detect tumor regions stained with cytokeratin.
- DetectCytokeratinCV() - Constructor for class qupath.opencv.DetectCytokeratinCV
- detection() - Method in class qupath.opencv.dnn.OpenCVDnn.Builder
-
Set the model type to be
OpenCVDnn.ModelType.DETECTION
. - DETECTION - Enum constant in enum class qupath.opencv.dnn.OpenCVDnn.ModelType
-
Refers to
DetectionModel
. - detectionCentroidDistances() - Static method in class qupath.lib.scripting.QP
-
Deprecated.retained only for compatibility of v0.2.0 milestone releases; use instead #detectionCentroidDistances(boolean)
- detectionCentroidDistances(boolean) - Static method in class qupath.lib.scripting.QP
-
Compute the distance for all detection object centroids to the closest detection with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
- detectionCentroidDistances(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
- detectionCentroidDistances(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
-
Compute the distance for all detection object centroids to the closest detection with each valid, not-ignored classification and add the result to the detection measurement list.
- detectionCentroidDistances2D(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
-
Compute the distance between the centroids of all detections, for all available classifications.
- detectionDisplayModeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Property representing the current
OverlayOptions.DetectionDisplayMode
. - DetectionPluginTools - Class in qupath.lib.plugins
-
Helper methods to convert ObjectDetectors into runnable tasks, which take care of resolving overlaps when using ParallelTileObjects after the detection is complete and firing notification events in a PathObjectHierarchy.
- DetectionPluginTools() - Constructor for class qupath.lib.plugins.DetectionPluginTools
- detections() - Method in class qupath.lib.classifiers.object.ObjectClassifiers.ClassifyByMeasurementBuilder
-
Set the filter to accept all detection objects only.
- DETECTIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- DETECTIONS - Enum constant in enum class qupath.lib.objects.PathObjectFilter
-
Accept detection objects (no subtypes, e.g.
- DETECTIONS_ALL - Enum constant in enum class qupath.lib.objects.PathObjectFilter
-
Accept detection objects (all subtypes)
- DETECTIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
- detectionsToCells(Collection<? extends PathObject>, double, double) - Static method in class qupath.lib.objects.CellTools
-
Create cell objects by expanding the (nucleus) ROIs from existing detections to approximate the full cell boundary.
- detectionStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Preferred stroke thickness to use when drawing detections ROIs.
- detectionToAnnotationDistances() - Static method in class qupath.lib.scripting.QP
-
Deprecated.retained only for compatibility of v0.2.0 milestone releases; use instead #detectionToAnnotationDistances(boolean)
- detectionToAnnotationDistances(boolean) - Static method in class qupath.lib.scripting.QP
-
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
- detectionToAnnotationDistances(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
- detectionToAnnotationDistances(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
-
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
- detectionToAnnotationDistances(ImageData<?>, boolean, boolean) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
- detectionToAnnotationDistancesSigned(boolean) - Static method in class qupath.lib.scripting.QP
-
Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list for the current ImageData.
- detectionToAnnotationDistancesSigned(ImageData<?>, boolean) - Static method in class qupath.lib.analysis.DistanceTools
-
Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
- detectionToAnnotationDistancesSigned(ImageData<?>, boolean) - Static method in class qupath.lib.scripting.QP
-
Compute the signed distance for all detection object centroids to the closest annotation with each valid, not-ignored classification and add the result to the detection measurement list.
- detectionTreeDisplayModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Define how detections should be displayed in lists and tree views.
- detectTMACoresFromBinary(ByteProcessor, double, int, int, Roi) - Static method in class qupath.imagej.detect.dearray.TMADearrayer
-
Detect TMA cores from a (low-resolution) whole slide image that has been thresholded to give a binary image.
- determinant() - Method in class qupath.lib.color.ColorDeconvMatrix3x3
-
Calculate the determinant of the matrix.
- df - Static variable in class qupath.lib.display.DirectServerChannelInfo
- df - Static variable in class qupath.lib.gui.viewer.recording.ViewTracker
- Dialogs - Class in qupath.lib.gui.dialogs
-
Collection of static methods to help with showing information to a user, as well as requesting some basic input.
- Dialogs() - Constructor for class qupath.lib.gui.dialogs.Dialogs
- Dialogs.Builder - Class in qupath.lib.gui.dialogs
-
Builder class to create a custom
Dialog
. - Dialogs.DialogButton - Enum Class in qupath.lib.gui.dialogs
-
Possible buttons pressed in a yes/no/cancel dialog.
- difference(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
-
Compute the difference between two ROIs.
- DilateAnnotationPlugin<T> - Class in qupath.lib.plugins.objects
-
Plugin to create new annotations by expanding the size of existing annotations.
- DilateAnnotationPlugin() - Constructor for class qupath.lib.plugins.objects.DilateAnnotationPlugin
- DilateAnnotationPlugin.LineCap - Enum Class in qupath.lib.plugins.objects
-
Line cap to use for annotation expansion.
- dim() - Method in interface qupath.lib.geom.Point
-
Number of values used to represent this point.
- dim() - Method in class qupath.lib.geom.Point2
- DirectServerChannelInfo - Class in qupath.lib.display
-
ChannelInfo intended for use with a single or multichannel image (possibly fluorescence) where the pixel's value is used to scale a single color according to a specified display range according to the following rules: If the pixel's value is >= maxDisplay, the pure color is used. If the pixel's value is <= minDisplay, the black is used. Otherwise, a scaled version of the color is used The end result is like having a lookup table (LUT) that stretches from black to the 'pure' color specified, but without actually generating the LUT.
- DirectServerChannelInfo(ImageData<BufferedImage>, int) - Constructor for class qupath.lib.display.DirectServerChannelInfo
-
Constructor.
- disabled(boolean) - Method in class qupath.lib.gui.ActionTools.ActionBuilder
-
Set the disabled property of the action.
- disabled(ObservableValue<Boolean>) - Method in class qupath.lib.gui.ActionTools.ActionBuilder
-
Bind the disabled property of the action to an
ObservableValue
, bidirectionally if possible. - disableUpdatesProperty() - Method in class qupath.lib.gui.panes.AnnotationPane
-
Property that may be used to prevent updates on every hierarchy or selection change event.
- disableUpdatesProperty() - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
-
Property that may be used to prevent updates on every hierarchy or selection change event.
- display(ImageDisplay) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
-
Deprecated.use
RenderedImageServer.Builder.renderer(ImageRenderer)
instead (since anImageDisplay
is also anImageRenderer
. - displayMode() - Method in class qupath.lib.display.ImageDisplay
-
Get the value of
ImageDisplay.useInvertedBackgroundProperty()
- distance(double, double) - Method in class qupath.lib.geom.Point2
-
Calculate the distance between this point and a specified x and y location.
- distance(Point) - Method in class qupath.lib.geom.Point2
- distance(Point) - Method in interface qupath.lib.geom.Point
-
Calculate the distance to another point, with the same
Point.dim()
. - distance(Point2) - Method in class qupath.lib.geom.Point2
-
Calculate the distance between this point and another point.
- distanceSq(double, double) - Method in class qupath.lib.geom.Point2
-
Calculate the squared distance between this point and a specified x and y location.
- distanceSq(Point) - Method in class qupath.lib.geom.Point2
- distanceSq(Point) - Method in interface qupath.lib.geom.Point
-
Calculate the squared distance to another point, with the same
Point.dim()
. - distanceSq(OpenCVTools.IndexedPixel) - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
-
Get the euclidean distance to another pixel, based upon the inds array and assuming unit spacing for all dimensions.
- distanceToAnnotations2D(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands
-
Compute the distance between all detections and the closest annotation, for all annotation classifications.
- DistanceTools - Class in qupath.lib.analysis
-
Static methods for calculating distances between objects.
- DistanceTools() - Constructor for class qupath.lib.analysis.DistanceTools
- div(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
-
Divide array elements by a constant.
- div(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
-
Per-element division of two arrays.
- divide(double...) - Static method in class qupath.opencv.ops.ImageOps.Core
-
Divide all pixels by a constant.
- dnn(DnnModel<?>, int, int, Padding, String...) - Static method in class qupath.opencv.ops.ImageOps.ML
-
Apply a
DnnModel
to pixels to generate a prediction. - DnnModel<T> - Interface in qupath.opencv.dnn
-
Wrapper for a deep learning model in a pipeline using OpenCV.
- DnnModelBuilder<T> - Interface in qupath.opencv.dnn
-
Builder to create a
DnnModel
fromDnnModelParams
. - 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 aBufferedImage
if necessary, or return the original image unchanged if it is already aBufferedImage
. - 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 anImageRegion
. - 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 specifiedPathClass
es. - 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.MultiscaleFeature
s 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
PathObject
s before export (objects returningtrue
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 aPathObjectPredicates.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 SuiteGeometry
objects. - GeometryTools() - Constructor for class qupath.lib.roi.GeometryTools
- GeometryTools.GeometryConverter - Class in qupath.lib.roi
- GeometryTools.GeometryConverter.Builder - Class in qupath.lib.roi
-
Builder to help define how ROIs and Geometry objects should be converted.
- geometryToROI(Geometry, ImagePlane) - Static method in class qupath.lib.roi.GeometryTools
-
Convert a JTS Geometry to a QuPath ROI.
- geometryToShape(Geometry) - Static method in class qupath.lib.roi.GeometryTools
-
Convert a JTS Geometry to a java.awt.Shape.
- geq(Mat, double) - Static method in class qupath.opencv.tools.GroovyCV
-
Apply a greater than or equal to threshold.
- geq(Mat, Mat) - Static method in class qupath.opencv.tools.GroovyCV
-
Apply a greater than or equal to threshold between two arrays.
- get(int) - Method in interface qupath.lib.geom.Point
-
Get the value of the ordinate for the specified dimension.
- get(int) - Method in class qupath.lib.geom.Point2
- get(int) - Method in class qupath.opencv.dnn.DnnShape
-
Get the length of the specified dimension.
- get(String) - Method in interface qupath.lib.measurements.MeasurementList
-
Get value for the measurement with the specified name.
- get(String) - Method in interface qupath.lib.projects.ResourceManager.Manager
-
Retrieve a resource by name.
- get2D(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
-
Get a 2D Gaussian scale.
- get3DAnisotropic(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
-
Get a 3D anisotropic Gaussian scale.
- get3DIsotropic(double) - Static method in class qupath.opencv.tools.LocalNormalization.SmoothingScale
-
Get a 3D isotropic Gaussian scale.
- getAcceleratorText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get a String representation of any accelerator for the command
- getActionProperty(MenuItem) - Static method in class qupath.lib.gui.ActionTools
-
Retrieve an Action stored within the properties of a menu item, or null if no action is found.
- getActionProperty(Node) - Static method in class qupath.lib.gui.ActionTools
-
Retrieve an Action stored within the properties of a node, or null if no action is found.
- getActiveTool() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the active
PathTool
for this viewer. - getActiveToolIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- getAllFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the collection of recorded frames.
- getAllImageSupports(URI, String...) - Static method in class qupath.lib.images.servers.ImageServers
-
Get all
ImageServerBuilder.UriImageSupport
that claim to be able to open the specified URI with optional args. - getAllNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getAllNames() - Method in interface qupath.lib.gui.measure.PathTableData
-
Return an ordered list of all names, including both numeric measurements and
String
values. - getAllNeighbors() - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
-
Get a list of neighbors for all objects.
- getAllObjects() - Static method in class qupath.lib.scripting.QP
-
Get all objects in the current hierarchy, including the root object.
- getAllObjects(boolean) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Get all the objects in the hierarchy, optionally including the root object.
- getAllObjects(boolean) - Static method in class qupath.lib.scripting.QP
-
Get all objects in the current hierarchy.
- getAllPathClassesVisible() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getAllPoints() - Method in class qupath.lib.roi.AreaROI
-
Beware this method! This will return all polygon points (useful e.g.
- getAllPoints() - Method in class qupath.lib.roi.EllipseROI
-
Since ellipses aren't represented internally with simple polygon points, this currently returns only 4 points (rather more diamond-like that would be ideal).
- getAllPoints() - Method in class qupath.lib.roi.GeometryROI
- getAllPoints() - Method in interface qupath.lib.roi.interfaces.ROI
-
Get a list of points representing the vertices of the ROI.
- getAllPoints() - Method in class qupath.lib.roi.LineROI
- getAllPoints() - Method in class qupath.lib.roi.PointsROI
- getAllPoints() - Method in class qupath.lib.roi.PolygonROI
- getAllPoints() - Method in class qupath.lib.roi.PolylineROI
- getAllPoints() - Method in class qupath.lib.roi.RectangleROI
- getAllSelectedObjects() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get all currently-selected objects from the hierarchy.
- getAllThumbnails() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get thumbnails for all z-slices & time points
- getAllTileRequests() - Method in interface qupath.lib.images.servers.TileRequestManager
-
Get
TileRequest
objects for all tiles that this server supports. - getAllTimes() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
-
Retrieve a sorted array containing all times where 'something happened' (observed or censored).
- getAlphaComposite() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
- getAnalysisTabPane() - Method in class qupath.lib.gui.QuPathGUI
-
Access the main tab pane shown in the QuPath window.
- getAncestorList(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
-
Return a list of object ancestors, starting from the root object and ending with PathObject (assuming that the object is part of a hierarchy with a root).
- getAncestorTMACore(PathObject) - Static method in class qupath.lib.objects.PathObjectTools
-
Get the TMA core object that contains a specified PathObject, or null if the object is not contained within a TMA core.
- getAnnotatedActions(Object) - Static method in class qupath.lib.gui.ActionTools
-
Actions can be parsed from the accessible (usually public) fields of any object, as well as methods annotated with
ActionTools.ActionMethod
. - getAnnotationObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Get all annotation objects in the hierarchy.
- getAnnotationObjects() - Static method in class qupath.lib.scripting.QP
-
Get a list of the current annotation objects.
- getArea() - Method in class qupath.lib.roi.RectangleROI
- getArea() - Method in class qupath.lib.roi.AreaROI
- getArea() - Method in class qupath.lib.roi.GeometryROI
- getArea() - Method in interface qupath.lib.roi.interfaces.ROI
-
Get the area of this ROI.
- getArea() - Method in class qupath.lib.roi.LineROI
- getArea() - Method in class qupath.lib.roi.PointsROI
- getArea() - Method in class qupath.lib.roi.PolygonROI
- getArea() - Method in class qupath.lib.roi.PolylineROI
- getArea(ROI) - Static method in class qupath.lib.roi.RoiTools
-
Get an
Area
object representing a ROI. - getARGB(Color) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a packed int (ARGB) representation of a Color object.
- getArgs() - Method in class qupath.lib.images.servers.ImageServerBuilder.DefaultImageServerBuilder
-
Get the args array.
- getArgs() - Method in class qupath.lib.scripting.ScriptParameters
-
Get an optional array of string arguments passed to the script.
- getArray() - Method in class qupath.lib.color.StainVector
-
Get the stain vector as a 3 element array (red, green, blue).
- getArray(boolean) - Method in class qupath.imagej.tools.PixelImageIJ
- getArray(boolean) - Method in interface qupath.lib.analysis.images.SimpleModifiableImage
-
Request the pixel array representing all the pixels in this image, returned row-wise.
- getAssociatedImage(String) - Method in class qupath.lib.images.servers.AbstractImageServer
- getAssociatedImage(String) - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
- getAssociatedImage(String) - Method in interface qupath.lib.images.servers.ImageServer
-
Get the image for a given associated image name.
- getAssociatedImage(String) - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
- getAssociatedImageList() - Method in class qupath.lib.images.servers.AbstractImageServer
- getAssociatedImageList() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
- getAssociatedImageList() - Method in interface qupath.lib.images.servers.ImageServer
-
Get a list of 'associated images', e.g.
- getAssociatedImageList() - Method in class qupath.lib.images.servers.openslide.OpenslideImageServer
- getAtRisk(double) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
-
Get the number at risk at a specified time.
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.CssLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.JsonLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.MarkdownLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.PlainLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.XmlLanguage
- getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.YamlLanguage
- getAutoCompletor() - Method in class qupath.lib.scripting.languages.ScriptLanguage
-
Get the
ScriptAutoCompletor
object that takes care of this language's auto-completion. - getAvailableFeatures(Collection<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
-
Get a set containing the names of all measurements found in the measurement lists of a specified object collection.
- getAvailableLanguages() - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Get the available script languages.
- getAvailablePathClasses() - Method in class qupath.lib.gui.QuPathGUI
-
Create a default list model for storing available PathClasses.
- getAvailableSyntaxes() - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
-
Get the available script syntaxes.
- getAvailableTools() - Method in class qupath.lib.gui.QuPathGUI
-
Get a list of the current available tools.
- getAveragedPixelSize() - Method in class qupath.lib.images.servers.ImageServerMetadata
-
Get the averaged pixel size in microns, if available - or Double.NaN otherwise.
- getAveragedPixelSize() - Method in class qupath.lib.images.servers.PixelCalibration
-
Get an average of
PixelCalibration.getPixelWidth()
andPixelCalibration.getPixelHeight()
. - getAveragedPixelSizeMicrons() - Method in class qupath.lib.images.servers.PixelCalibration
-
Get the average of the pixel width and height in microns if possible, or Double.NaN if the pixel size is not available.
- getBackingListEntries() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
-
Access the underlying entries, for which getEntries provides a filtered view.
- getBaseClass() - Method in class qupath.lib.objects.classes.PathClass
-
Get the 'base' class, i.e.
- getBaseDirectory(Project<?>) - Static method in class qupath.lib.projects.Projects
-
Get the base directory of a project stored on the local file system.
- getBasePathClass(PathObject) - Static method in class qupath.lib.scripting.QP
-
Get a base class - which is either a valid PathClass which is *not* an intensity class, or else null.
- getBaseStyle() - Method in class qupath.lib.gui.scripting.richtextfx.stylers.MarkdownStyler
-
Returns
"-fx-font-family: sans-serif"
to indicate the text should not be formatted as code by default. - getBaseStyle() - Method in interface qupath.lib.gui.scripting.richtextfx.stylers.ScriptStyler
-
Optionally return a base style for the code area.
- getBatchIndex() - Method in class qupath.lib.scripting.ScriptParameters
-
Get the index of the current image for batch processing, where 0 is the first and
getBatchSize() - 1
is the last. - getBatchSaveResult() - Method in class qupath.lib.scripting.ScriptParameters
-
Get whether changes to the image data should be saved.
- getBatchSize() - Method in class qupath.lib.scripting.ScriptParameters
-
Get the number of images being batch processed, or 1 if just a single image is being processed.
- getBinIndexForValue(double, double) - Method in class qupath.lib.analysis.stats.Histogram
-
Get the index of the bin that should contain the specified value.
- getBinLeftEdge(int) - Method in class qupath.lib.analysis.stats.Histogram
-
Get the lower edge for a specified bin.
- getBinRightEdge(int) - Method in class qupath.lib.analysis.stats.Histogram
-
Get the upper edge for a specified bin.
- getBinWidth(int) - Method in class qupath.lib.analysis.stats.Histogram
-
Get the width of a bin, which is the difference between its upper and lower edges.
- getBitsPerPixel() - Method in enum class qupath.lib.images.servers.PixelType
-
Number of bits per pixel.
- getBlobFunction() - Method in interface qupath.opencv.dnn.DnnModel
-
Get the function that can convert one or more OpenCV Mats into a blob supported by the prediction function for the first (or only) input.
- getBlobFunction() - Method in class qupath.opencv.dnn.OpenCVDnn
- getBlobFunction(String) - Method in interface qupath.opencv.dnn.DnnModel
-
Get the function that can convert one or more OpenCV Mats into a blob supported by the prediction function for a specified input layer.
- getBlobFunction(String) - Method in class qupath.opencv.dnn.OpenCVDnn
- getBlue() - Method in class qupath.lib.color.StainVector
-
Get the blue component of the (normalized) stain vector.
- getBlueOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
-
Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
- getBooleanParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Get a boolean parameter value (or its default) for the specified key.
- getBorderColor() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the border color set for this viewer.
- getBoundaryClass(PathClass) - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
-
Get the classification to be used for the annotation boundary, given the classification of the annotated region.
- getBoundaryDistance(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
-
Get the Euclidean distance between the boundaries of two ROIs.
- getBoundaryDistance(ROI, ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
-
Get the calibrated Euclidean distance between the boundaries of two ROIs using specified pixel sizes.
- getBoundaryLabels() - Method in class qupath.lib.images.servers.LabeledImageServer
-
Get an unmodifiable map of classifications and their corresponding boundary labels, if available.
- getBoundaryStrategy() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining
-
Get the strategy for handling the boundaries of area annotations.
- getBoundaryThickness() - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
-
Get the boundary thickness, in pixels.
- getBounds(ImageRegion) - Static method in class qupath.lib.awt.common.AwtTools
-
Create a
Rectangle
corresponding to the x,y,width,height of anImageRegion
. - 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 anImageRegion
. - getBounds(ROI) - Static method in class qupath.lib.awt.common.AwtTools
- getBounds2D(ROI) - Static method in class qupath.lib.awt.common.AwtTools
-
Create a
Rectangle2D
corresponding to bounding box of aROI
. - 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 aROI
. - getBoundsHeight() - Method in class qupath.lib.roi.RectangleROI
- getBoundsHeight() - Method in class qupath.lib.roi.AreaROI
- getBoundsHeight() - Method in class qupath.lib.roi.GeometryROI
- getBoundsHeight() - Method in interface qupath.lib.roi.interfaces.ROI
-
Returns the height of the ROI bounding box.
- getBoundsHeight() - Method in class qupath.lib.roi.LineROI
- getBoundsHeight() - Method in class qupath.lib.roi.PointsROI
- getBoundsHeight() - Method in class qupath.lib.roi.PolygonROI
- getBoundsHeight() - Method in class qupath.lib.roi.PolylineROI
- getBoundsWidth() - Method in class qupath.lib.roi.RectangleROI
- getBoundsWidth() - Method in class qupath.lib.roi.AreaROI
- getBoundsWidth() - Method in class qupath.lib.roi.GeometryROI
- getBoundsWidth() - Method in interface qupath.lib.roi.interfaces.ROI
-
Returns the width of the ROI bounding box.
- getBoundsWidth() - Method in class qupath.lib.roi.LineROI
- getBoundsWidth() - Method in class qupath.lib.roi.PointsROI
- getBoundsWidth() - Method in class qupath.lib.roi.PolygonROI
- getBoundsWidth() - Method in class qupath.lib.roi.PolylineROI
- getBoundsX() - Method in class qupath.lib.roi.RectangleROI
- getBoundsX() - Method in class qupath.lib.roi.AreaROI
- getBoundsX() - Method in class qupath.lib.roi.GeometryROI
- getBoundsX() - Method in interface qupath.lib.roi.interfaces.ROI
-
Returns the x coordinate for the top left of the ROI bounding box.
- getBoundsX() - Method in class qupath.lib.roi.LineROI
- getBoundsX() - Method in class qupath.lib.roi.PointsROI
- getBoundsX() - Method in class qupath.lib.roi.PolygonROI
- getBoundsX() - Method in class qupath.lib.roi.PolylineROI
- getBoundsY() - Method in class qupath.lib.roi.RectangleROI
- getBoundsY() - Method in class qupath.lib.roi.AreaROI
- getBoundsY() - Method in class qupath.lib.roi.GeometryROI
- getBoundsY() - Method in interface qupath.lib.roi.interfaces.ROI
-
Returns the y coordinate for the top left of the ROI bounding box.
- getBoundsY() - Method in class qupath.lib.roi.LineROI
- getBoundsY() - Method in class qupath.lib.roi.PointsROI
- getBoundsY() - Method in class qupath.lib.roi.PolygonROI
- getBoundsY() - Method in class qupath.lib.roi.PolylineROI
- getBrushDiameter() - Method in class qupath.lib.gui.viewer.tools.BrushTool
- getBrushDiameter() - Method in class qupath.process.gui.WandToolCV
-
Don't actually need the diameter for calculations here, but it's helpful for setting the cursor
- getBuilder() - Method in class qupath.lib.images.servers.AbstractImageServer
- getBuilder() - Method in interface qupath.lib.images.servers.ImageServer
-
Get a ServerBuilder capable of building a server the same as this one.
- getBuilders() - Method in class qupath.lib.images.servers.ImageServerBuilder.UriImageSupport
-
Get a list of ServerBuilders, one for each image that can be read based on the specified URI.
- getBuildString() - Method in class qupath.lib.gui.BuildInfo
-
Get the build String, or null if no build String is available.
- getBuildString() - Static method in class qupath.lib.gui.QuPathGUI
-
Get a String representing the QuPath version & build time.
- getBytesPerPixel() - Method in enum class qupath.lib.images.servers.PixelType
-
Number of bytes per pixel.
- getC() - Method in class qupath.lib.regions.ImagePlane
-
Get the channel index.
- getC() - Method in class qupath.lib.roi.RectangleROI
- getC() - Method in interface qupath.lib.roi.interfaces.ROI
-
Get channel index, or -1 if the ROI relates to all available channels.
- getC() - Method in class qupath.opencv.tools.OpenCVTools.IndexedPixel
-
Get channel index.
- getCache() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCache() - Method in class qupath.lib.images.servers.AbstractImageServer
-
Get the internal cache.
- getCache(Class<T>) - Static method in class qupath.lib.images.servers.ImageServerProvider
-
Get the cache in use for image tiles of a specific type.
- getCachedColor(int, int, int) - Static method in class qupath.lib.color.ColorToolsAwt
-
Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
- getCachedColor(int, int, int) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
- getCachedColor(int, int, int, int) - Static method in class qupath.lib.color.ColorToolsAwt
-
Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
- getCachedColor(int, int, int, int) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color object, possibly from a shared map (used to avoid creating too many objects unnecessarily).
- getCachedColor(Integer) - Static method in class qupath.lib.color.ColorToolsAwt
-
Get cached color.
- getCachedColor(Integer) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get cached color.
- getCachedColor(Integer, boolean) - Static method in class qupath.lib.color.ColorToolsAwt
-
Get cached color, explicitly stating whether alpha should be included or not.
- getCachedColor(Integer, boolean) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get cached color, explicitly stating whether alpha should be included or not.
- getCachedRegion(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCachedStroke(double) - Static method in class qupath.lib.gui.viewer.PathHierarchyPaintingHelper
-
Get a
BasicStroke
with the specified thickness. - getCachedThumbnail(ImageServer<BufferedImage>, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCachedTile(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
- getCachedTile(TileRequest) - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
- getCachedTile(TileRequest) - Method in class qupath.lib.images.servers.AbstractImageServer
-
Get a cached tile, or null if the tile has not been cached.
- getCachedTile(TileRequest) - Method in interface qupath.lib.images.servers.ImageServer
-
Get a cached tile, or null if the tile has not been cached.
- getCachedTilesForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
-
Get a map of all cached tiles pertaining to a specific ImageServer.
- getCaretPosition() - Method in interface qupath.lib.gui.scripting.EditableText
-
Get the current caret position.
- getCaretPosition() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
-
Gets the value of the property caretPosition.
- getCaretPosition() - Method in class qupath.lib.gui.scripting.TextAreaControl
-
Gets the value of the property caretPosition.
- getCaseID() - Method in class qupath.lib.objects.TMACoreObject
-
Get the case ID metadata value.
- getCategory() - Method in class qupath.lib.gui.panes.PreferencePane.PropertyItem
- getCellObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Get all cell objects in the hierarchy.
- getCellObjects() - Static method in class qupath.lib.scripting.QP
-
Get a list of the current cell objects.
- getCenterPixelX() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the x-coordinate of the pixel currently centered in the viewer, in the full size image space.
- getCenterPixelY() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the y-coordinate of the pixel currently centered in the viewer, in the full size image space.
- getCentroidDistance(ROI, ROI) - Static method in class qupath.lib.roi.RoiTools
-
Get the Euclidean distance between the centroids of two ROIs.
- getCentroidDistance(ROI, ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
-
Get the calibrated Euclidean distance between the centroids of two ROIs using specified pixel sizes.
- getCentroidX() - Method in class qupath.lib.roi.RectangleROI
- getCentroidX() - Method in class qupath.lib.roi.AreaROI
-
Get the x coordinate of the ROI centroid;
- getCentroidX() - Method in class qupath.lib.roi.GeometryROI
- getCentroidX() - Method in interface qupath.lib.roi.interfaces.ROI
-
Returns the x coordinate for the ROI centroid.
- getCentroidX() - Method in class qupath.lib.roi.LineROI
- getCentroidX() - Method in class qupath.lib.roi.PointsROI
- getCentroidX() - Method in class qupath.lib.roi.PolygonROI
- getCentroidX() - Method in class qupath.lib.roi.PolylineROI
-
The centroid for a
Polyline
here is represented by the centroid of its bounding box. - getCentroidY() - Method in class qupath.lib.roi.RectangleROI
- getCentroidY() - Method in class qupath.lib.roi.AreaROI
-
Get the y coordinate of the ROI centroid;
- getCentroidY() - Method in class qupath.lib.roi.GeometryROI
- getCentroidY() - Method in interface qupath.lib.roi.interfaces.ROI
-
Returns the y coordinate for the ROI centroid.
- getCentroidY() - Method in class qupath.lib.roi.LineROI
- getCentroidY() - Method in class qupath.lib.roi.PointsROI
- getCentroidY() - Method in class qupath.lib.roi.PolygonROI
- getCentroidY() - Method in class qupath.lib.roi.PolylineROI
-
The centroid for a
Polyline
here is represented by the centroid of its bounding box. - getChangedObjects() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
-
The objects that were affected by whichever changes were made.
- getChannel() - Method in class qupath.lib.analysis.images.ContourTracing.ChannelThreshold
-
Get the channel to threshold.
- getChannel() - Method in class qupath.lib.display.DirectServerChannelInfo
-
Get the channel number.
- getChannel(int) - Method in class qupath.lib.images.servers.AbstractImageServer
- getChannel(int) - Method in interface qupath.lib.images.servers.ImageServer
-
Request information for one channel (0-based index).
- getChannel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata
-
Get the specified channel.
- getChannelIndex(ImageServer<?>, String) - Static method in class qupath.lib.images.servers.ServerTools
-
Get the index of the first channel of a server with a specified channel name.
- getChannelList(String...) - Static method in class qupath.lib.images.servers.ImageChannel
-
Convert an array of channel names into a list of
ImageChannel
using default colors. - getChannels() - Method in class qupath.lib.images.servers.ImageServerMetadata
-
Get an unmodifiable list of all channels.
- getChannels(List<ImageChannel>) - Method in interface qupath.opencv.ops.ImageOp
-
Get appropriate channels to reflect the output of this transform.
- getChannels(ImageData<BufferedImage>) - Method in interface qupath.opencv.ops.ImageDataOp
-
Get appropriate channels to reflect the output of this transform, given the input.
- getChannelType() - Method in class qupath.lib.images.servers.ImageServerMetadata
-
Get the channel type, which can be used to interpret the channels.
- getChart() - Method in class qupath.lib.gui.charts.HistogramPanelFX
-
Get the
AreaChart
depicting the histogram. - getChartDataAsString(XYChart<Number, Number>) - Static method in class qupath.lib.gui.charts.ChartTools
-
Get a string representation of chart data, in such a way that it could be pasted into a spreadsheet.
- getCheckpoints() - Method in class qupath.lib.common.Timeit
-
Get an list of all the checkpoints.
- getChildObjects() - Method in class qupath.lib.objects.PathObject
-
Get a collection of child objects.
- getChildObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject
-
Get a collection containing all child objects.
- getChildObjectsAsArray() - Method in class qupath.lib.objects.PathObject
-
Get a defensive copy of child objects as an array.
- getChoiceParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Get a choice parameter value (or its default) for the specified key.
- getChoices() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
-
Get a list of available choices.
- getChooser(Window) - Static method in class qupath.lib.gui.dialogs.Dialogs
-
Get a
QuPathChooser
instance linked to a specific window. - getCircularity(ROI) - Static method in class qupath.lib.roi.RoiTools
-
Get circularity measurement for Area ROIs, calculated as
4 * PI * (area / perimeter^2)
. - getCircularity(ROI, double, double) - Static method in class qupath.lib.roi.RoiTools
-
Get circularity measurement for area ROIs, with optional pixel calibration, calculated as
4 * PI * (area / perimeter^2)
. - getCircularStructuringElement(int) - Static method in class qupath.opencv.tools.OpenCVTools
-
Deprecated.
OpenCVTools.createDisk(int, boolean)
gives more reliable shapes. - getClassification(ImageServer<BufferedImage>, int, int, int, int) - Static method in class qupath.opencv.ml.pixel.PixelClassifierTools
-
Request the classification for a specific pixel.
- getClassificationLabels() - Method in class qupath.lib.classifiers.pixel.PixelClassifierMetadata
-
Map between integer labels and classifications.
- getClassificationLabels() - Method in class qupath.lib.images.servers.ImageServerMetadata
-
Get map between labels and classification names.
- getClassifications() - Method in class qupath.lib.objects.PathObject
-
Get the components of the
PathClass
as an unmodifiable set. - getClassifier() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
-
Get the PixelClassifier performing the classification.
- getClassifyBoundaryStrategy(PathClass, double) - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy
-
Create a boundary strategy that trains a classifier for a specific PathClass for annotation boundaries.
- getClassProbability() - Method in class qupath.lib.objects.PathObject
-
Request the classification probability, or Double.NaN if no probability is available.
- getClassProbability() - Method in class qupath.lib.objects.PathROIObject
- getClassProbability() - Method in class qupath.lib.objects.PathRootObject
- getClipboardText(boolean) - Static method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getClusters(BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
-
Get clusters of connected objects, where connections are made between neighboring objects that meet the specified predicate.
- getColor() - Method in class qupath.lib.color.StainVector
-
Get a Color that (roughly) corresponds to color represented by this stain vector.
- getColor() - Method in interface qupath.lib.display.ChannelDisplayInfo
-
Predominate color used when this ChannelDisplayInfo uses a Color LUT (e.g.
- getColor() - Method in class qupath.lib.display.DirectServerChannelInfo
- getColor() - Method in class qupath.lib.images.servers.ImageChannel
-
Color used to display the output channel
- getColor() - Method in class qupath.lib.objects.classes.PathClass
-
Get the color that should be used to display objects with this classification.
- getColor() - Method in class qupath.lib.objects.PathObject
-
Return any stored color as a packed RGB value.
- getColor(double, double, double) - Method in interface qupath.lib.color.ColorMaps.ColorMap
-
Get a packed ARGB representation of the (interpolated) color at the specified value,.
- getColorDeconvolutionStains() - Method in class qupath.lib.images.ImageData
-
Get the stains defined for this image, or null if this is not a brightfield image suitable for color deconvolution.
- getColorDeconvolutionStainsAsString(ColorDeconvolutionStains, int) - Static method in class qupath.lib.color.ColorDeconvolutionStains
-
Get a String representation of the stains and background.
- getColorForObject(PathObject) - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the display color for a specified object, according to the settings of this mapper.
- getColorMap() - Method in class qupath.lib.gui.ColorMapCanvas
-
Return the currently displayed
ColorMaps.ColorMap
. - getColorMapper() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the color mapper, which is effectively a lookup table.
- getColorMaps() - Static method in class qupath.lib.color.ColorMaps
-
Get an unmodifiable map representing all the currently-available colormaps.
- getColorModel() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
-
Get the
ColorModel
for this renderer (may be null). - getColorModel() - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
- getColorModel() - Method in class qupath.lib.images.servers.ChannelTransformFeatureServer
- getColorModel(ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
- getColorRGB() - Method in class qupath.lib.objects.PathObject
-
Deprecated.since v0.4.0, use
PathObject.getColor()
instead. - getColorRGB(int...) - Static method in class qupath.lib.scripting.QP
-
Deprecated.Use instead
QP.makeRGB(int, int, int)
orQP.makeARGB(int, int, int, int)
- getColors(ColorMaps.ColorMap, int, boolean) - Static method in class qupath.lib.color.ColorMaps
-
Get an array of packed RGB values for a specific colormap.
- getColorWithOpacity(Color, double) - Static method in class qupath.lib.color.ColorToolsAwt
-
Get a color with a specified opacity, setting the alpha channel accordingly.
- getColorWithOpacity(Integer, double) - Static method in class qupath.lib.color.ColorToolsAwt
-
Get a color with a specified opacity, based on the packed RGB values in an Integer.
- getColorWithOpacity(Color, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Derived a Color from an existing one, setting the alpha component to match the desired opacity.
- getColorWithOpacityFX(Integer, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color from a packed RGB value, setting the alpha component to match the desired opacity.
- getCommandPath() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
-
Get a string representation of the menu path for this command, including the menu path and the text.
- getComparator() - Static method in class qupath.lib.scripting.languages.AutoCompletions
-
Get a comparator to order completions.
- getCompatibleObjects(ImageData<T>) - Method in class qupath.lib.classifiers.object.AbstractObjectClassifier
- getCompatibleObjects(ImageData<T>) - Method in interface qupath.lib.classifiers.object.ObjectClassifier
-
Get the objects from an
ImageData
that are compatible with this classifier. - getCompatibleWriters(Class<T>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
-
Get a list of compatible ImageWriters for a specific image class.
- getCompatibleWriters(ImageServer<T>, String) - Static method in class qupath.lib.images.writers.ImageWriterTools
-
Get a list of compatible ImageWriters compatible with a specific server.
- getCompletions(String, int) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
- getCompletions(String, int) - Method in interface qupath.lib.scripting.languages.ScriptAutoCompletor
-
Get a list of possible auto-completions for the given text with the caret at the specified position.
- getCompletionText() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion
-
Get the text that should be inserted for the full completion.
- getConfigPath() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Try to get the path to the config file.
- getConfigUri() - Method in class qupath.opencv.dnn.OpenCVDnn
-
Get the path to the model configuration, if required.
- getConnectedClusters() - Method in class qupath.opencv.features.DelaunayTriangulation
-
Get a list of PathObjects that are connected to each other in this triangulation.
- getConnectedNodes(Collection<PathObject>, Collection<double[]>) - Method in class qupath.opencv.features.DelaunayTriangulation
-
Deprecated.
- getConnectedNodes(PathObject, Collection<PathObject>) - Method in class qupath.opencv.features.DelaunayTriangulation
-
Get all the PathObjects immediately connected to the specified object, adding the points into a collection (or creating a new one).
- getConnectedObjects(PathObject) - Method in class qupath.lib.objects.DefaultPathObjectConnectionGroup
- getConnectedObjects(PathObject) - Method in interface qupath.lib.objects.PathObjectConnectionGroup
-
Get all the connections to a specified PathObject stored in this group.
- getConnectedObjects(PathObject) - Method in class qupath.opencv.features.DelaunayTriangulation
- getConnectionGroups() - Method in class qupath.lib.objects.PathObjectConnections
-
Get an unmodifiable list containing all connections groups.
- getConnections(PathObject) - Method in class qupath.lib.objects.PathObjectConnections
-
Get all the connections to a specified PathObject.
- getContents(Parent, Collection<Node>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
-
Get the nodes that are included within a
Parent
, optionally adding other nodes recursively. - getContentsOfType(Parent, Class<T>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
-
Get the nodes of type T that are contained within a
Parent
, optionally adding other nodes recursively. - getContextMenu() - Method in class qupath.lib.gui.scripting.richtextfx.CodeAreaControl
- getContextMenu() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
-
Get the context menu for the control.
- getContextMenu() - Method in class qupath.lib.gui.scripting.TextAreaControl
- getConvexHull() - Method in class qupath.lib.roi.AreaROI
-
Default implementation using JTS.
- getConvexHull() - Method in class qupath.lib.roi.EllipseROI
- getConvexHull() - Method in interface qupath.lib.roi.interfaces.ROI
-
Get a ROI representing the convex hull of this ROI.
- getConvexHull() - Method in class qupath.lib.roi.LineROI
- getConvexHull() - Method in class qupath.lib.roi.PointsROI
- getConvexHull() - Method in class qupath.lib.roi.RectangleROI
- getConvexHull(List<Point2>) - Static method in class qupath.lib.roi.ConvexHull
-
TODO: Consider a more efficient convex hull calculation.
- getCoreClasses() - Static method in class qupath.lib.gui.scripting.QPEx
-
Get a list of core classes that are likely to be useful for scripting.
- getCoreClasses() - Static method in class qupath.lib.scripting.QP
-
Get a list of core classes that are likely to be useful for scripting.
- getCountsForBin(int) - Method in class qupath.lib.analysis.stats.Histogram
-
Get the histogram counts for the specified bin.
- getCountSum() - Method in class qupath.lib.analysis.stats.Histogram
-
Sum of all histogram counts.
- getCreationTimestamp() - Method in interface qupath.lib.projects.Project
-
Request a timestamp from when the project was created.
- getCropRegion() - Method in class qupath.lib.images.servers.CroppedImageServer
-
Get the region being cropped, in terms of the bounding box within the base ImageServer.
- getCssStylesPath() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get the path to where user directory for storing CSS styles.
- getCurrentConsoleControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getCurrentDataFileVersion() - Static method in class qupath.lib.io.PathIO
-
Get the current preferred data file version.
- getCurrentEditorControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
- getCurrentHierarchy() - Static method in class qupath.lib.scripting.QP
-
Get the
PathObjectHierarchy
of the currentImageData
. - 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 currentImageData
. - getCurrentServerPath() - Static method in class qupath.lib.scripting.QP
-
Get the path to the
ImageServer
of the currentImageData
. - 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()
orQuPathViewer.zoomOut()
. - getDensityType() - Method in class qupath.lib.analysis.heatmaps.DensityMaps.DensityMapParameters
-
Get the normalization type of the density map.
- getDerivedBoundaryStrategy(double) - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy
-
Create a boundary strategy that trains a classifier for a PathClass derived from the original classification for annotation boundaries.
- getDerivedPathClass(PathClass, String) - Static method in class qupath.lib.scripting.QP
-
Get a PathClass with the specified name, derived from another PathClass.
- getDerivedPathClass(PathClass, String, Integer) - Static method in class qupath.lib.objects.classes.PathClassFactory
-
Deprecated.since v0.4.0, use
PathClass.getInstance(PathClass, String, Integer)
- getDerivedPathClass(PathClass, String, Integer) - Static method in class qupath.lib.scripting.QP
-
Get a PathClass with the specified name, derived from another PathClass.
- getDescendantObjects(Collection<PathObject>) - Method in class qupath.lib.objects.PathObject
-
Get a collection containing all descendant objects.
- getDescendantObjects(PathObject, Collection<PathObject>, Class<? extends PathObject>) - Static method in class qupath.lib.objects.PathObjectTools
-
Get all descendant objects with a specified type.
- getDescription() - Method in class qupath.imagej.detect.cells.SubcellularDetection
- getDescription() - Method in class qupath.imagej.detect.cells.WatershedCellDetection
- getDescription() - Method in class qupath.imagej.detect.cells.WatershedCellMembraneDetection
- getDescription() - Method in class qupath.imagej.detect.dearray.TMADearrayerPluginIJ
- getDescription() - Method in class qupath.imagej.detect.tissue.PositivePixelCounterIJ
- getDescription() - Method in class qupath.imagej.detect.tissue.SimpleTissueDetection2
- getDescription() - Method in class qupath.imagej.gui.IJExtension
- getDescription() - Method in class qupath.imagej.gui.ImageJMacroRunner
- getDescription() - Method in class qupath.imagej.images.servers.ImageJServerBuilder
- getDescription() - Method in class qupath.imagej.superpixels.DoGSuperpixelsPlugin
- getDescription() - Method in class qupath.imagej.superpixels.SLICSuperpixelsPlugin
- getDescription() - Method in class qupath.lib.algorithms.CoherenceFeaturePlugin
- getDescription() - Method in class qupath.lib.algorithms.HaralickFeaturesPlugin
- getDescription() - Method in class qupath.lib.algorithms.IntensityFeaturesPlugin
- getDescription() - Method in class qupath.lib.algorithms.LocalBinaryPatternsPlugin
- getDescription() - Method in class qupath.lib.algorithms.TilerPlugin
- getDescription() - Method in class qupath.lib.extension.svg.SvgExtension
- getDescription() - Method in interface qupath.lib.gui.extensions.QuPathExtension
-
A short description of the extension for displaying in the main GUI.
- getDescription() - Method in class qupath.lib.gui.panes.PreferencePane.PropertyItem
- getDescription() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
-
Get a user-friendly description of the style.
- getDescription() - Method in class qupath.lib.gui.scripting.richtextfx.RichScriptEditorExtension
- getDescription() - Method in class qupath.lib.images.servers.bioformats.BioFormatsOptionsExtension
- getDescription() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerBuilder
- getDescription() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
-
Get the image description, as stored in a TIFF, or null if no description is available.
- getDescription() - Method in interface qupath.lib.images.servers.ImageServerBuilder
-
Get a short, human-readable description for display in a GUI.
- getDescription() - Method in class qupath.lib.images.servers.JsonImageServerBuilder
- getDescription() - Method in class qupath.lib.images.servers.openslide.OpenslideServerBuilder
- getDescription() - Method in class qupath.lib.objects.PathAnnotationObject
-
Get a free text description previously set for this annotation.
- getDescription() - Method in class qupath.lib.plugins.objects.DilateAnnotationPlugin
- getDescription() - Method in class qupath.lib.plugins.objects.FillAnnotationHolesPlugin
- getDescription() - Method in class qupath.lib.plugins.objects.FindConvexHullDetectionsPlugin
- getDescription() - Method in class qupath.lib.plugins.objects.RefineAnnotationsPlugin
- getDescription() - Method in class qupath.lib.plugins.objects.ShapeFeaturesPlugin
- getDescription() - Method in class qupath.lib.plugins.objects.SmoothFeaturesPlugin
- getDescription() - Method in class qupath.lib.plugins.objects.SplitAnnotationsPlugin
- getDescription() - Method in class qupath.lib.plugins.objects.TileClassificationsToAnnotationsPlugin
- getDescription() - Method in interface qupath.lib.plugins.PathPlugin
-
Get a brief description of the plugin's purpose & operation.
- getDescription() - Method in interface qupath.lib.projects.ProjectImageEntry
-
Get a description; this is free text describing the image.
- getDescription() - Method in class qupath.opencv.CellCountsCV
- getDescription() - Method in class qupath.opencv.DetectCytokeratinCV
- getDescription() - Method in class qupath.opencv.features.DelaunayClusteringPlugin
- getDescription() - Method in class qupath.opencv.WatershedNucleiCV
- getDescription() - Method in class qupath.process.gui.ProcessingExtension
- getDetails() - Method in class qupath.imagej.images.writers.TiffWriterIJ
- getDetails() - Method in class qupath.imagej.images.writers.ZipWriterIJ
- getDetails() - Method in interface qupath.lib.images.writers.ImageWriter
-
Get further details of the writer, which may be displayed to a user.
- getDetails() - Method in class qupath.lib.images.writers.JpegWriter
- getDetails() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
- getDetails() - Method in class qupath.lib.images.writers.PngWriter
- getDetectionDisplayMode() - Method in class qupath.lib.gui.viewer.OverlayOptions
-
Get the current
OverlayOptions.DetectionDisplayMode
. - getDetectionObjects() - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Get all detection objects in the hierarchy (including sub-classes of detections).
- getDetectionObjects() - Static method in class qupath.lib.scripting.QP
-
Get a list of the current detection objects.
- getDeterminant() - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian
-
Get the determinant for each pixel.
- getDeterminant() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
- getDeterminant() - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
- getDisplayableImageName(ImageServer<?>) - Static method in class qupath.lib.images.servers.ServerTools
-
Get an ImageServer name suitable for displaying.
- getDisplayedClipShape(Shape) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Transform a clip shape into image coordinates for this viewer.
- getDisplayedColor(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get a Color appropriate for displaying an object.
- getDisplayedColorARGB(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX
-
Get the color with which an object should be displayed, as a packaged ARGB integer.
- getDisplayedName() - Method in class qupath.lib.objects.PathObject
-
Request an object name in a form suitable for displaying.
- getDisplayedRegionShape() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a shape corresponding to the region of the image currently visible in this viewer.
- getDisplayMaxValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the measurement value that maps to the last color in the color mapper.
- getDisplayMinValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Get the measurement value that maps to the first color in the color mapper.
- getDisplayText() - Method in interface qupath.lib.scripting.languages.AutoCompletions.Completion
-
Get the text that should be displayed for this completion.
- getDouble(int) - Method in interface qupath.lib.analysis.stats.ArrayWrappers.ArrayWrapper
-
Extract one entry from the array, converting to double as necessary.
- getDoubleParameterValue(String) - Method in class qupath.lib.plugins.parameters.ParameterList
-
Get a double parameter value (or its default) for the specified key.
- getDoubleValues(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
- getDoubleValues(String) - Method in interface qupath.lib.gui.measure.PathTableData
-
Get all double values for all items.
- getDownsample() - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
-
Get the downsample used within the mini viewers.
- getDownsample() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
-
Get the downsample factor for this level.
- getDownsample() - Method in class qupath.lib.images.servers.TileRequest
-
Get the downsample value for this tile.
- getDownsample() - Method in class qupath.lib.regions.RegionRequest
-
Get the requested downsample factor, defining the resolution at which pixels should be returned.
- getDownsampleFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the current downsample factor.
- getDownsampleFactor() - Method in interface qupath.lib.images.PathImage
-
Get the downsample factor originally used when obtaining the image from an ImageServer; will be 1 if the image is full-resolution.
- getDownsampleFactor(ImageServer<?>, double) - Static method in class qupath.lib.images.servers.ServerTools
-
Calculate a downsample factor for a server given a preferred pixel size.
- getDownsampleForLevel(int) - Method in class qupath.lib.images.servers.ImageServerMetadata
-
Get the downsample factor for a specific resolution level.
- getDownsampleForResolution(int) - Method in class qupath.lib.images.servers.AbstractImageServer
- getDownsampleForResolution(int) - Method in interface qupath.lib.images.servers.ImageServer
-
Get the downsample factor for a specified resolution level, where level 0 is the full resolution image and nResolutions() - 1 is the lowest resolution available.
- getDummyColorModel(int) - Static method in class qupath.lib.color.ColorModelFactory
-
Get a dummy ColorModel instance.
- getEdgeMax() - Method in class qupath.lib.analysis.stats.Histogram
-
Get the maximum edge of the histogram.
- getEdgeMin() - Method in class qupath.lib.analysis.stats.Histogram
-
Get the minimum edge of the histogram.
- getEdgeRange() - Method in class qupath.lib.analysis.stats.Histogram
-
Get the histogram edge range, defined as the maximum edge - the minimum edge.
- getEigenvalues(boolean) - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian
-
Get the eigenvalues, ranked from highest to lowest.
- getEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
- getEigenvalues(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
- getEigenvectors(boolean) - Method in interface qupath.opencv.tools.MultiscaleFeatures.Hessian
-
Get the eigenvectors, returned in the same order as the eigenvalues.
- getEigenvectors(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian2D
- getEigenvectors(boolean) - Method in class qupath.opencv.tools.MultiscaleFeatures.Hessian3D
- getEmptyTile(int, int) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
- getEmptyTile(int, int, boolean) - Method in class qupath.lib.images.servers.AbstractTileableImageServer
-
Create an empty tile for this server, using the default color model.
- getEngineByName(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
-
Get the
ScriptEngine
based on its name. - getEntry(ImageData<T>) - Method in interface qupath.lib.projects.Project
-
Request a
ProjectImageEntry
associated with anImageData
- getEntryPath() - Method in interface qupath.lib.projects.ProjectImageEntry
-
Get a path to the data for this image entry, or null if this entry is not stored on the local file system.
- getErrorWriter() - Method in class qupath.lib.scripting.ScriptParameters
-
Get the error writer for script output.
- getEvents() - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
-
Get an unmodifiable list of all events.
- getEventsAtTime(double) - Method in class qupath.lib.analysis.stats.survival.KaplanMeierData
-
Get the number of events at a specified time (exactly).
- getEventType() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
-
Get the hierarchy event type.
- getExcludeColumns() - Method in class qupath.lib.gui.tools.MeasurementExporter
-
Returns the list of columns to exclude from export.
- getExcludeOutsideRange() - Method in class qupath.lib.gui.tools.MeasurementMapper
-
Returns true if objects with values outside the specified min/max range have the min/max colors returned, false if null should be returned instead.
- getExtension(File) - Static method in class qupath.lib.common.GeneralTools
-
Get filename extension.
- getExtension(String) - Static method in class qupath.lib.common.GeneralTools
-
Get extension from a filename.
- getExtensionClassLoader() - Static method in class qupath.lib.gui.QuPathGUI
-
Get the
ClassLoader
used to load extensions. - getExtensionDirectory() - Static method in class qupath.lib.gui.QuPathGUI
-
Directory containing extensions.
- getExtensions() - Method in class qupath.imagej.images.writers.TiffWriterIJ
- getExtensions() - Method in class qupath.imagej.images.writers.ZipWriterIJ
- getExtensions() - Method in interface qupath.lib.images.writers.ImageWriter
-
Get the file extensions used by the image writer.
- getExtensions() - Method in class qupath.lib.images.writers.JpegWriter
- getExtensions() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
- getExtensions() - Method in class qupath.lib.images.writers.PngWriter
- getExtensions() - Method in class qupath.lib.scripting.languages.ScriptLanguage
-
Get an unmodifiable set containing the possible extensions for this language.
- getExtensionsPath() - Static method in class qupath.lib.gui.prefs.PathPrefs
-
Get the path to where extensions should be stored.
- getEyeFixatedIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- getEyePointIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
- getFeature(int) - Method in class qupath.lib.analysis.features.HaralickFeatures
-
Get the value of the specified feature.
- getFeatureImportance() - Method in class qupath.opencv.ml.OpenCVClassifiers.RTreesClassifier
-
Request the variable importance values from the last trained RTrees classifier, if available.
- getFeatureName(int) - Method in class qupath.lib.analysis.features.HaralickFeatures
-
Get the name of the specified feature.
- getFeatureNames() - Method in interface qupath.opencv.ml.objects.features.FeatureExtractor
- getFeatureOp() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining
-
Get an
ImageDataOp
used for feature calculation. - getFile() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the file associated with this
ViewTracker
. - getFile() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
-
Get the underlying file.
- getFile() - Method in interface qupath.lib.images.servers.FileFormatInfo.ImageCheckType
-
Get a File object representing the local image file - or null if no file could be found.
- getFile() - Method in class qupath.lib.scripting.ScriptParameters
-
Get the file where the script is located.
- getFilesOnly() - Method in class qupath.lib.images.servers.bioformats.BioFormatsServerOptions
-
Returns true if Bio-Formats is restricted to support only local files, not other URLs.
- getFill() - Method in class qupath.lib.gui.charts.HistogramPanelFX.HistogramData
-
Get the histogram fill color.
- getFillAnnotations() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getFillDetections() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getFilledPolygonROIs(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling
-
Get filled PolygonRois for connected pixels with the same value in an image.
- getFilledPolygonROIsExperimental(ImageProcessor) - Static method in class qupath.imagej.processing.RoiLabeling
-
Experimental 8-connected ROI creation; non-zero pixels considered within objects
- getFilledPolygonROIsFromLabels(ImageProcessor, int) - Static method in class qupath.imagej.processing.RoiLabeling
-
Get filled Polygon ROIs using distinct labels, creating a map between labels and ROIs.
- getFilteredNeighbors(BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
-
Get a list of neighbors for all objects, filtering out objects that do not meet specified criteria.
- getFilteredNeighbors(PathObject, BiPredicate<PathObject, PathObject>) - Method in class qupath.lib.analysis.DelaunayTools.Subdivision
-
Get a list of neighbors for a specified object, filtering out objects that do not meet specified criteria.
- getFlattenedMenuItems(boolean, MenuItem...) - Static method in class qupath.lib.gui.tools.MenuTools
-
Get a flattened list of all menu items recursively.
- getFlattenedMenuItems(List<? extends MenuItem>, boolean) - Static method in class qupath.lib.gui.tools.MenuTools
-
Get a flattened list of all menu items recursively.
- getFlattenedObjectList(List<PathObject>) - Method in class qupath.lib.objects.hierarchy.PathObjectHierarchy
-
Get a flattened list containing all PathObjects in the hierarchy (including from the root object).
- getFlattenedObjectList(PathObject, List<PathObject>, boolean) - Static method in class qupath.lib.objects.PathObjectTools
-
Get all descendant objects as a flattened list.
- getFontSize() - Method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
-
Get the font size as a CSS-compatible string.
- getFontSize() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getFormat() - Method in class qupath.lib.images.servers.bioformats.BioFormatsImageServer
-
Get the format String, as returned by Bio-Formats
IFormatReader.getFormat()
. - getFrame(int) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the frame at the specified
index
. - getFrameForTime(long) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the frame visible at the specified
timestamp
(in ms). - getFrameIndexForTime(long) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return the index of the frame visible at the specified
timestamp
(in ms). - getFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
-
Return an unmodifiable list of all the frames stored by this view tracker.
- getFramework() - Method in class qupath.opencv.dnn.DnnModelParams
-
Get the name of the deep learning framework that may be used.
- getFramework() - Method in class qupath.opencv.dnn.OpenCVDnn
-
Get the framework used to create the model.
- getFullLocationString(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a string to summarize the pixel found below the most recent known mouse location, or "" if the mouse is outside this viewer.
- getFullMagnification() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the full magnification for the image.
- getGamma() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the gamma value used for this viewer.
- getGammaOp() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get a
LookupOp
that can perform any requested gamma correction in this viewer. - getGaussianDeriv(double, int, int) - Static method in class qupath.opencv.tools.OpenCVTools
-
Get filter coefficients for a 1D Gaussian (derivative) kernel.
- getGaussianDerivKernel(double, int, boolean) - Static method in class qupath.opencv.tools.OpenCVTools
-
Get filter coefficients for a 1D Gaussian (derivative) kernel.
- getGeoJsonDataFormat() - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
-
Get a
DataFormat
suitable for storing GeoJSON data on a clipboard. - getGeometry() - Method in class qupath.lib.roi.RectangleROI
- getGeometry() - Method in class qupath.lib.roi.AreaROI
- getGeometry() - Method in class qupath.lib.roi.GeometryROI
- getGeometry() - Method in interface qupath.lib.roi.interfaces.ROI
-
Returns a org.locationtech.jts.geom.Geometry object.
- getGeometry() - Method in class qupath.lib.roi.PolygonROI
- getGeometryFactory() - Method in class qupath.lib.gui.viewer.tools.BrushTool
- getGreen() - Method in class qupath.lib.color.StainVector
-
Get the green component of the (normalized) stain vector.
- getGreenOpticalDensities(int[], double, float[]) - Static method in class qupath.lib.color.ColorDeconvolutionHelper
-
Convert red channel of packed rgb pixel to optical density values, using a specified maximum value.
- getGridHeight() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
- getGridHeight() - Method in interface qupath.lib.objects.hierarchy.TMAGrid
-
Number of cores along the vertical axis of the grid.
- getGridLines() - Method in class qupath.lib.gui.viewer.OverlayOptions
- getGridWidth() - Method in class qupath.lib.objects.hierarchy.DefaultTMAGrid
- getGridWidth() - Method in interface qupath.lib.objects.hierarchy.TMAGrid
-
Number of cores along the horizontal axis of the grid.
- getHalo() - Method in class qupath.opencv.ml.PatchClassifierParams
-
Get the 'halo' around the output.
- getHandles() - Method in class qupath.lib.roi.RoiEditor
-
Get all the handles for the current ROI being edited, or an empty list if no handles are available.
- getHazardRatio() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
-
Get the calculated hazard ratio.
- getHazardRatioLowerConfidence() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
-
Get the lower bound of the hazard ratio confidence interval.
- getHazardRatioUpperConfidence() - Method in class qupath.lib.analysis.stats.survival.LogRankTest.LogRankResult
-
Get the upper bound of the hazard ratio confidence interval.
- getHeight() - Method in class qupath.imagej.tools.PixelImageIJ
- getHeight() - Method in interface qupath.lib.analysis.images.SimpleImage
-
Get the image height.
- getHeight() - Method in class qupath.lib.geom.ImmutableDimension
-
Get the ImmutableDimension height.
- getHeight() - Method in class qupath.lib.images.servers.AbstractImageServer
- getHeight() - Method in interface qupath.lib.images.servers.ImageServer
-
Height of the full-resolution image in pixels.
- getHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata
-
Get the full-resolution image height.
- getHeight() - Method in class qupath.lib.images.servers.ImageServerMetadata.ImageResolutionLevel
-
Get the image height at this level.
- getHeight() - Method in class qupath.lib.regions.ImageRegion
-
Get the height of the region bounding box.
- getHelpText() - Method in class qupath.lib.plugins.parameters.ChoiceParameter
- getHelpText() - Method in interface qupath.lib.plugins.parameters.Parameter
-
Get a description of the meaning of the Parameter; may be displayed e.g.
- getHessian() - Method in class qupath.opencv.tools.MultiscaleFeatures.MultiscaleResultsBuilder.FeatureMap
-
Get the
MultiscaleFeatures.Hessian
associated with these features. - getHierarchy() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the object hierarchy for the current image data, or null if no image data is available.
- getHierarchy() - Method in class qupath.lib.images.ImageData
-
Get the object hierarchy.
- getHierarchy() - Method in class qupath.lib.objects.hierarchy.events.PathObjectHierarchyEvent
-
The hierarchy to which this event refers.
- getHierarchy(PluginRunner<T>) - Method in class qupath.lib.plugins.AbstractPlugin
-
Get the hierarchy from a PluginRunner, or null if no hierarchy is available.
- getHistogram() - Method in class qupath.lib.gui.charts.HistogramPanelFX.HistogramData
-
Get the histogram.
- getHistogram(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
-
Returns a histogram for a ChannelInfo, or none if no histogram is available (e.g.
- getHistogramData() - Method in class qupath.lib.gui.charts.HistogramPanelFX
-
Get all histogram data objects.
- getHistoryWorkflow() - Method in class qupath.lib.images.ImageData
-
Get a workflow representing a history of the processing steps applied to the ImageData.
- getIcon() - Method in interface qupath.lib.gui.viewer.tools.PathTool
-
Get the icon of the tool.
- getID() - Method in class qupath.lib.objects.PathObject
-
Get the ID for this object.
- getID() - Method in interface qupath.lib.projects.ProjectImageEntry
-
Get a unique ID to represent this entry.
- getID() - Method in class qupath.opencv.dnn.DnnTools.DNNLayer
-
Layer ID.
- getImage() - Method in interface qupath.lib.images.PathImage
-
Get the pixel data (image).
- getImageClass() - Method in class qupath.imagej.images.writers.ZipWriterIJ
- getImageClass() - Method in class qupath.lib.images.servers.AbstractImageServer
- getImageClass() - Method in interface qupath.lib.images.servers.ImageServer
-
Get the class of the image representation returned by this ImageServer.
- getImageClass() - Method in class qupath.lib.images.writers.JpegWriter
- getImageClass() - Method in interface qupath.lib.images.writers.ImageWriter
-
Get the class of supported images.
- getImageClass() - Method in class qupath.lib.images.writers.ome.OMETiffWriter
- getImageData() - Method in class qupath.lib.classifiers.pixel.PixelClassificationImageServer
-
Get the underlying ImageData used for classification.
- getImageData() - Method in class qupath.lib.display.DirectServerChannelInfo
- getImageData() - Method in class qupath.lib.display.ImageDisplay
-
Get the current image data
- getImageData() - Method in class qupath.lib.gui.QuPathGUI
-
Get the value of
QuPathGUI.imageDataProperty()
. - getImageData() - Method in class qupath.lib.gui.viewer.QuPathViewer
-
Get the image data currently being displayed within thie viewer.
- getImageData() - Method in class qupath.lib.plugins.AbstractPluginRunner
- getImageData() - Method in class qupath.lib.plugins.CommandLinePluginRunner
- getImageData() - Method
MeasurementList.put(String, double)
instead