Index

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

A

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
Deprecated.
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.
actionImageJDirectory - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
actionImportROIs - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
actionIntensity - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
 
actionLegacyMacroRunner - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
Deprecated.
actionLoadObjectClassifier - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
 
actionLoadPixelClassifier - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
 
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.
actionPositiveCellDetection - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
actionScriptRunner - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
actionShowImageJ - 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
 
actionTrainingImage - Variable in class qupath.process.gui.ProcessingExtension.OtherCommands
 
addRunnableTasks(ImageData<BufferedImage>, PathObject, List<Runnable>) - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 
addToWorkflow() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Request that the script is stored in the workflow history when it is run for an ImageData.
addToWorkflow(boolean) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally request that the script is stored in the workflow history when it is run for an ImageData.
ANNOTATION - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
 
ANNOTATIONS - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
ANY_CLASS_OR_NONE - Static variable in class qupath.process.gui.commands.density.DensityMapUI
Ignore classification entirely (i.e.
ANY_POSITIVE_CLASS - Static variable in class qupath.process.gui.commands.density.DensityMapUI
Accept any positive classification, including 1+, 2+, 3+.
ANY_SPECIFIED_CLASS - Static variable in class qupath.process.gui.commands.density.DensityMapUI
Any classification, but not no classification.
applyToObjects(ImageJScriptRunner.ApplyToObjects) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify the objects that the script should be applied to.

B

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.
BoundaryStrategy - Class in qupath.process.gui.commands.ml
Helper class for handling the boundaries of training annotations when creating a pixel classifier.
build() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Build a new ImageJScriptRunner with the parameters specified in this builder.
build() - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Build the pane
builder() - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Create a new builder for an instance of ImageJScriptRunner.
builder(ImageJScriptRunner.ImageJScriptParameters) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Create a new builder for an instance of ImageJScriptRunner, initializing using the provided parameters.

C

CELL - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
 
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 - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
channelIndices(int...) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally specify a subset of image channels to pass to ImageJ.
channelNames(String...) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally specify a subset of image channels to pass to ImageJ, based on channel names.
channels(Collection<? extends ColorTransforms.ColorTransform>) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally specify channels to pass to ImageJ.
channels(ColorTransforms.ColorTransform, ColorTransforms.ColorTransform...) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally specify channels to pass to ImageJ.
ClassificationResolution - Class in qupath.process.gui.commands.ml
Wrapper for a PixelCalibration to be used to define classifier resolution.
clearChildObjects() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Request that the child objects are removed from any objects that are passed to the script runner.
clearChildObjects(boolean) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally request that the child objects are removed from any objects that are passed to the script runner.
closeOpenImages(boolean) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Request that any images left open after the macro are closed.
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).
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.
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.
createDetectionOrPointAnnotation(ROI) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Function to create an annotation object from any PointsROI, and detection object from any other ROI.
createInstance(QuPathGUI) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
Create a new instance.
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.
createNewAnnotation(MouseEvent, double, double) - Method in class qupath.process.gui.WandToolEventHandler
 
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.
createObjectsFromROIs(ImagePlus, Collection<? extends Roi>, double, Function<ROI, PathObject>, 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.
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.
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.
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.
createShape(MouseEvent, double, double, boolean, Geometry) - Method in class qupath.process.gui.WandToolEventHandler
 
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
 

D

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.
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.
DETECTION - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
 
DETECTIONS - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
doAddToWorkflow() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Query whether the script should be logged in the history of the ImageData.
doCloseOpenImages() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Request that any lingering open images are closed after the script has run.
doCopy(ActionEvent) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
 
doCut(ActionEvent) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
 
doPaste(ActionEvent) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
 
doRedo(ActionEvent) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
 
doRemoveChildObjects() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Query whether child objects should be removed from the parent object after the script is complete.
doSetOverlay() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Query whether the Overlay should be set when an image is passed to ImageJ.
doSetRoi() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Query whether the Roi should be set when an image is passed to ImageJ.
doUndo(ActionEvent) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
 
downsample(DownsampleCalculator) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify how images should be downsampled when passing them to ImageJ.

E

ensureCursorType(Cursor) - Method in class qupath.process.gui.WandToolEventHandler
 
equals(Object) - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
 
equals(Object) - Method in class qupath.process.gui.commands.ml.ClassificationResolution
 
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.
extractOverlay(PathObjectHierarchy, RegionRequest, OverlayOptions, Predicate<PathObject>) - Static method in class qupath.imagej.gui.IJExtension
Extract an ImageJ overlay for the specified region.
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.

F

file(String) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify the path to a file containing the script or macro.
FIXED_DOWNSAMPLE - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.ResolutionOption
Use a fixed downsample value;
fixedDownsample(double) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Use a fixed downsample value when passing images to ImageJ.
fromJson(String) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Create a script runner from a JSON representation of ImageJScriptRunner.ImageJScriptParameters.
fromMap(Map<String, ?>) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Create a script runner from a map representation of ImageJScriptRunner.ImageJScriptParameters.
fromParams(ImageJScriptRunner.ImageJScriptParameters) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Create a script runner from the specified parameters.

G

getActiveRoiToObjectFunction() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get a function to convert an ImageJ active Roi into a QuPath object.
getApplyToObjects() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get the objects to which this script should be applied.
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.
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.
getBrushDiameter() - Method in class qupath.process.gui.WandToolEventHandler
Don't actually need the diameter for calculations here, but it's helpful for setting the cursor
getChannels() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
 
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.
getCurrentParent() - Method in class qupath.process.gui.WandToolEventHandler
 
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.
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.
getDescription() - Method in class qupath.imagej.gui.IJExtension
 
getDescription() - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 
getDescription() - Method in class qupath.process.gui.ProcessingExtension
 
getDownsample() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get the calculator used to determine how much to downsample image regions that will be send to ImageJ.
getFeatureOp() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining
Get an ImageDataOp used for feature calculation.
getImageJIcon(int, int) - Static method in class qupath.imagej.gui.IJExtension
Try to read the ImageJ icon from its jar.
getImageJInstance() - Static method in class qupath.imagej.gui.IJExtension
Get an instance of ImageJ, or start one, for interactive use (with GUI displayed).
getImageJPath() - Static method in class qupath.imagej.gui.IJExtension
Get the path for a local ImageJ installation, if set.
getLabelMap() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining.ClassifierTrainingData
Get the map of classifications to labels.
getLastResultsDescription() - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 
getName() - Method in class qupath.imagej.gui.IJExtension
 
getName() - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 
getName() - Method in class qupath.process.gui.commands.ml.ClassificationResolution
Get the simple name for this resolution.
getName() - Method in class qupath.process.gui.ProcessingExtension
 
getObjectsToProcess(PathObjectHierarchy, ImageJScriptRunner.ApplyToObjects) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Query which objects in a hierarchy would be used with the specified ImageJScriptRunner.ApplyToObjects value.
getOverlayRoiToObjectFunction() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get a function to convert an ImageJ Roi on an Overlay into a QuPath object.
getPadding() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get the padding to add around the ROI.
getParentObjects(ImageData<BufferedImage>) - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 
getPixelCalibration() - Method in class qupath.process.gui.commands.ml.ClassificationResolution
Get the PixelCalibration used to apply this resolution.
getQuPathVersion() - Method in class qupath.imagej.gui.IJExtension
Returns the version stored within this jar, because it is matched to the QuPath version.
getQuPathVersion() - Method in class qupath.process.gui.ProcessingExtension
Returns the version stored within this jar, because it is matched to the QuPath version.
getResolution() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining
Get the resolution at which the training should occur.
getScriptEngineName() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get the name of the script engine to use, or null if no script engine is specified.
getSkipBoundaryStrategy() - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy
Create a boundary strategy that ignores boundaries, not using them for classifier training.
getStage() - Method in class qupath.process.gui.commands.density.DensityMapDialog
Get the stage.
getSupportedParentObjectClasses() - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 
getTaskRunner() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get a task runner for running script tasks.
getText() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.ImageJScriptParameters
Get the text of the macro or script.
getTitle() - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
Get the title to use for this window.
getTrainData() - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining.ClassifierTrainingData
Get training data.
getVersion() - Method in class qupath.process.gui.ProcessingExtension
 
getViewer() - Method in class qupath.process.gui.WandToolEventHandler
 
getWandSensitivity() - Static method in class qupath.process.gui.WandToolEventHandler
Query the wand sensitivity value, which influences how similar local intensity values must be for the wand region growing.
getWandSigmaPixels() - Static method in class qupath.process.gui.WandToolEventHandler
Query the Gaussian sigma value used to smooth the image when applying the wand.
getWandUseOverlays() - Static method in class qupath.process.gui.WandToolEventHandler
Query whether the wand tool should be influenced by pixel values painted on image overlays.
GRAY - Enum constant in enum class qupath.process.gui.WandToolEventHandler.WandType
Grayscale image
GROOVY - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.LanguageOption
Groovy language
groovyText(String) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify the exact text for an ImageJ macro.

H

handle(MouseEvent) - Method in class qupath.process.gui.WandToolEventHandler
 
hashCode() - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
 
hashCode() - Method in class qupath.process.gui.commands.ml.ClassificationResolution
 

I

IJExtension - Class in qupath.imagej.gui
QuPath extension & associated static helper methods used to support integration of ImageJ with QuPath.
IJExtension() - Constructor for class qupath.imagej.gui.IJExtension
 
IJExtension.IJExtensionCommands - Class in qupath.imagej.gui
Commands to install with the ImageJ extension.
IMAGE - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
ImageJMacroRunner - Class in qupath.imagej.gui
Deprecated.
since v0.6.0; use ImageJScriptRunner and ImageJScriptRunnerControllerinstead.
ImageJMacroRunner(QuPathGUI) - Constructor for class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
Constructor.
imageJPathProperty() - Static method in class qupath.imagej.gui.IJExtension
Property representing the path to a local ImageJ installation, or null if no path has been set.
ImageJScriptRunner - Class in qupath.imagej.gui.scripts
Class to run ImageJ macros and scripts.
ImageJScriptRunner(ImageJScriptRunner.ImageJScriptParameters) - Constructor for class qupath.imagej.gui.scripts.ImageJScriptRunner
 
ImageJScriptRunner.ApplyToObjects - Enum Class in qupath.imagej.gui.scripts
Enum representing the objects that the script should be applied to.
ImageJScriptRunner.Builder - Class in qupath.imagej.gui.scripts
 
ImageJScriptRunner.ImageJScriptParameters - Class in qupath.imagej.gui.scripts
Class to store parameters used to run ImageJ macros or scripts from QuPath.
ImageJScriptRunner.PathObjectType - Enum Class in qupath.imagej.gui.scripts
 
ImageJScriptRunnerController - Class in qupath.imagej.gui.scripts
Controller class for the ImageJ script runner.
ImageJScriptRunnerController.LanguageOption - Enum Class in qupath.imagej.gui.scripts
Options for the script language.
ImageJScriptRunnerController.ResolutionOption - Enum Class in qupath.imagej.gui.scripts
Options for specifying how the resolution of an image region is determined.
installDefaultFeatureClassificationBuilder(ImageDataTransformerBuilder) - Static method in class qupath.process.gui.commands.ml.PixelClassifierPane
Add to the list of default feature calculator builders that will be available when this pane is opened.
installExtension(QuPathGUI) - Method in class qupath.imagej.gui.IJExtension
 
installExtension(QuPathGUI) - Method in class qupath.process.gui.ProcessingExtension
 

L

LAB_DISTANCE - Enum constant in enum class qupath.process.gui.WandToolEventHandler.WandType
Color image converted to CIELAB, Euclidean distance calculated
labelText(String) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Prompt to include beside the resource name text field
LARGEST_DIMENSION - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.ResolutionOption
Resize so that the width and height are ≤ a fixed length;
LoadResourceCommand<S> - Class in qupath.process.gui.commands.ui
Create commands for displaying pixel classifiers and density maps.

M

MACRO - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.LanguageOption
ImageJ macro language
macroText(String) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify the exact text for an ImageJ macro.
main(String[]) - Static method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Example program to log a script.
maxDimension(int) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Resize images to have a width and height ≤ a specified value when passing images to ImageJ.
mouseClicked(MouseEvent) - Method in class qupath.process.gui.WandToolEventHandler
 
mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.process.gui.WandToolEventHandler
 

N

NONE - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
 
nThreads(int) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify the number of parallel threads to use.

O

ObjectClassifierCommand - Class in qupath.process.gui.commands
Command used to create and show a suitable dialog box for interactive display of OpenCV classifiers.
ObjectClassifierCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.ObjectClassifierCommand
Constructor.
ObjectClassifierLoadCommand - Class in qupath.process.gui.commands
Command to apply a pre-trained object classifier to an image.
ObjectClassifierLoadCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.ObjectClassifierLoadCommand
Constructor.
openMacro(Path) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
 
overlayToAnnotations() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert Rois on the overlay of the current image at the end of the script to QuPath annotation objects.
overlayToDetections() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert Rois on the overlay of the current image at the end of the script to QuPath detection objects.
overlayToObjects(ImageJScriptRunner.PathObjectType) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert Rois on the overlay of the current image at the end of the script to the specified QuPath object type.
overlayToTiles() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert Rois on the overlay of the current image at the end of the script to QuPath tile objects.

P

padding(int) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify how much padding to add around the ROI.
parseArgument(ImageData<BufferedImage>, String) - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 
PIXEL_SIZE - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.ResolutionOption
Resize to a target pixel size.
PixelClassifierCommand - Class in qupath.process.gui.commands
Open GUI for the current viewer to train a new pixel classifier.
PixelClassifierCommand() - Constructor for class qupath.process.gui.commands.PixelClassifierCommand
 
PixelClassifierPane - Class in qupath.process.gui.commands.ml
Main user interface for interactively training a PixelClassifier.
PixelClassifierPane(QuPathGUI) - Constructor for class qupath.process.gui.commands.ml.PixelClassifierPane
Constructor.
PixelClassifierTraining - Class in qupath.process.gui.commands.ml
Helper class for training a pixel classifier.
PixelClassifierTraining(ImageDataOp) - Constructor for class qupath.process.gui.commands.ml.PixelClassifierTraining
Create a new pixel classifier helper, to support generating training data.
PixelClassifierTraining.ClassifierTrainingData - Class in qupath.process.gui.commands.ml
Wrapper for training data.
PixelClassifierUI - Class in qupath.process.gui.commands.ml
Helper class for generating standardized UI components for pixel classification.
PixelClassifierUI() - Constructor for class qupath.process.gui.commands.ml.PixelClassifierUI
 
pixelSize(PixelCalibration) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Resize images to have a target pixel value when passing images to ImageJ.
pixelSizeMicrons(double) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Resize images to have a target pixel value in µm when passing images to ImageJ.
ProcessingExtension - Class in qupath.process.gui
General-purpose processing and machine learning commands.
ProcessingExtension() - Constructor for class qupath.process.gui.ProcessingExtension
 
ProcessingExtension.ObjectClassificationCommands - Class in qupath.process.gui
 
ProcessingExtension.OpenCVCommands - Class in qupath.process.gui
Commands based on OpenCV.
ProcessingExtension.OtherCommands - Class in qupath.process.gui
 
ProcessingExtension.PixelClassificationCommands - Class in qupath.process.gui
 
project(ObjectExpression<Project<BufferedImage>>) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Current project
ProjectClassifierBindings - Class in qupath.process.gui.commands.ml
Class to help with formatting text fields for entering pixel and object classifier names.
ProjectClassifierBindings() - Constructor for class qupath.process.gui.commands.ml.ProjectClassifierBindings
 
promptToCreateNewMacro() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunnerController
 
promptToCreateObjects(ImageData<BufferedImage>, PixelClassifier, String) - Static method in class qupath.process.gui.commands.ml.PixelClassifierUI
Prompt the user to create objects directly from the pixels of an ImageServer.
promptToCreateTrainingImage(Project<BufferedImage>, List<PathClass>) - Static method in class qupath.process.gui.commands.CreateTrainingImageCommand
Prompt to create a training image, based upon annotations throughout a project.

Q

QuPath_Send_Overlay_to_QuPath - Class in qupathj
ImageJ plugin for sending back all the ROIs on an ImageJ overlay to QuPath.
QuPath_Send_Overlay_to_QuPath() - Constructor for class qupathj.QuPath_Send_Overlay_to_QuPath
 
QuPath_Send_ROI_to_QuPath - Class in qupathj
ImageJ plugin for sending back the active ROI from ImageJ to QuPath.
QuPath_Send_ROI_to_QuPath() - Constructor for class qupathj.QuPath_Send_ROI_to_QuPath
 
qupath.imagej.gui - package qupath.imagej.gui
User interface commands and extensions linking ImageJ and QuPath.
qupath.imagej.gui.scripts - package qupath.imagej.gui.scripts
Classes for running ImageJ macros through QuPath.
qupath.process.gui - package qupath.process.gui
General-purpose image processing and machine learning commands.
qupath.process.gui.commands - package qupath.process.gui.commands
QuPath commands relevant for machine learning.
qupath.process.gui.commands.density - package qupath.process.gui.commands.density
UI classes to support density maps.
qupath.process.gui.commands.ml - package qupath.process.gui.commands.ml
Interfaces and helper classes for using machine learning in QuPath.
qupath.process.gui.commands.ui - package qupath.process.gui.commands.ui
Reusable UI classes to support processing commands.
qupathj - package qupathj
ImageJ plugins to install within QuPath's embedded ImageJ instance to enable exchanging ROIs and objects.

R

refineGeometryByParent(Geometry) - Method in class qupath.process.gui.WandToolEventHandler
 
refineROIByParent(ROI) - Method in class qupath.process.gui.WandToolEventHandler
 
requestParentClipping(MouseEvent) - Method in class qupath.process.gui.WandToolEventHandler
 
requestPixelSnapping() - Method in class qupath.process.gui.WandToolEventHandler
 
resetConstrainingObjects() - Method in class qupath.process.gui.WandToolEventHandler
 
RGB - Enum constant in enum class qupath.process.gui.WandToolEventHandler.WandType
Color image (default behavior in v0.1.2 and before)
roiToAnnotation() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert any active Roi at the end of the script to a QuPath annotation object.
roiToDetection() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert any active Roi at the end of the script to a QuPath detection object.
roiToObject(ImageJScriptRunner.PathObjectType) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert any active Roi at the end of the script to the specified QuPath object type.
roiToTile() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Convert any active Roi at the end of the script to a QuPath tile object.
run() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Run the script for the 'current' image data, as requested from QP.
run() - Method in class qupath.process.gui.commands.CellIntensityClassificationCommand
 
run() - Method in class qupath.process.gui.commands.CreateChannelTrainingImagesCommand
 
run() - Method in class qupath.process.gui.commands.CreateCompositeClassifierCommand
 
run() - Method in class qupath.process.gui.commands.CreateRegionAnnotationsCommand
 
run() - Method in class qupath.process.gui.commands.DensityMapCommand
 
run() - Method in class qupath.process.gui.commands.ExportTrainingRegionsCommand
 
run() - Method in class qupath.process.gui.commands.ObjectClassifierCommand
 
run() - Method in class qupath.process.gui.commands.ObjectClassifierLoadCommand
 
run() - Method in class qupath.process.gui.commands.PixelClassifierCommand
 
run() - Method in class qupath.process.gui.commands.SimpleThresholdCommand
 
run() - Method in class qupath.process.gui.commands.SingleMeasurementClassificationCommand
 
run() - Method in class qupath.process.gui.commands.SplitProjectTrainingCommand
 
run() - Method in class qupath.process.gui.commands.ui.LoadResourceCommand
 
run(String) - Method in class qupathj.QuPath_Send_Overlay_to_QuPath
 
run(String) - Method in class qupathj.QuPath_Send_ROI_to_QuPath
 
run(ImageData<BufferedImage>) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Run the script for the specified image data.
runPlugin(TaskRunner, ImageData<BufferedImage>, String) - Method in class qupath.imagej.gui.ImageJMacroRunner
Deprecated.
 

S

savedName(StringProperty) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Property to store the saved name; this is useful if the name is required externally
SaveResourcePaneBuilder<T> - Class in qupath.process.gui.commands.ui
Small JavaFX pane to support saving object/pixel classifiers and density maps within a project in a standardized way.
SaveResourcePaneBuilder(Class<T>, ObjectExpression<? extends T>) - Constructor for class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Constructor.
scriptEngine(String) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify the name of any script engine to use.
scriptFile(File) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify a file containing the script or macro.
scriptFile(Path) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify a path to the script or macro.
SELECTED - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
SEP - Variable in class qupath.process.gui.ProcessingExtension.ObjectClassificationCommands
 
SEP - Variable in class qupath.process.gui.ProcessingExtension.PixelClassificationCommands
 
SEP_0 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
SEP_1 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
SEP_2 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
SEP_2B - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
SEP_3 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
SEP_4 - Variable in class qupath.imagej.gui.IJExtension.IJExtensionCommands
 
setBoundaryStrategy(BoundaryStrategy) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining
Set the strategy for handling the boundaries of area annotations.
setFeatureOp(ImageDataOp) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining
Set the ImageDataOp used to calculate features.
setImageJOverlay() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Add any QuPath objects within the field of view to an ImageJ overlay.
setImageJOverlay(boolean) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally add any QuPath objects within the field of view to an ImageJ overlay.
setImageJPath(String) - Static method in class qupath.imagej.gui.IJExtension
Set the path for a local ImageJ installation, if required.
setImageJRoi() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Set the ROI for the QuPath object being set as a Roi on the ImagePlus.
setImageJRoi(boolean) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Optionally set the ROI for the QuPath object being set as a Roi on the ImagePlus.
setResolution(PixelCalibration) - Method in class qupath.process.gui.commands.ml.PixelClassifierTraining
Set the resolution at which the training should occur.
setThickness(BoundaryStrategy, double) - Static method in class qupath.process.gui.commands.ml.BoundaryStrategy
Create a boundary strategy with the specified thickness.
setWandSensitivity(double) - Static method in class qupath.process.gui.WandToolEventHandler
Set the wand sensitivity value, which influences how similar local intensity values must be for the wand region growing.
setWandSigmaPixels(double) - Static method in class qupath.process.gui.WandToolEventHandler
Set the Gaussian sigma value used to smooth the image when applying the wand.
setWandUseOverlays(boolean) - Static method in class qupath.process.gui.WandToolEventHandler
Set whether the wand tool should be influenced by pixel values painted on image overlays.
SimpleThresholdCommand - Class in qupath.process.gui.commands
Apply simple thresholding to an image via the pixel classification framework to support thresholding at any resolution, optionally with visual feedback via an overlay.
SimpleThresholdCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.SimpleThresholdCommand
Constructor.
SingleMeasurementClassificationCommand - Class in qupath.process.gui.commands
Command to (sub)classify objects based on a single measurement.
SingleMeasurementClassificationCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.SingleMeasurementClassificationCommand
Constructor.
SplitProjectTrainingCommand - Class in qupath.process.gui.commands
Divide a project into training, validation and test sets but flagging individual image entries.
SplitProjectTrainingCommand(QuPathGUI) - Constructor for class qupath.process.gui.commands.SplitProjectTrainingCommand
Constructor.

T

taskRunner(TaskRunner) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Provide an optional task runner.
test() - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Test the script for the 'current' image data, as requested from QP.
test(ImageData<BufferedImage>) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner
Test the script for the specified image data.
text(String) - Method in class qupath.imagej.gui.scripts.ImageJScriptRunner.Builder
Specify the exact text for the script or macro.
textFieldPrompt(String) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Prompt to include beside the resource name text field
TILE - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
 
TILES - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
title(String) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Title to display in any dialogs
TMA_CORE - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
 
TMA_CORES - Enum constant in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
tooltip(ObservableValue<String>) - Method in class qupath.process.gui.commands.ui.SaveResourcePaneBuilder
Text to include in any tooltip.
toString() - Method in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
 
toString() - Method in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.ResolutionOption
 
toString() - Method in class qupath.process.gui.commands.ml.BoundaryStrategy
 
toString() - Method in class qupath.process.gui.commands.ml.ClassificationResolution
 
TRAIN_VALIDATION_TEST_METADATA_KEY - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand
Metadata key for the flag indicating the image type (Train, Validation, Test or None).

U

updateDefaults(ImageData<BufferedImage>) - Method in class qupath.process.gui.commands.density.DensityMapDialog
Update default parameters with a specified ImageData.
updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.process.gui.WandToolEventHandler
 
useOverlays - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
 

V

VALUE_NONE - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand
Metadata value for unassigned images.
VALUE_TEST - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand
Metadata value for test images.
VALUE_TRAINING - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand
Metadata value for training images.
VALUE_VALIDATION - Static variable in class qupath.process.gui.commands.SplitProjectTrainingCommand
Metadata value for validation images.
valueOf(String) - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.LanguageOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.ResolutionOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.process.gui.WandToolEventHandler.WandType
Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.ApplyToObjects
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunner.PathObjectType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.LanguageOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.imagej.gui.scripts.ImageJScriptRunnerController.ResolutionOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.process.gui.WandToolEventHandler.WandType
Returns an array containing the constants of this enum class, in the order they are declared.

W

WandPreferences() - Constructor for class qupath.process.gui.WandToolEventHandler.WandPreferences
 
wandSensitivity - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
 
wandSensitivityProperty() - Static method in class qupath.process.gui.WandToolEventHandler
Property representing the wand sensitivity value, which influences how similar local intensity values must be for the wand region growing.
wandSigma - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
 
wandSigmaPixelsProperty() - Static method in class qupath.process.gui.WandToolEventHandler
Property representing the Gaussian sigma value used to smooth the image when applying the wand.
WandToolEventHandler - Class in qupath.process.gui
Wand tool, which acts rather like the brush - except that it expands regions (sometimes rather too eagerly?) based upon local pixel values.
WandToolEventHandler(QuPathGUI) - Constructor for class qupath.process.gui.WandToolEventHandler
Constructor.
WandToolEventHandler.WandPreferences - Class in qupath.process.gui
 
WandToolEventHandler.WandType - Enum Class in qupath.process.gui
Enum reflecting different color images that may be used by the Wand tool.
wandType - Variable in class qupath.process.gui.WandToolEventHandler.WandPreferences
 
wandTypeProperty() - Static method in class qupath.process.gui.WandToolEventHandler
Property specifying whether the wand tool should be influenced by pixel values painted on image overlays.
wandUseOverlaysProperty() - Static method in class qupath.process.gui.WandToolEventHandler
Property specifying whether the wand tool should be influenced by pixel values painted on image overlays.
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