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All Classes and Interfaces|All Packages|Constant Field Values

A

AbstractImageOverlay - Class in qupath.lib.gui.viewer.overlays
Abstract PathOverlay with additional properties relevant when drawing BufferedImages.
AbstractImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
 
AbstractImageRenderer - Class in qupath.lib.gui.images.stores
Abstract ImageRenderer, which adds a timestamp variable.
AbstractImageRenderer() - Constructor for class qupath.lib.gui.images.stores.AbstractImageRenderer
 
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
accelerator(ObservableValue<KeyCombination>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Bind the accelerator property of the action to an ObservableValue, bidirectionally if possible.
accelerator(KeyCombination) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Set the accelerator property of the action.
acceleratorTextProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
ActionAccelerator - Annotation Interface in qupath.lib.gui.actions.annotations
Annotation used to specify a preferred accelerator for an an action.
actionBuilder() - Static method in class qupath.lib.gui.actions.ActionTools
Create an ActionTools.ActionBuilder with no properties set.
actionBuilder(String, Consumer<ActionEvent>) - Static method in class qupath.lib.gui.actions.ActionTools
Create an ActionTools.ActionBuilder with the specified text and event handler.
actionBuilder(Consumer<ActionEvent>) - Static method in class qupath.lib.gui.actions.ActionTools
Create an ActionTools.ActionBuilder with the specified event handler.
ActionConfig - Annotation Interface in qupath.lib.gui.actions.annotations
Annotation indicating the a key in the external resources file containing the menu, text and (optional) description.
ActionIcon - Annotation Interface in qupath.lib.gui.actions.annotations
Default icon for an action.
ActionMenu - Annotation Interface in qupath.lib.gui.actions.annotations
Annotation indicating the menu path where an action should be installed.
ActionMethod - Annotation Interface in qupath.lib.gui.actions.annotations
Annotation indicating that a method should be converted to an Action if possible.
Actions() - Constructor for class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
Actions() - Constructor for class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
 
ActionTools - Class in qupath.lib.gui.actions
Helper methods for generating and configuring Actions and UI elements.
ActionTools() - Constructor for class qupath.lib.gui.actions.ActionTools
 
ActionTools.ActionBuilder - Class in qupath.lib.gui.actions
Builder class for custom Action objects.
ACTIVE_SERVER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
activeToolProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the activeTool property of this tracker.
activeViewerProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
Get a read-only property representing the currently active viewer.
ADD_COLUMN_AFTER - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
 
ADD_COLUMN_BEFORE - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
 
ADD_ROW_AFTER - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
 
ADD_ROW_BEFORE - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
 
addActions - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
AddActions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.AddActions
 
addAllRegions(ImageServer<BufferedImage>, int) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Add all regions for a specific level of an ImageServer.
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.
addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
Deprecated.
use PropertyItemBuilder instead
addChoicePropertyPreference(Property<T>, ObservableList<T>, Class<? extends T>, String, String, String, boolean) - Method in class qupath.lib.gui.panes.PreferencePane
Deprecated.
use PropertyItemBuilder instead
addColorPropertyPreference(IntegerProperty, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
Deprecated.
use PropertyItemBuilder instead
addColumn(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
 
addCompletion(AutoCompletions.Completion) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
 
addCompletions(Collection<? extends AutoCompletions.Completion>) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
 
addCompletions(AutoCompletions.Completion...) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
 
addDirectoryPropertyPreference(Property<String>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
Deprecated.
use PropertyItemBuilder instead
addFileDropHandler(DragDropImportListener.DropHandler<File>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
Add a new File DropHandler.
addGridRow(GridPane, int, int, String, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Add a row of nodes.
AdditiveChannelInfo - Class in qupath.lib.display
Class for combining channels additively, then providing controls on the resulting RGB image.
AdditiveChannelInfo(ImageData<BufferedImage>, List<DirectServerChannelInfo>) - Constructor for class qupath.lib.display.AdditiveChannelInfo
 
addJsonDropHandler(DragDropImportListener.DropHandler<JsonElement>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
Add a new DropHandler specifically for JSON elements.
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.
addParameterChangeListener(ParameterChangeListener) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Add a ParameterChangeListener to be notified as the user modifies parameters.
addPropertyPreference(Property<T>, Class<? extends T>, String, String, String) - Method in class qupath.lib.gui.panes.PreferencePane
Deprecated.
use PropertyItemBuilder instead
addRow(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
 
addSeries(String, double[], double[]) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create and add a scatterplot using arrays of numeric values.
addSeries(String, double[], double[], List<T>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create and add a scatterplot series using collections of numeric values, with an associated custom object.
addSeries(String, double[], double[], T[]) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create and add a scatterplot using collections of numeric values, with an associated custom object.
addSeries(String, Collection<? extends Number>, Collection<? extends Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create and add a scatterplot using collections of numeric values.
addSeries(String, Collection<? extends T>, Function<T, Number>, Function<T, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Add values extracted from objects within a specified collection.
addSeries(String, Collection<XYChart.Data<Number, Number>>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create and add a scatterplot series from existing data.
addSeries(XYChart.Series<Number, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create a scatterplot series from existing data.
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.
addTextAppendableFX(TextAppendable) - Static method in class qupath.lib.gui.logging.LogManager
Register a TextAppendable that will be accept logging events and be updated on the JavaFX Application thread.
addThreshold(double) - Method in class qupath.lib.gui.charts.ChartThresholdPane
Add a threshold value.
addThreshold(double, Color) - Method in class qupath.lib.gui.charts.ChartThresholdPane
Add a threshold value with its display color.
addThreshold(ObservableNumberValue) - Method in class qupath.lib.gui.charts.ChartThresholdPane
Add a threshold value.
addTileListener(TileListener<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
addViewerListener(QuPathViewerListener) - Method in class qupath.lib.gui.viewer.QuPathViewer
Add a viewer listener.
alertType(Alert.AlertType) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Create a dialog styled as a specified alert type.
ALL - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
All log messages
ALL_WINDOWS - Enum constant in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
Use the system menubar for all windows.
allDetections() - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify that detection measurements (only) should be export.
allredMinPercentagePositiveProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
The minimum positive percentage of cells for Allred proportion score to be non-zero.
ALWAYS - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
Always display
alwaysPaintSelected - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
alwaysPaintSelectedObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Always paint selected objects in the viewer, even if the opacity setting is 0.
AnalyzeMenuActions - Class in qupath.lib.gui.actions.menus
 
AnalyzeMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
ANNOTATION_COPY_TO_PLANE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
ANNOTATION_DUPLICATE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
annotationActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
AnnotationActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
AnnotationPane - Class in qupath.lib.gui.panes
Component for displaying annotations within the active image.
AnnotationPane(QuPathGUI) - Constructor for class qupath.lib.gui.panes.AnnotationPane
Constructor.
AnnotationPane(QuPathGUI, ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.AnnotationPane
Constructor.
annotations() - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify that annotation measurements (only) should be export.
ANNOTATIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
ANNOTATIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
annotationStrokeThickness - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
annotationStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Preferred stroke thickness to use when drawing annotation ROIs.
ANY_ANNOTATIONS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
Regions overlapping the ROIs of any annotations
ANY_ANNOTATIONS_BOUNDS - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
Regions overlapping the bounding box of any annotations
ANY_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
AppearancePreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
 
append(Collection<? extends PathObjectValueFactory>) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
append(PathObjectValueFactory...) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
appendFrame(ViewRecordingFrame) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Append frame to the collection of frames.
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.TextAreaControl
 
applyDisplaySettings(String) - Static method in class qupath.lib.gui.scripting.QPEx
Apply the display settings with the specified name or file path to the current version.
applyDisplaySettings(ImageDisplaySettings) - Static method in class qupath.lib.gui.scripting.QPEx
Apply the display settings to the current viewer.
applyDisplaySettings(QuPathViewer, ImageDisplaySettings) - Static method in class qupath.lib.gui.scripting.QPEx
Apply the display settings to the specified viewer.
applyLastAnnotationToActiveViewer() - Method in class qupath.lib.gui.viewer.ViewerManager
 
applySettingsToDisplay(ImageDisplay, ImageDisplaySettings) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
Apply the settings to the display, if they are compatible.
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>, 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.gui.charts.HistogramChart.DisplayMode
Show as areas.
ARROW_DOUBLE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Arrow drawing tool, with arrowhead at both ends
ARROW_DOUBLE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ARROW_END - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Arrow drawing tool, with arrowhead at the end
ARROW_END_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ARROW_START - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Arrow drawing tool, with arrowhead at the start
ARROW_START_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ATTACH_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
ATTACH_VIEWER - Variable in class qupath.lib.gui.actions.ViewerActions
 
attachActiveViewerToGrid() - Method in class qupath.lib.gui.viewer.ViewerManager
Insert the currently active viewer back into the viewer grid.
attachViewerToGrid(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
Attach the specified viewer to the viewer grid, if possible.
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.
AutomateActions - Class in qupath.lib.gui.actions
Default actions associated with QuPath's 'Automate' (scripting) menu.
AutomateActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.AutomateActions
 
AutomateMenuActions - Class in qupath.lib.gui.actions.menus
 
AutomateMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
autorangeToFullDataProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Get a property representing whether to use the entire dataset when calculating axis limits automatically.
autoSaturationPercent - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
autoSetAnnotationClassProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Classification that should automatically be applied to all new annotations.
autoSetDisplayRange(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
Automatically set the display range for a channel, using the default saturation defined in PathPrefs.autoBrightnessContrastSaturationPercentProperty().
autoSetDisplayRange(ChannelDisplayInfo, double) - Method in class qupath.lib.display.ImageDisplay
Automatically set the display range for a channel.
autoUpdate - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
 
autoUpdate - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
autoUpdateCheckProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Check for updates when launching QuPath, if possible.
availableChannels() - Method in class qupath.lib.display.ImageDisplay
Read-only observable list 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.

B

backgroundColor - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
backgroundColor(int, boolean) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify a base color.
backgroundColor(Color) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify a base color.
badges - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
 
BAR - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode
Show as bars.
barChart() - Static method in class qupath.lib.gui.charts.Charts
Create a Charts.ScatterChartBuilder for generating a custom scatter plot.
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
 
BILINEAR - Enum constant in enum class qupath.lib.gui.viewer.ImageInterpolation
Bilinear interpolation.
bindLocale() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
 
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.
BOUNDARIES_ONLY - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
Show only cell boundaries.
BRIGHTNESS_CONTRAST - Variable in class qupath.lib.gui.actions.CommonActions
 
BRIGHTNESS_CONTRAST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
BrightnessContrastChannelPane - Class in qupath.lib.gui.commands.display
A pane responsible for the display and selection of channels from an image display.
BrightnessContrastChannelPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
 
BrightnessContrastCommand - Class in qupath.lib.gui.commands
Command to show a Brightness/Contrast dialog to adjust the image display.
BrightnessContrastCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.BrightnessContrastCommand
Constructor.
BrightnessContrastHistogramPane - Class in qupath.lib.gui.commands.display
A pane to display a histogram for brightness/contrast adjustment, allowing the user to select min/max values.
BrightnessContrastHistogramPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
 
BrightnessContrastSettingsPane - Class in qupath.lib.gui.commands.display
A pane to save and load display settings, using a ResourceManager.
BrightnessContrastSettingsPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane
 
BrightnessContrastSliderPane - Class in qupath.lib.gui.commands.display
A pane containing sliders for adjusting the min/max display range and gamma value associated with an ImageDisplay.
BrightnessContrastSliderPane() - Constructor for class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
 
browseDirectory(File) - Static method in class qupath.lib.gui.tools.GuiTools
Open the directory containing a file for browsing.
browseURI(URI) - Static method in class qupath.lib.gui.tools.GuiTools
Try to open a URI in a web browser.
BRUSH - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Brush drawing tool
BRUSH_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
BRUSH_TOOL - Variable in class qupath.lib.gui.ToolManager
 
brushCreateNewObjectsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Create new objects by default when drawing with the Brush tool.
brushDiameter - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
brushDiameterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Default brush tool diameter, in pixels.
brushScaleByMag - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
brushScaleByMagProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Optionally scale the default brush tool diameter by the viewer magnification (downsample value).
BrushToolEventHandler - Class in qupath.lib.gui.viewer.tools.handlers
Tool for drawing (and subtract from) freehand regions, optionally adapting brush size to magnification.
BrushToolEventHandler() - Constructor for class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
BufferedImageOverlay - Class in qupath.lib.gui.viewer.overlays
An overlay used to display one or more BufferedImage objects on top of a primary image shown in a viewer.
BufferedImageOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Create an empty overlay without any images to display.
BufferedImageOverlay(OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Create an overlay to display multiple image regions.
BufferedImageOverlay(OverlayOptions, ImageRegion, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Create an overlay to display one specified image region.
BufferedImageOverlay(QuPathViewer, BufferedImage) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
BufferedImageOverlay(QuPathViewer, Map<ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Create an overlay to show an image rescaled to overlay the entire current image in the specified viewer.
BufferedImageOverlay(QuPathViewer, OverlayOptions, Map<? extends ImageRegion, BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Create an overlay to display multiple image regions.
bufferedImageProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get a read-only property representing the buffered image.
BUGS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
build() - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Create an Action with this builder.
build() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Build a chart according to the specified parameters.
build() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Build a chart according to the specified parameters.
build() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
build() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Build the dialog.
build() - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Create the rendered image server.
build() - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
builder() - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Create a new builder to generate a custom dialog.
Builder() - Constructor for class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
 
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;
BuildInfo - Class in qupath.lib.gui
Basic version information about the current QuPath build.
bundle() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
 
buttons(String...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the buttons to display in the dialog.
buttons(ButtonType...) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the buttons to display in the dialog.

C

cache - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
calibratedLocationString - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
canBeautify() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Returns true if ScriptSyntax.beautify(String) is capable of beautifying the text, false otherwise.
CANCEL - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
Deprecated.
"Cancel" option
cancelDirection(boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
Cancel either the x- or y-axis direction of the movement.
canCompress() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Returns true if ScriptSyntax.compress(String) is capable of compressing the text, false otherwise.
canRedo() - Method in class qupath.lib.gui.UndoRedoManager
True if it's possible to call redoOnce for the currently-active viewer in QuPath, false otherwise.
canUndo() - Method in class qupath.lib.gui.UndoRedoManager
True if it's possible to call undoOnce for the currently-active viewer in QuPath, false otherwise.
caretPositionProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Property for the current caret position.
caretPositionProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
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
 
cellDisplayActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
CellDisplayActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
 
cells() - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify that cell measurements (only) should be export.
CENTER_ALL - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
 
CENTER_OFFSCREEN - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
 
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
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
 
changed(ObservableValue<? extends QuPathViewer>, QuPathViewer, QuPathViewer) - Method in class qupath.lib.gui.UndoRedoManager
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.CountingDialogCommand
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.commands.PathObjectGridView
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.AnnotationPane
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.ImageDetailsPane
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.ProjectBrowser
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.SlideLabelView
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
 
changed(ObservableValue<? extends ImageData<BufferedImage>>, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
 
CHANNEL_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
ChannelColor - Class in qupath.lib.display.settings
A simple class to store the color of an image channel.
ChannelColor() - Constructor for class qupath.lib.display.settings.ChannelColor
 
ChannelDisplayInfo - Interface in qupath.lib.display
Interface used to control the display of single channels of image data, where 'single channel' means one value per pixel (in Java's parlance, one band for the SampleModel).
ChannelDisplayInfo.ModifiableChannelDisplayInfo - Interface in qupath.lib.display
Helper interface to indicate that the display ranges can be modified.
ChannelDisplayMode - Enum Class in qupath.lib.display
Display mode for an image channel, used in combination with ImageDisplay and ChannelDisplayInfo.
ChannelDisplayTransformServer - Class in qupath.lib.gui.images.servers
ImageServer that applies a color transform to an image.
ChannelSettings - Class in qupath.lib.display.settings
A simple class to store the main information needed by QuPath to display an image channel with a requested color and brightness/contrast setting.
ChannelSettings() - Constructor for class qupath.lib.display.settings.ChannelSettings
 
Charts - Class in qupath.lib.gui.charts
Helper class for generating interactive charts.
Charts() - Constructor for class qupath.lib.gui.charts.Charts
 
Charts.BarChartBuilder - Class in qupath.lib.gui.charts
Builder for creating scatter charts.
Charts.PieChartBuilder - Class in qupath.lib.gui.charts
Builder for creating pie charts.
Charts.ScatterChartBuilder - Class in qupath.lib.gui.charts
Builder for creating scatter charts.
ChartThresholdPane - Class in qupath.lib.gui.charts
Pane that can be used to contain an XYChart, adding adjustable thresholds to be displayed.
ChartThresholdPane(XYChart<Number, Number>) - Constructor for class qupath.lib.gui.charts.ChartThresholdPane
Note: xAxis and yAxis must be instances of NumberAxis.
ChartTools - Class in qupath.lib.gui.charts
Collection of static methods to help when working with JavaFX charts, and adapting these for QuPath's purposes.
ChartTools() - Constructor for class qupath.lib.gui.charts.ChartTools
 
CHECK_URIS - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
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.
CITE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
classifications(Collection<? extends PathObject>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Plot two measurements against one another for the specified objects.
ClassifyMenuActions - Class in qupath.lib.gui.actions.menus
 
ClassifyMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
clear() - Method in interface qupath.lib.gui.scripting.EditableText
Request clear the contents of the control.
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_CORES - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
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) - 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
 
clearThresholds() - Method in class qupath.lib.gui.charts.ChartThresholdPane
Clear all thresholds.
clipROIsForHierarchy - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
clipROIsForHierarchyProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request ROIs to be clipped and inserted as the right place in the hierarchy when drawing (to prevent overlapping ROIs being created accidentally).
clipToAllowed - Variable in class qupath.lib.display.AdditiveChannelInfo
 
clipToAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
 
close() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
 
close() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
close() - Method in class qupath.lib.gui.SharedThreadPoolManager
Shutdown any threadpools created by this manager.
closeProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Close the current project open in the QuPathGUI.
closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewer
Request that this viewer is closed.
closeViewer() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
 
closeViewer(QuPathViewer) - Method in class qupath.lib.gui.QuPathGUI
Close the image within a viewer, prompting to save changes if necessary.
CM_GRAYSCALE - Static variable in class qupath.lib.display.DirectServerChannelInfo
 
CM_GRAYSCALE_INVERTED - Static variable in class qupath.lib.display.DirectServerChannelInfo
 
COG - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
COLOR - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
Show using default color LUT (may be composite)
COLOR_DECONVOLUTION_REFINE - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
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.
colormapsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
Read only property representing the custom colormaps directory.
ColorModelRenderer - Class in qupath.lib.gui.images.stores
An ImageRenderer that uses a ColorModel.
ColorModelRenderer(ColorModel) - Constructor for class qupath.lib.gui.images.stores.ColorModelRenderer
Constructor.
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.
colorTMAProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
The default color used to display TMA core objects.
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
 
combineSelectedAnnotations(ImageData<?>, RoiTools.CombineOp) - Static method in class qupath.lib.gui.commands.Commands
Combine the selected annotations for the specified hierarchy.
comboPasteEscape - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
COMMAND_LIST - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
COMMAND_LIST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
commandBarDisplay - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
commandBarDisplayProperty() - Static method in class qupath.lib.gui.tools.CommandFinderTools
Property specifying where the command bar should be displayed relative to the main viewer window.
CommandFinderTools - Class in qupath.lib.gui.tools
Helper tools for creating components that enable fast access to menu commands via a filtered list.
CommandFinderTools() - Constructor for class qupath.lib.gui.tools.CommandFinderTools
 
CommandFinderTools.CommandBarDisplay - Enum Class in qupath.lib.gui.tools
Available modes for displaying the command bar.
CommandFinderTools.CommandEntry - Class in qupath.lib.gui.tools
Helper class to wrap summary data for a command to display in the list.
Commands - Class in qupath.lib.gui.commands
Helper class implementing simple 'single-method' commands for easy inclusion in the GUI.
Commands() - Constructor for class qupath.lib.gui.commands.Commands
 
CommonActions - Class in qupath.lib.gui.actions
Default actions associated with a specific QuPath instance.
CommonActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.CommonActions
 
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.
compressSourceAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
configureRecentItemsMenu(Menu, ObservableList<URI>, Consumer<URI>) - Static method in class qupath.lib.gui.tools.GuiTools
Configure a menu to displays recent items, stored in the form of URIs.
confirmation() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Create an confirmation alert dialog.
content(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify a Node to display within the dialog.
contentText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the dialog content text.
ContextHelpViewer - Class in qupath.lib.gui.commands
Help window providing context-dependent help.
CONTRAST - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
convertDetectionsToPoints(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands
Convert detection objects to point annotations based upon their ROI centroids.
convertToPercentages(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Request that pie chart values are converted to percentages for tooltips.
CONVEX_HULL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
CONVEX_POINTS - Variable in class qupath.lib.gui.actions.CommonActions
 
copy() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Request copy the current selection.
copy() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
COPY_ANNOTATION_OBJECTS - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
COPY_FULL_SCREENSHOT - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
COPY_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
COPY_VIEW - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
COPY_WINDOW - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
COPY_WINDOW_SCREENSHOT - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
copyAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
copyActions - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
CopyActions() - Constructor for class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
copyAnnotationsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Attempt to annotation objects to the system clipboard, if available
copySelectedAnnotationsToCurrentPlane(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
Copy the selected objects and add them to the plane currently active in the viewer.
copySelectedObjectsToClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Attempt to copy selected objects to the system clipboard, if available
copyTableContentsToClipboard(PathTableData<?>, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
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.
CountingDialogCommand - Class in qupath.lib.gui.commands
Command to open up a counting panel to aid with creating Point annotations.
CountingDialogCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.CountingDialogCommand
Constructor.
countProperty() - Method in class qupath.lib.gui.actions.InfoMessage
Read only property containing any count associated with the text (may be null).
countsTransformProperty() - Method in class qupath.lib.gui.charts.HistogramChart
Property to control how counts should be transformed before being shown in the histogram
create() - Static method in class qupath.lib.gui.SharedThreadPoolManager
Create a new instance
create() - Static method in class qupath.lib.gui.ToolManager
Create a new instance
create(boolean) - Static method in class qupath.lib.gui.tools.WebViews
Create a new WebView.
create(String, double, boolean, List<ChannelSettings>) - Static method in class qupath.lib.display.settings.ImageDisplaySettings
Create a new image display settings object.
create(String, float, float, ChannelColor, boolean) - Static method in class qupath.lib.display.settings.ChannelSettings
Create a new channel settings object.
create(String, String, String) - Static method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
Create a new GitHubProject.
create(String, Version, URI) - Static method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
create(Collection<? extends ImageServer<BufferedImage>>) - Static method in class qupath.lib.gui.panes.ServerSelector
 
create(QuPathGUI) - Static method in class qupath.lib.gui.viewer.ViewerManager
Create a new instance
create(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Create an overlay to display a live image that can be created from an existing ImageData.
create(OverlayOptions, Map<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Create an overlay to display a live image that can be created from an existing ImageData.
create(OverlayOptions, PixelClassifier) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Create an overlay to display the live application of a PixelClassifier to an image, using the default number of parallel threads for classification.
create(OverlayOptions, PixelClassifier, int) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Create an overlay to display the live application of a PixelClassifier to an image.
create(QuPathViewer) - Static method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
 
create(ImageData<?>, Collection<? extends PathObject>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a warpper containing the specified objects.
create(ImageData<?>, Predicate<PathObject>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a wrapper that includes all objects selected by the specified predicate.
create(ImageData<BufferedImage>) - Static method in class qupath.lib.display.ImageDisplay
Create a new image display, and set the specified image data.
CREATE_MANUAL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
CREATE_TILES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
createAction(Runnable) - Static method in class qupath.lib.gui.actions.ActionTools
Create an action whose event handler calls a runnable.
createAction(Runnable, String) - Static method in class qupath.lib.gui.actions.ActionTools
Create an action whose event handler calls a runnable, with a specified name.
createAllMenuActions(QuPathGUI) - Static method in class qupath.lib.gui.actions.menus.Menus
Create a collection of all the actions that should be installed in QuPath's main menubar.
createAnnotationView(QuPathGUI) - Static method in class qupath.lib.gui.commands.PathObjectGridView
Create a grid view for annotations.
createArrowEndEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createArrowStartEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createBrushEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createButton(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Create a button from an action, showing both the text and graphic if available.
createButtonWithGraphicOnly(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Create a button from an action, showing only the graphic and not any text.
createCanvasViewer(QuPathViewer, ImageServer<BufferedImage>, boolean) - Static method in class qupath.lib.gui.tools.PathObjectImageViewers
Create an item viewer to display a PathObject using a canvas.
createCheckBox(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Create a checkbox from an action.
createCheckMenuItem(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Create a menu item from an action that makes use of a selected property.
createCheckMenuItem(Action, ToggleGroup) - Static method in class qupath.lib.gui.actions.ActionTools
Create a menu item from an action that makes use of a selected property.
createColorTransformServer(ImageServer<BufferedImage>, List<ChannelDisplayInfo>) - Static method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
Create an ImageServer for which the channels are created dynamically from a list of ChannelDisplayInfos.
createColumnGrid(int) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Create a GridPane containing columns that resize similarly to Swing's GridLayout().
createColumnGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Create a GridPane containing columns that resize similarly to Swing's GridLayout().
createColumnGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Create a GridPane containing columns that resize similarly to Swing's GridLayout(), where controls have their widths bound to their parent.
createCommandFinderDialog(QuPathGUI) - Static method in class qupath.lib.gui.tools.CommandFinderTools
Create a dialog showing a filtered list of menu commands, for fast selection.
createCommandFinderPane(QuPathGUI, Node, ObjectProperty<CommandFinderTools.CommandBarDisplay>) - Static method in class qupath.lib.gui.tools.CommandFinderTools
Create a component that contains a TextField for entering menu commands to run quickly.
createContext(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Create a ScriptContext containing information from the ScriptParameters.
createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
 
createDefaultRGBImage(int, int) - Method in class qupath.lib.gui.images.servers.RenderedImageServer
 
createDoubleArrowEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createEllipseEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createExtendedTool(PathTool...) - Static method in class qupath.lib.gui.viewer.tools.PathTools
 
createFeatureDisplayOverlay(OverlayOptions, Function<ImageData<BufferedImage>, ImageServer<BufferedImage>>, ImageRenderer) - Static method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
createFontAwesome(char) - Static method in class qupath.lib.gui.tools.IconFactory
Create a node from a FontAwesome Glyph with the default size for toolbars.
createFontAwesome(char, int) - Static method in class qupath.lib.gui.tools.IconFactory
Create a node from a FontAwesome Glyph with the default size for toolbars.
createForObservableViewer(ObservableValue<? extends QuPathViewer>) - Static method in class qupath.lib.gui.UndoRedoManager
 
createFromBuilders(Collection<? extends ImageServerBuilder.ServerBuilder<BufferedImage>>) - Static method in class qupath.lib.gui.panes.ServerSelector
 
createFullImageAnnotation(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
Create a full image annotation for the image in the specified viewer.
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.
createHiddenInstance() - Static method in class qupath.lib.gui.QuPathGUI
Create a new QuPath instance that is not visible (i.e.
createHistogramData(Histogram, Integer) - Static method in class qupath.lib.gui.charts.HistogramChart
Create a HistogramData object to wrap a histogram & some info about its display.
createHistogramData(Histogram, Color) - Static method in class qupath.lib.gui.charts.HistogramChart
Create a HistogramData object to wrap a histogram & some info about its display.
createIconImage(IconFactory.PathIcons, int) - Static method in class qupath.lib.gui.tools.IconFactory
Create an image from a default icon glyph.
createID() - Method in class qupath.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
 
createImageChoicePane(QuPathGUI, List<ProjectImageEntry<BufferedImage>>, List<ProjectImageEntry<BufferedImage>>, String) - Static method in class qupath.lib.gui.dialogs.ProjectDialogs
Populates a given ListSelectionView with all the project entries.
createImageDataAction(Consumer<ImageData<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI
Create an Action that depends upon an ImageData.
createImageDataAction(Consumer<ImageData<BufferedImage>>, String) - Method in class qupath.lib.gui.QuPathGUI
Create an Action that depends upon an ImageData.
createImageRegionStore() - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreFactory
Create an ImageRegionStore using a default tile cache size, based upon the available memory and user preferences.
createImageRegionStore(long) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreFactory
Create an ImageRegionStore with a specified tile cache size, in bytes.
createImageViewer(QuPathViewer, ImageServer<BufferedImage>, boolean) - Static method in class qupath.lib.gui.tools.PathObjectImageViewers
Create an item viewer to display a PathObject using an ImageView.
createInstance(Stage) - Static method in class qupath.lib.gui.QuPathGUI
Static method to launch QuPath on the JavaFX Application thread.
createInstance(Stage, HostServices) - Static method in class qupath.lib.gui.QuPathGUI
Static method to launch QuPath from a JavaFX application.
createJsonTreeBrowser(String, Object) - Static method in class qupath.lib.gui.panes.ObjectTreeBrowser
Create a TreeTableView showing the names and values of fields within a JsonElement.
createLeftRightTitledPane(String, Node...) - Static method in class qupath.lib.gui.tools.GuiTools
Create a TitledPane with a text heading aligned to the left, and additional content (usually one or more buttons) aligned to the right.
createLeftRightTitledPane(Node, Node) - Static method in class qupath.lib.gui.tools.GuiTools
Create a TitledPane with content aligned to the left and right of the title.
createLicensesWindow(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Create a window summarizing license information for QuPath and its third party dependencies.
createLineEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createListCell() - Static method in class qupath.lib.gui.tools.PathObjectLabels
Create a ListCell for displaying a PathObject using the default PathObject.toString() method.
createListCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
Create a ListCell for displaying a PathObject using a custom method to create a string representation of the object.
createListSelectionView() - Static method in class qupath.lib.gui.tools.GuiTools
Create a new ListSelectionView.
createLogFiles - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
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.
createMeasurementMapDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Create a dialog for displaying measurement maps.
createMemoryMonitorDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Create a dialog to monitor memory usage.
createMenu(String, Object...) - Static method in class qupath.lib.gui.tools.MenuTools
Create a menu, optionally add new menu items with MenuTools.addMenuItems(List, Object...).
createMenuItem(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Create a menu item from an action.
createMoreButton(ContextMenu, Side) - Static method in class qupath.lib.gui.tools.GuiTools
Create a Button with a standardized icon and tooltip text to indicate 'More', which triggers a ContextMenu when clicked.
createMoveEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createNewAnnotation(MouseEvent, double, double) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Create a new annotation and set it in the current viewer.
createNewChart() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
createNewChart() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
createNewChart() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
createNewChart(Axis<Number>, Axis<Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
createNewChart(Axis<String>, Axis<Number>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
createNewEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
createNewROI(MouseEvent, double, double, ImagePlane) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
createNode(int, int, IconFactory.PathIcons) - Static method in class qupath.lib.gui.tools.IconFactory
Create a node from a default icon glyph.
createNode(FontAwesome.Glyph) - Static method in class qupath.lib.gui.tools.IconFactory
Create a node from a FontAwesome Glyph with the default size for toolbars.
createNode(FontAwesome.Glyph, int) - Static method in class qupath.lib.gui.tools.IconFactory
Create a node from a FontAwesome Glyph.
createObjectDescriptionsDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Create a stage to display object descriptions.
createObjectTreeBrowser(String, Object) - Static method in class qupath.lib.gui.panes.ObjectTreeBrowser
Create a TreeTableView showing the names and values of object fields, accessed via reflection.
createPane() - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
 
createPane() - Static method in class qupath.lib.gui.tools.PathObjectLabels
Create a PathObjectLabels.PathObjectMiniPane using the default PathObject.toString() method.
createPane(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
Create a PathObjectLabels.PathObjectMiniPane using a custom method to create a string representation of the object.
createPane(ObservableValue<ImageData<T>>) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
 
createPane(ObservableValue<ImageData<T>>, boolean) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
 
createPathObjectIcon(PathObject, int, int) - Static method in class qupath.lib.gui.tools.IconFactory
Create an icon depicting a PathObject.
createPersistentPreference(String, boolean) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, double) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, int) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, long) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, String) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, T, Class<T>) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create a persistent property, which is one that will be saved to/reloaded from the user preferences.
createPersistentPreference(String, T, Function<T, String>, Function<String, T>) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create a persistent property representing any object serializable as a String, which will be saved to/reloaded from the user preferences.
createPersistentUriList(String, int, String...) - Static method in class qupath.lib.gui.prefs.PathPrefs
Create an observable list backed by preferences to store URIs.
createPlaceholderText(String) - Static method in class qupath.lib.gui.tools.GuiTools
Create a Text object for use as a placeholder in a list or table.
createPlugin(Class<? extends PathPlugin>) - Method in class qupath.lib.gui.QuPathGUI
Create a plugin from a specified class.
createPluginAction(String, Class<? extends PathPlugin>, String) - Method in class qupath.lib.gui.QuPathGUI
Create an action for a plugin to be run through this QuPath instance.
createPluginAction(String, PathPlugin<BufferedImage>, String) - Method in class qupath.lib.gui.QuPathGUI
Create an Action to call the specified plugin for the current image.
createPointsEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createPolygonEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createPolylineEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createPreferencesDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Show a dialog to adjust QuPath preferences.
createProjectAction(Consumer<Project<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI
Create an Action that depends upon a Project.
createPropertySheetItem(Property<T>, Class<? extends T>) - Static method in class qupath.lib.gui.panes.PreferencePane
Deprecated.
use PropertyItemBuilder instead
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.
createRectangleEventHandler() - Static method in class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
createRelativePathProperty(String) - Method in class qupath.lib.gui.UserDirectoryManager
Create a read only property for a relative path of the user subdirectory.
createRenderedServer(QuPathViewer) - Static method in class qupath.lib.gui.images.servers.RenderedImageServer
Create an ImageServer that returns tiles based on how approximately they would appear within the viewer.
createRenderedServer(ImageServer<BufferedImage>, ImageRenderer) - Static method in class qupath.lib.gui.images.servers.RenderedImageServer
Create an ImageServer that converts the image to RGB using the specified ImageRenderer.
createROIIcon(ROI, int, int, Color) - Static method in class qupath.lib.gui.tools.IconFactory
Create an icon depicting a ROI.
createRotateImageDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Create a dialog for rotating the image in the current viewer (for display only).
createRowGrid(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Create a GridPane containing rows that resize similarly to Swing's GridLayout().
createRowGridControls(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Create a GridPane containing columns that resize similarly to Swing's GridLayout(), while also resizing contained objects to have the corresponding widths.
createSelectableAction(ObservableValue<Boolean>) - Static method in class qupath.lib.gui.actions.ActionTools
Create an unnamed action with its Action.selectedProperty() bound to a specified property.
createSelectableAction(ObservableValue<Boolean>, String) - Static method in class qupath.lib.gui.actions.ActionTools
Create an action with its Action.selectedProperty() bound to a specified property.
createSelectableAction(ObservableValue<Boolean>, String, Node, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
Create an action with its Action.selectedProperty() bound to a specified property, with optional graphic and accelerator.
createSelectableCommandAction(ObservableBooleanValue) - Static method in class qupath.lib.gui.actions.ActionTools
 
createSelectableCommandAction(SelectableItem<T>) - Static method in class qupath.lib.gui.actions.ActionTools
 
createSelectableCommandAction(SelectableItem<T>, String) - Static method in class qupath.lib.gui.actions.ActionTools
Create an action from a selectable icon.
createSelectableCommandAction(SelectableItem<T>, String, Node, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
 
createSelectableCommandAction(SelectableItem<T>, ObservableValue<String>, ObservableValue<Node>, KeyCombination) - Static method in class qupath.lib.gui.actions.ActionTools
 
createSeparator() - Static method in class qupath.lib.gui.actions.ActionTools
Create an action indicating that a separator should be added (e.g.
createSeries(String, double[], double[]) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create a scatterplot using arrays of numeric values.
createSeries(String, double[], double[], List<T>) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create a scatterplot using collections of numeric values, with an associated custom object.
createSeries(String, double[], double[], T[]) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create a series of data using collections of numeric values, with an associated custom object.
createSeries(String, Collection<? extends Number>, Collection<? extends Number>) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create a series using collections of numeric values.
createSeries(String, Collection<? extends T>, Function<T, Number>, Function<T, Number>) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create a data series extracted from objects within a specified collection.
createSeriesFromMeasurements(Collection<? extends PathObject>, String, String) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Create a data series from two measurements for the specified objects.
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
 
createShape(MouseEvent, double, double, boolean, Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Create a new Geometry using the specified tool, assuming a user click/drag at the provided x & y coordinates.
createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.QuPathGUI
Deprecated.
createSharedPoolCompletionService(Class<V>) - Method in class qupath.lib.gui.SharedThreadPoolManager
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.
createSingleStageAction(Supplier<Stage>, String) - Static method in class qupath.lib.gui.commands.Commands
Create a named command that generates a persistent single dialog on demand.
createSingleThreadExecutor(Object) - Method in class qupath.lib.gui.QuPathGUI
Deprecated.
createSpecifyAnnotationDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Create a stage to prompt the user to specify an annotation to add.
createTableCell(QuPathViewer, ImageServer<BufferedImage>, boolean, double) - Static method in class qupath.lib.gui.tools.PathObjectImageViewers
Create a table cell to show an object.
createTaskRunner() - Static method in class qupath.lib.gui.scripting.QPEx
Create a task runner with the default number of threads defined by ThreadTools.getParallelism().
createTaskRunner(int) - Static method in class qupath.lib.gui.scripting.QPEx
Create a task runner with the specified number of threads.
createTileWorker(ImageServer<BufferedImage>, RegionRequest, Map<RegionRequest, BufferedImage>, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
createTmaCoreView(QuPathGUI) - Static method in class qupath.lib.gui.commands.PathObjectGridView
Create a grid view for TMA core objects.
createToggleButton(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Create a toggle button from an action, showing both the text and graphic if available.
createToggleButtonWithGraphicOnly(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Create a toggle button from an action, showing only the graphic and not any text.
createTool(EventHandler<MouseEvent>, String, Node) - Static method in class qupath.lib.gui.viewer.tools.PathTools
Create a tool from the specified MouseEvent handler.
createTool(EventType<T>, EventHandler<T>, String, Node) - Static method in class qupath.lib.gui.viewer.tools.PathTools
Create a tool from the specified event handler.
createTreeCell() - Static method in class qupath.lib.gui.tools.PathObjectLabels
Create a TreeCell for displaying a PathObject using the default PathObject.toString() method.
createTreeCell(Function<PathObject, String>) - Static method in class qupath.lib.gui.tools.PathObjectLabels
Create a TreeCell for displaying a PathObject using a custom method to create a string representation of the object.
createValues(PathObjectListWrapper) - Method in class qupath.lib.gui.measure.MeasurementListValueFactory
 
createValues(PathObjectListWrapper) - Method in class qupath.lib.gui.measure.MetadataValueFactory
 
createValues(PathObjectListWrapper) - Method in interface qupath.lib.gui.measure.PathObjectValueFactory
Create the lazy values for the objects contained in the wrapper.
createViewer() - Method in class qupath.lib.gui.viewer.ViewerManager
Create a viewer, adding it to the stored array but not adding it to any component (which is left up to the calling code to handle)
createViewerAction(Consumer<QuPathViewer>) - Method in class qupath.lib.gui.QuPathGUI
Create an Action that depends upon an QuPathViewer.
createWindow(QuPathGUI) - Static method in class qupath.lib.gui.panes.ObjectDescriptionPane
 
createWorkflowDisplayDialog(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Create a dialog to show the workflow history for the current image data.
createZoomCommand(QuPathGUI, int) - Static method in class qupath.lib.gui.commands.Commands
Create a zoom in/out command action.
cssDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
Read only property representing the css directory.
CssLanguage - Class in qupath.lib.gui.scripting.languages
Class for representing CSS in QuPath.
currentChannelProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Get the currently-selected channel.
currentChannelVisible() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Read-only property indicating whether the currently-selected channel is visible, i.e.
currentLanguageProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
currentSyntaxProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
cursorTrackingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the cursorTracking property of this tracker.
cut() - Method in 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
 

D

data(Map<?, ? extends Number>) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify data for the pie chart as a map.
dataItemAdded(XYChart.Series<Number, Number>, int, XYChart.Data<Number, Number>) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
 
dataItemRemoved(XYChart.Data<Number, Number>, XYChart.Series<Number, Number>) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
 
DEBUG - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
Debug logging (a lot of messages)
decelerate() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
Stop moving, by smoothly decelerating.
DECIMAL_PLACES_DEFAULT - Static variable in class qupath.lib.gui.tools.MeasurementExporter
Constant representing that the number of decimal places to use when exporting measurements can be chosen automatically.
decimalPlaces(int) - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify how many decimal places to use for numeric output.
DEFAULT - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
JavaFX default.
DEFAULT_DECIMAL_PLACES - Static variable in interface qupath.lib.gui.measure.PathTableData
The default number of decimal places when converting floating point values to strings.
DEFAULT_DELIMITER - Static variable in interface qupath.lib.gui.measure.PathTableData
The default delimiter to use.
DEFAULT_PREFIX - Static variable in class qupath.lib.gui.images.servers.PathHierarchyImageServer
Prefix used for the path of all instances of this class.
DefaultAutoCompletor - Class in qupath.lib.gui.scripting.completors
Default auto-completor for JVM-based languages, optionally including QuPath default imports.
DefaultAutoCompletor() - Constructor for class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
Constructor, using the default Java code completions for QuPath.
DefaultAutoCompletor(Collection<? extends AutoCompletions.Completion>) - Constructor for class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
Constructor.
defaultColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
DefaultImageRegionStore - Class in qupath.lib.gui.images.stores
An ImageRegionStore suitable for either Swing or JavaFX applications.
defaultLocaleDisplayProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get a property for setting the default Locale for Locale.Category.DISPLAY.
defaultLocaleFormatProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get a property for setting the default Locale for Locale.Category.FORMAT.
defaultLocaleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get a property for setting the default Locale.
DefaultPathObjectValueFactoryBuilder - Class in qupath.lib.gui.measure
 
DefaultPathObjectValueFactoryBuilder() - Constructor for class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
DefaultScriptEditor - Class in qupath.lib.gui.scripting
Default multilingual script editor.
DefaultScriptEditor(QuPathGUI) - Constructor for class qupath.lib.gui.scripting.DefaultScriptEditor
Constructor.
DefaultScriptLanguage - Class in qupath.lib.gui.scripting.languages
Default implementation for a ScriptLanguage, based on a ScriptEngine.
DefaultScriptLanguage(String, Collection<String>, ScriptAutoCompletor) - Constructor for class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Constructor for a ExecutableLanguage.
DefaultScriptLanguage(ScriptEngineFactory) - Constructor for class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Constructor for a ExecutableLanguage based on a ScriptEngineFactory.
DefaultScriptLanguage.ImportStatementGenerator - Interface in qupath.lib.gui.scripting.languages
Interface defining how the import statements should be generated for the language.
defaultStringFunction(PathClass) - Static method in class qupath.lib.gui.tools.PathClassListCell
Default function to convert a PathClass to a string.
DELETE_ALL - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
DELETE_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
DELETE_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
DELETE_IMAGE_BOUNDARY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
DELETE_SELECTED_BOUNDARY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
DELETE_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
deleteActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
DeleteActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
DeleteObjectsOnBoundsCommand - Class in qupath.lib.gui.commands
Interactive command to remove objects with ROIs that touch or overlap the boundary of other objects.
DeleteObjectsOnBoundsCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.DeleteObjectsOnBoundsCommand
 
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.TextAreaControl
 
DEMOS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
deregisterTool(QuPathViewer) - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
 
deregisterTool(QuPathViewer) - Method in interface qupath.lib.gui.viewer.tools.PathTool
Deregister the tool from the viewer.
deselect() - Method in interface qupath.lib.gui.scripting.EditableText
Deselect any currently-selected text.
deselect() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
DETACH_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
DETACH_VIEWER - Variable in class qupath.lib.gui.actions.ViewerActions
 
detachActiveViewerFromGrid() - Method in class qupath.lib.gui.viewer.ViewerManager
Detach the currently active viewer from the viewer grid, if possible.
detachViewerFromGrid(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
Detach the specified viewer from the viewer grid, if possible.
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.
DETECTIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
DETECTIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
DETECTIONS_FILL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
detectionStrokeThicknessProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Preferred stroke thickness to use when drawing detections ROIs.
detectionTreeDisplayModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Define how detections should be displayed in lists and tree views.
detectonStrokeThickness - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
df - Static variable in class qupath.lib.display.DirectServerChannelInfo
 
df - Static variable in class qupath.lib.gui.viewer.recording.ViewTracker
 
Dialogs - Class in qupath.lib.gui.dialogs
Deprecated.
since v0.5.0.
Dialogs() - Constructor for class qupath.lib.gui.dialogs.Dialogs
Deprecated.
 
Dialogs.Builder - Class in qupath.lib.gui.dialogs
Deprecated.
Dialogs.DialogButton - Enum Class in qupath.lib.gui.dialogs
Deprecated.
Possible buttons pressed in a yes/no/cancel dialog.
DIR_COLORMAPS - Static variable in class qupath.lib.gui.UserDirectoryManager
Name of subdirectory containing colormaps.
DIR_CSS - Static variable in class qupath.lib.gui.UserDirectoryManager
Name of subdirectory containing css files for styling.
DIR_EXTENSIONS - Static variable in class qupath.lib.gui.UserDirectoryManager
Name of subdirectory containing extensions.
DIR_LOCALIZATION - Static variable in class qupath.lib.gui.UserDirectoryManager
Name of subdirectory containing properties files for localization.
DIR_LOGS - Static variable in class qupath.lib.gui.UserDirectoryManager
Name of subdirectory containing log files.
DIR_SCRIPTS - Static variable in class qupath.lib.gui.UserDirectoryManager
Name of subdirectory containing shared scripts.
DirectServerChannelInfo - Class in qupath.lib.display
ChannelInfo intended for use with a single or multichannel image (possibly fluorescence) where the pixel's value is used to scale a single color according to a specified display range according to the following rules: If the pixel's value is >= maxDisplay, the pure color is used. If the pixel's value is <= minDisplay, the black is used. Otherwise, a scaled version of the color is used The end result is like having a lookup table (LUT) that stretches from black to the 'pure' color specified, but without actually generating the LUT.
DirectServerChannelInfo(ImageData<BufferedImage>, int) - Constructor for class qupath.lib.display.DirectServerChannelInfo
Constructor.
disabled(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Set the disabled property of the action.
disabled(ObservableValue<Boolean>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Bind the disabled property of the action to an ObservableValue, bidirectionally if possible.
disableGammaAdjustmentProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
Prevent gamma from being adjusted.
disableMinMaxAdjustmentProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
Prevent the min and max sliders from being adjusted.
disableToggleMenuItemsProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Property to disable options to toggle the visibility of channels.
disableUpdatesProperty() - Method in class qupath.lib.gui.panes.AnnotationPane
Property that may be used to prevent updates on every hierarchy or selection change event.
disableUpdatesProperty() - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
Property that may be used to prevent updates on every hierarchy or selection change event.
display(ImageDisplay) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
displayMode() - Method in class qupath.lib.display.ImageDisplay
displayModeProperty() - Method in class qupath.lib.gui.charts.HistogramChart
Property to control how the histogram is displayed, either using areas or bars.
DisplaySettingUtils - Class in qupath.lib.display.settings
Utility class for working with image display and image display settings objects.
DisplaySettingUtils() - Constructor for class qupath.lib.display.settings.DisplaySettingUtils
 
displayToSettings(ImageDisplay, String) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
Create a new image display settings object from the image display.
DISTANCE_CENTROIDS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
DISTANCE_TO_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
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.
DocGenerator - Class in qupath.lib.gui.tools
Command line tool to export icons and markdown documentation for QuPath commands.
DocGenerator() - Constructor for class qupath.lib.gui.tools.DocGenerator
 
doCopy() - Method in class qupath.lib.gui.FileCopier
Perform the copying.
doCreateLogFilesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request a log file to be generated.
DOCS - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
doesSomething() - Method in class qupath.lib.display.AdditiveChannelInfo
 
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
 
doLogCountsProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
Property to control whether the histogram shows pixel counts, or the natural logarithm of the counts.
doubleClickToZoom - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
doubleClickToZoomProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request that double-clicking the viewer can be used to zoom in.
DOWNLOAD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
DownsampledShapeCache - Class in qupath.lib.gui.viewer
Helper class for managing simplified versions of a shape for rendering shapes at lower resolutions.
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.
DragDropImportListener - Class in qupath.lib.gui.viewer
Drag and drop support for main QuPath application, which can support a range of different object types (Files, URLs, Strings,..)
DragDropImportListener(QuPathGUI) - Constructor for class qupath.lib.gui.viewer.DragDropImportListener
Constructor.
DragDropImportListener.DropHandler<T> - Interface in qupath.lib.gui.viewer
Interface to define a new drop handler.
DrawingPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
duplicateSelectedAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Duplicate the selected annotations.

E

EditableText - Interface in qupath.lib.gui.scripting
Interface for objects that manage editable text, including a caret position and selection.
EditMenuActions - Class in qupath.lib.gui.actions.menus
 
EditMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
EditMenuActions.CopyActions - Class in qupath.lib.gui.actions.menus
 
editSelectedAnnotation(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Prompt to edit the selected annotation by translation and rotation.
ELLIPSE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Ellipse drawing tool
ELLIPSE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ELLIPSE_TOOL - Variable in class qupath.lib.gui.ToolManager
 
enableFreehand - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
enableFreehandToolsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Enable polygon/polyline tools to support 'freehand' mode; this means that if the ROI is started by dragging, then it will end by lifting the mouse (rather than requiring a double-click).
ensureCursorType(Cursor) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Ensure that the specified cursor is set in the current viewer.
ensureCursorType(Cursor) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
Ensure that the specified cursor is set in the current viewer.
ensureDuplicatableGlyph(Glyph) - Static method in class qupath.lib.gui.tools.GuiTools
Ensure that a Glyph is 'duplicatable', without losing its key properties.
ensureDuplicatableGlyph(Glyph, boolean) - Static method in class qupath.lib.gui.tools.GuiTools
Ensure that a Glyph is 'duplicatable', optionally retaining any fill.
equals(Object) - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
 
error() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Create an error alert dialog.
error(String) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an error message with static text.
error(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an error message with static text and a count.
error(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
Create a error message to show a count of errors.
error(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an error message.
error(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an error message with a count.
ERROR - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType
Error or exception.
ERROR - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
Error logging (only if something goes recognizably wrong)
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.
eventCountProperty() - Method in class qupath.lib.display.ImageDisplay
Counter for the number of display changes that have been made.
EVERYWHERE - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
Accept all requests
excludeColumns(String...) - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify the columns that will be excluded during the export.
execute(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
 
execute(ScriptParameters) - Method in class qupath.lib.gui.scripting.languages.MarkdownLanguage
 
EXPAND_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
expandableContent(Node) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify a Node to display within the dialog as expandable content, not initially visible.
expandChartClip(Chart, double) - Static method in class qupath.lib.gui.charts.ChartTools
Expand the clip region for a chart.
expandToWindowProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the property indicating whether the image should grow to fill the window (while maintaining its aspect ratio).
EXPORT - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
EXPORT_GEOJSON - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
EXPORT_IMAGE_LIST - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
EXPORT_ORIGINAL - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
 
EXPORT_RENDERED - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
 
exportImageActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
ExportImageActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ExportImageActions
 
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.
ExportObjectsCommand - Class in qupath.lib.gui.commands
Command to export object(s) in GeoJSON format to an output file.
exportPreferences(OutputStream) - Static method in class qupath.lib.gui.prefs.PathPrefs
Export preferences to a stream.
exportSnapshotActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
ExportSnapshotActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
 
exportTMAData(String, double) - Static method in class qupath.lib.gui.scripting.QPEx
Export TMA summary data for the current image.
exportTMAData(ImageData<BufferedImage>, String, double) - Static method in class qupath.lib.gui.scripting.QPEx
Export TMA summary data for the specified image.
exportType(Class<? extends PathObject>) - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify what type of object should be exported.
ExtendedPathTool - Class in qupath.lib.gui.viewer.tools
 
ExtensionPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ExtensionPreferences
 
EXTENSIONS - Variable in class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
 
EXTENSIONS_ONLY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
Check for extensions on GitHub only (not new QuPath releases)
extensionsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
Read only property representing the extensions directory.
ExtensionsMenuActions - Class in qupath.lib.gui.actions.menus
 
ExtensionsMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
EXTRACT_REGION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
eyeTrackingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the eyeTracking property of this tracker.

F

FileCopier - Class in qupath.lib.gui
Copy files to an output directory, prompting the user if necessary.
FileCopier() - Constructor for class qupath.lib.gui.FileCopier
 
FileMenuActions - Class in qupath.lib.gui.actions.menus
 
FileMenuActions(QuPathGUI) - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions
 
FileMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
FileMenuActions.ExportImageActions - Class in qupath.lib.gui.actions.menus
 
FileMenuActions.ExportSnapshotActions - Class in qupath.lib.gui.actions.menus
 
FileMenuActions.ProjectActions - Class in qupath.lib.gui.actions.menus
 
FileMenuActions.TmaActions - Class in qupath.lib.gui.actions.menus
 
FILL_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
FILL_ANNOTATIONS - Variable in class qupath.lib.gui.actions.OverlayActions
 
FILL_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
FILL_DETECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
 
FILL_HOLES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
fillAnnotationsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
fillDetectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
filter(Predicate<PathObject>) - Method in class qupath.lib.gui.tools.MeasurementExporter
Filter the PathObjects before export (objects returning true for the predicate will be included).
findAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
fireImageDataChanged(ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
fireVisibleRegionChangedEvent(Shape) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
fontProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
Get the current selected font.
fontSizeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
forAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a wrapper including all annotations.
forCells(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a wrapper containing all cells.
forceOverlayUpdate() - Method in class qupath.lib.gui.viewer.QuPathViewer
Force the overlay displaying detections and annotations to be repainted.
forDetections(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a wrapper including all detections.
forRoot(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a wrapper including only the root object.
forTiles(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a wrapper containing all tile objects.
forTmaCores(ImageData<?>) - Static method in class qupath.lib.gui.measure.PathObjectListWrapper
Create a wrapper containing all TMA cores.
FORUM - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
fromPackedARGB(int) - Static method in class qupath.lib.display.settings.ChannelColor
Create a channel color from a packed ARGB value.
fromRGB(int, int, int) - Static method in class qupath.lib.display.settings.ChannelColor
Create a channel color from 8-bit RGB values.
fromString(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
Get the ScriptLanguage object corresponding to the specified String.
FULL_SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
Full screenshot, including items outside of QuPath.

G

gammaProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the gamma property for this viewer.
gammaValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
Value of the gamma slider.
GeneralPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
GESTURES_ALL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
 
GESTURES_NONE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
 
GESTURES_ROTATE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
 
GESTURES_SCROLL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
 
GESTURES_ZOOM - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
 
getAcceleratorText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
Get a String representation of any accelerator for the command
getActionProperty(MenuItem) - Static method in class qupath.lib.gui.actions.ActionTools
Retrieve an Action stored within the properties of a menu item, or null if no action is found.
getActionProperty(Node) - Static method in class qupath.lib.gui.actions.ActionTools
Retrieve an Action stored within the properties of a node, or null if no action is found.
getActions() - Method in class qupath.lib.gui.actions.menus.AnalyzeMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.AutomateMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.ClassifyMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.EditMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.ExtensionsMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.FileMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.HelpMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.MeasureMenuActions
 
getActions() - Method in interface qupath.lib.gui.actions.menus.MenuActions
Get all the actions to include in the menu, in order.
getActions() - Method in class qupath.lib.gui.actions.menus.ObjectsMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.TMAMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.ViewMenuActions
 
getActions() - Method in class qupath.lib.gui.actions.menus.WindowMenuActions
 
getActiveTool() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the active PathTool for this viewer.
getActiveToolIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
getActiveViewer() - Method in class qupath.lib.gui.viewer.ViewerManager
getAllFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the collection of recorded frames.
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.
getAllPathClassesVisible() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
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
getAllViewers() - Method in class qupath.lib.gui.QuPathGUI
Get an unmodifiable observable list of all viewers.
getAllViewers() - Method in class qupath.lib.gui.viewer.ViewerManager
Get an observable list of viewers.
getAlphaComposite() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
 
getAnalysisTabPane() - Method in class qupath.lib.gui.QuPathGUI
Access the main tab pane shown in the QuPath window.
getAnnotatedActions(Object) - Static method in class qupath.lib.gui.actions.ActionTools
Actions can be parsed from the accessible (usually public) fields of any object, as well as methods annotated with ActionMethod.
getARGB(Color) - Static method in class qupath.lib.gui.tools.ColorToolsFX
Get a packed int (ARGB) representation of a Color object.
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
 
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.ImageJMacroLanguage
 
getAutoCompletor() - Method in class qupath.lib.gui.scripting.languages.XmlLanguage
 
getAutomateActions() - Method in class qupath.lib.gui.QuPathGUI
Get the automated actions associated with this QuPath instance.
getAutorangeToFullData() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
getAvailableLanguages() - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
Get the available script languages.
getAvailablePathClasses() - Method in class qupath.lib.gui.QuPathGUI
Get an observable list of available PathClasses.
getAvailableSyntaxes() - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
Get the available script syntaxes.
getAvailableTools() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
 
getBackingList() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Access all the objects used to generate the table.
getBackingListEntries() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Deprecated.
getBlue() - Method in class qupath.lib.display.settings.ChannelColor
Get the blue value.
getBorderColor() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the border color set for this viewer.
getBrushDiameter() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
getBufferedImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the buffered image.
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.
getCache() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
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.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.gui.tools.ColorToolsFX
Get cached color.
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.PathObjectPainter
Get a BasicStroke with the specified thickness.
getCachedThumbnail(ImageServer<BufferedImage>, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
getCachedTile(ImageServer<BufferedImage>, RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
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.TextAreaControl
Gets the value of the caretPosition property.
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.
getChannel() - Method in class qupath.lib.display.DirectServerChannelInfo
Get the channel number.
getChannels() - Method in class qupath.lib.display.AdditiveChannelInfo
Get an unmodifiable list of the channels that are merged here for display.
getChannels() - Method in class qupath.lib.display.settings.ImageDisplaySettings
Get all the available channels.
getChartDataAsString(XYChart<Number, Number>) - Static method in class qupath.lib.gui.charts.ChartTools
Get a string representation of chart data, in such a way that it could be pasted into a spreadsheet.
getChooser(Window) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Get a QuPathChooser instance linked to a specific window.
getCitationUrl() - Static method in class qupath.lib.gui.Urls
Get a URL pointing to a page that explains how to cite this version of QuPath in a publication.
getClipboardText(boolean) - Static method in class qupath.lib.gui.scripting.DefaultScriptEditor
Get the text from the system clipboard, optionally escaping characters.
getColor() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getColor() - Method in interface qupath.lib.display.ChannelDisplayInfo
Predominate color used when this ChannelDisplayInfo uses a Color LUT (e.g.
getColor() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getColor() - Method in class qupath.lib.display.settings.ChannelSettings
Get the color used to display the channel, or null if a color is not relevant.
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.
getColormapsDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
Get the path to where colormaps should be written.
getColorModel() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
Get the ColorModel for this renderer (may be null).
getColorModel() - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
 
getColorModel(ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
 
getColorScheme() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
Get the color scheme.
getColorWithOpacity(Color, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX
Derived a Color from an existing one, setting the alpha component to match the desired opacity.
getColorWithOpacityFX(Integer, double) - Static method in class qupath.lib.gui.tools.ColorToolsFX
Get a Color from a packed RGB value, setting the alpha component to match the desired opacity.
getCommandPath() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
Get a string representation of the menu path for this command, including the menu path and the text.
getCommonActions() - Method in class qupath.lib.gui.QuPathGUI
Get the common actions associated with this QuPath instance.
getCompletions(String, int) - Method in class qupath.lib.gui.scripting.completors.DefaultAutoCompletor
 
getConfigPath() - Static method in class qupath.lib.gui.prefs.PathPrefs
Try to get the path to the config file.
getContents(Parent, Collection<Node>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Get the nodes that are included within a Parent, optionally adding other nodes recursively.
getContentsOfType(Parent, Class<T>, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Get the nodes of type T that are contained within a Parent, optionally adding other nodes recursively.
getContextMenu() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Get the context menu for the control.
getContextMenu() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
getCoreClasses() - Static method in class qupath.lib.gui.scripting.QPEx
Get a list of core classes that are likely to be useful for scripting.
getCount() - Method in class qupath.lib.gui.actions.InfoMessage
Counts associated with the message, or -1 if the count is null.
getCountsTransform() - Method in class qupath.lib.gui.charts.HistogramChart
Get the current counts transform.
getCssStylesPath() - Method in class qupath.lib.gui.UserDirectoryManager
Get the path to where user directory for storing CSS styles.
getCurrentConsoleControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
getCurrentEditorControl() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
getCurrentImages(QuPathGUI) - Static method in class qupath.lib.gui.dialogs.ProjectDialogs
Get the ProjectImageEntry for each of the current images open in QuPath, if available.
getCurrentLanguage() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Gets the value of the currentLanguage property.
getCurrentParent() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
getCurrentParent() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
getCurrentROI() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the current ROI, i.e.
getCurrentScriptTab() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
getCurrentSyntax() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Gets the value of the currentSyntax property.
getCurrentText() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
getCurrentViewer() - Static method in class qupath.lib.gui.scripting.QPEx
Get the active viewer in the current QuPath instance.
getCursor() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the current cursor for this viewer
getCustomOverlayLayers() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get direct access to the custom overlay list.
getCustomPixelLayerOverlay() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the custom pixel layer overlay, or null if it has not be set.
getDataMaxValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
Get the maximum measurement value from the objects passed to the constructor of this mapper.
getDataMinValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
Get the minimum measurement value from the objects passed to the constructor of this mapper.
getDefaultAutoCompletor(String) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Default method to get a suitable auto completor for the given language name.
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.
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.
getDefaultQuPathUserDirectory() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get the default location for extensions.
getDefaultScriptName() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
 
getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
getDefaultWindowTitle() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
getDefaultZoomFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
The amount by which the downsample factor is scaled for one increment of QuPathViewer.zoomIn() or QuPathViewer.zoomOut().
getDescription() - Method in interface qupath.lib.gui.extensions.QuPathExtension
A short description of the extension for displaying in the main GUI.
getDescription() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
Get a user-friendly description of the style.
getDetectionDisplayMode() - Method in class qupath.lib.gui.viewer.OverlayOptions
getDisplayedClipShape(Shape) - Method in class qupath.lib.gui.viewer.QuPathViewer
Transform a clip shape into image coordinates for this viewer.
getDisplayedColor(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX
Get a Color appropriate for displaying an object.
getDisplayedColorARGB(PathObject) - Static method in class qupath.lib.gui.tools.ColorToolsFX
Get the color with which an object should be displayed, as a packaged ARGB integer.
getDisplayedImageName(ImageData<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI
Get the image name to display for a specified image.
getDisplayedRegionShape() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get a shape corresponding to the region of the image currently visible in this viewer.
getDisplayMaxValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
Get the measurement value that maps to the last color in the color mapper.
getDisplayMinValue() - Method in class qupath.lib.gui.tools.MeasurementMapper
Get the measurement value that maps to the first color in the color mapper.
getDisplayMode() - Method in class qupath.lib.gui.charts.HistogramChart
Get the histogram display mode.
getDocsUrl() - Static method in class qupath.lib.gui.Urls
Get the base URL for the QuPath documentation (independent of version).
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.
getDownsampleFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the current downsample factor.
getEngineByName(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
Get the ScriptEngine based on its name.
getExcludeColumns() - Method in class qupath.lib.gui.tools.MeasurementExporter
Returns the list of columns to exclude from export.
getExcludeOutsideRange() - Method in class qupath.lib.gui.tools.MeasurementMapper
Returns true if objects with values outside the specified min/max range have the min/max colors returned, false if null should be returned instead.
getExpandToWindow() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Query whether the image is allowed to expand beyond its preferred width and height to fill the window.
getExtensionCatalogManager() - Static method in class qupath.lib.gui.QuPathGUI
 
getExtensionsDocsUrl() - Static method in class qupath.lib.gui.Urls
Get a URL pointing to a page that explains how to install QuPath extensions.
getExtensionsPath() - Method in class qupath.lib.gui.UserDirectoryManager
Get the path to where extensions should be stored.
getEyeFixatedIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
getEyePointIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
getFile() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the file associated with this ViewTracker.
getFill() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData
Get the histogram fill color.
getFillAnnotations() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getFillDetections() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
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.
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
 
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.
getFullLocationString(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
Get a string to summarize the pixel found below the most recent known mouse location, or "" if the mouse is outside this viewer.
getFullMagnification() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the full magnification for the image.
getGamma() - Method in class qupath.lib.display.settings.ImageDisplaySettings
Get the requested vamma value for the viewer.
getGamma() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the gamma value used for this viewer.
getGammaOp() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get a LookupOp that can perform any requested gamma correction in this viewer.
getGeoJsonDataFormat() - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
Get a DataFormat suitable for storing GeoJSON data on a clipboard.
getGeometryFactory() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
getGitHubIssuesUrl() - Static method in class qupath.lib.gui.Urls
Get a URL pointing to the main GitHub issues page.
getGitHubRepoUrl() - Static method in class qupath.lib.gui.Urls
Get a URL pointing to the main QuPath GitHub repo.
getGreen() - Method in class qupath.lib.display.settings.ChannelColor
Get the green value.
getGridLines() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getHelpText(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Get help text for a measurement if available, or null if no help text is found.
getHideIfEmpty() - Method in class qupath.lib.gui.charts.HistogramChart
Query whether the chart is automatically hidden (visibility set to false) when there is no data.
getHierarchy() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the object hierarchy for the current image data, or null if no image data is available.
getHistogram() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData
Get the histogram.
getHistogram(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
Returns a histogram for a channel of the current image.
getHistogramData() - Method in class qupath.lib.gui.charts.HistogramChart
Get all histogram data objects.
getIcon() - Method in interface qupath.lib.gui.viewer.tools.PathTool
Get the icon of the tool.
getImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the JavaFX image.
getImageData() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getImageData() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getImageData() - Method in class qupath.lib.display.ImageDisplay
Get the current image data
getImageData() - Method in class qupath.lib.gui.QuPathGUI
getImageData() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the image data currently being displayed within thie viewer.
getImageDisplay() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the ImageDisplay object used to determine how the image is converted to RGB for display.
getImageList() - Method in class qupath.lib.gui.tools.MeasurementExporter
Returns the list of images (ProjectImageEntry).
getImageObjectClassificationString(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Get a string representing the object classification x & y location in the viewer component, or an empty String if no object is found.
getImagePlane() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the ImagePlane currently being displayed, including z and t positions.
getImageRegionStore() - Method in class qupath.lib.gui.QuPathGUI
Return the global DefaultImageRegionStore instance, used to cache and paint image tiles.
getImageRegionStore() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the region store used by this viewer for tile caching and painting.
getImageServer() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getImageServer() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getImportStatementGenerator() - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
getImportStatementGenerator() - Method in class qupath.lib.gui.scripting.languages.GroovyLanguage
 
getImportStatements(Collection<Class<?>>) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Get the import statements as a String, to add at the beginning of the executed script.
getImportStatments(Collection<Class<?>>) - Method in interface qupath.lib.gui.scripting.languages.DefaultScriptLanguage.ImportStatementGenerator
 
getIncludeColumns() - Method in class qupath.lib.gui.tools.MeasurementExporter
Returns the list of columns to include in the export.
getInfoMessage() - Method in class qupath.lib.gui.commands.ContextHelpViewer
Get a message that may be used to create a badge indicating that info or warning messages are available.
getInfoMessage() - Method in class qupath.lib.gui.commands.LogViewerCommand
Get a string expression to draw attention to error messages.
getInstallationUrl() - Static method in class qupath.lib.gui.Urls
Get a URL pointing to a page that explains how to install this version of QuPath.
getInstance() - Static method in class qupath.lib.gui.BuildInfo
Get the shared BuildInfo instance.
getInstance() - Static method in class qupath.lib.gui.QuPathGUI
Get the static instance of the current QuPath GUI.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.CssLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.GroovyLanguage
Get the static instance of this class, using the default code completions.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.ImageJMacroLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.JsonLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.MarkdownLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.PlainLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.PropertiesLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.XmlLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.scripting.languages.YamlLanguage
Get the static instance of this class.
getInstance() - Static method in class qupath.lib.gui.UserDirectoryManager
Get the singleton instance of the UserDirectoryManager.
getInstance(QuPathGUI) - Static method in class qupath.lib.gui.commands.ContextHelpViewer
Get the single ContextHelpViewer instance associated with a specific QuPath instance.
getInstance(QuPathGUI) - Static method in class qupath.lib.gui.WelcomeStage
 
getInstanceWithCompletions(Collection<? extends AutoCompletions.Completion>) - Static method in class qupath.lib.gui.scripting.languages.GroovyLanguage
Get an instead of this class that uses the specified code completions, rather than the defaults.
getInterpolation() - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
Get the preferred method of interpolation to use for display.
getItem() - Method in class qupath.lib.gui.SelectableItem
Get the current item.
getItems() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
 
getItems() - Method in interface qupath.lib.gui.measure.PathTableData
Get internal list of the items used to provide measurements.
getJavadocViewer() - Method in class qupath.lib.gui.JavadocViewerRunner
Get a reference to the viewer launched by the JavadocViewerCommand.
getLanguage() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Get any language stored for text to be displayed by this control.
getLanguageFromExtension(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
Return the first ScriptLanguage compatible with the specified extension (can be runnable or not).
getLanguageFromName(String) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
Given a file name, determine the associated language - or null if no suitable (supported) language can be found.
getLanguageNames() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Get a set of the scripting languages supported by this syntax.
getLastChangeTimestamp() - Method in class qupath.lib.display.ImageDisplay
Get the event count, which is here used as an alternative to a timestamp.
getLastChangeTimestamp() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
 
getLastChangeTimestamp() - Method in interface qupath.lib.gui.images.stores.ImageRenderer
Timestamp of the last change.
getLastTime() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the time associated with the last recorded frame.
getLatestCommit() - Method in class qupath.lib.gui.BuildInfo
Get reference to the latest git commit, if known, or null if this has not be preserved.
getLineCommentString() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Get the String that represents the start of a comment line.
getLineWidth() - Method in class qupath.lib.gui.charts.ChartThresholdPane
Get the threshold line width.
getLivePrediction() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Query whether live prediction is turned on.
getLocalizationDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
Get the path to where localization property files should be written.
getLocalizedResourceManager() - Static method in class qupath.lib.gui.localization.QuPathResources
Get a localized resource manager, which can be used to manage localized strings, and update these whenever the locale preferences are updated.
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
 
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in interface qupath.lib.gui.viewer.overlays.AbstractOverlay.LocationStringFunction
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in interface qupath.lib.gui.viewer.overlays.PathOverlay
Get a location string to display when showing a specified image.
getLocationString(ImageData<BufferedImage>, double, double, int, int) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
 
getLocationStringFunction() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
 
getLogDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
Get the path to where log files should be written.
getLogMessageCounts() - Method in class qupath.lib.gui.commands.LogViewerCommand
Get the counts of all messages logged by the log viewer.
getLogViewerCommand() - Method in class qupath.lib.gui.QuPathGUI
Get the log viewer associated with this QuPath instance.
getLongText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
Get the long text (description) for the command, if available.
getMagnification() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the magnification for the image within this viewer, or Double.NaN if no image is present.
getMagnificationString(QuPathViewer) - Static method in class qupath.lib.gui.tools.GuiTools
Get an appropriate String to represent the magnification of the image currently in the viewer.
getMaxAllowed() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getMaxAllowed() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getMaxAllowed() - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the max allowed display value.
getMaxDisplay() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getMaxDisplay() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getMaxDisplay() - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the max display value.
getMaxDisplay() - Method in class qupath.lib.display.settings.ChannelSettings
Get the requested maximum display value for the channel, This should be used with the last entry in any lookup table.
getMaxDownsample() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the maximum downsample value supported by this viewer.
getMaxPoints() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
getMaxROIHandleSize() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the maximum size for which ROI handles may be drawn.
getMaxThreads() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Get the maximum number of threads that may be used during live prediction.
getMeasurementMapper() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getMeasurementNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
 
getMeasurementNames() - Method in interface qupath.lib.gui.measure.PathTableData
Get the names of all numeric measurements.
getMenu(String, boolean) - Method in class qupath.lib.gui.QuPathGUI
Get a reference to an existing menu from the main QuPath menubar, optionally creating a new menu if it is not present.
getMenu(List<Menu>, String, boolean) - Static method in class qupath.lib.gui.tools.MenuTools
Get a reference to an existing menu, optionally creating a new menu if it is not present.
getMenuBar() - Method in class qupath.lib.gui.QuPathGUI
Get the menubar for the main QuPath application.
getMenuItem() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
Get the menu item corresponding to this command.
getMenuPath() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
Get a String representation of the menu containing this command.
getMessageType() - Method in class qupath.lib.gui.actions.InfoMessage
Type of the message.
getMetadataNames() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Get the names of all columns corresponding to metadata (String) values.
getMethod() - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the ColorTransformer.ColorTransformMethod associated with this channel, or null if no method is relevant.
getMinAllowed() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getMinAllowed() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getMinAllowed() - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the min allowed display value.
getMinDisplay() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getMinDisplay() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getMinDisplay() - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the min display value.
getMinDisplay() - Method in class qupath.lib.display.settings.ChannelSettings
Get the requested minimum display value for the channel.
getMinDownsample() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the minimum downsample value supported by this viewer.
getModel() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
getMousePointIfRequired() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
getMousePosition() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the current cursor position within this viewer, or null if the cursor is outside the viewer.
getName() - Method in class qupath.lib.display.AdditiveChannelInfo
 
getName() - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the channel name.
getName() - Method in class qupath.lib.display.DirectServerChannelInfo
 
getName() - Method in class qupath.lib.display.settings.ChannelSettings
Get the name of the channel.
getName() - Method in class qupath.lib.display.settings.ImageDisplaySettings
Get the name of the settings.
getName() - Method in class qupath.lib.gui.actions.menus.AnalyzeMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.AutomateMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.ClassifyMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.EditMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.ExtensionsMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.FileMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.HelpMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.MeasureMenuActions
 
getName() - Method in interface qupath.lib.gui.actions.menus.MenuActions
Get the name of the menu.
getName() - Method in class qupath.lib.gui.actions.menus.ObjectsMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.TMAMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.ViewMenuActions
 
getName() - Method in class qupath.lib.gui.actions.menus.WindowMenuActions
 
getName() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
Get the name.
getName() - Method in interface qupath.lib.gui.extensions.QuPathExtension
A readable name for the extension.
getName() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
Get the release name (any text).
getName() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the name of the image.
getName() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
Get a user-friendly name for the style.
getName() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the name of this ViewTracker.
getName() - Method in interface qupath.lib.gui.viewer.tools.PathTool
Get the name of the tool
getNavigationAccelerationProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get whether to apply the navigation acceleration (& deceleration) effects or not.
getNewConsole() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
getNewEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
getNode() - Method in interface qupath.lib.gui.tools.PathObjectImageViewers.ItemViewer
Get the node to display
getNode() - Method in class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane
Get the node to display.
getNumBins() - Method in class qupath.lib.gui.charts.HistogramDisplay
Get the requested number of bins used for the histogram.
getNumericValue(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
 
getNumericValue(T, String) - Method in interface qupath.lib.gui.measure.PathTableData
Get the numeric value from an item for the specific measurement.
getObjectClassificationString(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Get a string representing the object classification x & y location in the viewer component, or an empty String if no object is found.
getOpacity() - Method in class qupath.lib.gui.viewer.OverlayOptions
Get the global opacity for overlay drawing.
getOpacity() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
Get opacity, between 0 (completely transparent) and 1 (completely opaque).
getOriginalChannelName() - Method in class qupath.lib.display.DirectServerChannelInfo
Get the original channel name, extracted for the current ImageData if available.
getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
 
getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
 
getOriginalMetadata() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
 
getOverlayActions() - Method in class qupath.lib.gui.QuPathGUI
Get the actions associated with the viewer overlay options.
getOverlayLayers() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get an unmodifiable list containing the overlay layers, in order.
getOverlayOptions() - Method in class qupath.lib.gui.actions.OverlayActions
Get the overlay options controlled by these actions.
getOverlayOptions() - Method in class qupath.lib.gui.QuPathGUI
Return the global OverlayOptions instance, used to control display within viewers by default.
getOverlayOptions() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
Get the overlay options, which may influence the display of this overlay.
getOverlayOptions() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the overlay options that control the viewer display.
getOverlayOptions() - Method in class qupath.lib.gui.viewer.ViewerManager
Get the overlay options shared by all viewers created by this manager.
getOverrideSystemMenuBar() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Get the current value of the override property, which specifies whether the system menubar should not be used by any window - no matter what the value of SystemMenuBar.systemMenubarProperty().
getOwner() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
Get the owner.
getPane() - Method in class qupath.lib.gui.charts.HistogramDisplay
Get the pane containing the histogram and associated UI components, for addition to a scene.
getPane() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
Get the pane containing the scatter plot and associated UI components, for addition to a scene.
getPane() - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
Get the pane containing all mini viewers, which can be added to a scene for display.
getPane() - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Get the Pane that can be displayed.
getPane() - Method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
 
getPane() - Method in class qupath.lib.gui.panes.AnnotationPane
Get the pane for display.
getPane() - Method in class qupath.lib.gui.panes.ImageDetailsPane
Get the Pane component for addition to a scene.
getPane() - Method in class qupath.lib.gui.panes.MeasurementMapPane
Get the pane, which can be added to a scene for display.
getPane() - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
Get the pane for display.
getPane() - Method in class qupath.lib.gui.panes.PreferencePane
Get a pane to display.
getPane() - Method in class qupath.lib.gui.panes.ProjectBrowser
Get the Pane component for addition to a scene.
getPane() - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
Get the Pane containing the table and a filter field.
getPane() - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
Get the pane to add to a scene.
getParameterEnabled(String) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Returns true if a parameter exists with the given key and is enabled (and is therefore editable).
getParameterEnabled(Parameter<?>) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Returns true if a parameter is enabled (and is therefore editable).
getParameters() - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Get the ParameterList displayed in this panel.
getPathClassColor(PathClass) - Static method in class qupath.lib.gui.tools.ColorToolsFX
Get a Color appropriate for displaying a PathClass.
getPenManager() - Static method in class qupath.lib.gui.viewer.tools.QuPathPenManager
Get the current PenInputManager.
getPixelClassificationRegionFilter() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getPixelClassificationServer(ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Get the ImageServer that would be used by this overlay for the specified ImageData.
getPixelLayer(ImageData<?>) - Static method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Request the pixel layer from an ImageData.
getPlaceholderText() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the placeholder text to show if no image is available.
getPointOpacity() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
getPointRadius() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
getPredicateTextField() - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
Get the predict text field that is used to filter measurements.
getPreferencePane() - Method in class qupath.lib.gui.QuPathGUI
Get a reference to the PreferencePane.
getPreferredOverlayColor() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
Return the preferred overlay color.
getPressure() - Method in interface qupath.lib.gui.viewer.tools.QuPathPenManager.PenInputManager
Returns a pressure value, between 0 and 1.
getPreviousSelectedTool() - Method in class qupath.lib.gui.ToolManager
getProject() - Method in class qupath.lib.gui.QuPathGUI
Get the value of QuPathGUI.projectProperty().
getProjection() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
Gets the value of the projection property.
getPropertySheet() - Method in class qupath.lib.gui.panes.PreferencePane
Get the property sheet for this PreferencePane.
getQuPath() - Method in class qupath.lib.gui.actions.CommonActions
Get the QuPath instance associated with these actions.
getQuPath() - Static method in class qupath.lib.gui.scripting.QPEx
Get the current QuPath instance.
getQuPathVersion() - Method in interface qupath.lib.gui.extensions.QuPathExtension
Get a QuPath version for which this extension was written.
getRecentProjectList() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get a list of the most recent projects that were opened.
getRecentScriptsList() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get a list of the most recent scripts that were opened.
getRed() - Method in class qupath.lib.display.settings.ChannelColor
Get the red value.
getRegion() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Get the region representing this control, so it may be added to a scene.
getRegion() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
getRegion() - Method in class qupath.lib.gui.viewer.ViewerManager
Get the region node that can be added to a scene graph to display the viewers.
getRegionMap() - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Get an unmodifiable Map containing image regions to paint on this overlay.
getRelativePathOrNull(String) - Method in class qupath.lib.gui.UserDirectoryManager
 
getRenderer() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Get the ImageRenderer used with this overlay, which may be null.
getRenderer() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
Get the ImageRenderer used with this overlay, which may be null.
getRenderer() - Method in class qupath.lib.gui.viewer.QuPathViewer
Request a renderer that converts image tiles into RGB images.
getRepo() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
Get the repo.
getRepository() - Method in interface qupath.lib.gui.extensions.GitHubProject
Get the GitHub repository associated with the project.
getRequestedCursor() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
getResourcesForProject(Project<?>) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
Get the resource manager for image display settings from a project.
getRGB(float, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
Get a suitable RGB value for displaying a pixel with the specified value
getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
 
getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
 
getRGB(BufferedImage, int[], ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the RGB values that would be used to display all the pixels of an image
getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
 
getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
 
getRGB(BufferedImage, int, int, ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
Get the RGB value that would be used to display a particular pixel
getRGB(Color) - Static method in class qupath.lib.gui.tools.ColorToolsFX
Get a packed int (ARGB) representation of a Color object, omitting the alpha component.
getRGBThumbnail() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get a thumbnail representing the image as displayed by this viewer.
getRngSeed() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
getROIEditor() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the RoiEditor used by this viewer.
getRootLogLevel() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level, as set by this manager.
getRotation() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the current rotation; angle in radians.
getRowStrings() - Method in interface qupath.lib.gui.measure.PathTableData
Get a list of Strings representing table data for all items.
getRowStrings(String, int, Predicate<String>) - Method in interface qupath.lib.gui.measure.PathTableData
Get a list of Strings representing table data for all items.
getRowStrings(Collection<? extends T>, String, int, Predicate<String>) - Method in interface qupath.lib.gui.measure.PathTableData
Get a list of Strings representing table data for specific items.
getSaturationPercent() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the percentage of pixels to use when applying auto contrast settings to a non-8-bit image.
getScaledNavigationSpeed() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get navigation speed scaled as a proportion and forced to be in the range 0-1.
getScaledRGBInstance(BufferedImage, int, int) - Static method in class qupath.lib.gui.tools.GuiTools
Get a scaled (RGB or ARGB) image, achieving reasonable quality even when scaling down by a considerably amount.
getScaledScrollSpeed() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get scroll speed scaled as a proportion and forced to be in the range 0-1.
getScriptEditor() - Method in class qupath.lib.gui.QuPathGUI
Get a reference to the current ScriptEditor (which may or may not be open at the moment).
getScriptsDirectoryPath() - Method in class qupath.lib.gui.UserDirectoryManager
Get the path to where shared script files should be written.
getSelectedClassVisibilityMode() - Method in class qupath.lib.gui.viewer.OverlayOptions
getSelectedObject() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the currently-selected object from the hierarchy.
getSelectedText() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
getSelectedText() - Method in interface qupath.lib.gui.scripting.EditableText
Get the selected text as a string.
getSelectedText() - Method in class qupath.lib.gui.scripting.TextAreaControl
Gets the value of the selectedText property.
getSelectedTool() - Method in class qupath.lib.gui.ToolManager
getSelection() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Get the range of the currently-selected text.
getSelection() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
getSelectionEnd() - Method in interface qupath.lib.gui.scripting.EditableText
Get the ending position for any selection (exclusive).
getSelectionEnd() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
 
getSelectionLength() - Method in interface qupath.lib.gui.scripting.EditableText
Get the selection length, or 0 if there is no selection.
getSelectionModeAction() - Method in class qupath.lib.gui.ToolManager
Return the action associated with 'selection mode'.
getSelectionModel() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Get the selection model for the channels.
getSelectionStart() - Method in interface qupath.lib.gui.scripting.EditableText
Get the starting position for any selection (inclusive).
getSelectionStart() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
 
getSeparator() - Method in class qupath.lib.gui.tools.MeasurementExporter
Returns the separator used in between measurements.
getSerializationExtension() - Static method in class qupath.lib.gui.prefs.PathPrefs
File extension used for serialization of ImageData (without the dot)
getServer() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the ImageServer for the current image displayed within the viewer, or null if no image is displayed.
getServerBounds() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get an ImageRegion representing the full width and height of the current image.
getServerHeight() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the height in pixels of the full resolution of the current image, or 0 if no image is currently open.
getServerType() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
 
getServerType() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
 
getServerType() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
 
getServerWidth() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the width in pixels of the full resolution of the current image, or 0 if no image is currently open.
getShapeForDownsample(ROI, double) - Static method in class qupath.lib.gui.viewer.DownsampledShapeCache
Get the shape for a particular downsample.
getSharedInstance() - Static method in class qupath.lib.gui.viewer.OverlayOptions
Get a shared OverlayOptions instance that makes some properties persistent.
getSharedInstance() - Static method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
Get a shared instance with persistence properties.
getShowAllRGBTransforms() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request that all available color transforms are shown for RGB images.
getShowAnnotations() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowCellBoundaries() - Method in class qupath.lib.gui.viewer.OverlayOptions
Query the current OverlayOptions.DetectionDisplayMode to see if cell boundary ROIs should be drawn.
getShowCellNuclei() - Method in class qupath.lib.gui.viewer.OverlayOptions
Query the current OverlayOptions.DetectionDisplayMode to see if nuclei ROIs should be drawn.
getShowConnections() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowDetections() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowGrid() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowLocation() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
getShowNames() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowObjectPredicate() - Method in class qupath.lib.gui.viewer.OverlayOptions
getShowOverview() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
getShowPixelClassification() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowScalebar() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
getShowTMACoreLabels() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowTMAGrid() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getShowZProjectControls() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
getSingleThreadExecutor(Object) - Method in class qupath.lib.gui.SharedThreadPoolManager
Get a reusable executor using a single thread, creating a new executor if needed.
getSize() - Method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
 
getSkipMissingCoresProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Return whether the viewer skips missing TMA cores when navigating TMA grids with arrow keys.
getSpaceX() - Method in class qupath.lib.gui.viewer.GridLines
Horizontal spacing between lines for any counting grid.
getSpaceY() - Method in class qupath.lib.gui.viewer.GridLines
Vertical spacing between lines for any counting grid.
getStage() - Method in class qupath.lib.gui.commands.ContextHelpViewer
Get the help viewer stage.
getStage() - Method in class qupath.lib.gui.commands.PathObjectGridView
Get the stage used to show the grid view.
getStage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the stage used to display the image.
getStage() - Method in class qupath.lib.gui.QuPathGUI
Get the main QuPath stage.
getStage() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Get the stage for this script editor.
getStage() - Method in class qupath.lib.gui.tma.TMASummaryViewer
Deprecated.
Get the stage for display.
getStartTime() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the time associated with the first recorded frame.
getStartX() - Method in class qupath.lib.gui.viewer.GridLines
Starting x coordinate for any counting grid (usually 0).
getStartY() - Method in class qupath.lib.gui.viewer.GridLines
Starting y coordinate for any counting grid (usually 0).
getStaticImportStatements(Collection<Class<?>>) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Get the static import statements as a String, to add at the beginning of the executed script.
getStaticImportStatments(Collection<Class<?>>) - Method in interface qupath.lib.gui.scripting.languages.DefaultScriptLanguage.ImportStatementGenerator
 
getString(String) - Static method in class qupath.lib.gui.localization.QuPathResources
Get a string from the main ResourceBundle used for the QuPath user interface.
getString(String, String) - Static method in class qupath.lib.gui.localization.QuPathResources
 
getStringValue(PathObject, String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
 
getStringValue(PathObject, String, int) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
 
getStringValue(T, String) - Method in interface qupath.lib.gui.measure.PathTableData
Get a string representation of the value.
getStringValue(T, String, int) - Method in interface qupath.lib.gui.measure.PathTableData
Get a string value, converting to a fixed number of decimal places if the column is numeric.
getStroke() - Method in class qupath.lib.gui.charts.HistogramChart.HistogramData
Get the histogram stroke color.
getStyleColorScheme() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
Get the color scheme of the current style, or the system color scheme if no other is available.
getStyles() - Method in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
 
getStyleSheet() - Static method in class qupath.lib.gui.tools.WebViews
 
getSwitchToGrayscaleChannel() - Method in class qupath.lib.display.ImageDisplay
getSynchronizeViewers() - Method in class qupath.lib.gui.viewer.ViewerManager
Gets the value of the synchronizeViewers property.
getSyntaxFromName(String) - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
Get a script syntax from a specified language name.
getTable() - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
Get the TableView.
getTableModelString(PathTableData<T>, String, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
Get a single String representing the data in a table.
getTableModelStrings(PathTableData<T>, String, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
Get a list of Strings representing table data.
getTabString() - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
String to insert when tab key pressed
getText() - Method in class qupath.lib.gui.actions.InfoMessage
Text of the message.
getText() - Method in interface qupath.lib.gui.scripting.EditableText
Get all the text in the editor;
getText() - Method in class qupath.lib.gui.scripting.TextAreaControl
Gets the value of the text property.
getText() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
Get the name of the command.
getTextField(Parameter<?>, int, String) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
 
getThickStrokeWidth(double) - Method in class qupath.lib.gui.viewer.OverlayOptions
Get the requested stroke thickness to use when drawing ROIs that should be represented with 'thick' lines (annotations, TMA cores).
getThis() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
getThis() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
getThis() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
getThreadPoolManager() - Method in class qupath.lib.gui.QuPathGUI
Get a SharedThreadPoolManager to help with submitting tasks in other threads.
getThresholds() - Method in class qupath.lib.gui.charts.ChartThresholdPane
Get a list of all thresholds.
getThumbnail() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get a thumbnail representing the image as displayed by this viewer.
getThumbnail(ImageServer<BufferedImage>, int, int, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
getThumbnailRGB(ImageServer<BufferedImage>) - Static method in class qupath.lib.gui.commands.ProjectCommands
Get an RGB thumbnail for an image server, suitable for showing as a project thumbnail.
getTileCacheSize() - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
Get the tile cache size, in bytes.
getTileRequest(ImageServer<BufferedImage>, double, double, double, int, int) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreHelpers
Given an ImageServer, determine the boundaries of the image tile that contains specified x, y coordinates.
getTilesToRequest(ImageServer<?>, Shape, double, int, int, List<RegionRequest>) - Static method in class qupath.lib.gui.images.stores.ImageRegionStoreHelpers
Given ImageServer, determine the boundaries of the image tiles that would be needed to paint a specified shape (defined by coordinates in the full-resolution image space).
getTool(String) - Static method in class qupath.lib.gui.viewer.tools.PathTools
Return the PathTool corresponding to the specified String.
getToolAction(PathTool) - Method in class qupath.lib.gui.ToolManager
Get the action that corresponds to a specific PathTool, creating a new action if one does not already exist.
getToolBar() - Method in class qupath.lib.gui.QuPathGUI
Get the main toolbar.
getToolManager() - Method in class qupath.lib.gui.QuPathGUI
Get the ToolManager that handles available and selected tools.
getTools() - Method in class qupath.lib.gui.ToolManager
Get a read-only list of all available tools.
getTPosition() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the currently-visible time point.
getTransformedValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.ImageDisplay
Get a string representation of a transformed pixel value, using the currently-selected channels.
getType() - Method in class qupath.lib.gui.tools.MeasurementExporter
Returns the type of path objects used in the export.
getUndoRedoManager() - Method in class qupath.lib.gui.QuPathGUI
Get the UndoRedoManager, which can be useful if needing to clear it in cases where available memory is low.
getUniqueID() - Method in class qupath.lib.gui.images.stores.AbstractImageRenderer
 
getUniqueID() - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
 
getUniqueID() - Method in interface qupath.lib.gui.images.stores.ImageRenderer
Get a unique key, which will be used for caching.
getUri() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
Get a URI to download the release (may be null if no URI is available).
getURIs() - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
 
getURIs() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
 
getUrlString() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
Get the URL for the main repo.
getUseExactSelectedClasses() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
getUsefulValue(PathObject, double) - Method in class qupath.lib.gui.tools.MeasurementMapper
 
getUserForumUrl() - Static method in class qupath.lib.gui.Urls
Get a URL pointing to the main QuPath user forum.
getUserPath() - Method in class qupath.lib.gui.UserDirectoryManager
Get the user path where additional files may be stored.
getUserPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
Deprecated.
since v0.5.0 - avoid direct use of the Preferences object, since this may be invalidated by a call to PathPrefs.resetPreferences()
getValue(BufferedImage, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
 
getValue(BufferedImage, int, int) - Method in interface qupath.lib.display.SingleChannelDisplayInfo
Extract the value for a single pixel of an image.
getValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
 
getValueAsString(BufferedImage, int, int) - Method in class qupath.lib.display.AdditiveChannelInfo
 
getValueAsString(BufferedImage, int, int) - Method in interface qupath.lib.display.ChannelDisplayInfo
Get a string representation of a pixel's value.
getValues(BufferedImage, int, int, int, int, float[]) - Method in class qupath.lib.display.DirectServerChannelInfo
 
getValues(BufferedImage, int, int, int, int, float[]) - Method in interface qupath.lib.display.SingleChannelDisplayInfo
Extract values for a square of pixels from an image.
getVersion() - Method in class qupath.lib.gui.BuildInfo
Get the version, or null if the version is unknown.
getVersion() - Method in interface qupath.lib.gui.extensions.QuPathExtension
Get the version of the current extension.
getVersion() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
Get the semantic version.
getVersion() - Static method in class qupath.lib.gui.QuPathGUI
Get the current QuPath version.
getVersionedDocsUrl() - Static method in class qupath.lib.gui.Urls
Get the base URL for the QuPath documentation, specifically for this software version.
getVersionedDocsUrl(String) - Static method in class qupath.lib.gui.Urls
Get the base URL for the QuPath documentation for this software version, including a relative component to link to a specific page (without leading slash).
getView() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the main JavaFX component representing this viewer.
getViewer() - Method in class qupath.lib.gui.QuPathGUI
Get the currently active viewer.
getViewer() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
getViewer() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
getViewerActions() - Method in class qupath.lib.gui.QuPathGUI
Get the associations associated with QuPath image viewers.
getViewerManager() - Method in class qupath.lib.gui.actions.ViewerActions
 
getViewerManager() - Method in class qupath.lib.gui.QuPathGUI
Get the viewer manager, which gives access to all the viewers available within this QuPath instance.
getWindow(String) - Static method in class qupath.lib.gui.scripting.QPEx
Access a window currently open within QuPath by its title.
getYouTubeUrl() - Static method in class qupath.lib.gui.Urls
Get a URL pointing to the QuPath YouTube channel.
getZoomToFitDownsampleFactor() - Method in class qupath.lib.gui.viewer.QuPathViewer
 
getZPosition() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the currently-visible z-slice.
GITHUB - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
GitHubProject - Interface in qupath.lib.gui.extensions
Helper class to represent a project hosted on GitHub.
GitHubProject.GitHubRepo - Class in qupath.lib.gui.extensions
Helper class to represent a GitHub repository.
graphic(ObservableValue<Node>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Bind the graphic property of the action to an ObservableValue, bidirectionally if possible.
graphic(Node) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Set the graphic property of the action.
GRAYSCALE - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
Show using a grayscale LUT (black to white)
GRID - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
GRID_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
GRID_SPACING - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
GRID_SPACING - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
GRID_SPACING - Variable in class qupath.lib.gui.actions.OverlayActions
 
GRID_TMA - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
GridLines - Class in qupath.lib.gui.viewer
Simple class used for storing information related to GridLines that may be painted over an image.
GridLines() - Constructor for class qupath.lib.gui.viewer.GridLines
 
gridLinesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
GridOverlay - Class in qupath.lib.gui.viewer.overlays
An overlay used to show a (counting) grid on top of an image.
GridOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.GridOverlay
Constructor.
gridScaleMicrons - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
gridScaleMicronsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Define counting grid optionally displayed on any viewer using microns rather than pixel coordinates.
gridSpacingX - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
gridSpacingXProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Horizontal spacing between lines for any counting grid.
gridSpacingY - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
gridSpacingYProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Vertical spacing between lines for any counting grid.
gridStartXProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Starting x coordinate for any counting grid (usually 0).
gridStartYProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Starting y coordinate for any counting grid (usually 0).
GROOVY - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
GroovyAutoCompletor - Class in qupath.lib.gui.scripting.completors
Auto completion support for Groovy.
GroovyAutoCompletor() - Constructor for class qupath.lib.gui.scripting.completors.GroovyAutoCompletor
Constructor using the default code completions for QuPath.
GroovyAutoCompletor(Collection<? extends AutoCompletions.Completion>) - Constructor for class qupath.lib.gui.scripting.completors.GroovyAutoCompletor
Constructor that supports a custom set of completions.
GroovyLanguage - Class in qupath.lib.gui.scripting.languages
Class for the representation of the Groovy programming language in QuPath.
GuiTools - Class in qupath.lib.gui.tools
Assorted static methods to help with JavaFX and QuPath GUI-related tasks.
GuiTools() - Constructor for class qupath.lib.gui.tools.GuiTools
 
GuiTools.SnapshotType - Enum Class in qupath.lib.gui.tools
Kinds of snapshot image that can be created for QuPath.

H

handle(DragEvent) - Method in class qupath.lib.gui.viewer.DragDropImportListener
 
handle(MouseEvent) - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
 
handle(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
handle(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
handleBackspace(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Handle a backspace.
handleDrop(QuPathViewer, List<T>) - Method in interface qupath.lib.gui.viewer.DragDropImportListener.DropHandler
Handle drop onto a viewer.
handleLeftParenthesis(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Handle left parentheses (.
handleLineComment(EditableText) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Handle line comments.
handleNewLine(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Handle a new line.
handleQuotes(EditableText, boolean, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Handle single/double quotes.
handleRightParenthesis(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Handle right parentheses ).
handleTabPress(EditableText, boolean) - Method in interface qupath.lib.gui.scripting.syntax.ScriptSyntax
Handle tab key.
hasActiveToolTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return whether this ViewTracker tracks the active tool.
hasAlpha() - Method in class qupath.lib.gui.images.servers.RenderedImageServer
 
hasBundleForLocale(String, Locale) - Static method in class qupath.lib.gui.localization.QuPathResources
 
hasCursorTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return whether this ViewTracker tracks the cursor.
hasDefaultBundleForLocale(Locale) - Static method in class qupath.lib.gui.localization.QuPathResources
 
hasEyeTrackingData() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return whether this ViewTracker tracks the eye.
hashCode() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
 
hasJavaPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
Attempt to load user JVM defaults - may fail if packager.jar (and any required native library) isn't found.
hasServer() - Method in class qupath.lib.gui.viewer.QuPathViewer
Returns true if there is currently an ImageServer being displayed in this viewer.
hasString(String) - Static method in class qupath.lib.gui.localization.QuPathResources
 
hasString(String, String) - Static method in class qupath.lib.gui.localization.QuPathResources
 
hasUnseenErrors() - Method in class qupath.lib.gui.commands.LogViewerCommand
Boolean binding indicating whether there are any unseen errors.
hasZAndT() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return whether this ViewTracker has Z and T information.
headerText(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the dialog header text.
height - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
height - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
height - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
height(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Set the preferred height of the chart.
height(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Set the preferred height of the chart.
height(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the preferred height of the chart.
height(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the dialog height.
HELP - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
HELP_VIEWER - Variable in class qupath.lib.gui.actions.CommonActions
 
HELP_VIEWER - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
HelpMenuActions - Class in qupath.lib.gui.actions.menus
 
HelpMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
HIDE_SELECTED - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
Hide classes that are included in the selected class collection.
hideIfEmptyProperty() - Method in class qupath.lib.gui.charts.HistogramChart
Property controlling whether the chart should be hidden if there is no data.
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.commands.PathObjectGridView
 
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.AnnotationPane
 
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
 
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
 
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.UndoRedoManager
 
hierarchyChanged(PathObjectHierarchyEvent) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
hierarchyDisplayMode - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
HierarchyOverlay - Class in qupath.lib.gui.viewer.overlays
An overlay capable of painting a PathObjectHierarchy, except for any TMA grid (which is handled by TMAGridOverlay).
HierarchyOverlay(DefaultImageRegionStore, OverlayOptions, ImageData<BufferedImage>) - Constructor for class qupath.lib.gui.viewer.overlays.HierarchyOverlay
Constructor.
HistogramChart - Class in qupath.lib.gui.charts
JavaFX chart for displaying histograms.
HistogramChart() - Constructor for class qupath.lib.gui.charts.HistogramChart
 
HistogramChart.CountsTransformMode - Enum Class in qupath.lib.gui.charts
Enum to specify how the counts are displayed.
HistogramChart.DisplayMode - Enum Class in qupath.lib.gui.charts
Display mode for the histogram.
HistogramChart.HistogramData - Class in qupath.lib.gui.charts
Helper class for representing data that may be visualized with a HistogramChart.
HistogramData(Histogram, Color) - Constructor for class qupath.lib.gui.charts.HistogramChart.HistogramData
Wrapper for histogram & data relevant to its display.
HistogramDisplay - Class in qupath.lib.gui.charts
Wrapper close to enable the generation and display of histograms relating to a data table.
HistogramDisplay(PathTableData<?>, boolean) - Constructor for class qupath.lib.gui.charts.HistogramDisplay
Constructor.
HISTORY_SCRIPT - Variable in class qupath.lib.gui.actions.AutomateActions
 
HISTORY_SCRIPT - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
 
HISTORY_SHOW - Variable in class qupath.lib.gui.actions.AutomateActions
 
HISTORY_SHOW - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
 
HOVER - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
Display only when the cursor hovers nearby
HtmlRenderer - Interface in qupath.lib.gui.scripting.languages
Marker interface that indicates an executable language renders HTML.
HUGE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
 

I

IconFactory - Class in qupath.lib.gui.tools
Factory class for creating icons.
IconFactory() - Constructor for class qupath.lib.gui.tools.IconFactory
 
IconFactory.PathIcons - Enum Class in qupath.lib.gui.tools
Default icons for QuPath commands.
iconProperty() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
 
iconProperty() - Method in interface qupath.lib.gui.viewer.tools.PathTool
Property giving the icon that should be used for the tool
image() - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify that whole-image measurements (only) should be export.
IMAGE - Enum constant in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
Accept all requests for the image where the region is non-empty
IMAGE_NAME - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
 
imageData - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
imageData - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
imageData - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify an ImageData object.
imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify an ImageData object.
imageData(ImageData<?>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify an ImageData object.
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.UndoRedoManager
 
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
Called with the image data within a viewer has changed.
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
imageDataChanged(QuPathViewer, ImageData<BufferedImage>, ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.ViewerManager
 
imageDataProperty() - Method in class qupath.lib.gui.commands.PathObjectGridView
 
imageDataProperty() - Method in class qupath.lib.gui.QuPathGUI
Read-only property containing the image open within the currently-active viewer.
imageDataProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
Property for the image data currently being displayed within this viewer.
imageDataProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
Read-only property containing the image open within the currently-active viewer.
ImageDetailsPane - Class in qupath.lib.gui.panes
A panel used for displaying basic info about an image, e.g.
ImageDetailsPane(ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.ImageDetailsPane
Constructor.
ImageDisplay - Class in qupath.lib.display
Class used to look after the color transforms that may be applied to an image, including brightness/contrast settings.
ImageDisplay() - Constructor for class qupath.lib.display.ImageDisplay
Constructor.
imageDisplayObjectProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane
The current image display.
imageDisplayProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Property for the image display that should be shown and managed by this pane.
imageDisplayProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
The image display to which the sliders are applied.
ImageDisplaySettings - Class in qupath.lib.display.settings
A simple class to store the main information needed by QuPath to display an image, in a JSON-friendly form.
ImageDisplaySettings() - Constructor for class qupath.lib.display.settings.ImageDisplaySettings
 
ImageInterpolation - Enum Class in qupath.lib.gui.viewer
Supported interpolation methods when displaying images.
IMAGEJ_MACRO - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
ImageJMacroCompletor - Class in qupath.lib.gui.scripting.completors
And autocompletor for the ImageJ macro language.
ImageJMacroCompletor() - Constructor for class qupath.lib.gui.scripting.completors.ImageJMacroCompletor
Constructor.
ImageJMacroLanguage - Class in qupath.lib.gui.scripting.languages
 
imageList(List<ProjectImageEntry<BufferedImage>>) - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify the list of images (ProjectImageEntry) to export.
imageNameProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get a read-only property indicating the name of the image.
imagePointToComponentPoint(Point2D, Point2D, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
Convert a coordinate from the the full-resolution image into the corresponding pixel coordinate in the viewer - optionally constraining it to any viewer component bounds.
imageProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get a read-only property representing the JavaFX image.
ImageRegionRenderer - Interface in qupath.lib.gui.images.stores
Interface for painting regions of an ImageServer onto a Graphics object.
ImageRegionStoreFactory - Class in qupath.lib.gui.images.stores
Factory for creating an ImageRegionStore.
ImageRegionStoreFactory() - Constructor for class qupath.lib.gui.images.stores.ImageRegionStoreFactory
 
ImageRegionStoreHelpers - Class in qupath.lib.gui.images.stores
Helper methods related to image region storage.
ImageRegionStoreHelpers() - Constructor for class qupath.lib.gui.images.stores.ImageRegionStoreHelpers
 
ImageRenderer - Interface in qupath.lib.gui.images.stores
Interface for objects capable of converting a BufferedImage for rendering using Graphics2D.
imageTypeSettingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Specify how setting the image type should be handled for images when they are opened for the first time.
imageUpdated - Variable in class qupath.lib.gui.viewer.QuPathViewer
Flag used to indicate that the image was updated for a repaint (otherwise it's assumed only the overlay may have changed)
IMPORT_IMAGES - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
IMPORT_IMAGES_LEGACY - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
importDearrayedTMAData(File) - Static method in class qupath.lib.gui.tma.TMADataIO
Import a TMA grid from an exported TMA analysis file, i.e.
importPreferences(InputStream) - Static method in class qupath.lib.gui.prefs.PathPrefs
Import preferences from a stream.
INACTIVE_SERVER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
includeImage(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
includeMeasurementList(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
includeObjectCounts(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
includeObjectMetadata(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
includeObjectProperties(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
includeOnlyColumns(String...) - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify the columns that will be included in the export.
includePixelClassification(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
includeRoiProperties(boolean) - Method in class qupath.lib.gui.measure.DefaultPathObjectValueFactoryBuilder
 
info(String) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an information message with static text.
info(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an information message with static text and a count.
info(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
Create a information message to show a count of messages.
info(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an information message.
info(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
Create an information message with a count.
INFO - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType
Information only.
INFO - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
Info logging (default)
INFO - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
INFO - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
infoMessage() - Method in class qupath.lib.gui.commands.BrightnessContrastCommand
Get a string expression to draw attention to any warnings associated with the current display settings.
InfoMessage - Class in qupath.lib.gui.actions
An informative message that should be shown to the user.
InfoMessage.MessageType - Enum Class in qupath.lib.gui.actions
The type of message, which can be used for styling.
information() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Create an information alert dialog.
initializeForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
initializeForServer(ImageServer<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
 
INPUT_DISPLAY - Variable in class qupath.lib.gui.actions.CommonActions
 
INPUT_DISPLAY - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
inputFiles(Collection<File>) - Method in class qupath.lib.gui.FileCopier
Collection of files to copy.
InputOutputPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
 
inputPaths(Collection<Path>) - Method in class qupath.lib.gui.FileCopier
Collection of paths representing files to copy.
INSERT_INTO_HIERARCHY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
insertAllDefaultImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
insertDetectionMeasurementsAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
insertMuAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
insertObjectClassifiersAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
insertPixelClassifiersAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
insertQPExImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
insertQPImportAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
insertSelectedObjectsInHierarchy(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Insert the selected objects in the hierarchy, resolving positions accordingly.
insertText(int, String) - Method in interface qupath.lib.gui.scripting.EditableText
Request inserting the specified text.
insertText(int, String) - Method in class qupath.lib.gui.scripting.TextAreaControl
 
installActions(Collection<? extends Action>) - Method in class qupath.lib.gui.QuPathGUI
Install the specified actions.
installCommand(String, Runnable) - Method in class qupath.lib.gui.QuPathGUI
Install a new command in QuPath.
installDragAndDropHandler(QuPathGUI) - Static method in class qupath.lib.gui.commands.TMACommands
Command to install a drag and drop file handler for exported TMA data.
installExtension(QuPathGUI) - Method in interface qupath.lib.gui.extensions.QuPathExtension
Install the extension for a QuPathGUI instance.
installGroovyCommand(String, File) - Method in class qupath.lib.gui.QuPathGUI
Install a Groovy script as a new command in QuPath.
installGroovyCommand(String, String) - Method in class qupath.lib.gui.QuPathGUI
Install a Groovy script as a new command in QuPath.
installImageDataCommand(String, Consumer<ImageData<BufferedImage>>) - Method in class qupath.lib.gui.QuPathGUI
Install a new command in QuPath that takes the current ImageData as input.
installInfoMessage(Action, ObjectExpression<InfoMessage>) - Static method in class qupath.lib.gui.actions.ActionTools
Install an optional info message to the action.
installLanguage(ScriptLanguage) - Static method in class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
Install a new script language.
installRangePrompt(Slider) - Static method in class qupath.lib.gui.tools.GuiTools
Install a mouse click listener to prompt the user to input min/max values for a slider.
installStyles(Collection<File>) - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
Handle installing CSS files (which can be used to style QuPath).
installSyntax(ScriptSyntax) - Static method in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
Install a new ScriptSyntax programmatically.
installTool(PathTool, KeyCodeCombination) - Method in class qupath.lib.gui.ToolManager
Install a new tool for interacting with viewers.
INTENSITY_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
InteractiveObjectImporter - Class in qupath.lib.gui.commands
Static methods to import object(s) from different sources.
interpolateBilinear - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
interpolationProperty() - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
The preferred method of interpolation to use for display.
invertBackground() - Method in class qupath.lib.display.settings.ImageDisplaySettings
Get whether the background should be shown 'inverted'.
invertColors() - Method in enum class qupath.lib.display.ChannelDisplayMode
 
INVERTED_COLOR - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
Show using color LUT with an inverted background
INVERTED_GRAYSCALE - Enum constant in enum class qupath.lib.display.ChannelDisplayMode
Show using an inverted grayscale LUT (white to black)
invertScrolling - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
invertScrollingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Invert the scrolling direction of the mouse applied to the viewer.
invertZSlider - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
invertZSliderProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Invert the z-slider for the viewer.
isAdditive() - Method in class qupath.lib.display.AdditiveChannelInfo
 
isAdditive() - Method in interface qupath.lib.display.ChannelDisplayInfo
Returns true if this channel can be used additively to create a composite image display; returns false if this channel wants all the color information to itself, so can't be displayed with others.
isAdditive() - Method in class qupath.lib.display.DirectServerChannelInfo
 
isBrightnessContrastRescaled() - Method in class qupath.lib.display.AdditiveChannelInfo
 
isBrightnessContrastRescaled() - Method in class qupath.lib.display.DirectServerChannelInfo
 
isBrightnessContrastRescaled() - Method in interface qupath.lib.display.ChannelDisplayInfo
Returns true if rescaling according to min & max display levels is applied, false if the full display range is used.
isCompatible(ImageDisplay) - Method in class qupath.lib.display.ImageDisplay
Check if an image display is 'compatible' with this one.
isEmpty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Query if the table is empty, i.e.
isEmpty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return whether the collection of recorded frames is empty.
isEmptyRegion(RegionRequest) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
Returns true if there are no objects to be painted within the requested region.
isEraser() - Method in interface qupath.lib.gui.viewer.tools.QuPathPenManager.PenInputManager
Query if there is a pen currently being used as an eraser.
iseScrollGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
isHidden(PathObject) - Method in class qupath.lib.gui.viewer.OverlayOptions
Query whether an object should be hidden.
isImageDataChanging() - Method in class qupath.lib.gui.viewer.QuPathViewer
Returns true between the time setImageData has been called, and before the first repaint has been completed.
isInteractive() - Method in class qupath.lib.gui.charts.ChartThresholdPane
isInteractiveProperty() - Method in class qupath.lib.gui.charts.ChartThresholdPane
Property indicating whether thresholds can be adjusted interactively.
isLastFrame(ViewRecordingFrame) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return whether the specified frame is the last one recorded.
isLocationVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
Returns true if the cursor location is visible, false otherwise.
isModified() - Method in class qupath.lib.gui.scripting.ScriptTab
Return
isModifiedProperty() - Method in class qupath.lib.gui.scripting.ScriptTab
Return the isModifiedProperty of this script tab (true if the script is modified, i.e.
isMutable() - Method in class qupath.lib.display.DirectServerChannelInfo
 
isMutable() - Method in interface qupath.lib.display.SingleChannelDisplayInfo
Check if SingleChannelDisplayInfo.getValue(BufferedImage, int, int) returns fixed values, or if they are dependent on other properties of the ImageData.
isNumericMeasurement(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Query whether a named measurement returns a numeric value only.
isOverviewVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
Returns true if the image overview is visible, false otherwise.
isPathClassHidden(PathClass) - Method in class qupath.lib.gui.viewer.OverlayOptions
Query whether objects with a specified classification should be displayed or hidden.
isReadOnly() - Method in class qupath.lib.gui.QuPathGUI
Query whether QuPath is in 'read-only' mode.
isRecording() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return whether this is currently recording.
isRedoable() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Returns true if 'redo' can be applied to the control.
isRedoable() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
isResizable() - Method in class qupath.lib.gui.ColorMapCanvas
 
isRotated() - Method in class qupath.lib.gui.viewer.QuPathViewer
Returns true if viewer.getRotation() != 0.
isScalebarVisible() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
Returns true if the scalebar is visible, false otherwise.
isSelectable(Action) - Static method in class qupath.lib.gui.actions.ActionTools
Specify that an Action has a meaningful 'selected' status.
isSelected() - Method in class qupath.lib.gui.SelectableItem
Returns true if the value of the selected property equals SelectableItem.getItem().
isShowing() - Method in class qupath.lib.display.settings.ChannelSettings
Get whether the channel should be displayed.
isShowing() - Method in class qupath.lib.gui.viewer.QuPathViewer
Returns true if the viewer is visible, and attached to a scene.
isSpaceDown() - Method in class qupath.lib.gui.viewer.QuPathViewer
Returns true if the spacebar was pressed when this component was focussed, and is still being held down.
isStandalone() - Method in class qupath.lib.gui.QuPathGUI
Query whether this is a standalone QuPathGUI instance, as flagged during startup.
isStringMeasurement(String) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Query whether a named measurement returns a String value only.
isSubtractMode(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
isToolSwitchingEnabled() - Method in class qupath.lib.gui.ToolManager
Returns true if the user is able to activate another PathTool, false otherwise.
isUndoable() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Returns true if 'undo' can be applied to the control.
isUndoable() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
isValid() - Method in class qupath.lib.gui.tools.MeasurementMapper
Query if the mapper is valid.
isVisible() - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
Check overlay visibility status.
isVisible() - Method in class qupath.lib.gui.viewer.overlays.GridOverlay
 
isVisible() - Method in class qupath.lib.gui.viewer.overlays.TMAGridOverlay
 

J

JAVA_IMPORTER - Static variable in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Java-like import statements
JavadocViewerRunner - Class in qupath.lib.gui
A command to show a JavadocViewer in a standalone window.
JavadocViewerRunner(Stage) - Constructor for class qupath.lib.gui.JavadocViewerRunner
Create the command.
join(Collection<? extends PathObjectValueFactory>) - Static method in interface qupath.lib.gui.measure.PathObjectValueFactory
Join multiple factories for a collection to create all of their values.
join(PathObjectValueFactory...) - Static method in interface qupath.lib.gui.measure.PathObjectValueFactory
Join multiple factories to create all of their values.
JSON - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
JsonLanguage - Class in qupath.lib.gui.scripting.languages
Class for the representation of JSON syntax in QuPath.

K

keepDisplaySettings - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
keepDisplaySettingsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Retain display settings (channel colors, brightness/contrast) when opening new images that have the same properties (channels, channel names, bit-depths).
KEYBOARD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
killRunningScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 

L

LARGE - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
 
LARGE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
 
lastChangeTimestamp() - Method in class qupath.lib.gui.viewer.OverlayOptions
Get a property representing the timestamp of the last recorded change for any property.
launchInstanceFromSwing() - Static method in class qupath.lib.gui.QuPathGUI
Static method to launch QuPath from within a Swing/AWT application.
launchTMADataViewer(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Open new window with the TMA data viewer.
layers(Collection<PathOverlay>) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify one or more overlay layers as a collection.
layers(PathOverlay...) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify one or more overlay layers.
legend(boolean) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify whether the legend should be shown or not.
legend(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify whether the legend should be shown or not.
legend(boolean) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify whether the legend should be shown or not.
legend(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify the side of the chart where the legend should be shown.
legend(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify the side of the chart where the legend should be shown.
legend(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify the side of the chart where the legend should be shown.
legend(Side) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify the side of the chart where the legend should be shown.
legend(Side) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify the side of the chart where the legend should be shown.
legend(Side) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify the side of the chart where the legend should be shown.
legendSide - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
legendSide - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
legendSide - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
legendVisible - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
legendVisible - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
legendVisible - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
LICENSE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
licenseMessage - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
limitDatapoints(int) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Choose the maximum number of supported datapoints per series.
LINE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Line drawing tool
LINE_OR_ARROW - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Extended PathTool that can switch between drawing lines or arrows.
LINE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
LINE_TOOL - Variable in class qupath.lib.gui.ToolManager
 
lineWidthProperty() - Method in class qupath.lib.gui.charts.ChartThresholdPane
Line width property used for displaying threshold lines.
loadDisplaySettings(String) - Static method in class qupath.lib.gui.scripting.QPEx
Load a display settings object from a file path or from the current project.
localeDefault - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
 
localeDisplay - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
 
localeFormat - Variable in class qupath.lib.gui.panes.PreferencePane.LocalePreferences
 
LocalePreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.LocalePreferences
 
localizationDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
Read only property representing the localization directory.
locateFile(String) - Static method in class qupath.lib.gui.scripting.QPEx
Locate a specified file based upon its name or path, with a search depth of 4.
locateFile(String, int) - Static method in class qupath.lib.gui.scripting.QPEx
Locate a specified file based upon its name or path.
LOCATION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
locationFontSize - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
locationFontSizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Preferred font size for the location text in the viewer.
locationUpdated - Variable in class qupath.lib.gui.viewer.QuPathViewer
Flag used to indicate that the visible region in the viewer has changed
LOCK_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
 
lockActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
LockActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
 
lockSelectedToolProperty() - Method in class qupath.lib.gui.ToolManager
Property to request that the selected tool be locked.
LOG_DELIMITER - Static variable in class qupath.lib.gui.viewer.recording.ViewTracker
 
LOG_VIEWER - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
LOGARITHM - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
Natural logarithm of raw bin counts.
logDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
Read only property representing the log file directory.
logLevel - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
LogManager - Class in qupath.lib.gui.logging
Manage logging levels.
LogManager() - Constructor for class qupath.lib.gui.logging.LogManager
 
LogManager.LogLevel - Enum Class in qupath.lib.gui.logging
Available log levels.
logToFile(File) - Static method in class qupath.lib.gui.logging.LogManager
Request logging to the specified file.
LogViewerCommand - Class in qupath.lib.gui.commands
A viewer for log messages.
LogViewerCommand(Window) - Constructor for class qupath.lib.gui.commands.LogViewerCommand
Constructor.
longText(String) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Set the long text property of the action.
longText(ObservableValue<String>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Bind the long text property of the action to an ObservableValue, bidirectionally if possible.
longTextProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
lookupAccelerator(String) - Method in class qupath.lib.gui.QuPathGUI
Get the action or menu item associated with an accelerator.
lookupAccelerator(KeyCombination) - Method in class qupath.lib.gui.QuPathGUI
Get the action or menu item associated with an key combination.
lookupActionByText(String) - Method in class qupath.lib.gui.QuPathGUI
Search for an action based upon its text (name) property.
lookupMenuItem(String, String...) - Method in class qupath.lib.gui.QuPathGUI
Search for a menu item based upon its path.

M

main(String[]) - Static method in class qupath.lib.gui.tools.DocGenerator
 
MAIN_SCENE - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
Snapshot of the full Scene of the main QuPath Window.
MAIN_WINDOW_SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
Screenshot of the full QuPath window as it currently appears, including any overlapping windows.
MAKE_INVERSE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
makeChartInteractive(Chart, NumberAxis, NumberAxis) - Static method in class qupath.lib.gui.charts.ChartTools
Make it possible to select chart regions to zoom in, and scroll to navigate around it.
makeFullScreenshot() - Static method in class qupath.lib.gui.tools.GuiTools
Make a BufferedImage snapshot of the full screen.
makeInverseAnnotation(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Make an inverse annotation for the selected objects, storing the command in the history workflow.
makeProgressMonitor() - Method in class qupath.lib.gui.TaskRunnerFX
 
makeSnapshot() - Static method in class qupath.lib.gui.tools.GuiTools
Make a BufferedImage snapshot of the current GUI.
makeSnapshot(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
Make a snapshot (image) showing what is currently displayed in a QuPath window or the active viewer within QuPath, as determined by the SnapshotType.
makeSnapshot(QuPathGUI, QuPathViewer, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
Make a snapshot (image) showing what is currently displayed in a QuPath window or the specified viewer, as determined by the SnapshotType.
makeSnapshotFX(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
Make a snapshot as a JavaFX Image, using the current viewer if a viewer is required.
makeSnapshotFX(QuPathGUI, QuPathViewer, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.tools.GuiTools
Make a snapshot as a JavaFX Image.
makeViewerSnapshot() - Static method in class qupath.lib.gui.tools.GuiTools
Make a BufferedImage snapshot of the current viewer.
makeViewerSnapshot(QuPathViewer) - Static method in class qupath.lib.gui.tools.GuiTools
Make a BufferedImage snapshot of the specified viewer.
manageChildMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Request that a menubar is managed as a child menubar.
manageMainMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Request that a menubar is managed as a main menubar.
MANAGER - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
MAPS - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
MarkdownLanguage - Class in qupath.lib.gui.scripting.languages
Class for the representation of JSON syntax in QuPath.
markerOpacity - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
markerOpacity - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
markerOpacity - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify the marker opacity.
markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify the marker opacity.
markerOpacity(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify the marker opacity.
maskImageNames - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
maskImageNamesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request that image names are hidden within the user interface.
MATCH_VIEWER_RESOLUTIONS - Variable in class qupath.lib.gui.actions.ViewerActions
 
matchResolutions() - Method in class qupath.lib.gui.viewer.ViewerManager
Match the display resolutions (downsamples) of all viewers to match the current viewer.
maxAllowed - Variable in class qupath.lib.display.AdditiveChannelInfo
 
maxAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
 
maxClipboardObjects - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
maxDisplay - Variable in class qupath.lib.display.AdditiveChannelInfo
 
maxDisplay - Variable in class qupath.lib.display.DirectServerChannelInfo
 
maxHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
 
maxMemoryGB - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
maxMemoryMBProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Get property representing the maximum memory for the Java Virtual Machine, applied after restarting the application.
maxObjectsToClipboardProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
The maximum number of objects that can be copied to the system clipboard.
maxPointsProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Get a property representing the maximum number of points that the plot will display.
maxUndoHierarchySize - Variable in class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
 
maxUndoHierarchySizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
The requested maximum number of objects in a hierarchy for which QuPath should support undo/redo.
maxUndoLevels - Variable in class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
 
maxUndoLevelsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
The requested maximum number of undo levels that QuPath should support.
maxValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
The maximum value displayed on the histogram.
maxValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
Value of the maximum slider.
maxWidth(double) - Method in class qupath.lib.gui.ColorMapCanvas
 
MEASURE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
MEASURE_ANNOTATIONS - Variable in class qupath.lib.gui.actions.CommonActions
 
MEASURE_DETECTIONS - Variable in class qupath.lib.gui.actions.CommonActions
 
MEASURE_GRID_ANNOTATIONS - Variable in class qupath.lib.gui.actions.CommonActions
 
MEASURE_GRID_TMA_CORES - Variable in class qupath.lib.gui.actions.CommonActions
 
MEASURE_TMA - Variable in class qupath.lib.gui.actions.CommonActions
 
MeasurementExportCommand - Class in qupath.lib.gui.commands
Dialog box to export measurements
MeasurementExportCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.MeasurementExportCommand
Creates a simple GUI for MeasurementExporter.
MeasurementExporter - Class in qupath.lib.gui.tools
Helper class for exporting the measurements of one or more entries in a project.
MeasurementExporter() - Constructor for class qupath.lib.gui.tools.MeasurementExporter
 
MeasurementListValueFactory - Class in qupath.lib.gui.measure
Measurements that only extract metadata from objects.
MeasurementListValueFactory() - Constructor for class qupath.lib.gui.measure.MeasurementListValueFactory
 
MeasurementMapPane - Class in qupath.lib.gui.panes
Component used for displaying measurement maps, whereby detection objects are recolored according to measurement values.
MeasurementMapPane(QuPathGUI) - Constructor for class qupath.lib.gui.panes.MeasurementMapPane
Constructor.
MeasurementMapper - Class in qupath.lib.gui.tools
Helpers class that can be used to map an object's measurement to a color (packed RGB int).
MeasurementMapper(ColorMaps.ColorMap, String, Collection<? extends PathObject>) - Constructor for class qupath.lib.gui.tools.MeasurementMapper
Constructor.
measurementMapperProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
MeasurementPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
 
measurements(Collection<? extends PathObject>, String, String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Plot two measurements against one another for the specified objects.
MeasureMenuActions - Class in qupath.lib.gui.actions.menus
 
MeasureMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
MEDIUM - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
 
MEDIUM - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
 
MEMORY_MONITOR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
MEMORY_MONITOR - Variable in class qupath.lib.gui.actions.CommonActions
 
MEMORY_MONITOR - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
menu() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
 
MenuActions - Interface in qupath.lib.gui.actions.menus
Common interface to define the contents of a menu in terms of actions.
menuPathProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
Menus - Class in qupath.lib.gui.actions.menus
Generate actions for installation in QuPath's main menubar.
Menus() - Constructor for class qupath.lib.gui.actions.menus.Menus
 
menusToMarkdown() - Static method in class qupath.lib.gui.tools.CommandFinderTools
Create a markdown representation of the menus for inclusion in the documentation, using the current QuPath instance.
menusToMarkdown(QuPathGUI, Writer) - Static method in class qupath.lib.gui.tools.CommandFinderTools
Write a markdown representation of the menus for inclusion in the documentation.
MenuTools - Class in qupath.lib.gui.tools
Static methods to help with creating and populating JavaFX menus.
MenuTools() - Constructor for class qupath.lib.gui.tools.MenuTools
 
MERGE_SELECTED - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
mergeSelectedAnnotations(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Merge the currently-selected annotations for an image, replacing them with a single new annotation.
METADATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
MetadataValueFactory - Class in qupath.lib.gui.measure
Measurements that only extract metadata from objects.
MetadataValueFactory() - Constructor for class qupath.lib.gui.measure.MetadataValueFactory
 
MIME_TYPE_GEOJSON - Static variable in class qupath.lib.gui.commands.InteractiveObjectImporter
Mime type for GeoJson
minAllowed - Variable in class qupath.lib.display.AdditiveChannelInfo
 
minAllowed - Variable in class qupath.lib.display.DirectServerChannelInfo
 
minDisplay - Variable in class qupath.lib.display.AdditiveChannelInfo
 
minDisplay - Variable in class qupath.lib.display.DirectServerChannelInfo
 
minHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
 
MINI_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
minimumPyramidDimension - Variable in class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
 
MiniViewerManager(QuPathViewer, Collection<? extends ChannelDisplayInfo>) - Constructor for class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
MiniViewers - Class in qupath.lib.gui.commands
Command to open a small viewer window, which displays a detail from the current image depending on where the cursor is over the image.
MiniViewers() - Constructor for class qupath.lib.gui.commands.MiniViewers
 
MiniViewers.MiniViewerManager - Class in qupath.lib.gui.commands
A manager for one or more mini-viewers, where the 'more' means a separate viewer per channel.
minPyramidDimensionProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Minimum image width or height before pyramidalizing (if required).
MINUS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
minValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
The minimum value displayed on the histogram.
minValueProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
Value of the minimum slider.
minWidth(double) - Method in class qupath.lib.gui.ColorMapCanvas
 
modality(Modality) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the modality of the dialog.
modelProperty() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
Get property representing the model used with this display.
mouseClicked(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mouseClicked(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
mouseDragged(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mouseDragged(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
mouseEntered(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
mouseEntered(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mouseExited(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
mouseExited(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mouseLocationToImage(MouseEvent, boolean, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
mouseMoved(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mouseMoved(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
mousePressed(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mousePressed(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
mouseReleased(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
mouseReleased(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
MOVE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Move tool
MOVE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
MOVE_TOOL - Variable in class qupath.lib.gui.ToolManager
 
MoveToolEventHandler - Class in qupath.lib.gui.viewer.tools.handlers
The MoveTool is used for quite a lot of things, movement-related: movement around an image (panning), moving ROIs (translating) and moving individual 'handles' of ROIs (resizing/reshaping)
MoveToolEventHandler() - Constructor for class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
MoveToolEventHandler.ViewerMover - Class in qupath.lib.gui.viewer.tools.handlers
Helper class for panning a QuPathViewer (reasonably) smoothly.
multipointToolProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Create multiple points within the same annotation when using the counting tool.
multitouchActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
MultitouchActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
 
MULTIVIEW_ADD_COLUMN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_ADD_ROW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_CLOSE_VIEWER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
MULTIVIEW_GRID_1x1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_GRID_1x2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_GRID_2x1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_GRID_2x2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_GRID_3x3 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_GRID_ACTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
MULTIVIEW_MATCH_RESOLUTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
MULTIVIEW_REMOVE_COLUMN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_REMOVE_ROW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_RESET_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
MULTIVIEW_SYNCHRONIZE_VIEWERS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
multiviewActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
MultiviewActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
MultiviewGridActions() - Constructor for class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 

N

NAME - Static variable in class qupath.lib.gui.scripting.languages.ImageJMacroLanguage
Constant representing the name of this language.
NAME_OBJECT_ID - Static variable in class qupath.lib.gui.measure.ObservableMeasurementTableData
The name used for the Object ID column
nameProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the String property of this ViewTracker.
nameProperty() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
 
nameProperty() - Method in interface qupath.lib.gui.viewer.tools.PathTool
Property giving the name of the tool
navigationAcceleration - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
navigationAccelerationProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Apply acceleration/deceleration effects when holding and releasing navigation key.
navigationSpeed - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
navigationSpeedProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Percentage to scale navigation speed.
NEAREST - Enum constant in enum class qupath.lib.gui.viewer.ImageInterpolation
Nearest neighbor interpolation.
NEVER - Enum constant in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
Don't use the system menubar for any windows.
NEVER - Enum constant in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
Never display
newDetectionRendering - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
newDetectionRenderingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Flag to enable the new rendering strategy for detections.
nFrames() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the number of recorded frames.
NO - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
Deprecated.
"No" option
NO_SHUFFLE_SEED - Static variable in class qupath.lib.gui.charts.PathObjectScatterChart
Seed value to use to specify that no shuffling should be applied before displaying the objects.
NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
Don't check for any updates automatically
NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
Do not show detections
NONE - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
Do not set the image type
nonModal() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify that the dialog should be non-modal.
NORMALIZED - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
Normalized bin counts, so that the sum of all counts is 1.0.
NUCLEI_AND_BOUNDARIES - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
Show both cell boundaries and cell nuclei, where available.
NUCLEI_ONLY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
NUCLEI_ONLY - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
Show only cell nuclei.
numCommandThreadsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Property specifying the preferred number of threads QuPath should use for multithreaded commands.
numThreads - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 

O

OBJECT_IMPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
ObjectDescriptionPane<T> - Class in qupath.lib.gui.panes
Wraps a pane used to display an object description, if one is available.
ObjectPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
ObjectsMenuActions - Class in qupath.lib.gui.actions.menus
 
ObjectsMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
ObjectsMenuActions.AnnotationActions - Class in qupath.lib.gui.actions.menus
 
ObjectsMenuActions.DeleteActions - Class in qupath.lib.gui.actions.menus
 
ObjectsMenuActions.LockActions - Class in qupath.lib.gui.actions.menus
 
ObjectsMenuActions.SelectActions - Class in qupath.lib.gui.actions.menus
 
ObjectTreeBrowser - Class in qupath.lib.gui.panes
Simple browser for exploring fields (including private fields) within an object by reflection.
ObjectTreeBrowser() - Constructor for class qupath.lib.gui.panes.ObjectTreeBrowser
 
ObservableMeasurementTableData - Class in qupath.lib.gui.measure
A table data model to supply observable measurements of PathObjects.
ObservableMeasurementTableData() - Constructor for class qupath.lib.gui.measure.ObservableMeasurementTableData
 
OFF - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
Turn off logging
opacityProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
Property representing the global opacity for overlay drawing.
opacityTMAMissingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
The default opacity to use when display TMA core objects, between 0 and 1.
OPEN_IMAGE - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
OPEN_IMAGE_OR_URL - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
openFile(File) - Static method in class qupath.lib.gui.tools.GuiTools
Try to open a file in the native application.
openImage(QuPathViewer, String) - Method in class qupath.lib.gui.QuPathGUI
 
openImage(QuPathViewer, String, boolean, boolean) - Method in class qupath.lib.gui.QuPathGUI
Open a new whole slide image server, or ImageData.
openImageEntry(ProjectImageEntry<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI
Open the image represented by the specified ProjectImageEntry.
openInBrowser(String) - Static method in class qupath.lib.gui.QuPathGUI
Try to launch a browser window for a specified URL.
openSavedData(QuPathViewer, File, boolean, boolean) - Method in class qupath.lib.gui.QuPathGUI
Open a saved data file within a particular viewer, optionally keeping the same ImageServer as is currently open.
outputPath(String) - Method in class qupath.lib.gui.FileCopier
Name of the output directory.
outputPath(Path) - Method in class qupath.lib.gui.FileCopier
Path representing the output directory.
OverlayActions - Class in qupath.lib.gui.actions
Actions that interact with OverlayOptions.
OverlayActions(OverlayOptions) - Constructor for class qupath.lib.gui.actions.OverlayActions
 
overlayOpacity(double) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify the opacity for overlay layers.
OverlayOptions - Class in qupath.lib.gui.viewer
Default class for storing overlay display options.
OverlayOptions() - Constructor for class qupath.lib.gui.viewer.OverlayOptions
Constructor, using default values.
OverlayOptions(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.OverlayOptions
Constructor, initializing values based on an existing OverlayOptions object.
OverlayOptions.ClassVisibilityMode - Enum Class in qupath.lib.gui.viewer
Visibility modes for classes.
OverlayOptions.DetectionDisplayMode - Enum Class in qupath.lib.gui.viewer
Display modes for cells and other detections.
overrideSystemMenuBarProperty() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Property requesting that the system menubar should never be used for managed menubars.
OVERVIEW - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
owner(Window) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the dialog owner.

P

paintComponent(Graphics) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
paintConnections(DelaunayTools.Subdivision, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Paint connections between objects from a DelaunayTools.Subdivision.
paintConnections(PathObjectConnections, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Deprecated.
v0.6.0 as #paintConnections(DelaunayTools.Subdivision, PathObjectHierarchy, Graphics2D, Color, double, ImagePlane) is preferred
paintHandles(List<Point2>, Graphics2D, double, double, Color, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Paint the handles onto a Graphics object, if we have a suitable (non-point) ROI.
paintHandles(RoiEditor, Graphics2D, double, double, Color, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Paint the handles onto a Graphics object, if we have a suitable (non-point) ROI.
paintImage(Canvas, Image) - Static method in class qupath.lib.gui.tools.GuiTools
Paint an image centered within a canvas, scaled to be as large as possible while maintaining its aspect ratio.
paintImage(Canvas, Image, double) - Static method in class qupath.lib.gui.tools.GuiTools
Paint an image centered within a canvas, scaled by the specified scale factor.
paintObject(PathObject, Graphics2D, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Paint an object (or, more precisely, its ROI).
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
 
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
 
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.GridOverlay
 
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
 
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in interface qupath.lib.gui.viewer.overlays.PathOverlay
Paint the overlay to a graphics object.
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
 
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.TMAGridOverlay
 
paintOverlay(Graphics2D, ImageRegion, double, ImageData<BufferedImage>, boolean) - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
 
paintRegion(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
paintRegion(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer) - Method in interface qupath.lib.gui.images.stores.ImageRegionRenderer
Paint an image region.
paintRegionCompletely(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, ImageObserver, ImageRenderer, long) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
Similar to paintRegion, but wait until all the tiles have arrived (or abort if it is taking too long)
paintRegionCompletely(ImageServer<BufferedImage>, Graphics, Shape, int, int, double, ImageObserver, ImageRenderer, long) - Method in interface qupath.lib.gui.images.stores.ImageRegionRenderer
Similar to ImageRegionRenderer.paintRegion(ImageServer, Graphics, Shape, int, int, double, BufferedImage, ImageObserver, ImageRenderer), but wait until all the tiles have arrived (or abort if it is taking too long).
paintSelectedBoundsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Specify whether the bounding box of selected objects should be painted.
paintShape(Shape, Graphics2D, Color, Stroke, Color) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Paint the specified shape with specified stroke and fill colors.
paintSpecifiedObjects(Graphics2D, Collection<? extends PathObject>, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Paint the specified objects.
paintTMAGrid(Graphics2D, TMAGrid, OverlayOptions, PathObjectSelectionModel, double) - Static method in class qupath.lib.gui.viewer.PathObjectPainter
Paint the specified tissue microarray grid.
paintViewer(Graphics, int, int) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
PaneTools - Class in qupath.lib.gui.tools
Deprecated.
since v0.5.0; GridPaneUtils contains many of the features.
PaneTools() - Constructor for class qupath.lib.gui.tools.PaneTools
Deprecated.
 
parameterChanged(ParameterList, String, boolean) - Method in class qupath.lib.gui.charts.HistogramDisplay
 
ParameterPanelFX - Class in qupath.lib.gui.dialogs
A panel for displaying a list of parameters suitably to aid with creating JavaFX GUIs.
ParameterPanelFX(ParameterList) - Constructor for class qupath.lib.gui.dialogs.ParameterPanelFX
Create a ParameterPanelFX.
parent(Window) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Set the parent window.
parent(Window) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Set the parent window.
parent(Window) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the parent window.
parseAnnotations(Action, AnnotatedElement) - Static method in class qupath.lib.gui.actions.ActionTools
Parse annotations relating to an action, updating the properties of the action.
parseAnnotations(Action, AnnotatedElement, String) - Static method in class qupath.lib.gui.actions.ActionTools
Parse annotations relating to an action, updating the properties of the action with an optional base menu.
parseDisplaySettings(JsonElement) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
Parse the JSON element into an image display settings object, if possible.
parseDisplaySettings(Path) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
Parse the JSON element into an image display settings object.
paste() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Request paste from the system clipboard.
paste() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
PASTE - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
PASTE_TO_PLANE - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
pasteAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
pasteAndEscapeAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
pasteFromClipboard(QuPathGUI, boolean) - Static method in class qupath.lib.gui.commands.Commands
Attempt to paste objects from the system clipboard to the current image, if available; otherwise, check for text on the clipboard and paste it into a new script editor tab
pasteFromClipboard(ScriptEditorControl<?>, boolean) - Static method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
PathClassListCell - Class in qupath.lib.gui.tools
A cell for displaying PathClass objects in a list view or combo box.
PathClassListCell() - Constructor for class qupath.lib.gui.tools.PathClassListCell
Create a list cell using the default string function.
PathClassListCell(Function<PathClass, String>) - Constructor for class qupath.lib.gui.tools.PathClassListCell
Create a list cell using the specified string function.
PathHierarchyImageServer - Class in qupath.lib.gui.images.servers
A special ImageServer implementation that doesn't have a backing image, but rather constructs tiles on request from a PathObjectHierarchy and its detection objects.
PathHierarchyImageServer(ImageData<BufferedImage>, OverlayOptions) - Constructor for class qupath.lib.gui.images.servers.PathHierarchyImageServer
Constructor.
PathObjectGridView - Class in qupath.lib.gui.commands
Grid display of objects.
PathObjectGridView.GridDisplaySize - Enum Class in qupath.lib.gui.commands
 
PathObjectHierarchyView - Class in qupath.lib.gui.panes
Component for showing a tree-based view of the object hierarchy.
PathObjectHierarchyView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.PathObjectHierarchyView
Constructor.
PathObjectHierarchyView(QuPathGUI, ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.PathObjectHierarchyView
Constructor.
PathObjectImageViewers - Class in qupath.lib.gui.tools
Helper class for working with thumbnail images relating to path objects.
PathObjectImageViewers() - Constructor for class qupath.lib.gui.tools.PathObjectImageViewers
 
PathObjectImageViewers.ItemViewer<S,T> - Interface in qupath.lib.gui.tools
Interface for managing a node that can display an item.
PathObjectLabels - Class in qupath.lib.gui.tools
Create standardized ListCell and TreeCell instances for displaying a PathObject, or a generic pane to use elsewhere.
PathObjectLabels() - Constructor for class qupath.lib.gui.tools.PathObjectLabels
 
PathObjectLabels.PathObjectMiniPane - Class in qupath.lib.gui.tools
Manage a small pane that can be used to display a PathObject.
PathObjectListWrapper - Class in qupath.lib.gui.measure
Helper class to wrap a collection of PathObjects that should be measured.
PathObjectMiniPane(Function<PathObject, String>) - Constructor for class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane
Constructor using a custom string extraction function.
PathObjectPainter - Class in qupath.lib.gui.viewer
Static methods to assist with painting PathObjects.
PathObjectScatterChart - Class in qupath.lib.gui.charts
An interactive ScatterChart implementation for showing large(ish) numbers of PathObject, optionally linked to a QuPathViewer.
PathObjectScatterChart(QuPathViewer) - Constructor for class qupath.lib.gui.charts.PathObjectScatterChart
Create an interactive scatter plot using the current viewer
PathObjectValueFactory - Interface in qupath.lib.gui.measure
Interface defining a way to create lazy values from an image and associated objects.
PathOverlay - Interface in qupath.lib.gui.viewer.overlays
Interface defining an overlay to paint on top of a viewer.
PathPrefs - Class in qupath.lib.gui.prefs
Central storage of QuPath preferences.
PathPrefs() - Constructor for class qupath.lib.gui.prefs.PathPrefs
 
PathPrefs.AutoUpdateType - Enum Class in qupath.lib.gui.prefs
Options for automatic updating checking of QuPath and/or extensions.
PathPrefs.DetectionTreeDisplayModes - Enum Class in qupath.lib.gui.prefs
Enum for different ways that detections can be displayed in lists and trees.
PathPrefs.FontSize - Enum Class in qupath.lib.gui.prefs
Enum to control font size.
PathPrefs.ImageTypeSetting - Enum Class in qupath.lib.gui.prefs
Enum defining how setting the image type should be handled for new images.
PathTableData<T> - Interface in qupath.lib.gui.measure
Interface defining a table model that enables measurement names to be mapped to string or numeric values (as appropriate).
PathTool - Interface in qupath.lib.gui.viewer.tools
Interface defining how a toolbar tool interacts with a viewer.
PathToolEventHandlers - Class in qupath.lib.gui.viewer.tools.handlers
 
PathToolEventHandlers() - Constructor for class qupath.lib.gui.viewer.tools.handlers.PathToolEventHandlers
 
PathTools - Class in qupath.lib.gui.viewer.tools
Default PathTool implementations.
PathTools() - Constructor for class qupath.lib.gui.viewer.tools.PathTools
 
pieChart() - Static method in class qupath.lib.gui.charts.Charts
Create a Charts.PieChartBuilder for generating a custom pie chart.
PIXEL_CLASSIFICATION - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
pixelClassificationFilterRegionProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
PixelClassificationOverlay - Class in qupath.lib.gui.viewer.overlays
PathOverlay that gives the results of pixel classification.
pixelSnapping - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
placeholderText - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
placeholderTextProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the placeholder text to show if no image is available.
placeholderTextProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
String property to hold text that should be displayed whenever no image is open in the viewer.
PLAIN - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
PlainLanguage - Class in qupath.lib.gui.scripting.languages
Class for the representation of plain text in QuPath.
PLAYBACK_PLAY - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
pointOpacityProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Get a property representing the opacity of all data points.
pointRadius - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
pointRadiusProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Get a property representing the radius of all data points.
pointRadiusProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Radius of the circle used to draw individual points in a point annotation (in pixels).
POINTS - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Points annotation and counting tool
POINTS_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
POINTS_TOOL - Variable in class qupath.lib.gui.ToolManager
 
POLYGON - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Polygon drawing tool (closed)
POLYGON_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
POLYGON_TOOL - Variable in class qupath.lib.gui.ToolManager
 
POLYLINE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Polyline drawing tool (open)
POLYLINE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
POLYLINE_TOOL - Variable in class qupath.lib.gui.ToolManager
 
populateAnnotationsMenu(QuPathGUI, ContextMenu) - Static method in class qupath.lib.gui.tools.GuiTools
Populate a ContextMenu with standard options to operate on selected annotation objects.
populateAnnotationsMenu(QuPathGUI, Menu) - Static method in class qupath.lib.gui.tools.GuiTools
Populate a Menu with standard options to operate on selected annotation objects.
positionCaret(int) - Method in interface qupath.lib.gui.scripting.EditableText
Set the caret position to the specified index
positionCaret(int) - Method in class qupath.lib.gui.scripting.TextAreaControl
 
postProcess(Collection<? extends PathTask>) - Method in class qupath.lib.gui.TaskRunnerFX
 
PreferencePane - Class in qupath.lib.gui.panes
QuPath's preference pane, giving a means to modify many of the properties within PathPrefs.
PreferencePane() - Constructor for class qupath.lib.gui.panes.PreferencePane
 
PreferencePane.AppearancePreferences - Class in qupath.lib.gui.panes
 
PreferencePane.DrawingPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.ExtensionPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.GeneralPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.InputOutputPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.LocalePreferences - Class in qupath.lib.gui.panes
 
PreferencePane.MeasurementPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.ObjectPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.ScriptingPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.UndoRedoPreferences - Class in qupath.lib.gui.panes
 
PreferencePane.ViewerPreferences - Class in qupath.lib.gui.panes
 
PREFERENCES - Variable in class qupath.lib.gui.actions.CommonActions
 
PREFERENCES - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
preferReturnToMove() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Returns false.
prefHeight(double) - Method in class qupath.lib.gui.ColorMapCanvas
 
prefHeight(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the preferred height of the dialog pane.
prefWidth(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the preferred width of the dialog pane.
previousSelectedToolProperty() - Method in class qupath.lib.gui.ToolManager
Property storing the previous tool that was selected.
progressMonitor(DoubleConsumer) - Method in class qupath.lib.gui.tools.MeasurementExporter
Set a progress monitor to be notified during export.
PROJECT_ADD_IMAGES - Variable in class qupath.lib.gui.actions.CommonActions
 
PROJECT_CLOSE - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
PROJECT_NEW - Variable in class qupath.lib.gui.actions.CommonActions
 
PROJECT_NEW - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
PROJECT_OPEN - Variable in class qupath.lib.gui.actions.CommonActions
 
PROJECT_OPEN - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
projectActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
ProjectActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
ProjectBrowser - Class in qupath.lib.gui.panes
Component for previewing and selecting images within a project.
ProjectBrowser(QuPathGUI) - Constructor for class qupath.lib.gui.panes.ProjectBrowser
Constructor.
ProjectCommands - Class in qupath.lib.gui.commands
Helper class implementing simple 'single-method' commands related to projects.
ProjectCommands() - Constructor for class qupath.lib.gui.commands.ProjectCommands
 
ProjectDialogs - Class in qupath.lib.gui.dialogs
Dialogs specifically related to managing projects.
ProjectDialogs() - Constructor for class qupath.lib.gui.dialogs.ProjectDialogs
 
projectionProperty() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
 
projectProperty() - Method in class qupath.lib.gui.QuPathGUI
Read-only property representing the currently-open project.
PROMPT - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
Prompt the user to specified the image type
promptForDirectory(File) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt user to select a directory.
promptForDirectory(String, File) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt user to select a directory.
promptForFile(File) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt user to select a file.
promptForFile(String...) - Static method in class qupath.lib.gui.scripting.QPEx
Prompt the user to select a file from a file chooser.
promptForFile(String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt the user for a file with some kind of file dialog.
promptForFilePathOrURL(String, String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt user to select a file or input a URL.
promptForMultipleFiles(String, File, String, String...) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt to open a list of files.
promptForParentObjects(String, ImageData<?>, boolean, Collection<Class<? extends PathObject>>) - Static method in class qupath.lib.gui.tools.GuiTools
Get the parent objects to use when running the plugin, or null if no suitable parent objects are found.
promptForSliderRange(Slider) - Static method in class qupath.lib.gui.tools.GuiTools
Prompt the user to input min/max values for a slider.
promptToAddColumnAfterSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to add a column to a TMA grid after the column containing the currently-selected object.
promptToAddColumnBeforeSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to add a column to a TMA grid before the column containing the currently-selected object.
promptToAddNoteToSelectedCores(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to type a node to associate with the selected TMA cores.
promptToAddRowAfterSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to add a row to a TMA grid after the row containing the currently-selected object.
promptToAddRowBeforeSelected(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to add a row to a TMA grid before the row containing the currently-selected object.
promptToAddShapeFeatures(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Prompt to add shape features for selected objects.
promptToCheckURIs(Project<?>, boolean) - Static method in class qupath.lib.gui.commands.ProjectCommands
Check the URIs within a project, prompting the user to correct any broken links if required.
promptToClearAllSelectedObjects(ImageData<?>) - Static method in class qupath.lib.gui.tools.GuiTools
Prompt user to select all currently-selected objects (except TMA core objects).
promptToCreateProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Prompt the user to select an empty directory, and use this to create a new project and set it as active.
promptToCreateTMAGrid(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt the user to manually create a new TMA grid.
promptToDeleteObjects(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands
Prompt to delete objects of a specified type, or all objects.
promptToDeleteTMAGridColumn(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to delete a column from a TMA grid.
promptToDeleteTMAGridRow(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to delete a row from a TMA grid.
promptToEditClass(PathClass) - Static method in class qupath.lib.gui.commands.Commands
Prompt to edit the name/color of a class.
promptToEstimateStainVectors(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Prompt to estimate stain vectors for the specified image, using any current region of interest.
promptToExportImageList(Project<?>) - Static method in class qupath.lib.gui.commands.ProjectCommands
Prompt to export a text file containing a list of image paths for a project.
promptToExportImageRegion(QuPathViewer, boolean) - Static method in class qupath.lib.gui.commands.Commands
Prompt to export the current image region selected in the viewer.
promptToExportTMAData(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to export summary TMA data for a specific image to a directory.
promptToImportImages(QuPathGUI, String...) - Static method in class qupath.lib.gui.commands.ProjectCommands
Show prompt for the user to select images to import into the current project in QuPath, choosing a suitable ImageServerBuilder.
promptToImportImages(QuPathGUI, ImageServerBuilder<BufferedImage>, String...) - Static method in class qupath.lib.gui.commands.ProjectCommands
Show prompt for the user to select images to import into the current project in QuPath.
promptToImportLegacyProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.ProjectCommands
Prompt the user to select a legacy project file, and then import the images into the current project.
promptToImportObjects(PathObjectHierarchy, Collection<? extends PathObject>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
Import a collection of objects to an object hierarchy, prompting to confirm and asking whether to update IDs.
promptToImportObjectsFromFile(ImageData<BufferedImage>, File) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
Prompt to import objects read from a file.
promptToImportObjectsProjectEntry(ImageData<BufferedImage>, ProjectImageEntry<?>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
Prompt to import objects from a project entry.
promptToImportTMAData(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to import TMA data for the specified image data.
promptToOpenImageFile() - Method in class qupath.lib.gui.QuPathGUI
Show a file chooser to open a new image in the current viewer.
promptToOpenImageFileOrUri() - Method in class qupath.lib.gui.QuPathGUI
Show a dialog to open a new image in the current viewer, with support for entering a URL (rather than requiring a local file only).
promptToOpenProject(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Prompt the user to open an existing project and set it as active.
promptToPasteObjectsFromClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
Prompt to paste objects from the system clipboard, if possible.
promptToRelabelTMAGrid(ImageData<?>) - Static method in class qupath.lib.gui.commands.TMACommands
Prompt to relabel the core names within a TMA grid.
promptToRemoveSelectedObject(PathObject, PathObjectHierarchy) - Static method in class qupath.lib.gui.tools.GuiTools
Prompt to remove a single, specified selected object.
promptToResetPreferences() - Static method in class qupath.lib.gui.commands.Commands
Reset QuPath's preferences, after confirming with the user.
promptToResolveHierarchy(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Resolve parent-child relationships within the object hierarchy.
promptToSaveFile(String, File, String, String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt user to select a file path to save.
promptToSaveFile(String, File, String, Map<String, String>) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Prompt user to select a file path to save, providing zero or more file extensions as an option.
promptToSaveImageData(QuPathGUI, ImageData<BufferedImage>, boolean) - Static method in class qupath.lib.gui.commands.Commands
Prompt to save the specified ImageData.
promptToSelectImage(String, boolean) - Method in class qupath.lib.gui.panes.ServerSelector
Prompt to select a single ImageServer.
promptToSelectImages(String) - Method in class qupath.lib.gui.panes.ServerSelector
Prompt to select multiple ImageServers.
promptToSelectObjectsByClassification(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Prompt to select objects according to their classifications.
promptToSetActiveAnnotationProperties(PathObjectHierarchy) - Static method in class qupath.lib.gui.tools.GuiTools
Prompt the user to set properties for the currently-selected annotation(s).
promptToSetFontSize() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Update the font size for the script editor and console.
promptToSetGridLineSpacing(OverlayOptions) - Static method in class qupath.lib.gui.commands.Commands
Prompt to input the spacing for the grid lines optionally displayed on viewers.
promptToSetImageType(ImageData<BufferedImage>, ImageData.ImageType) - Static method in class qupath.lib.gui.panes.ImageDetailsPane
Prompt the user to set the ImageData.ImageType for the image.
promptToSimplifySelectedAnnotations(ImageData<?>, double) - Static method in class qupath.lib.gui.commands.Commands
Show a prompt to selected annotations in a hierarchy.
promptToUpdateUris(Collection<T>, URI, URI, boolean) - Static method in class qupath.lib.gui.commands.UpdateUrisCommand
Show dialog prompting the user to update URIs for missing files.
PROPERTIES - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
PropertiesLanguage - Class in qupath.lib.gui.scripting.languages
Class for the representation of properties and config files in QuPath.
propertyChange(PropertyChangeEvent) - Method in class qupath.lib.gui.panes.ImageDetailsPane
 
propertyChange(PropertyChangeEvent) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
 
putActionProperty(MenuItem, Action) - Static method in class qupath.lib.gui.actions.ActionTools
Add an Action to the properties of a MenuItem, so that it may be retrieved later.
putActionProperty(Node, Action) - Static method in class qupath.lib.gui.actions.ActionTools
Add an Action to the properties of a Node, so that it may be retrieved later.
PYTHON - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
PYTHON_IMPORTER - Static variable in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
Pythonic import statements
PythonAutoCompletor - Class in qupath.lib.gui.scripting.completors
Auto completion support for Python.
PythonAutoCompletor() - Constructor for class qupath.lib.gui.scripting.completors.PythonAutoCompletor
Constructor.

Q

QPEx - Class in qupath.lib.gui.scripting
Alternative to QP offering static methods of use for scripting, along with some extra methods that require access of GUI features.
QPEx() - Constructor for class qupath.lib.gui.scripting.QPEx
 
QUIT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
QUPATH_AND_EXTENSIONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
Check for QuPath and extensions on GitHub
QUPATH_ONLY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
Check for QuPath updates only
QUPATH_STARTUP - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
qupath.lib.display - package qupath.lib.display
Classes to control the display of images in a QuPathViewer.
qupath.lib.display.settings - package qupath.lib.display.settings
Classes to support storing and retrieving image display settings.
qupath.lib.gui - package qupath.lib.gui
The main QuPath user interface.
qupath.lib.gui.actions - package qupath.lib.gui.actions
Classes to manage Actions.
qupath.lib.gui.actions.annotations - package qupath.lib.gui.actions.annotations
Annotations that can be used to configure actions.
qupath.lib.gui.actions.menus - package qupath.lib.gui.actions.menus
Classes to store actions that correspond to QuPath's main menus.
qupath.lib.gui.charts - package qupath.lib.gui.charts
Classes for plotting and charting.
qupath.lib.gui.commands - package qupath.lib.gui.commands
Commands shown within the main QuPath interface.
qupath.lib.gui.commands.display - package qupath.lib.gui.commands.display
Extra package to organize the classes related to the Brightness/Contrast command.
qupath.lib.gui.commands.objects - package qupath.lib.gui.commands.objects
 
qupath.lib.gui.dialogs - package qupath.lib.gui.dialogs
Helper classes for creating dialogs, prompts and filt choosers within QuPath.
qupath.lib.gui.extensions - package qupath.lib.gui.extensions
Interface to define QuPath extensions.
qupath.lib.gui.images.servers - package qupath.lib.gui.images.servers
Custom ImageServers that depend upon the QuPath interface and image display settings.
qupath.lib.gui.images.stores - package qupath.lib.gui.images.stores
Classes for requesting, caching and drawing image tiles.
qupath.lib.gui.localization - package qupath.lib.gui.localization
 
qupath.lib.gui.logging - package qupath.lib.gui.logging
Support for logging.
qupath.lib.gui.measure - package qupath.lib.gui.measure
Classes related to extracting, calculating and displaying measurements.
qupath.lib.gui.measure.ui - package qupath.lib.gui.measure.ui
 
qupath.lib.gui.panes - package qupath.lib.gui.panes
Panes used to display information in the QuPath interface.
qupath.lib.gui.prefs - package qupath.lib.gui.prefs
Custom preferences.
qupath.lib.gui.scripting - package qupath.lib.gui.scripting
Scripting through the QuPath interface.
qupath.lib.gui.scripting.completors - package qupath.lib.gui.scripting.completors
Classes for auto-completion in QuPath's script editor.
qupath.lib.gui.scripting.languages - package qupath.lib.gui.scripting.languages
Language and syntax definitions for QuPath scripting.
qupath.lib.gui.scripting.syntax - package qupath.lib.gui.scripting.syntax
Classes for syntax help in QuPath's script editor.
qupath.lib.gui.tma - package qupath.lib.gui.tma
Display, summarize and query tissue microarray analysis results.
qupath.lib.gui.tools - package qupath.lib.gui.tools
Assorted helper classes for the QuPath interface.
qupath.lib.gui.viewer - package qupath.lib.gui.viewer
QuPath image viewing and display.
qupath.lib.gui.viewer.overlays - package qupath.lib.gui.viewer.overlays
Support for overlays, which may be painted on top of QuPathViewers.
qupath.lib.gui.viewer.recording - package qupath.lib.gui.viewer.recording
Record and display field of view changes made within a QuPathViewer.
qupath.lib.gui.viewer.tools - package qupath.lib.gui.viewer.tools
Drawing and navigation tools for the QuPath toolbar.
qupath.lib.gui.viewer.tools.handlers - package qupath.lib.gui.viewer.tools.handlers
 
QuPathApp - Class in qupath.lib.gui
Launcher application to start QuPath.
QuPathApp() - Constructor for class qupath.lib.gui.QuPathApp
 
QuPathExtension - Interface in qupath.lib.gui.extensions
Simple interface for QuPath extensions.
QuPathGUI - Class in qupath.lib.gui
Main GUI for QuPath, written using JavaFX.
QuPathPenManager - Class in qupath.lib.gui.viewer.tools
Helper class for managing pressure-sensitive input.
QuPathPenManager() - Constructor for class qupath.lib.gui.viewer.tools.QuPathPenManager
 
QuPathPenManager.PenInputManager - Interface in qupath.lib.gui.viewer.tools
Interface defining minimal behavior for a pen input device.
QuPathResources - Class in qupath.lib.gui.localization
Load strings from the default resource bundle.
QuPathResources() - Constructor for class qupath.lib.gui.localization.QuPathResources
 
QuPathStyleManager - Class in qupath.lib.gui.prefs
Class to facilitate the use of different styles within QuPath.
QuPathStyleManager() - Constructor for class qupath.lib.gui.prefs.QuPathStyleManager
 
QuPathStyleManager.Fonts - Enum Class in qupath.lib.gui.prefs
Available font families.
QuPathStyleManager.StyleOption - Interface in qupath.lib.gui.prefs
Interface defining a style that may be applied to QuPath.
QuPathTMAViewer - Class in qupath.lib.gui.tma
Standalone viewer for looking at TMA summary results.
QuPathTMAViewer() - Constructor for class qupath.lib.gui.tma.QuPathTMAViewer
 
QuPathViewer - Class in qupath.lib.gui.viewer
JavaFX component for viewing a (possibly large) image, along with overlays.
QuPathViewer(DefaultImageRegionStore, OverlayOptions) - Constructor for class qupath.lib.gui.viewer.QuPathViewer
Create a new viewer.
QuPathViewerListener - Interface in qupath.lib.gui.viewer
Interface for defining a listener that needs to know whenever the data related to a QuPathViewer has changed in some way - such as by changing the underlying ImageData, or by moving the field of view.
QuPathViewerPlus - Class in qupath.lib.gui.viewer
A whole slide viewer with optional extras...
QuPathViewerPlus(DefaultImageRegionStore, OverlayOptions, ViewerPlusDisplayOptions) - Constructor for class qupath.lib.gui.viewer.QuPathViewerPlus
Create a new viewer.

R

random(Random) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the random number generator.
RAW - Enum constant in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
Raw bin counts.
readFile(File) - Method in class qupath.lib.gui.scripting.ScriptTab
Read the file, set the editor's text area with the content of the file and return the detected language (based on the file extension).
readObjectsFromClipboard(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.InteractiveObjectImporter
Try to read objects from the system clipboard.
readOnlyProperty() - Method in class qupath.lib.gui.QuPathGUI
Property indicating whether QuPath is in 'read-only' mode.
readPathObjects() - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
 
readRegion(RegionRequest) - Method in class qupath.lib.gui.images.servers.ChannelDisplayTransformServer
 
readTile(TileRequest) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
 
readTile(TileRequest) - Method in class qupath.lib.gui.images.servers.RenderedImageServer
 
RECENT_COMMAND_LIST - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
RECENT_COMMANDS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
recordingProperty() - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Return the recording property of this ViewTracker.
RECTANGLE - Static variable in class qupath.lib.gui.viewer.tools.PathTools
Rectangle drawing tool
RECTANGLE_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
RECTANGLE_TOOL - Variable in class qupath.lib.gui.ToolManager
 
redo() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Request redo.
redo() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
REDO - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
redoAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
redoOnce() - Method in class qupath.lib.gui.UndoRedoManager
Request to 'redo' the last 'undone' hierarchy change for the current active viewer.
refineGeometryByParent(Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
 
refineGeometryByParent(Geometry) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
 
refineROIByParent(ROI) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Apply clipping based on the current parent object.
refineROIByParent(ROI) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
Apply clipping based on the current parent object.
refresh() - Method in class qupath.lib.gui.commands.PathObjectGridView
Refresh the data in the grid view
refresh() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
Refresh the current style.
REFRESH - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
REFRESH_DUPLICATE_OBJECT_IDS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
REFRESH_OBJECT_IDS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
refreshAllEditors() - Method in class qupath.lib.gui.panes.PreferencePane
Request that all the property editors are regenerated.
refreshChannelOptions() - Method in class qupath.lib.display.ImageDisplay
Refresh the channel options.
refreshCombo() - Method in class qupath.lib.gui.charts.HistogramDisplay
Refresh the available measurements.
refreshData() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Recalculate the values of all data points.
refreshFileContents() - Method in class qupath.lib.gui.scripting.ScriptTab
 
refreshHistogram() - Method in class qupath.lib.gui.charts.HistogramDisplay
Refresh the currently-displayed histogram (e.g.
refreshList(ListView<T>) - Static method in class qupath.lib.gui.tools.GuiTools
Refresh a ListView in the Application thread.
refreshObjectIDs(ImageData<?>, boolean) - Static method in class qupath.lib.gui.commands.Commands
Refresh object IDs to ensure uniqueness.
refreshProject() - Method in class qupath.lib.gui.panes.ProjectBrowser
Refresh the current project, updating the displayed entries.
refreshProject() - Method in class qupath.lib.gui.QuPathGUI
Refresh the project, updating the display if required.
refreshScatterPlot() - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
Refresh the scatter plot, in case the underlying data has been updated.
refreshSliders() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
Refresh the sliders, to ensure they match with the current channel.
refreshTitle() - Method in class qupath.lib.gui.QuPathGUI
Refresh the title bar in the main QuPath window.
refreshTitles() - Method in class qupath.lib.gui.viewer.ViewerManager
Request that viewers refresh their titles.
RegionFilter - Interface in qupath.lib.gui.viewer
Define the area of an image to which pixel classification should be applied.
RegionFilter.StandardRegionFilters - Enum Class in qupath.lib.gui.viewer
Standard classification regions (hopefully all you will ever need).
registerRequest(TileListener<BufferedImage>, ImageServer<BufferedImage>, Shape, double, int, int) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
Register a request so that the tile request queue will be populated, including potentially for nearby tiles (i.e.
registerTool(QuPathViewer) - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
 
registerTool(QuPathViewer) - Method in interface qupath.lib.gui.viewer.tools.PathTool
Register the tool on the viewer.
RELABEL - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
relativeToUserDirectory() - Method in class qupath.lib.gui.FileCopier
Specify that the copying is relative to the QuPath user directory.
RELOAD_DATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
reloadImageData(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Reload the specified image data from a previously saved version,if available.
REMOVE_COLUMN - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
 
REMOVE_FRAGMENTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
REMOVE_ROW - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
 
removeActions - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
RemoveActions() - Constructor for class qupath.lib.gui.actions.menus.TMAMenuActions.Actions.RemoveActions
 
removeColumn(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
Try to remove the column containing the specified viewer, notifying the user if this isn't possible.
removeFileDropHandler(DragDropImportListener.DropHandler<File>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
Remove a File DropHandler.
removeJsonDropHandler(DragDropImportListener.DropHandler<JsonElement>) - Method in class qupath.lib.gui.viewer.DragDropImportListener
Remove a JSON DropHandler.
removeOnImageBounds(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Delete all objects touching the image boundary.
removeParameterChangeListener(ParameterChangeListener) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Remove a ParameterChangeListener.
removeRow(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
Try to remove the row containing the specified viewer, notifying the user if this isn't possible.
removeTextAppendableFX(TextAppendable) - Static method in class qupath.lib.gui.logging.LogManager
Deregister a TextAppendable so that it will no longer be informed of logging events.
removeTileListener(TileListener<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
removeViewerListener(QuPathViewerListener) - Method in class qupath.lib.gui.viewer.QuPathViewer
Remove a viewer listener.
RenderedImageServer - Class in qupath.lib.gui.images.servers
An ImageServer that can display a rendered image, with optional overlays.
RenderedImageServer.Builder - Class in qupath.lib.gui.images.servers
Builder to create an ImageServer to display rendered images, with optional overlay layers.
renderer(ImageRenderer) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify the ImageRenderer that controls conversion to RGB.
rendererProperty() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Get the ImageRenderer property used with this overlay.
rendererProperty() - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
Get the ImageRenderer property used with this overlay.
repaint() - Method in class qupath.lib.gui.viewer.QuPathViewer
Request that the viewer is repainted.
repaintAllViewers() - Method in class qupath.lib.gui.viewer.ViewerManager
Request that all viewers are repainted as soon as possible.
repaintEntireImage() - Method in class qupath.lib.gui.viewer.QuPathViewer
Request that the entire image is repainted, including the thumbnail.
repaintEntireImage() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
 
repaintTimestamp() - Method in class qupath.lib.gui.viewer.QuPathViewer
Get the timestamp referring to the last time this viewer was repainted.
replaceSelection(String) - Method in interface qupath.lib.gui.scripting.EditableText
Insert the specified text, replacing any existing selection.
replaceSelection(String) - Method in class qupath.lib.gui.scripting.TextAreaControl
 
requestAutomaticUpdateCheck() - Method in class qupath.lib.gui.QuPathGUI
Request an automated update check in a background thread.
requestCancelDirection(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
Requests that the viewer cancels either the x- or y-axis direction.
requestClose() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
requestClose() - Method in interface qupath.lib.gui.scripting.ScriptEditor
Attempt to close the editor, saving changes if requested.
requestDecelerate() - Method in class qupath.lib.gui.viewer.QuPathViewer
Request that a viewer decelerate any existing panning smoothly.
requestFocus() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Request that the control is focused.
requestFocus() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
requestFollowCaret() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Request that the X and Y scrolls are adjusted to ensure the caret is visible.
requestFullUpdateCheck() - Method in class qupath.lib.gui.QuPathGUI
Request a manual update check in a background thread.
requestImageTile(ImageServer<BufferedImage>, RegionRequest, Map<RegionRequest, BufferedImage>, boolean) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
Request an image tile.
requestParentClipping(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Query whether parent clipping should be applied.
requestParentClipping(MouseEvent) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
Query whether parent clipping should be applied.
requestPixelSnapping() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Returns true if the tool requests that pixel coordinates be snapped to integer values.
requestPixelSnapping() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
Returns true if the tool requests that pixel coordinates be snapped to integer values.
requestStartMoving(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Request that the viewer start panning with a velocity determined by dx and dy.
requestStopMoving() - Method in class qupath.lib.gui.viewer.QuPathViewer
Request that the viewer stop any panning immediately.
requestUserDirectory(boolean) - Static method in class qupath.lib.gui.commands.Commands
Request the current user directory, optionally prompting the user to request a directory if none is available.
requiresTileRegion(String, ImageRegion) - Method in interface qupath.lib.gui.images.stores.TileListener
Check if the listener requires a particular tile.
requiresTileRegion(String, ImageRegion) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
RESET_DETECTION_CLASSIFICATIONS - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
 
RESET_METADATA - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
RESET_PREFERENCES - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
RESET_SELECTION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
resetAllSliders() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
Reset all sliders to their default values.
resetAvailablePathClasses() - Method in class qupath.lib.gui.QuPathGUI
Populate the availablePathClasses with a default list.
resetClassifications(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands
Select objects that are instances of a specified class, logging an appropriate method in the workflow.
resetConstrainingObjects() - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
Reset the constraining objects.
resetConstrainingObjects() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
Reset the constraining objects.
resetCustomPixelLayerOverlay() - Method in class qupath.lib.gui.viewer.QuPathViewer
Reset the custom pixel layer overlay to null.
resetGridSize() - Method in class qupath.lib.gui.viewer.ViewerManager
 
resetImage() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Remove the image.
resetImageData() - Method in class qupath.lib.gui.viewer.overlays.HierarchyOverlay
Reset the last image data.
resetImageData() - Method in class qupath.lib.gui.viewer.QuPathViewer
Reset the image data to null.
resetMeasurementMapper() - Method in class qupath.lib.gui.viewer.OverlayOptions
Reset any MeasurementMapper, so that measurements are not used to determine object colors.
resetMinimumRepaintSpacingMillis() - Method in class qupath.lib.gui.viewer.QuPathViewer
Return to processing all repainting requests.
resetPreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
Reset the preferences to their defaults.
resetSelection(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Reset the selection for an image.
resetShowObjectPredicate() - Method in class qupath.lib.gui.viewer.OverlayOptions
resetTMAMetadata(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Reset TMA metadata, if available.
resizable() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Make the dialog resizable (but default it is not).
resize(double, double) - Method in class qupath.lib.gui.ColorMapCanvas
 
RESOLVE_HIERARCHY - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
resourceManagerProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSettingsPane
The resource manager used to handle saving/loading.
returnToMove - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
returnToMoveModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request that the GUI returns to using the PAN tool after a ROI is drawn.
RIGID_OBJECT_EDITOR - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
rngSeedProperty() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Get a property representing the random number generator's seed for subsampling.
rootLogLevelProperty() - Static method in class qupath.lib.gui.logging.LogManager
Property representing the current requested root log level.
ROTATE_IMAGE - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
rotationProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
Return the rotation property of this viewer.
run() - Method in class qupath.lib.gui.commands.BrightnessContrastCommand
 
run() - Method in class qupath.lib.gui.commands.CountingDialogCommand
 
run() - Method in class qupath.lib.gui.commands.MeasurementExportCommand
 
run() - Method in class qupath.lib.gui.JavadocViewerRunner
 
run() - Method in class qupath.lib.gui.tma.TMAExplorer
 
run() - Method in class qupath.lib.gui.tools.DocGenerator
 
run() - Method in class qupath.lib.gui.viewer.recording.ViewTrackerControlPane
 
run(ImageData<?>) - Method in class qupath.lib.gui.commands.objects.SplitAnnotationsByLineCommand
Run the command for the specified image data.
runForImage(ImageData<?>) - Method in class qupath.lib.gui.commands.DeleteObjectsOnBoundsCommand
Run the command interactively for the specified image.
runGeoJsonExport(QuPathGUI) - Static method in class qupath.lib.gui.commands.ExportObjectsCommand
Run the path object GeoJSON export command.
runGeoJsonObjectExport(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Show a dialog to export object(s) to a GeoJSON file.
runObjectImport(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Show a dialog to import object(s) from a file.
runPlugin(String, String) - Static method in class qupath.lib.gui.scripting.QPEx
 
runPlugin(String, ImageData<?>, String) - Static method in class qupath.lib.gui.scripting.QPEx
 
runPlugin(PathPlugin<BufferedImage>, String, boolean) - Method in class qupath.lib.gui.QuPathGUI
Run a plugin, interactively (i.e.
runProjectScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
runProjectScriptNoSaveAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
runScript(File, String) - Method in class qupath.lib.gui.QuPathGUI
Convenience method to execute a script.
runScriptAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
runSelectedAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
runTasks(String, Collection<? extends Runnable>) - Method in class qupath.lib.gui.TaskRunnerFX
 

S

SANS_SERIF - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
Preferred sans-serif font.
saturationPercentProperty() - Method in class qupath.lib.gui.panes.SimpleImageViewer
Get the percentage of any non-8-bit image that should be saturated when applying auto contrast settings.
SAVE_DATA - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
SAVE_DATA_AS - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
saveAnnotationMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save annotation measurements for the current image.
saveAnnotationMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save annotation measurements for the specified image.
saveCellMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save cell measurements for the current image.
saveChannelColorProperties() - Method in class qupath.lib.display.ImageDisplay
Save color channels in the ImageData properties.
saveDetectionMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save detection measurements for the current image.
saveDetectionMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save detection measurements for the specified image.
saveImageMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save whole image measurements for the current image.
saveImageMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save whole image measurements for the specified image.
saveMeasurements(Class<? extends PathObject>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save measurements for the current image for objects of a fixed type.
saveMeasurements(ImageData<?>, Class<? extends PathObject>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save measurements for the specified image for objects of a fixed type.
savePreferences() - Static method in class qupath.lib.gui.prefs.PathPrefs
Save the preferences.
saveSnapshot(QuPathGUI, GuiTools.SnapshotType) - Static method in class qupath.lib.gui.commands.Commands
Save an image snapshot, prompting the user to select the output file.
saveSnapshotWithDelay(QuPathGUI, GuiTools.SnapshotType, long) - Static method in class qupath.lib.gui.commands.Commands
Save an image snapshot after a specified delay, prompting the user to select the output file.
saveTableModel(PathTableData<?>, File, Collection<String>) - Static method in class qupath.lib.gui.measure.ui.SummaryMeasurementTable
Save the data from a table to a text file, using the default delimiter from PathPrefs.
saveTileMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save tile measurements for the current image.
saveTMAMeasurements(String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save TMA measurements for the current image.
saveTMAMeasurements(ImageData<?>, String, String...) - Static method in class qupath.lib.gui.scripting.QPEx
Save TMA measurements for the specified image.
scalebarFontSize - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
scalebarFontSizeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Preferred font size for the scalebar in the viewer.
scalebarFontWeight - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
scalebarFontWeightProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Preferred font weight in the viewer.
scalebarLineWidth - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
scalebarLineWidthProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Preferred line width for the scalebar.
scatterChart() - Static method in class qupath.lib.gui.charts.Charts
Create a Charts.ScatterChartBuilder for generating a custom scatter plot.
ScatterPlotDisplay - Class in qupath.lib.gui.charts
A wrapper around PathObjectScatterChart for displaying data about PathObject measurements.
ScatterPlotDisplay() - Constructor for class qupath.lib.gui.charts.ScatterPlotDisplay
Create a scatter plot from a table of PathObject measurements.
SCREENSHOT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
SCRIPT_EDITOR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
SCRIPT_EDITOR - Variable in class qupath.lib.gui.actions.AutomateActions
 
SCRIPT_EDITOR - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
 
SCRIPT_INTERPRETER - Variable in class qupath.lib.gui.actions.AutomateActions
 
SCRIPT_INTERPRETER - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
 
ScriptEditor - Interface in qupath.lib.gui.scripting
Minimal interface for a script editor that the GUI can call.
ScriptEditorControl<T> - Interface in qupath.lib.gui.scripting
Basic script editor control using JavaFX.
ScriptingPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ScriptingPreferences
 
ScriptLanguageProvider - Class in qupath.lib.gui.scripting.languages
Class with static methods to fetch all the available ScriptLanguages.
ScriptLanguageProvider() - Constructor for class qupath.lib.gui.scripting.languages.ScriptLanguageProvider
 
scriptRunning() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Observable value indicating whether a script is currently running or not.
scriptsDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
Read only property representing the shared scripts directory.
scriptsPath - Variable in class qupath.lib.gui.panes.PreferencePane.ExtensionPreferences
 
scriptsPath - Variable in class qupath.lib.gui.panes.PreferencePane.ScriptingPreferences
 
scriptsPathProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Path to a directory containing scripts for quick-access through the user interface.
ScriptSyntax - Interface in qupath.lib.gui.scripting.syntax
Interface for classes that apply some syntax formatting to an EditableText.
ScriptSyntaxProvider - Class in qupath.lib.gui.scripting.syntax
Class with static methods to fetch all the available ScriptSyntaxes.
ScriptSyntaxProvider() - Constructor for class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
ScriptTab - Class in qupath.lib.gui.scripting
Class representing a script tab (e.g.
scrollSpeed - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
scrollSpeedProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Percentage to scale scroll speed for zooming etc.
SELECT_ALL_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SELECT_ALL_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SELECT_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SELECT_BY_CLASSIFICATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SELECT_BY_PLANE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SELECT_CELLS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SELECT_TILES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SELECT_TMA_CORES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
selectable(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Sets the selectable property of the action.
SelectableItem<T> - Class in qupath.lib.gui
Helper class for managing items when only one of them may be selected.
SelectableItem(ObjectProperty<T>, T) - Constructor for class qupath.lib.gui.SelectableItem
Constructor.
selectActions - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
SelectActions() - Constructor for class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
selectAllObjects(ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Select all objects (excluding the root object) in the imageData.
selected(boolean) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Set the selected property of the action.
selected(ObservableValue<Boolean>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Bind the selected property of the action to an ObservableValue, bidirectionally if possible.
selectedChannelProperty() - Method in class qupath.lib.gui.commands.display.BrightnessContrastSliderPane
The channel to which the sliders are applied.
selectedChannels() - Method in class qupath.lib.display.ImageDisplay
Read-only observable list containing the channels currently selected for display.
selectedClassesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
selectedClassVisibilityModeProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
Request that only exact matches to classes in OverlayOptions.selectedClassesProperty() should be hidden.
selectedColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
SelectedMeasurementTableView - Class in qupath.lib.gui.panes
Component to show measurements for a currently-selected object.
SelectedMeasurementTableView(ObservableValue<ImageData<BufferedImage>>) - Constructor for class qupath.lib.gui.panes.SelectedMeasurementTableView
Constructor.
selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.UndoRedoManager
 
selectedObjectChanged(QuPathViewer, PathObject) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
Called when the primary selected object has changed in a viewer.
selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
selectedObjectChanged(QuPathViewer, PathObject) - Method in class qupath.lib.gui.viewer.ViewerManager
 
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.AnnotationPane
 
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.PathObjectHierarchyView
 
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.panes.SelectedMeasurementTableView
 
selectedPathObjectChanged(PathObject, PathObject, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
selectedProperty() - Method in class qupath.lib.gui.SelectableItem
Property representing the item that has been selected (which may or may not be the same as SelectableItem.getItem()).
selectedScriptProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Get a property representing the current selected ScriptTab.
selectedStyleProperty() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
Get the current selected style.
selectedTextProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Text currently selected in the editor control.
selectedTextProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
selectedTool() - Method in class qupath.lib.gui.viewer.tools.ExtendedPathTool
 
selectedToolProperty() - Method in class qupath.lib.gui.ToolManager
Property containing the currently-selected PathTool.
SELECTION_MODE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
SELECTION_MODE - Variable in class qupath.lib.gui.ToolManager
 
selectionModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Convert drawing tools to select objects, rather than creating new objects.
selectionModeStatus() - Static method in class qupath.lib.gui.prefs.PathPrefs
 
selectObjectsByClass(ImageData<?>, Class<? extends PathObject>) - Static method in class qupath.lib.gui.commands.Commands
Select objects that are instances of a specified class, logging an appropriate method in the workflow.
selectObjectsByClassification(ImageData<?>, PathClass...) - Static method in class qupath.lib.gui.commands.Commands
Select objects by classification, logging the step (if performed) in the history workflow.
selectObjectsOnCurrentPlane(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
Select all the objects on the current plane of the viewer.
selectRange(int, int) - Method in interface qupath.lib.gui.scripting.EditableText
Set the range of the selected text.
selectRange(int, int) - Method in class qupath.lib.gui.scripting.TextAreaControl
 
sendLogToConsoleProperty() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Boolean property indicating whether the console should display the log, rather than directly-printed information.
sendQuitRequest() - Method in class qupath.lib.gui.QuPathGUI
Request to quit QuPath.
SEP - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
 
SEP_0 - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
SEP_0 - Variable in class qupath.lib.gui.actions.menus.AutomateMenuActions.Actions
 
SEP_0 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
SEP_0 - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
SEP_0 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_00 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.CopyActions
 
SEP_00 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
SEP_00 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
SEP_01 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
SEP_01 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
SEP_02 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewActions
 
SEP_02 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultiviewGridActions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ExtensionsMenuActions.Actions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.TMAMenuActions.Actions
 
SEP_1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_2 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
SEP_2 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
SEP_2 - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
SEP_2 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.DeleteActions
 
SEP_2 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SEP_2 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_22 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ProjectActions
 
SEP_3 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
 
SEP_3 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
SEP_3 - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
SEP_3 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.SelectActions
 
SEP_3 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
SEP_4 - Variable in class qupath.lib.gui.actions.menus.ClassifyMenuActions.Actions
 
SEP_4 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
SEP_4 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
SEP_4 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_5 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
SEP_5 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SEP_5 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_6 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
SEP_6 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SEP_6 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_7 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
SEP_7 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SEP_7 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_8 - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
SEP_8 - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SEP_8 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SEP_9 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.MultitouchActions
 
separator(String) - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify the separator used between measurement values.
series(String, String[], double[]) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Create a bar chart using arrays of String values and associated numeric values.
series(String, String[], double[], List<T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Create a bar chart using collections of String values and associated numeric values, with an associated custom object.
series(String, String[], double[], T[]) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Create a bar chart using collections String values and associated numeric values, with an associated custom object.
series(String, Collection<? extends String>, Collection<T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Create a bar chart using collections of numeric values.
series(String, Collection<? extends T>, Function<T, PathClass>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Plot values extracted from objects within a specified collection.
series(String, Collection<XYChart.Data<String, Number>>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Create a bar chart from existing data plots.
series(String, Map<String, T>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Create a bar chart using a map of String values and associated numeric values.
SERIF - Enum constant in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
Preferred serif font.
ServerSelector - Class in qupath.lib.gui.panes
Helper class for selecting one image server out of a collection.
setAccelerator(String, String) - Method in class qupath.lib.gui.QuPathGUI
Set an accelerator for the specified menu command.
setAccelerator(MenuItem, KeyCombination) - Method in class qupath.lib.gui.QuPathGUI
Set the accelerator for the specified menu item.
setAccelerator(Action, KeyCombination) - Method in class qupath.lib.gui.QuPathGUI
Set the accelerator for the specified action.
setActiveTool(PathTool) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the active PathTool for input to this viewer.
setActiveViewer(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
Sets the value of the activeViewer property.
setAll() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level to LogLevel.ALL.
setAlphaComposite(Graphics2D) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
 
setAutorangeToFullData(boolean) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
setBorderColor(Color) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the border color for this viewer.
setCenterPixelLocation(double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the image pixel to display in the center of the viewer (using image pixel coordinates at the full-resolution)
setChannelDisplayRange(int, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
Set the minimum and maximum display range for the current ImageData for a channel identified by number.
setChannelDisplayRange(String, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
Set the minimum and maximum display range for the current ImageData for a channel identified by name.
setChannelDisplayRange(ImageData<BufferedImage>, int, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
Set the minimum and maximum display range for the specified ImageData for a channel identified by number.
setChannelDisplayRange(ImageData<BufferedImage>, String, double, double) - Static method in class qupath.lib.gui.scripting.QPEx
Set the minimum and maximum display range for the specified ImageData for a channel identified by name.
setChannelSelected(ChannelDisplayInfo, boolean) - Method in class qupath.lib.display.ImageDisplay
Set the selection of a channel on or off.
setColorMap(ColorMaps.ColorMap) - Method in class qupath.lib.gui.ColorMapCanvas
Set the ColorMaps.ColorMap to display to the one with the specified list index.
setColorMapper(ColorMaps.ColorMap) - Method in class qupath.lib.gui.tools.MeasurementMapper
Set a new color mapper.
setColorModel(ColorModel) - Method in class qupath.lib.gui.images.stores.ColorModelRenderer
Set the color model to use.
setColorModel(ColorModel) - Method in class qupath.lib.gui.viewer.overlays.BufferedImageOverlay
Optionally set a custom ColorModel.
setContextMenu(ContextMenu) - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Set the context menu for the control.
setContextMenu(ContextMenu) - Method in class qupath.lib.gui.scripting.TextAreaControl
 
setCountsTransform(HistogramChart.CountsTransformMode) - Method in class qupath.lib.gui.charts.HistogramChart
Set the current counts transform.
setCursor(Cursor) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the requested cursor to display in this viewer
setCustomPixelLayerOverlay(PathOverlay) - Method in class qupath.lib.gui.viewer.QuPathViewer
Optionally set a custom overlay to use for the pixel layer.
setData(Collection<? extends PathObject>, Function<PathObject, Number>, Function<PathObject, Number>) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Set the data to display in the plot.
setDataFromTable(Collection<? extends PathObject>, PathTableData<PathObject>, String, String) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
Set the data to display in the plot from a table model.
setDebug() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level to DEBUG.
setDetectionDisplayMode(OverlayOptions.DetectionDisplayMode) - Method in class qupath.lib.gui.viewer.OverlayOptions
setDisplayMaxValue(double) - Method in class qupath.lib.gui.tools.MeasurementMapper
Set the measurement value that maps to the last color in the color mapper.
setDisplayMinValue(double) - Method in class qupath.lib.gui.tools.MeasurementMapper
Set the measurement value that maps to the first color in the color mapper.
setDisplayMode(HistogramChart.DisplayMode) - Method in class qupath.lib.gui.charts.HistogramChart
Set the histogram display mode.
setDoFasterRepaint(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set flag to indicate that repaints should prefer speed over accuracy.
setDownsample(double) - Method in class qupath.lib.gui.commands.MiniViewers.MiniViewerManager
Set the downsample to use within the mini viewers.
setDownsampleFactor(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the downsample factor for this viewer.
setDownsampleFactor(double, double, double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set downsample factor, so that the specified coordinate in the image space is not shifted in the viewer afterwards.
setDownsampleFactor(double, double, double, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set downsample factor, so that the specified coordinate in the image space is not shifted in the viewer afterwards.
setError() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level to LogLevel.ERROR.
setExcludeOutsideRange(boolean) - Method in class qupath.lib.gui.tools.MeasurementMapper
Specify whether out-of-range values should be excluded.
setExpandToWindow(boolean) - Method in class qupath.lib.gui.panes.SimpleImageViewer
Control whether the image should be allowed to expand beyond its preferred width and height to fill the window.
setFile(File) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Set the file for this ViewTracker.
setFillAnnotations(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show annotation objects 'filled' in viewers.
setFillDetections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show detection objects 'filled' in viewers.
setFillHeight(Boolean, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the GridPane.setFillHeight(Node, Boolean) property for specified nodes.
setFillWidth(Boolean, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the GridPane.setFillWidth(Node, Boolean) property for specified nodes.
setFontSize(float) - Method in class qupath.lib.gui.viewer.OverlayOptions
Set the requested font size for the 'Show names' option
setGamma(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the gamma value for this viewer.
setGridLines(GridLines) - Method in class qupath.lib.gui.viewer.OverlayOptions
Set the GridLines object that defines how a counting grid may be show in viewers
setGridSize(int, int) - Method in class qupath.lib.gui.viewer.ViewerManager
Set the grid to have a specific number of rows and columns.
setHGrowPriority(Priority, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the GridPane.setHgrow(Node, Priority) property for specified nodes.
setHideChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Request that the specified channel is hidden.
setHideIfEmpty(boolean) - Method in class qupath.lib.gui.charts.HistogramChart
Request that the chart is automatically hidden (visibility set to false) when there is no data.
setImageData(ImageData<?>, Collection<? extends PathObject>) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Set the ImageData and a collection of objects to measure.
setImageData(ImageData<BufferedImage>) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the current image for this viewer.
setImageData(ImageData<BufferedImage>, boolean) - Method in class qupath.lib.display.ImageDisplay
Set the ImageData to a new value
setImageType - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
setInfo() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level to DEBUG.
setInputFile(File) - Method in class qupath.lib.gui.tma.TMASummaryViewer
Deprecated.
Set the input file for the summary viewer.
setInterpolation(Graphics2D) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
 
setInterpolation(ImageInterpolation) - Method in class qupath.lib.gui.viewer.overlays.AbstractImageOverlay
Set the preferred method of interpolation to use for display.
setIsInteractive(boolean) - Method in class qupath.lib.gui.charts.ChartThresholdPane
setItem(S) - Method in interface qupath.lib.gui.tools.PathObjectImageViewers.ItemViewer
Set the item to display
setLanguage(ScriptLanguage) - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Set the language for text to be displayed by this control.
setLineChartLegendLines(Chart, double) - Static method in class qupath.lib.gui.charts.ChartTools
Charts tend to show their legends with circular/square markers...
setLineWidth(double) - Method in class qupath.lib.gui.charts.ChartThresholdPane
Set the threshold line width.
setLivePrediction(boolean) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Turn on or off live prediction.
setLocationStringFunction(AbstractOverlay.LocationStringFunction) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
Set a custom function to calculate a location string for the overlay.
setLUTColor(int, int, int) - Method in class qupath.lib.display.DirectServerChannelInfo
Set the 'maximum' color, which defines the lookup table to use.
setMagnification(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the downsample factor based upon magnification values.
setMaxDisplay(float) - Method in class qupath.lib.display.AdditiveChannelInfo
 
setMaxDisplay(float) - Method in class qupath.lib.display.DirectServerChannelInfo
 
setMaxDisplay(float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo
Set the max display value for this channel.
setMaxHeight(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the max height property for the specified regions.
setMaxPoints(int) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
setMaxThreads(int) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Set the maximum number of threads that may be used during live prediction.
setMaxWidth(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the max width property for the specified regions.
setMeasurementMapper(MeasurementMapper) - Method in class qupath.lib.gui.viewer.OverlayOptions
Set the MeasurementMapper that defines how detections should be color coded according to their measurement values in viewers
setMetadata(ImageServerMetadata) - Method in class qupath.lib.gui.images.servers.PathHierarchyImageServer
Throws an exception - metadata should not be set for a hierarchy image server directly.
setMinDisplay(float) - Method in class qupath.lib.display.AdditiveChannelInfo
 
setMinDisplay(float) - Method in class qupath.lib.display.DirectServerChannelInfo
 
setMinDisplay(float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo
Set the min display value for this channel.
setMinHeight(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the min height property for the specified regions.
setMinimumRepaintSpacingMillis(long) - Method in class qupath.lib.gui.viewer.QuPathViewer
Prevent frequent repaints (temporarily) by setting a minimum time that must have elapsed after the previous repaint for a new one to be triggered.
setMinMaxAllowed(float, float) - Method in class qupath.lib.display.AdditiveChannelInfo
 
setMinMaxAllowed(float, float) - Method in class qupath.lib.display.DirectServerChannelInfo
 
setMinMaxAllowed(float, float) - Method in interface qupath.lib.display.ChannelDisplayInfo.ModifiableChannelDisplayInfo
Set the maximum permissible range for the image display.
setMinMaxDisplay(ChannelDisplayInfo, float, float) - Method in class qupath.lib.display.ImageDisplay
Set the min/max display values for a specified ChannelDisplayInfo.
setMinWidth(double, Region...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the min width property for the specified regions.
setModel(PathTableData<PathObject>) - Method in class qupath.lib.gui.charts.ScatterPlotDisplay
setName(String) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Set the name of this ViewTracker.
setNumBins(int) - Method in class qupath.lib.gui.charts.HistogramDisplay
Set the number of bins for the histogram.
setNumericParameterValue(String, Number) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Set a numeric parameter value (either int or double).
setNumericParameterValueRange(String, double, double) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Set the minimum and maximum value for a numeric parameter.
setOff() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level to LogLevel.OFF.
setOpacity(double) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
Set opacity between 0 (completely transparent) and 1 (completely opaque).
setOpacity(float) - Method in class qupath.lib.gui.viewer.OverlayOptions
Set global opacity for overlay drawing.
setOptionalParameters(boolean, boolean, boolean, boolean) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Set optional parameters for this ViewTracker.
setOverrideSystemMenuBar(boolean) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Set the current value of the override property, which optionally specifies whether the system menubar should not be used by any window - no matter what the value of SystemMenuBar.systemMenubarProperty().
setParameterEnabled(String, boolean) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Set the enabled status of a parameter by key, to determine if it can be edited.
setParameterEnabled(Parameter<?>, boolean) - Method in class qupath.lib.gui.dialogs.ParameterPanelFX
Set the enabled status of a parameter, to determine if it can be edited.
setPathClassHidden(PathClass, boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Request that objects with a particular PathClass not be displayed.
setPathObject(PathObject) - Method in class qupath.lib.gui.tools.PathObjectLabels.PathObjectMiniPane
Set the PathObject to display (may be null).
setPenManager(QuPathPenManager.PenInputManager) - Static method in class qupath.lib.gui.viewer.tools.QuPathPenManager
Set the PenInputManager.
setPieChartData(PieChart, Map<T, ? extends Number>, Function<T, String>, Function<T, Color>, boolean, boolean) - Static method in class qupath.lib.gui.charts.ChartTools
Set pie chart data from a count map.
setPixelClassificationRegionFilter(RegionFilter) - Method in class qupath.lib.gui.viewer.OverlayOptions
Control where pixel classifications should be calculated during live prediction
setPixelLayer(ImageData<BufferedImage>, ImageServer<BufferedImage>) - Static method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Set an ImageServer as a property in the ImageData.
setPlaceholderText(String) - Method in class qupath.lib.gui.panes.SimpleImageViewer
Set the placeholder text to show if no image is available.
setPointOpacity(double) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
setPointRadius(double) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
setPredicate(Predicate<? super PathObject>) - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Set a predicate used to filter the rows of the table.
setPreferredOverlayColor(Color) - Method in class qupath.lib.gui.viewer.overlays.AbstractOverlay
Set a preferred overlay color, which the overlay may or may not make use of.
setProject(Project<BufferedImage>) - Method in class qupath.lib.gui.panes.ProjectBrowser
Set the project.
setProject(Project<BufferedImage>) - Method in class qupath.lib.gui.QuPathGUI
Set the active project, triggering any necessary GUI updates.
setProjection(ZProjectedImageServer.Projection) - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
Sets the value of the projection property.
setReadOnly(boolean) - Method in class qupath.lib.gui.QuPathGUI
Specify whether QuPath should be in 'read-only' mode.
setRecording(boolean) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
Set the recording property of this ViewTracker.
setRenderer(ImageRenderer) - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Set the ImageRenderer to be used with this overlay.
setRenderer(ImageRenderer) - Method in class qupath.lib.gui.viewer.overlays.ZProjectOverlay
Set the ImageRenderer property used with this overlay.
setRngSeed(int) - Method in class qupath.lib.gui.charts.PathObjectScatterChart
setRootLogLevel(LogManager.LogLevel) - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level.
setRotation(double) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the rotation; angle in radians.
setSaturationPercent(double) - Method in class qupath.lib.gui.panes.SimpleImageViewer
Set the percentage of pixels to use when applying auto contrast settings to a non-8-bit image.
setScriptEditor(ScriptEditor) - Method in class qupath.lib.gui.QuPathGUI
Set a new ScriptEditor, which will be used from now on.
setSelectable(Action, boolean) - Static method in class qupath.lib.gui.actions.ActionTools
Set the selectable property for an action.
setSelected(boolean) - Method in class qupath.lib.gui.SelectableItem
Set the item to be selected.
setSelectedClassVisibilityMode(OverlayOptions.ClassVisibilityMode) - Method in class qupath.lib.gui.viewer.OverlayOptions
setSelectedObject(PathObject) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set selected object in the current hierarchy, without centering the viewer.
setSelectedObject(PathObject, boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set selected object in the current hierarchy, without centering the viewer.
setSelectedTool(PathTool) - Method in class qupath.lib.gui.ToolManager
Programmatically select the active PathTool.
setShowAnnotations(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show the annotations on the image.
setShowChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Request that the specified channel is shown.
setShowConnections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show connections between objects, if available.
setShowDetections(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show the objects as an overlay on the image.
setShowGrid(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Set whether a counting grid should be shown in viewers
setShowLocation(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
setShowNames(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show the object names on the image.
setShowObjectPredicate(Predicate<PathObject>) - Method in class qupath.lib.gui.viewer.OverlayOptions
setShowOverview(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
setShowPixelClassification(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show pixel classification overlays.
setShowScalebar(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
setShowTickLabels(boolean) - Method in class qupath.lib.gui.charts.HistogramChart
Request that tick labels are visible or not for both x and y axis.
setShowTMACoreLabels(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show TMA core names on top of the image.
setShowTMAGrid(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
Show the TMA grid on the image, if present.
setShowZProjectControls(boolean) - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
setSpaceDown(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewer
Notify this viewer that the isSpaceDown status should be changed.
setSpaceX(double) - Method in class qupath.lib.gui.viewer.GridLines
Set the horizontal spacing between lines for any counting grid.
setSpaceY(double) - Method in class qupath.lib.gui.viewer.GridLines
Set the vertical spacing between lines for any counting grid.
setSpinnersPosition(boolean) - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
Sets the Z and T spinner' position to allow space for command bar
setStyle() - Method in interface qupath.lib.gui.prefs.QuPathStyleManager.StyleOption
Set the style for the QuPath application.
setSwitchToGrayscaleChannel(ChannelDisplayInfo) - Method in class qupath.lib.display.ImageDisplay
setSynchronizeViewers(boolean) - Method in class qupath.lib.gui.viewer.ViewerManager
Sets the value of the synchronizeViewers property.
setText(String) - Method in interface qupath.lib.gui.scripting.EditableText
Set all the text in the editor.
setText(String) - Method in class qupath.lib.gui.scripting.TextAreaControl
Sets the value of the text property.
setTextFieldFromNumber(TextField, Number, String) - Static method in class qupath.lib.gui.dialogs.ParameterPanelFX
 
setThresholdColor(ObservableNumberValue, Color) - Method in class qupath.lib.gui.charts.ChartThresholdPane
Set the color of a specified threshold line.
setThresholds(Color, double...) - Method in class qupath.lib.gui.charts.ChartThresholdPane
Set thresholds, which are visualized as vertical lines.
settings(ImageDisplaySettings) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify the ImageDisplaySettings that control conversion to RGB.
settingsCompatibleWithDisplay(ImageDisplay, ImageDisplaySettings) - Static method in class qupath.lib.display.settings.DisplaySettingUtils
Check if the settings are compatible with the display.
setTMAEntriesFromImageData(ImageData<BufferedImage>) - Method in class qupath.lib.gui.tma.TMASummaryViewer
Deprecated.
Set the TMA entries from the TMACoreObjects of a specific ImageData.
setToExpandGridPaneHeight(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set constraints and max width values (where possible) so that the specified nodes fill all available vertical space in a GridPane.
setToExpandGridPaneWidth(Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set constraints and max width values (where possible) so that the specified nodes fill all available horizontal space in a GridPane.
setToolSwitchingEnabled(boolean) - Method in class qupath.lib.gui.ToolManager
Toggle whether the user is permitted to switch to a new active PathTool.
setTooltipFunction(Function<Double, String>) - Method in class qupath.lib.gui.ColorMapCanvas
Set the function that will take a value between 0 and 255 (from the color map) and output a displayable string
setTPosition(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the requested time point to be visible.
setTrace() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level to LogLevel.TRACE.
setupTarget(Node) - Method in class qupath.lib.gui.viewer.DragDropImportListener
Prepare a target node to accept drag and drop events.
setupTarget(Scene) - Method in class qupath.lib.gui.viewer.DragDropImportListener
Prepare a target scene to accept drag and drop events.
setUseExactSelectedClasses(boolean) - Method in class qupath.lib.gui.viewer.OverlayOptions
setUseGrayscaleLuts(boolean) - Method in class qupath.lib.display.ImageDisplay
setUseInvertedBackground(boolean) - Method in class qupath.lib.display.ImageDisplay
setUseMicrons(boolean) - Method in class qupath.lib.gui.viewer.GridLines
Specify whether to use calibrated units when calculating coordinates for any counting grid.
setUserPath(Path) - Method in class qupath.lib.gui.UserDirectoryManager
Set the user path where additional files may be stored.
setVGrowPriority(Priority, Node...) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Set the GridPane.setVgrow(Node, Priority) property for specified nodes.
setViewerDownsample(QuPathViewer, double) - Static method in class qupath.lib.gui.commands.Commands
Set the downsample factor for the specified viewer.
setWarn() - Static method in class qupath.lib.gui.logging.LogManager
Set the root log level to LogLevel.WARN.
setZPosition(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
Set the requested z-slice to be visible.
SHAPE_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
SharedThreadPoolManager - Class in qupath.lib.gui
Manager to simplify submitting short tasks in background threads using a shared ExecutorService.
show() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Add the chart to a stage, and show it in the Application thread.
show() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Add the chart to a stage, and show it in the Application thread.
show() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Add the chart to a stage, and show it in the Application thread.
show() - Method in class qupath.lib.gui.commands.LogViewerCommand
 
show() - Method in class qupath.lib.gui.commands.PathObjectGridView
Create the stage and show the grid view.
show() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Show the dialog.
SHOW_ANALYSIS_PANE - Variable in class qupath.lib.gui.actions.CommonActions
 
SHOW_ANALYSIS_PANEL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_ANNOTATIONS - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_CELL_BOUNDARIES - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
 
SHOW_CELL_BOUNDARIES - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_CELL_BOUNDARIES_AND_NUCLEI - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
 
SHOW_CELL_BOUNDARIES_AND_NUCLEI - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_CELL_CENTROIDS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
 
SHOW_CELL_CENTROIDS - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_CELL_NUCLEI - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.CellDisplayActions
 
SHOW_CELL_NUCLEI - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_CONNECTIONS - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
SHOW_CONNECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_CONNECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_DETECTIONS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_DETECTIONS - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_GRID - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_LICENSE - Variable in class qupath.lib.gui.actions.CommonActions
 
SHOW_LOCATION - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_LOCATION - Variable in class qupath.lib.gui.actions.ViewerActions
 
SHOW_LOG - Variable in class qupath.lib.gui.actions.CommonActions
 
SHOW_LOG - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_NAMES - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
SHOW_NAMES - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_NAMES - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_OBJECT_DESCRIPTIONS - Variable in class qupath.lib.gui.actions.CommonActions
 
SHOW_OBJECT_DESCRIPTIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.Actions
 
SHOW_OVERVIEW - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_OVERVIEW - Variable in class qupath.lib.gui.actions.ViewerActions
 
SHOW_PIXEL_CLASSIFICATION - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_PIXEL_CLASSIFICATION - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_POINTS_DIALOG - Variable in class qupath.lib.gui.actions.CommonActions
 
SHOW_SCALEBAR - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
SHOW_SCALEBAR - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_SCALEBAR - Variable in class qupath.lib.gui.actions.ViewerActions
 
SHOW_SELECTED - Enum constant in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
Show classes that are included in the selected class collection.
SHOW_TMA_GRID - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_TMA_GRID - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_TMA_GRID_LABELS - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_TMA_GRID_LABELS - Variable in class qupath.lib.gui.actions.OverlayActions
 
SHOW_Z_PROJECT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SHOW_Z_PROJECT - Variable in class qupath.lib.gui.actions.ViewerActions
 
showAnalysisPaneProperty() - Method in class qupath.lib.gui.QuPathGUI
 
showAndWait() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Show the dialog.
showAnnotationGridView(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Show a grid view for annotation objects.
showAnnotationMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for annotation objects from the current image.
showAnnotationMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Show a measurement table for all annotation objects.
showAnnotationMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for annotation objects from the specified image.
showAnnotationsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showCellMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for tile objects from the current image.
showCellMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Show a measurement table for all cell objects.
showCellMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for cell objects from the specified image.
showChannelViewer(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
Show a channel viewer window associated with a specific viewer.
showChoiceDialog(String, String, Collection<T>, T) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a choice dialog with a collection of choices (selection from ComboBox or similar).
showChoiceDialog(String, String, T[], T) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a choice dialog with an array of choices (selection from ComboBox or similar).
showConfirmDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a confirm dialog (OK/Cancel).
showConfirmDialog(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a confirm dialog (OK/Cancel).
showConnectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showDeprecatedCommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
showDetectionMeasurementManager(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Show a simple dialog for viewing (and optionally removing) detection measurements.
showDetectionMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for all detection objects from the current image.
showDetectionMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Show a measurement table for all detection objects.
showDetectionMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for all detection objects from the specified image.
showDetectionsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showEditor() - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
showEditor() - Method in interface qupath.lib.gui.scripting.ScriptEditor
Show the script editor.
showErrorMessage(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an error message.
showErrorMessage(String, Throwable) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an error message, displaying the localized message of a Throwable.
showErrorMessage(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an error message, with the content defined within a Node.
showErrorNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an error notification.
showErrorNotification(String, Throwable) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an error notification, displaying the localized message of a Throwable.
showExperimentalCommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
showExperimentalOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Flag to indicate that menu items marked 'experimental' should be shown to the user.
showGridProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showHistogram(String) - Method in class qupath.lib.gui.charts.HistogramDisplay
Show the histogram for a specified data column.
showImageNameInTitle - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
showImageNameInTitleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Property specifying if QuPath should show the image title in the main window title.
showInfoNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an info notification.
showingProperty() - Method in class qupath.lib.gui.panes.SlideLabelView
Property indicating whether the label is showing on screen or not.
showInputDialog(String, String, Double) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an input dialog requesting a numeric value.
showInputDialog(String, String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an input dialog requesting a String input.
showInputDisplayProperty() - Method in class qupath.lib.gui.QuPathGUI
Property to indicate whether the input display is currently showing
showInstalledExtensions(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Show a dialog displaying the extensions installed for a specified QuPath instance.
showLegacyOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Flag to indicate that the legacy options should be shown to the user - normally not desirable.
showLicenseMessageOnStartupProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Show a startup message about license when QuPath is launched.
showLocationProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
Show the cursor location.
showLocationProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
Show the cursor location.
showMeasurementTable(Predicate<PathObject>) - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for the current image.
showMeasurementTable(ImageData<BufferedImage>, Predicate<PathObject>) - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for the specified image.
showMeasurementTableObjectIDs - Variable in class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
 
showMeasurementTableObjectIDsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Specify whether measurement tables should show object IDs by default or not.
showMeasurementTableThumbnails - Variable in class qupath.lib.gui.panes.PreferencePane.MeasurementPreferences
 
showMeasurementTableThumbnailsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Specify whether measurement tables should show thumbnail images by default or not.
showMessageDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a standard message dialog.
showMessageDialog(String, Node) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a message dialog (OK button only), with the content contained within a Node.
showMiniViewer(QuPathViewer) - Static method in class qupath.lib.gui.commands.Commands
Show a mini viewer window associated with a specific viewer.
showNamesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showNoImageError(String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an error message that no image is available.
showNoImageError(String) - Static method in class qupath.lib.gui.tools.GuiTools
Show an error message that no image is available.
showNoProjectError(String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show an error message that no project is available.
showNoProjectError(String) - Static method in class qupath.lib.gui.tools.GuiTools
Show an error message that no project is available.
showObjectPredicateProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
Get the predicate used to determine whether an object should be displayed or hidden.
showOverviewProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
Show the overview image.
showOverviewProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
Show the overview image.
showParameterDialog(String, ParameterList) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a (modal) dialog for a specified ParameterList.
showParameterDialog(String, ParameterList) - Static method in class qupath.lib.gui.tools.GuiTools
Show a (modal) dialog for a specified ParameterList.
showPixelClassificationProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showPlainMessage(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a plain message.
showPlainNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a plain notification.
showPointHullsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Show the convex hull for point annotations within the viewer.
showProjectMetadataEditor(Project<?>) - Static method in class qupath.lib.gui.commands.ProjectCommands
Show the metadata editor for the specified project.
showScalebarProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
Show the scalebar.
showScalebarProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
Show the scalebar.
showScript(File) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
showScript(File) - Method in interface qupath.lib.gui.scripting.ScriptEditor
Show the script editor, opening an existing script file.
showScript(String, String) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
 
showScript(String, String) - Method in interface qupath.lib.gui.scripting.ScriptEditor
Show the script editor, including a new script with the specified name.
showScript(ScriptEditor, Workflow) - Static method in class qupath.lib.gui.panes.WorkflowCommandLogView
Show a script in the script editor based on the specified workflow.
showScriptEditor(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Show the script editor, or bring the window to the front if it is already open.
showScriptInterpreter(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Show a script interpreter window for a Qupath instance.
showStartupMessageProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Show a startup message when QuPath is launched.
showTable(ImageData<BufferedImage>, Predicate<PathObject>) - Method in class qupath.lib.gui.commands.SummaryMeasurementTableCommand
Show a measurement table for the specified image data.
showTextWindow(Window, String, String, Modality, boolean) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a window containing plain text, with the specified properties.
showTileMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for tile objects from the current image.
showTileMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for tile objects from the specified image.
showTMACommands - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
showTMACoreGridView(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Show a grid view for TMA core objects.
showTMACoreLabelsProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showTmaCoreMeasurementTable() - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for TMA core objects from the current image.
showTmaCoreMeasurementTable(ImageData<BufferedImage>) - Static method in class qupath.lib.gui.scripting.QPEx
Show a measurement table for TMA core objects from the specified image.
showTMAGridProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
 
showTMAMeasurementTable(QuPathGUI, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.commands.Commands
Show a measurement table for all TMA core objects.
showTMAOptionsProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Flag to indicate that the TMA menu should be shown to the user - only relevant when working with Tissue Microarrays.
showToolBarBadgesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Show badges on the toolbar, e.g.
showViewerPlaceholderTextProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Property to determine whether placeholder text should be shown when the viewer is empty.
showViewTracker(QuPathGUI) - Static method in class qupath.lib.gui.commands.Commands
Show a dialog to track the viewed region of an image.
showWarningNotification(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a warning notification.
showWithScreenSizeConstraints(Stage, double) - Static method in class qupath.lib.gui.tools.GuiTools
Show a stage, while ensuring that it cannot be larger than the screen size.
showWithSizeConstraints(Stage, double, double) - Static method in class qupath.lib.gui.tools.GuiTools
Show a stage, while ensuring that it cannot be larger the maximum dimensions provided This effectively sets the maximum dimensions of the stage, shows it, and then restores the previous maximum dimensions.
showWorkflowScript(QuPathGUI, ImageData<?>) - Static method in class qupath.lib.gui.commands.Commands
Show the QuPath script editor with a script corresponding to the command history of a specified image.
showYesNoCancelDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a Yes/No/Cancel dialog.
showYesNoDialog(String, String) - Static method in class qupath.lib.gui.dialogs.Dialogs
Deprecated.
Show a Yes/No dialog.
showZProjectControlsProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
Show z-projection overlay options, where relevant
showZProjectControlsProperty() - Method in class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
Show controls to view z-projection overlays, where available.
SIGNED_DISTANCE_TO_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
SimpleImageViewer - Class in qupath.lib.gui.panes
A simple viewer for a single image, with options to save or copy.
SimpleImageViewer() - Constructor for class qupath.lib.gui.panes.SimpleImageViewer
Create a new simple image viewer.
SIMPLIFY_SHAPE - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
simplifyTitledPane(TitledPane, boolean) - Static method in class qupath.lib.gui.tools.PaneTools
Deprecated.
Simplify the appearance of a TitledPane using CSS.
SingleChannelDisplayInfo - Interface in qupath.lib.display
ChannelDisplayInfo that determines colors based upon a single value for each pixel.
size(double, double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Set the preferred size of the chart.
size(double, double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Set the preferred size of the chart.
size(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the preferred size of the chart.
size(double, double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the dialog height.
skipMissingCores - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
skipMissingCoresProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Skip ('jump over') missing cores when navigating through TMA grids.
skipProjectUriChecks - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
skipProjectUriChecksProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Property to suppress checking whether image files exists in the project browser.
SLIDE_LABEL - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
SlideLabelView - Class in qupath.lib.gui.panes
A simple viewer for a slide label, tied to the current viewer.
SlideLabelView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.SlideLabelView
Constructor.
SMALL - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
 
SMALL - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
 
smartEditing - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
smartEditingAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
SMOOTHED_FEATURES - Variable in class qupath.lib.gui.actions.menus.AnalyzeMenuActions.Actions
 
SNAPSHOT_VIEWER_CONTENT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
 
SNAPSHOT_WINDOW - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
 
SNAPSHOT_WINDOW_CONTENT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.ExportSnapshotActions
 
SOURCE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
SPECIFY_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SPLIT_ANNOTATIONS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SPLIT_ANNOTATIONS_BY_LINES - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
SplitAnnotationsByLineCommand - Class in qupath.lib.gui.commands.objects
Command to split annotations using lines.
SplitAnnotationsByLineCommand() - Constructor for class qupath.lib.gui.commands.objects.SplitAnnotationsByLineCommand
 
splitViewer(QuPathViewer, boolean) - Method in class qupath.lib.gui.viewer.ViewerManager
 
start(Stage) - Method in class qupath.lib.gui.QuPathApp
 
start(Stage) - Method in class qupath.lib.gui.tma.QuPathTMAViewer
 
startMoving(double, double, boolean) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
Start moving, with initial velocity given by dx and dy.
startupMessage - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
startupScriptPath - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
startupScriptProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Path to a startup script that should be run immediately after QuPath's launch.
stop() - Method in class qupath.lib.gui.viewer.overlays.PixelClassificationOverlay
Stop the overlap, halting any pending tile requests.
stopMoving() - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
Stop moving immediately.
stopWaiting(RegionRequest) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
store(DefaultImageRegionStore) - Method in class qupath.lib.gui.images.servers.RenderedImageServer.Builder
Specify the region store used to paint the underlying image.
STYLE_PLACEHOLDER_TEXT - Static variable in class qupath.lib.gui.tools.GuiTools
Style class to use with placeholder text.
Subcommand - Interface in qupath.lib.gui.extensions
A subcommand for the command line interface.
submitShortTask(Runnable) - Method in class qupath.lib.gui.QuPathGUI
Deprecated.
submitShortTask(Runnable) - Method in class qupath.lib.gui.SharedThreadPoolManager
Submit a short task to a shared thread pool
SummaryMeasurementTable - Class in qupath.lib.gui.measure.ui
Control to show a table to view measurements and properties of PathObject.
SummaryMeasurementTable(ImageData<BufferedImage>, Predicate<PathObject>) - Constructor for class qupath.lib.gui.measure.ui.SummaryMeasurementTable
Create a new measurement table.
SummaryMeasurementTableCommand - Class in qupath.lib.gui.commands
Show a summary table for an object of a particular type (annotation, detection, TMA core...)
SummaryMeasurementTableCommand(QuPathGUI) - Constructor for class qupath.lib.gui.commands.SummaryMeasurementTableCommand
Command to show a summary measurement table, for PathObjects of a specified type (e.g.
supportsFile(File) - Method in class qupath.lib.gui.scripting.DefaultScriptEditor
Query whether a file represents a supported script.
supportsFile(File) - Method in interface qupath.lib.gui.scripting.ScriptEditor
Check if the script editor supports a particular file.
supportsSystemMenubar() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Returns true if the platform supports (or maybe supports) the system menubar.
switchToGrayscaleChannelProperty() - Method in class qupath.lib.display.ImageDisplay
Property indicating which channel should be used if ImageDisplay.useGrayscaleLutProperty() is turned on.
synchronizeViewersProperty() - Method in class qupath.lib.gui.viewer.ViewerManager
 
syncProject(Project<?>) - Static method in class qupath.lib.gui.panes.ProjectBrowser
Try to save a project, showing an error message if this fails.
SYSTEM_MENUBAR - Variable in class qupath.lib.gui.actions.menus.WindowMenuActions.Actions
 
systemMenubar - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
 
SystemMenuBar - Class in qupath.lib.gui.prefs
Helper class for managing MenuBar.useSystemMenuBarProperty() values based upon a property value.
SystemMenuBar() - Constructor for class qupath.lib.gui.prefs.SystemMenuBar
 
SystemMenuBar.SystemMenuBarOption - Enum Class in qupath.lib.gui.prefs
Enum specifying when and where the system menubar should be used.
systemMenubarProperty() - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Property used to specify whether the system menubar should be used for the main QuPath stage.

T

TABLE - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
tableDelimiterProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Delimiter to use when exporting tables.
TaskRunnerFX - Class in qupath.lib.gui
Plugin runner that takes care of showing progress (in the appropriate thread) using JavaFX components.
TaskRunnerFX(QuPathGUI) - Constructor for class qupath.lib.gui.TaskRunnerFX
Constructor.
TaskRunnerFX(QuPathGUI, int) - Constructor for class qupath.lib.gui.TaskRunnerFX
Constructor specifying the number of threads.
tempSelectionModeProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Temporarily request selection mode, without changing the value of #selectionModeProperty().
test(ImageData<?>, RegionRequest) - Method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
 
text(String) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Set the text property of the action.
text(ObservableValue<String>) - Method in class qupath.lib.gui.actions.ActionTools.ActionBuilder
Bind the text property of the action to an ObservableValue, bidirectionally if possible.
TextAppendable - Interface in qupath.lib.gui.logging
Interface to indicate anything for which text can be appended.
TextAreaControl - Class in qupath.lib.gui.scripting
Simple text area control (JavaFX) with basic operations and no styling support.
TextAreaControl(boolean) - Constructor for class qupath.lib.gui.scripting.TextAreaControl
Constructor to create a new text area and wrap it in a TextAreaControl.
TextAreaControl(TextArea, boolean) - Constructor for class qupath.lib.gui.scripting.TextAreaControl
Constructor to wrap an existing text area and wrap it in a TextAreaControl.
textProperty() - Method in class qupath.lib.gui.actions.InfoMessage
Read only property containing the message text.
textProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Text currently in the editor control.
textProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
textProperty() - Method in class qupath.lib.gui.tools.CommandFinderTools.CommandEntry
theme - Variable in class qupath.lib.gui.panes.PreferencePane.AppearancePreferences
 
tileAvailable(String, ImageRegion, BufferedImage) - Method in class qupath.lib.gui.viewer.QuPathViewer
 
tileAvailable(String, ImageRegion, T) - Method in interface qupath.lib.gui.images.stores.TileListener
Notify a listener that an image tile has been received read & is available.
tileBrush - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
tileCache - Variable in class qupath.lib.gui.panes.PreferencePane.GeneralPreferences
 
tileCachePercentageProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Requested percentage of available memory to use for tile caching.
TileListener<T> - Interface in qupath.lib.gui.images.stores
Interface for anything that needs to know when image tiles become available.
tileListeners - Variable in class qupath.lib.gui.images.stores.DefaultImageRegionStore
 
tiles() - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify that tile measurements (only) should be export.
TINY - Enum constant in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
 
TINY - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
 
title - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
title - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
title - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
title(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify the chart title.
title(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify the chart title.
title(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify the chart title.
title(String) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the dialog title.
title(String) - Method in class qupath.lib.gui.FileCopier
Title for any dialog.
TMA - Variable in class qupath.lib.gui.actions.menus.MeasureMenuActions.Actions
 
TMA_ADD_NOTE - Variable in class qupath.lib.gui.actions.CommonActions
 
TMA_DEARRAYING_DATA_EXTENSION - Static variable in class qupath.lib.gui.tma.TMADataIO
 
TMA_EXPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
 
TMA_GRID - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
TMA_IMPORT - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
 
TMA_VIEWER - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
 
tmaActions - Variable in class qupath.lib.gui.actions.menus.FileMenuActions.Actions
 
TmaActions() - Constructor for class qupath.lib.gui.actions.menus.FileMenuActions.TmaActions
 
tmaColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
TMACommands - Class in qupath.lib.gui.commands
Helper class implementing simple 'single-method' commands related to tissue microarrays for easy inclusion in the GUI.
TMACommands() - Constructor for class qupath.lib.gui.commands.TMACommands
 
tmaCores() - Method in class qupath.lib.gui.tools.MeasurementExporter
Specify that TMA core measurements (only) should be export.
TMADataIO - Class in qupath.lib.gui.tma
Static methods for exporting TMA data, optionally with small images.
TMADataIO() - Constructor for class qupath.lib.gui.tma.TMADataIO
 
TMAExplorer - Class in qupath.lib.gui.tma
The aim of this is to enable the exploration of TMA data from multiple images in a project.
TMAExplorer(QuPathGUI) - Constructor for class qupath.lib.gui.tma.TMAExplorer
Constructor.
tmaExportDownsample - Variable in class qupath.lib.gui.panes.PreferencePane.InputOutputPreferences
 
tmaExportDownsampleProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Default downsample factor to use when exporting TMA cores.
TMAGridOverlay - Class in qupath.lib.gui.viewer.overlays
An overlay capable of painting a TMA Grid.
TMAGridOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.TMAGridOverlay
Constructor.
TMAMenuActions - Class in qupath.lib.gui.actions.menus
 
TMAMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
TMAMenuActions.Actions.AddActions - Class in qupath.lib.gui.actions.menus
 
TMAMenuActions.Actions.RemoveActions - Class in qupath.lib.gui.actions.menus
 
tmaMissingOpacity - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
TMASummaryViewer - Class in qupath.lib.gui.tma
Deprecated.
since v0.4.0
TMASummaryViewer(Stage) - Constructor for class qupath.lib.gui.tma.TMASummaryViewer
Deprecated.
Constructor.
TOGGLE_SELECTED_OBJECTS_LOCKED - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
 
TOGGLE_SYNCHRONIZE_VIEWERS - Variable in class qupath.lib.gui.actions.ViewerActions
 
toggleShowHideChannel(ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Toggle the visibility of the specified channel.
toJSON(boolean) - Method in class qupath.lib.display.ImageDisplay
Create a JSON representation of the main components of the current display.
TOOLBAR_ICON_SIZE - Static variable in class qupath.lib.gui.QuPathGUI
Icon size to use in the main QuPath toolbar
ToolManager - Class in qupath.lib.gui
Manage (drawing) tool selection in a QuPath UI.
tooltips(boolean) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Request tooltips to be shown when the cursor hovers over the pie chart.
toStage() - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Add the chart to a stage, but do not show it.
toStage() - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Add the chart to a stage, but do not show it.
toStage() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Add the chart to a stage, but do not show it.
toString() - Method in class qupath.lib.display.AdditiveChannelInfo
 
toString() - Method in class qupath.lib.display.DirectServerChannelInfo
 
toString() - Method in class qupath.lib.gui.BuildInfo
 
toString() - Method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
 
toString() - Method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
 
toString() - Method in class qupath.lib.gui.extensions.GitHubProject.GitHubRepo
 
toString() - Method in class qupath.lib.gui.extensions.UpdateChecker.ReleaseVersion
 
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
 
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
 
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
 
toString() - Method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
 
toString() - Method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
 
toString() - Method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
 
toString() - Method in class qupath.lib.gui.scripting.ScriptTab
 
toString() - Method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
 
toString() - Method in enum class qupath.lib.gui.viewer.ImageInterpolation
 
toString() - Method in class qupath.lib.gui.viewer.QuPathViewer
 
toString() - Method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
 
totalBytes() - Method in class qupath.lib.gui.UndoRedoManager
The total number of bytes used for all viewers.
tPositionProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
Current t-position for the timepoint currently visible in the viewer.
TRACE - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
Trace logging (an awful lot of messages)
TRACKING_RECORD - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
TRACKING_REWIND - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
TRACKING_STOP - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
TRANSFER_ANNOTATION - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.AnnotationActions
 
TRANSLUCENT_BLACK_FX - Static variable in class qupath.lib.gui.tools.ColorToolsFX
Black with opacity at 50%.
TRANSLUCENT_WHITE_FX - Static variable in class qupath.lib.gui.tools.ColorToolsFX
White with opacity at 50%.
tryToInterpretMessage(Throwable, int, boolean) - Method in class qupath.lib.gui.scripting.languages.DefaultScriptLanguage
 
tryToSelect(PathObject, QuPathViewer, ImageData<?>, boolean, boolean) - Static method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Try to select an object if possible (e.g.

U

uiBlocked() - Method in class qupath.lib.gui.QuPathGUI
Observable value indicating that the user interface is/should be blocked.
undo() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Request undo.
undo() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
UNDO - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
UNDO - Variable in class qupath.lib.gui.actions.menus.EditMenuActions.Actions
 
undoAction - Variable in class qupath.lib.gui.scripting.DefaultScriptEditor
 
undoOnce() - Method in class qupath.lib.gui.UndoRedoManager
Request to 'undo' the last observed hierarchy change for the current active viewer.
UndoRedoManager - Class in qupath.lib.gui
Helper class to add undo/redo support to QuPath.
UndoRedoPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.UndoRedoPreferences
 
unlimitedDatapoints() - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Show all datapoints, without subsampling, even when this may cause performance issues.
UNLOCK_SELECTED_OBJECTS - Variable in class qupath.lib.gui.actions.menus.ObjectsMenuActions.LockActions
 
unmanageMenuBar(MenuBar) - Static method in class qupath.lib.gui.prefs.SystemMenuBar
Do not manage the system menubar status for the given menubar.
UPDATE - Variable in class qupath.lib.gui.actions.menus.HelpMenuActions.Actions
 
updateAffineTransform() - Method in class qupath.lib.gui.viewer.QuPathViewer
 
updateAffineTransform() - Method in class qupath.lib.gui.viewer.QuPathViewerPlus
 
updateAvailableStyles() - Static method in class qupath.lib.gui.prefs.QuPathStyleManager
Request that the list of available styles is updated.
updateAxisRange() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
 
updateChart(BarChart<String, Number>) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
updateChart(PieChart) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
updateChart(ScatterChart<Number, Number>) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
UpdateChecker - Class in qupath.lib.gui.extensions
Helper class to query for updates using GitHub's web API.
UpdateChecker() - Constructor for class qupath.lib.gui.extensions.UpdateChecker
 
UpdateChecker.ReleaseVersion - Class in qupath.lib.gui.extensions
Class to represent a release version.
updateCursor() - Method in class qupath.lib.gui.viewer.QuPathViewer
 
updateFromDisplay(ImageDisplay) - Method in class qupath.lib.display.ImageDisplay
Update the current display based upon a different display.
updateHistogram(ImageDisplay, ChannelDisplayInfo) - Method in class qupath.lib.gui.commands.display.BrightnessContrastHistogramPane
Update the histogram to show the data for the given channel.
updateImage(String, BufferedImage) - Method in class qupath.lib.gui.panes.SimpleImageViewer
Update the image using a buffered image.
updateImage(String, Image) - Method in class qupath.lib.gui.panes.SimpleImageViewer
Update the image using a JavaFX image.
updateItem(PathClass, boolean) - Method in class qupath.lib.gui.tools.PathClassListCell
 
updateLegend() - Method in class qupath.lib.gui.charts.PathObjectScatterChart
 
updateMeasurementList() - Method in class qupath.lib.gui.measure.ObservableMeasurementTableData
Update the entire measurement list for the current objects.
updateMeasurements() - Method in class qupath.lib.gui.panes.MeasurementMapPane
Update the measurements according to the current image
updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
 
updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
 
updateRGBAdditive(BufferedImage, int[], ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
Update an array of existing pixels (packed RGB) additively using the colors to display a specified image.
updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.AdditiveChannelInfo
 
updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in class qupath.lib.display.DirectServerChannelInfo
 
updateRGBAdditive(BufferedImage, int, int, int, ChannelDisplayMode) - Method in interface qupath.lib.display.ChannelDisplayInfo
Update an existing pixel (packed RGB) additively using the color used to display a specified one
updateTable() - Method in class qupath.lib.gui.commands.display.BrightnessContrastChannelPane
Ensure the table is up-to-date.
UpdateUrisCommand<T> - Class in qupath.lib.gui.commands
Fix broken URIs by using relative paths or prompting the user to select files.
updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.tools.handlers.BrushToolEventHandler
New annotations can be constrained while they are being drawn, to avoid overlaps with existing annotations or to ensure they are drawn within a parent annotation.
updatingConstrainingObjects(QuPathViewer, double, double, Collection<PathObject>) - Method in class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler
New annotations can be constrained while they are being drawn, to avoid overlaps with existing annotations or to ensure they are drawn within a parent annotation.
Urls - Class in qupath.lib.gui
Class to return core QuPath URLs centrally.
Urls() - Constructor for class qupath.lib.gui.Urls
 
useCalibratedLocationStringProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Show the cursor location on a viewer in calibrated units, rather than pixels.
useColorLUTs() - Method in class qupath.lib.display.ImageDisplay
useExactSelectedClassesProperty() - Method in class qupath.lib.gui.viewer.OverlayOptions
Property to control whether entries in OverlayOptions.selectedClassesProperty() should be used exactly, or should also include all related classes (i.e.
useGrayscaleLutProperty() - Method in class qupath.lib.display.ImageDisplay
Property that specifies whether grayscale lookup tables should be preferred to color lookup tables
useGrayscaleLuts() - Method in class qupath.lib.display.ImageDisplay
useInvertedBackground() - Method in class qupath.lib.display.ImageDisplay
useInvertedBackgroundProperty() - Method in class qupath.lib.display.ImageDisplay
Property that specifies whether the background should be inverted (i.e.
useMicrons() - Method in class qupath.lib.gui.viewer.GridLines
Query whether to use calibrated units when calculating coordinates for any counting grid.
useMultipoint - Variable in class qupath.lib.gui.panes.PreferencePane.DrawingPreferences
 
usePixelSnappingProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
If true, pixels should be snapped to integer coordinates when using the drawing tools.
UserDirectoryManager - Class in qupath.lib.gui
Helper class for managing a user directory, and associated subdirectories.
userDirectoryProperty() - Method in class qupath.lib.gui.UserDirectoryManager
Property representing the user directory.
useRotateGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
useRotateGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Support rotate gestures for touchscreens and trackpads.
userPathProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
A path where additional files may be stored, such as extensions and log files.
useScrollGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Support scroll gestures for touchscreens and trackpads.
useSelectedColor - Variable in class qupath.lib.gui.panes.PreferencePane.ObjectPreferences
 
useSelectedColorProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Use a specified color for highlighting selected objects in the viewer.
useSystemMenubarProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Deprecated.
useTileBrushProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request that the brush tool automatically uses any available tiles, rather than creating 'circles' as normal.
useZoomGestures - Variable in class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
useZoomGesturesProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Support zoom gestures for touchscreens and trackpads.

V

value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionAccelerator
String form of an accelerator, compatible with KeyCombination.valueOf(String).
value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionConfig
Key to external properties file.
value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionIcon
Icon to associate with the action's graphic property.
value() - Element in annotation interface qupath.lib.gui.actions.annotations.ActionMenu
Menu path, in the form "Menu>Submenu>Command name".
valueOf(String) - Static method in enum class qupath.lib.display.ChannelDisplayMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.actions.InfoMessage.MessageType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
Deprecated.
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.logging.LogManager.LogLevel
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.tools.IconFactory.PathIcons
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.viewer.ImageInterpolation
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
Returns the enum constant of this class with the specified name.
values() - Static method in enum class qupath.lib.display.ChannelDisplayMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.actions.InfoMessage.MessageType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.charts.HistogramChart.CountsTransformMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.charts.HistogramChart.DisplayMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.commands.PathObjectGridView.GridDisplaySize
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
Deprecated.
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.logging.LogManager.LogLevel
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.AutoUpdateType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.FontSize
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.PathPrefs.ImageTypeSetting
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.QuPathStyleManager.Fonts
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.prefs.SystemMenuBar.SystemMenuBarOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.tools.CommandFinderTools.CommandBarDisplay
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.tools.IconFactory.PathIcons
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.viewer.ImageInterpolation
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.ClassVisibilityMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.viewer.OverlayOptions.DetectionDisplayMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class qupath.lib.gui.viewer.RegionFilter.StandardRegionFilters
Returns an array containing the constants of this enum class, in the order they are declared.
VIEW_TRACKER - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
viewer - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
viewer - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
viewer - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify a viewer.
viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Specify a viewer.
viewer(QuPathViewer) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify a viewer.
VIEWER - Enum constant in enum class qupath.lib.gui.tools.GuiTools.SnapshotType
Snapshot of the current viewer content.
VIEWER_GRID_1x1 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
VIEWER_GRID_1x1 - Variable in class qupath.lib.gui.actions.ViewerActions
 
VIEWER_GRID_1x2 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
VIEWER_GRID_1x2 - Variable in class qupath.lib.gui.actions.ViewerActions
 
VIEWER_GRID_2x1 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
VIEWER_GRID_2x1 - Variable in class qupath.lib.gui.actions.ViewerActions
 
VIEWER_GRID_2x2 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
VIEWER_GRID_2x2 - Variable in class qupath.lib.gui.actions.ViewerActions
 
VIEWER_GRID_3x3 - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
VIEWER_GRID_3x3 - Variable in class qupath.lib.gui.actions.ViewerActions
 
ViewerActions - Class in qupath.lib.gui.actions
Actions that interact with one or more viewers.
ViewerActions(ViewerManager) - Constructor for class qupath.lib.gui.actions.ViewerActions
 
viewerBackgroundColorProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Color to paint behind any image.
viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.UndoRedoManager
 
viewerClosed(QuPathViewer) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
Called when a viewer is closed.
viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
viewerClosed(QuPathViewer) - Method in class qupath.lib.gui.viewer.ViewerManager
 
viewerGammaProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Requested gamma value applied to the image in each viewer (for display only).
viewerInterpolateBilinearProperty() - Static method in class qupath.lib.gui.prefs.PathPrefs
Request that images are displayed in viewers using bilinear interpolation.
ViewerManager - Class in qupath.lib.gui.viewer
Class to manage multiple QuPathViewer instances in a UI region.
ViewerMover(QuPathViewer) - Constructor for class qupath.lib.gui.viewer.tools.handlers.MoveToolEventHandler.ViewerMover
Constructor.
ViewerPlusDisplayOptions - Class in qupath.lib.gui.viewer
A group of properties determining what should be displayed for each viewer.
ViewerPlusDisplayOptions() - Constructor for class qupath.lib.gui.viewer.ViewerPlusDisplayOptions
 
ViewerPreferences() - Constructor for class qupath.lib.gui.panes.PreferencePane.ViewerPreferences
 
viewerProperty() - Method in class qupath.lib.gui.QuPathGUI
Property representing the viewer currently active.
ViewMenuActions - Class in qupath.lib.gui.actions.menus
 
ViewMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
ViewMenuActions.CellDisplayActions - Class in qupath.lib.gui.actions.menus
 
ViewMenuActions.MultitouchActions - Class in qupath.lib.gui.actions.menus
 
ViewMenuActions.MultiviewActions - Class in qupath.lib.gui.actions.menus
 
ViewMenuActions.MultiviewGridActions - Class in qupath.lib.gui.actions.menus
 
ViewMenuActions.ZoomActions - Class in qupath.lib.gui.actions.menus
 
ViewTracker - Class in qupath.lib.gui.viewer.recording
Default ViewTracker implementation.
ViewTrackerControlPane - Class in qupath.lib.gui.viewer.recording
Panel for viewing ViewTracker controls.
ViewTrackerControlPane(QuPathGUI) - Constructor for class qupath.lib.gui.viewer.recording.ViewTrackerControlPane
Create a ViewTrackerControlPane.
ViewTrackerDataMap - Class in qupath.lib.gui.viewer.recording
Class for storing the values of a data map as well as generating a proper BufferedImage with the appropriate pixel type.
visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.UndoRedoManager
 
visibleRegionChanged(QuPathViewer, Shape) - Method in interface qupath.lib.gui.viewer.QuPathViewerListener
Called when the visible region has changed in a viewer.
visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.viewer.recording.ViewTracker
 
visibleRegionChanged(QuPathViewer, Shape) - Method in class qupath.lib.gui.viewer.ViewerManager
 

W

WAND_TOOL - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
WARN - Enum constant in enum class qupath.lib.gui.actions.InfoMessage.MessageType
Warning.
WARN - Enum constant in enum class qupath.lib.gui.logging.LogManager.LogLevel
Warn logging (only if something is moderately important)
warning() - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Create a warning alert dialog.
warning(String) - Static method in class qupath.lib.gui.actions.InfoMessage
Create a warning message with static text.
warning(String, int) - Static method in class qupath.lib.gui.actions.InfoMessage
Create a warning message with static text and a count.
warning(ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
Create a warning message to show a count of warnings.
warning(ObservableValue<String>) - Static method in class qupath.lib.gui.actions.InfoMessage
Create a warning message.
warning(ObservableValue<String>, ObservableNumberValue) - Static method in class qupath.lib.gui.actions.InfoMessage
Create a warning message with a count.
WARNING - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
WebViews - Class in qupath.lib.gui.tools
Helper class for creating a WebView in a standardized way.
WebViews() - Constructor for class qupath.lib.gui.tools.WebViews
 
WelcomeStage - Class in qupath.lib.gui
Welcome page when launching QuPath.
WelcomeStage() - Constructor for class qupath.lib.gui.WelcomeStage
 
width - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
width - Variable in class qupath.lib.gui.charts.Charts.PieChartBuilder
 
width - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
width(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Set the preferred width of the chart.
width(double) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Set the preferred width of the chart.
width(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the preferred width of the chart.
width(double) - Method in class qupath.lib.gui.dialogs.Dialogs.Builder
Deprecated.
Specify the dialog width.
WindowMenuActions - Class in qupath.lib.gui.actions.menus
Actions associated with showing/hiding/centering windows, or other window-related features.
WindowMenuActions.Actions - Class in qupath.lib.gui.actions.menus
 
windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Title to use for the window, if the chart is shown.
windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.PieChartBuilder
Title to use for the window, if the chart is shown.
windowTitle(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Title to use for the window, if the chart is shown.
WITH_ICONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
Show detections with ROI icons
WITHOUT_ICONS - Enum constant in enum class qupath.lib.gui.prefs.PathPrefs.DetectionTreeDisplayModes
Show detections without ROI icons
workerComplete(TileWorker<BufferedImage>) - Method in class qupath.lib.gui.images.stores.DefaultImageRegionStore
Every TileWorker should call this when the task is done!
WorkflowCommandLogView - Class in qupath.lib.gui.panes
Show logged commands, and optionally generate a script.
WorkflowCommandLogView(QuPathGUI) - Constructor for class qupath.lib.gui.panes.WorkflowCommandLogView
Construct a view to display the workflow for the currently-active ImageData within a running QuPath instance.
WorkflowCommandLogView(QuPathGUI, Workflow) - Constructor for class qupath.lib.gui.panes.WorkflowCommandLogView
Construct a view displaying a static workflow (i.e.
workflowUpdated(Workflow) - Method in class qupath.lib.gui.panes.WorkflowCommandLogView
 
wrapTextProperty() - Method in interface qupath.lib.gui.scripting.ScriptEditorControl
Request wordwrap.
wrapTextProperty() - Method in class qupath.lib.gui.scripting.TextAreaControl
 
writeImage(Image, String) - Static method in class qupath.lib.gui.scripting.QPEx
Write a JavaFX image to the specified path.
writeRenderedImage(QuPathViewer, String) - Static method in class qupath.lib.gui.scripting.QPEx
Write a rendered image for the current viewer to the specified path.
writeRenderedImage(ImageData<BufferedImage>, String) - Static method in class qupath.lib.gui.scripting.QPEx
Write a rendered image to the specified path.
writeRenderedImageRegion(QuPathViewer, RegionRequest, String) - Static method in class qupath.lib.gui.scripting.QPEx
Write a rendered image region for the current viewer to the specified path.
writeRenderedImageRegion(ImageData<BufferedImage>, RegionRequest, String) - Static method in class qupath.lib.gui.scripting.QPEx
Write a rendered image region to the specified path.
writeTMAData(File, ImageData<BufferedImage>) - Static method in class qupath.lib.gui.tma.TMADataIO
Write TMA summary data, without any image export.
writeTMAData(File, ImageData<BufferedImage>, OverlayOptions, double) - Static method in class qupath.lib.gui.tma.TMADataIO
Write TMA data in a human-readable (and viewable) way, with JPEGs and TXT/CSV files.

X

xAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the upper bound for the x-axis.
xAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the lower bound for the x-axis.
xAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the lower and upper bounds for the x-axis.
xLabel - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
xLabel - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
xLabel(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify the x-axis label.
xLabel(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify the x-axis label.
XML - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
XmlLanguage - Class in qupath.lib.gui.scripting.languages
Class for representing XML in QuPath.

Y

YAML - Static variable in class qupath.lib.gui.scripting.syntax.ScriptSyntaxProvider
 
YamlLanguage - Class in qupath.lib.gui.scripting.languages
Class for the representation of YAML syntax in QuPath.
yAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Set the upper bound for the y-axis.
yAxisMax(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the upper bound for the y-axis.
yAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Set the lower bound for the y-axis.
yAxisMin(double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the lower bound for the y-axis.
yAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Set the lower and upper bounds for the y-axis.
yAxisRange(double, double) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Set the lower and upper bounds for the y-axis.
YES - Enum constant in enum class qupath.lib.gui.dialogs.Dialogs.DialogButton
Deprecated.
"Yes" option
yLabel - Variable in class qupath.lib.gui.charts.Charts.BarChartBuilder
 
yLabel - Variable in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
 
yLabel(String) - Method in class qupath.lib.gui.charts.Charts.BarChartBuilder
Specify the y-axis label.
yLabel(String) - Method in class qupath.lib.gui.charts.Charts.ScatterChartBuilder
Specify the y-axis label.

Z

Z_PROJECT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ZOOM_1 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
ZOOM_10 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
ZOOM_100 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
ZOOM_400 - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
ZOOM_IN - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ZOOM_IN - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
ZOOM_OUT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ZOOM_OUT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
ZOOM_TO_FIT - Enum constant in enum class qupath.lib.gui.tools.IconFactory.PathIcons
 
ZOOM_TO_FIT - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.ZoomActions
 
ZOOM_TO_FIT - Variable in class qupath.lib.gui.actions.ViewerActions
 
zoomActions - Variable in class qupath.lib.gui.actions.menus.ViewMenuActions.Actions
 
zoomIn() - Method in class qupath.lib.gui.viewer.QuPathViewer
Zoom in by one step.
zoomIn(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
Zoom in by a specified number of steps, where one 'step' indicates a minimal zoom increment.
zoomOut() - Method in class qupath.lib.gui.viewer.QuPathViewer
Zoom out by one step.
zoomOut(int) - Method in class qupath.lib.gui.viewer.QuPathViewer
Zoom out by a specified number of steps, where one 'step' indicates a minimal zoom increment.
zoomToFit() - Method in class qupath.lib.gui.viewer.QuPathViewer
Request that the downsample is set to contain the entire image, and the image is centered in the viewer.
zPositionProperty() - Method in class qupath.lib.gui.viewer.QuPathViewer
Current z-position for the z-slice currently visible in the viewer.
ZProjectOverlay - Class in qupath.lib.gui.viewer.overlays
 
ZProjectOverlay(OverlayOptions) - Constructor for class qupath.lib.gui.viewer.overlays.ZProjectOverlay
 
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