All Classes and Interfaces
Class
Description
Abstract
PathOverlay with additional properties relevant when drawing BufferedImages.Abstract
ImageRenderer, which adds a timestamp variable.Abstract class to help with implementing PathOverlays.
Define a function to perform the task of
PathOverlay.getLocationString(ImageData, double, double, int, int)Annotation used to specify a preferred accelerator for an an action.
Annotation indicating the a key in the external resources file containing
the menu, text and (optional) description.
Default icon for an action.
Annotation indicating the menu path where an action should be installed.
Annotation indicating that a method should be converted to an
Action if possible.Helper methods for generating and configuring Actions and UI elements.
Builder class for custom
Action objects.Class for combining channels additively, then providing controls on the resulting RGB image.
Component for displaying annotations within the active image.
Default actions associated with QuPath's 'Automate' (scripting) menu.
A pane responsible for the display and selection of channels from an image display.
Command to show a Brightness/Contrast dialog to adjust the image display.
A pane to display a histogram for brightness/contrast adjustment, allowing the user to select min/max values.
A pane to save and load display settings, using a
ResourceManager.A pane containing sliders for adjusting the min/max display range and gamma value
associated with an
ImageDisplay.Tool for drawing (and subtract from) freehand regions, optionally adapting brush size to magnification.
An overlay used to display one or more
BufferedImage objects on top of a primary image shown in a viewer.Basic version information about the current QuPath build.
A simple class to store the color of an image channel.
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).
Helper interface to indicate that the display ranges can be modified.
Display mode for an image channel, used in combination with
ImageDisplay and ChannelDisplayInfo.ImageServer that applies a color transform to an image.
A simple class to store the main information needed by QuPath to display an image channel
with a requested color and brightness/contrast setting.
Helper class for generating interactive charts.
Builder for creating scatter charts.
Builder for creating pie charts.
Builder for creating scatter charts.
Pane that can be used to contain an XYChart, adding adjustable thresholds to be displayed.
Collection of static methods to help when working with JavaFX charts,
and adapting these for QuPath's purposes.
Canvas to show the range of a ColorMap (i.e.
An
ImageRenderer that uses a ColorModel.Helper class for converting between packed RGB colors and Java's AWT representation, as well as creating some ColorModels for BufferedImages.
Helper tools for creating components that enable fast access to menu commands via a filtered list.
Available modes for displaying the command bar.
Helper class to wrap summary data for a command to display in the list.
Helper class implementing simple 'single-method' commands for easy inclusion in the GUI.
Default actions associated with a specific QuPath instance.
Help window providing context-dependent help.
Command to open up a counting panel to aid with creating Point annotations.
Class for representing CSS in QuPath.
Default auto-completor for JVM-based languages, optionally including QuPath default imports.
An ImageRegionStore suitable for either Swing or JavaFX applications.
Default multilingual script editor.
Default implementation for a
ScriptLanguage, based on a ScriptEngine.Interface defining how the import statements should be generated for the language.
Interactive command to remove objects with ROIs that touch or overlap the boundary of other objects.
Deprecated.
since v0.5.0.
Deprecated.
Possible buttons pressed in a yes/no/cancel dialog.
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.
Utility class for working with image display and image display settings objects.
Command line tool to export icons and markdown documentation for QuPath commands.
Helper class for managing simplified versions of a shape for rendering shapes at lower resolutions.
Drag and drop support for main QuPath application, which can support a range of different object types (Files, URLs, Strings,..)
Interface to define a new drop handler.
Interface for objects that manage editable text, including a caret position and selection.
Command to export object(s) in GeoJSON format to an output file.
Copy files to an output directory, prompting the user if necessary.
Helper class to represent a project hosted on GitHub.
Helper class to represent a GitHub repository.
Simple class used for storing information related to GridLines that may be painted over an image.
An overlay used to show a (counting) grid on top of an image.
Auto completion support for Groovy.
Class for the representation of the Groovy programming language in QuPath.
Assorted static methods to help with JavaFX and QuPath GUI-related tasks.
Kinds of snapshot image that can be created for QuPath.
An overlay capable of painting a
PathObjectHierarchy, except for any
TMA grid (which is handled by TMAGridOverlay).JavaFX chart for displaying histograms.
Enum to specify how the counts are displayed.
Display mode for the histogram.
Helper class for representing data that may be visualized with a
HistogramChart.Wrapper close to enable the generation and display of histograms relating to a data table.
Marker interface that indicates an executable language renders HTML.
Factory class for creating icons.
Default icons for QuPath commands.
A panel used for displaying basic info about an image, e.g.
Class used to look after the color transforms that may be applied to an image,
including brightness/contrast settings.
A simple class to store the main information needed by QuPath to display an image,
in a JSON-friendly form.
Supported interpolation methods when displaying images.
And autocompletor for the ImageJ macro language.
Interface for painting regions of an
ImageServer onto a Graphics object.Factory for creating an ImageRegionStore.
Helper methods related to image region storage.
Interface for objects capable of converting a
BufferedImage for rendering using Graphics2D.An informative message that should be shown to the user.
The type of message, which can be used for styling.
Static methods to import object(s) from different sources.
A command to show a
JavadocViewer
in a standalone window.Class for the representation of JSON syntax in QuPath.
Manage logging levels.
Available log levels.
A viewer for log messages.
Class for the representation of JSON syntax in QuPath.
Dialog box to export measurements
Helper class for exporting the measurements of one or more entries in a project.
Measurements that only extract metadata from objects.
Component used for displaying measurement maps, whereby detection objects are recolored
according to measurement values.
Helpers class that can be used to map an object's measurement to a color (packed RGB int).
Common interface to define the contents of a menu in terms of actions.
Generate actions for installation in QuPath's main menubar.
Static methods to help with creating and populating JavaFX menus.
Measurements that only extract metadata from objects.
Command to open a small viewer window, which displays a detail from
the current image depending on where the cursor is over the image.
A manager for one or more mini-viewers, where the 'more' means a separate viewer per channel.
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)
Helper class for panning a
QuPathViewer (reasonably) smoothly.Wraps a pane used to display an object description, if one is available.
Simple browser for exploring fields (including private fields) within an object by reflection.
A table data model to supply observable measurements of PathObjects.
Actions that interact with
OverlayOptions.Default class for storing overlay display options.
Visibility modes for classes.
Display modes for cells and other detections.
Deprecated.
since v0.5.0;
GridPaneUtils contains many of the features.A panel for displaying a list of parameters suitably to aid with creating JavaFX GUIs.
A cell for displaying
PathClass objects in a list view or combo box.A special
ImageServer implementation that doesn't have a backing image, but rather
constructs tiles on request from a PathObjectHierarchy and its detection objects.Grid display of objects.
Component for showing a tree-based view of the object hierarchy.
Helper class for working with thumbnail images relating to path objects.
Interface for managing a node that can display an item.
Manage a small pane that can be used to display a
PathObject.Helper class to wrap a collection of PathObjects that should be measured.
Static methods to assist with painting PathObjects.
An interactive
ScatterChart implementation for showing large(ish) numbers of PathObject,
optionally linked to a QuPathViewer.Interface defining a way to create lazy values from an image and associated objects.
Interface defining an overlay to paint on top of a viewer.
Central storage of QuPath preferences.
Options for automatic updating checking of QuPath and/or extensions.
Enum for different ways that detections can be displayed in lists and trees.
Enum to control font size.
Enum defining how setting the image type should be handled for new images.
Interface defining a table model that enables measurement names to be mapped to string or numeric values (as appropriate).
Interface defining how a toolbar tool interacts with a viewer.
Default
PathTool implementations.PathOverlay that gives the results of pixel classification.Class for the representation of plain text in QuPath.
QuPath's preference pane, giving a means to modify many of the properties within PathPrefs.
Component for previewing and selecting images within a project.
Helper class implementing simple 'single-method' commands related to projects.
Dialogs specifically related to managing projects.
Class for the representation of properties and config files in QuPath.
Auto completion support for Python.
Alternative to QP offering static methods of use for scripting,
along with some extra methods that require access of GUI features.
Launcher application to start QuPath.
Simple interface for QuPath extensions.
Main GUI for QuPath, written using JavaFX.
Helper class for managing pressure-sensitive input.
Interface defining minimal behavior for a pen input device.
Load strings from the default resource bundle.
Class to facilitate the use of different styles within QuPath.
Available font families.
Interface defining a style that may be applied to QuPath.
Standalone viewer for looking at TMA summary results.
JavaFX component for viewing a (possibly large) image, along with overlays.
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.
A whole slide viewer with optional extras...
Define the area of an image to which pixel classification should be applied.
Standard classification regions (hopefully all you will ever need).
An ImageServer that can display a rendered image, with optional overlays.
Builder to create an ImageServer to display rendered images, with optional overlay layers.
A wrapper around
PathObjectScatterChart for displaying data about PathObject measurements.Minimal interface for a script editor that the GUI can call.
Basic script editor control using JavaFX.
Class with static methods to fetch all the available ScriptLanguages.
Interface for classes that apply some syntax formatting to an
EditableText.Class with static methods to fetch all the available ScriptSyntaxes.
Class representing a script tab (e.g.
Helper class for managing items when only one of them may be selected.
Component to show measurements for a currently-selected object.
Helper class for selecting one image server out of a collection.
Manager to simplify submitting short tasks in background threads using a shared
ExecutorService.A simple viewer for a single image, with options to save or copy.
ChannelDisplayInfo that determines colors based upon a single value for each pixel.A simple viewer for a slide label, tied to the current viewer.
Command to split annotations using lines.
A subcommand for the command line interface.
Control to show a table to view measurements and properties of
PathObject.Show a summary table for an object of a particular type (annotation, detection, TMA core...)
Helper class for managing
MenuBar.useSystemMenuBarProperty() values based upon a property value.Enum specifying when and where the system menubar should be used.
Plugin runner that takes care of showing progress (in the appropriate thread) using JavaFX components.
Interface to indicate anything for which text can be appended.
Simple text area control (JavaFX) with basic operations and no styling support.
Interface for anything that needs to know when image tiles become available.
Helper class implementing simple 'single-method' commands related to tissue microarrays for easy inclusion in the GUI.
Static methods for exporting TMA data, optionally with small images.
The aim of this is to enable the exploration of TMA data from multiple images in a project.
An overlay capable of painting a TMA Grid.
Deprecated.
since v0.4.0
Manage (drawing) tool selection in a QuPath UI.
Helper class to add undo/redo support to QuPath.
Helper class to query for updates using GitHub's web API.
Class to represent a release version.
Fix broken URIs by using relative paths or prompting the user to select files.
Class to return core QuPath URLs centrally.
Helper class for managing a user directory, and associated subdirectories.
Actions that interact with one or more viewers.
Class to manage multiple
QuPathViewer instances in a UI region.A group of properties determining what should be displayed for each viewer.
Default ViewTracker implementation.
Panel for viewing ViewTracker controls.
Class for storing the values of a data map as well as generating a proper
BufferedImage with the appropriate pixel type.Helper class for creating a
WebView in a standardized way.Welcome page when launching QuPath.
Actions associated with showing/hiding/centering windows, or other window-related features.
Show logged commands, and optionally generate a script.
Class for representing XML in QuPath.
Class for the representation of YAML syntax in QuPath.