Package containing the main QuPath launcher.
Classes to enable cell detection, implemented with the help of ImageJ as an image processing library.
Classes to help with Tissue Microarray dearraying.
Classes to enable tissue detection by thresholding.
User interface commands and extensions linking ImageJ and QuPath.
ImageServerimplementation using ImageJ as the image reading library.
Image writers, using ImageJ as the writing library.
Static methods that add further processing methods when working with ImageJ images.
Classes to generate superpixels.
Helper classes and static methods for working with ImageJ images.
Feature calculation plugins.
Classes to aid with analysis.
Classes and static methods adding reusable processing and analysis functionality.
Classes to help with calculating features.
Classes and static methods associated with generating and querying heatmaps.
Helper interfaces and methods to write pixel processing algorithms.
Calculate simple statistics from arrays.
Helper classes for survival analysis.
Static classes and methods to help work with Java AWT.
Classes and interfaces to support machine learning classifiers.
Classes for object classification in QuPath.
Core support for pixel classification.
Classes to assist with color, including stain separation and color transforms.
General-purpose helper classes.
Classes to control the display of images in a
Write SVG images from QuPath using JFreeSVG (http://www.jfree.org/jfreesvg/).
Simple, immutable classes to represent points and dimensions.
The main QuPath user interface.
Classes for plotting and charting.
Commands shown within the main QuPath interface.
Helper classes for creating dialogs, prompts and filt choosers within QuPath.
Interface to define QuPath extensions.
Custom ImageServers that depend upon the QuPath interface and image display settings.
Classes for requesting, caching and drawing image tiles.
Support for logging.
Classes related to extracting, calculating and displaying measurements.
Panes used to display information in the QuPath interface.
Scripting through the QuPath interface.
Alternative script editor for QuPath using syntax highlighting thanks to RichTextFX (https://github.com/FXMisc/RichTextFX).
Display, summarize and query tissue microarray analysis results.
Assorted helper classes for the QuPath interface.
QuPath image viewing and display.
Support for overlays, which may be painted on top of
Record and display field of view changes made within a
Drawing and navigation tools for the QuPath toolbar.
ImageDataclass to represent the key data associated with an analyzed image.
Supports accessing pixels and metadata in QuPath.
Read images using Bio-Formats (https://www.openmicroscopy.org/bio-formats/).
Read images using OpenSlide (https://openslide.org/).
Supports for writing images of various kinds in various ways.
Write OME-TIFF images.
Supports reading and writing some core QuPath data structures.
Provides PathObjects, used to represent annotations and other image structures within QuPath.
Classes to represent the object hierarchy.
Events triggered when the hierarchy changes, such as objects being added, removed or reclassified.
Classes to support general analysis commands.
Plugins for manipulating objects and ROIs.
Defines classes for handling parameters used in interactive dialogs or as method arguments.
Classes and interfaces related to logging analysis steps to assist scripting and reproducibility.
Classes and interfaces related to projects, which are used to manage multiple images.
Defines immutable classes for representing image planes and regions.
Classes that define regions of interest (ROIs).
Interface that define regions of interest (ROIs).
Defines helper class for running scripts.
Detection plugins using OpenCV.
Classifiers using OpenCV's ml module.
QuPath classes to use OpenCV's DNN module.
Classes for feature calculation using OpenCV.
QuPath classes to apply machine learning to pixels and objects using OpenCV.
QuPath object classifiers using OpenCV.
Extract object features using OpenCV.
QuPath pixel classifiers using OpenCV.
Image operations, implemented with OpenCV.
Additional processing methods for use with OpenCV Mats.
General-purpose image processing and machine learning commands.
QuPath commands relevant for machine learning.
UI classes to support density maps.
Interfaces and helper classes for using machine learning in QuPath.
Reusable UI classes to support processing commands.
Legacy classes related to object classification.
ImageJ plugins to install within QuPath's embedded ImageJ instance to enable exchanging ROIs and objects.