Repositories list

• qupath-imglib2

  Public
  A Java library to link QuPath and ImgLib2

  Java

  •

  Apache License 2.0

  •1•1•1•1•Updated Oct 30, 2025Oct 30, 2025

• qupath

  Public
  QuPath - Open-source bioimage analysis for research

  groovyopencvmachine-learning+ 13imagejjavafximage-processinghistologycell-segmentationbioimage-informaticsdigital-pathology+ 6

  Java

  •

  GNU General Public License v3.0

  •312•1.2k•35•5•Updated Oct 29, 2025Oct 29, 2025

• log-viewer

  Public
  Java

  •

  Apache License 2.0

  •3•6•3•0•Updated Oct 28, 2025Oct 28, 2025

• qupath-catalog

  Public
  The catalog containing QuPath extensions developed by the QuPath team

  Apache License 2.0

  •1•1•2•0•Updated Oct 27, 2025Oct 27, 2025

• qupath-extension-omero

  Public
  QuPath extension to work with images through OMERO's APIs

  Java

  •

  Apache License 2.0

  •2•8•2•0•Updated Oct 27, 2025Oct 27, 2025

• qubalab

  Public
  Lab for quantitative bioimage analysis experiments in Python

  Python

  •

  Apache License 2.0

  •5•16•0•0•Updated Oct 22, 2025Oct 22, 2025

• qupath-extension-instanseg

  Public
  The official QuPath extension for InstanSeg

  Java

  •

  Apache License 2.0

  •6•28•5•0•Updated Oct 20, 2025Oct 20, 2025

• qupath.github.io

  Public
  GitHub pages site

  SCSS

  •

  MIT License

  •5•2•0•0•Updated Sep 25, 2025Sep 25, 2025

• qupath-docs

  Public
  QuPath documentation

  Python

  •24•20•8•1•Updated Sep 17, 2025Sep 17, 2025

• qupath-extension-training

  Public
  A QuPath extension to help with learning the software

  Java

  •

  Apache License 2.0

  •4•1•2•2•Updated Sep 12, 2025Sep 12, 2025

• qupath-fxtras

  Public
  Reusable JavaFX tools for QuPath (and beyond)

  Java

  •

  Apache License 2.0

  •4•6•2•1•Updated Sep 8, 2025Sep 8, 2025

• actions

  Public
  GitHub actions for QuPath and related repositories

  Shell

  •

  Apache License 2.0

  •1•0•0•0•Updated Sep 8, 2025Sep 8, 2025

• qupath-extension-stitching

  Public
  A QuPath extension to combine TIFF images

  Java

  •

  Apache License 2.0

  •0•1•1•0•Updated Aug 21, 2025Aug 21, 2025

• qupath-extension-template

  Public template
  Template to help create a new QuPath extension

  Java

  •12•21•0•0•Updated Aug 12, 2025Aug 12, 2025

• extension-manager

  Public
  A manager for catalogs and extensions.

  Java

  •

  Apache License 2.0

  •3•0•0•0•Updated Aug 8, 2025Aug 8, 2025

• qupath-extension-align

  Public
  QuPath extension to interactively align images

  Java

  •

  GNU General Public License v3.0

  •9•26•1•0•Updated Aug 7, 2025Aug 7, 2025

• qupath-extension-py4j

  Public
  A QuPath extension for linking up to Python via Py4J (https://www.py4j.org)

  Java

  •

  Apache License 2.0

  •3•1•0•0•Updated Jul 28, 2025Jul 28, 2025

• javadoc-viewer

  Public
  A simple JavaFX Javadoc viewer

  Java

  •

  Apache License 2.0

  •1•0•0•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-gradle-plugin

  Public
  Gradle plugins to help create QuPath extensions

  Java

  •

  Apache License 2.0

  •1•2•0•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-extension-bioimageio

  Public
  A QuPath extension for working with the Bioimage Model Zoo (https://bioimage.io)

  Java

  •

  Apache License 2.0

  •4•6•2•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-extension-djl

  Public
  A QuPath extension for working with Deep Java Library (https://djl.ai)

  Java

  •

  Apache License 2.0

  •6•8•1•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-extension-jpen

  Public
  QuPath extension using JPen for graphics tablet input

  Java

  •

  GNU General Public License v3.0

  •4•1•0•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-extension-liverquant

  Public
  A QuPath extension to run the Liverquant algorithm

  Java

  •

  Apache License 2.0

  •1•0•0•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-extension-snapshots

  Public
  A QuPath extension to help with making screenshots

  Java

  •

  Apache License 2.0

  •2•1•0•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-extension-stardist

  Public
  QuPath extension to run StarDist nucleus detection

  Java

  •

  Apache License 2.0

  •7•47•2•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-extension-wsinfer

  Public
  QuPath extension to work with WSInfer - https://wsinfer.readthedocs.io/

  Java

  •

  Apache License 2.0

  •10•26•3•1•Updated Jul 2, 2025Jul 2, 2025

• qupath-bioimageio-spec

  Public
  Support for parsing the BioImage Model Zoo spec in Java

  Java

  •

  MIT License

  •2•0•2•0•Updated Jul 2, 2025Jul 2, 2025

• qupath-gradle-scripting-project

  Public template
  Groovy

  •3•0•0•0•Updated Jul 2, 2025Jul 2, 2025

• openslide-jars

  Public
  Ruby

  •2•0•0•0•Updated Jul 2, 2025Jul 2, 2025

• c-blosc-jars

  Public
  JAR files for the c-blosc native library.

  1•2•0•0•Updated Jul 2, 2025Jul 2, 2025