Repositories list

• qupath-extension-omero

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

  Java

  •

  Apache License 2.0

  •22 forks•99 stars•33 issues•00 pull requests•Updated Jun 26, 2026Jun 26, 2026

• models

  Public
  Trained models for use with QuPath

  33 forks•1616 stars•00 issues•00 pull requests•Updated Jun 25, 2026Jun 25, 2026

• qupath-extension-stardist

  Public
  QuPath extension to run StarDist nucleus detection

  Java

  •

  Apache License 2.0

  •77 forks•4848 stars•22 issues•00 pull requests•Updated Jun 25, 2026Jun 25, 2026

• qupath

  Public
  QuPath - Open-source bioimage analysis for research

  groovyopencvmachine-learning+ 13

  groovyopencvmachine-learningimagejjavafximage-processinghistologycell-segmentationbioimage-informaticsdigital-pathology+ 6

  Java

  •

  GNU General Public License v3.0

  •353353 forks•1.4k1.4k stars•3030 issues•22 pull requests•Updated Jun 25, 2026Jun 25, 2026

• openslide-jars

  Public
  Ruby

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jun 24, 2026Jun 24, 2026

• qupath.github.io

  Public
  GitHub pages site

  SCSS

  •

  MIT License

  •55 forks•22 stars•00 issues•00 pull requests•Updated Jun 23, 2026Jun 23, 2026

• qupath-fxtras

  Public
  Reusable JavaFX tools for QuPath (and beyond)

  Java

  •

  Apache License 2.0

  •33 forks•66 stars•11 issue•11 pull request•Updated Jun 12, 2026Jun 12, 2026

• qupath-extension-bioimageio

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

  Java

  •

  Apache License 2.0

  •33 forks•55 stars•33 issues•00 pull requests•Updated May 13, 2026May 13, 2026

• extension-catalog-model

  Public
  A pydantic package for writing QuPath extension catalogs

  Python

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• qupath-extension-djl

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

  Java

  •

  Apache License 2.0

  •77 forks•1010 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• qupath-extension-template

  Public template
  Template to help create a new QuPath extension

  Java

  •1515 forks•2121 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• qupath-extension-training

  Public
  A QuPath extension to help with learning the software

  Java

  •

  Apache License 2.0

  •33 forks•11 star•00 issues•11 pull request•Updated Apr 23, 2026Apr 23, 2026

• qupath-imglib2

  Public
  A Java library to link QuPath and ImgLib2

  Java

  •

  Apache License 2.0

  •11 fork•11 star•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• qupath-catalog

  Public
  The catalog containing QuPath extensions developed by the QuPath team

  Apache License 2.0

  •33 forks•11 star•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• qupath-bioimageio-spec

  Public
  Support for parsing the BioImage Model Zoo spec in Java

  Java

  •

  MIT License

  •22 forks•00 stars•22 issues•00 pull requests•Updated Mar 30, 2026Mar 30, 2026

• qupath-extension-stitching

  Public
  A QuPath extension to combine TIFF images

  Java

  •

  Apache License 2.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• libczi-jars

  Public
  00 forks•00 stars•00 issues•00 pull requests•Updated Mar 16, 2026Mar 16, 2026

• qupath-gradle-scripting-project

  Public template
  Groovy

  •33 forks•00 stars•00 issues•00 pull requests•Updated Mar 9, 2026Mar 9, 2026

• log-viewer

  Public
  Java

  •

  Apache License 2.0

  •22 forks•66 stars•44 issues•11 pull request•Updated Mar 2, 2026Mar 2, 2026

• qupath-docs

  Public
  QuPath documentation

  Python

  •2525 forks•2222 stars•77 issues•11 pull request•Updated Mar 2, 2026Mar 2, 2026

• qubalab

  Public
  Lab for quantitative bioimage analysis experiments in Python

  Python

  •

  Apache License 2.0

  •55 forks•2020 stars•00 issues•00 pull requests•Updated Feb 16, 2026Feb 16, 2026

• javadoc-viewer

  Public
  A simple JavaFX Javadoc viewer

  Java

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 11, 2026Feb 11, 2026

• qupath-extension-omero-web

  Public
  QuPath extension to work with images through OMERO's web API

  Java

  •

  GNU General Public License v3.0

  •1111 forks•1010 stars•88 issues•00 pull requests•Updated Feb 10, 2026Feb 10, 2026

• qupath-extension-instanseg

  Public
  The official QuPath extension for InstanSeg

  Java

  •

  Apache License 2.0

  •55 forks•2929 stars•66 issues•00 pull requests•Updated Jan 21, 2026Jan 21, 2026

• extension-manager

  Public
  A manager for catalogs and extensions.

  Java

  •

  Apache License 2.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Jan 12, 2026Jan 12, 2026

• actions

  Public
  GitHub actions for QuPath and related repositories

  Shell

  •

  Apache License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jan 7, 2026Jan 7, 2026

• qupath-extension-wsinfer

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

  Java

  •

  Apache License 2.0

  •99 forks•2929 stars•11 issue•11 pull request•Updated Dec 3, 2025Dec 3, 2025

• i2k-qupath-for-python-programmers

  Public archive
  Jupyter Notebook

  •

  Apache License 2.0

  •22 forks•99 stars•00 issues•00 pull requests•Updated Nov 5, 2025Nov 5, 2025

• qupath-extension-align

  Public
  QuPath extension to interactively align images

  Java

  •

  GNU General Public License v3.0

  •1010 forks•2929 stars•11 issue•00 pull requests•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

  •33 forks•11 star•00 issues•00 pull requests•Updated Jul 28, 2025Jul 28, 2025