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https://github.com/qupath/qupath

QuPath - Open-source bioimage analysis for research
https://github.com/qupath/qupath

bioimage-analysis bioimage-informatics cell-analysis cell-segmentation computational-pathology digital-pathology groovy histology image-processing imagej javafx machine-learning opencv pathology tissue-microarray-analysis whole-slide-imaging

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QuPath - Open-source bioimage analysis for research

Host: GitHub
URL: https://github.com/qupath/qupath
Owner: qupath
License: gpl-3.0
Created: 2016-08-28T14:31:41.000Z (over 8 years ago)
Default Branch: main
Last Pushed: 2024-11-26T13:44:42.000Z (16 days ago)
Last Synced: 2024-11-26T14:35:19.112Z (16 days ago)
Topics: bioimage-analysis, bioimage-informatics, cell-analysis, cell-segmentation, computational-pathology, digital-pathology, groovy, histology, image-processing, imagej, javafx, machine-learning, opencv, pathology, tissue-microarray-analysis, whole-slide-imaging
Language: Java
Homepage: https://qupath.github.io
Size: 95.6 MB
Stars: 1,064
Watchers: 56
Forks: 282
Open Issues: 46
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md

Awesome Lists containing this project

AwesomeJavaFX - QuPath - Open source software for bioimage analysis. (Libraries, Tools and Projects)

README

        [![Image.sc forum](https://img.shields.io/badge/dynamic/json.svg?label=forum&url=https%3A%2F%2Fforum.image.sc%2Ftags%2Fqupath.json&query=%24.topic_list.tags.0.topic_count&colorB=brightgreen&suffix=%20topics&logo=data:image/png;base64,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)](https://forum.image.sc/tag/qupath)

[![Total downloads](https://img.shields.io/github/downloads/qupath/qupath/total?style=flat)](https://github.com/qupath/qupath/releases)

[![Latest release downloads](https://img.shields.io/github/downloads/qupath/qupath/latest/total?style=flat)](https://github.com/qupath/qupath/releases/latest)

[![Paper](https://zenodo.org/badge/DOI/10.1038/s41598-017-17204-5.svg)](https://doi.org/10.1038/s41598-017-17204-5)

[![Twitter](https://img.shields.io/twitter/follow/qupath?style=flat)](http://twitter.com/qupath)

# QuPath

**QuPath is open source software for bioimage analysis**.

Features include:

* Lots of tools to annotate and view images, including whole slide & microscopy images

* Workflows for brightfield & fluorescence image analysis

* New algorithms for common tasks, including cell segmentation, tissue microarray dearraying

* Interactive machine learning for object & pixel classification

* Customization, batch-processing & data interrogation by scripting

* Easy integration with other tools, including ImageJ

To **download QuPath**, go to the [Latest Releases](https://github.com/qupath/qupath/releases/latest) page.

For **documentation**, see [https://qupath.readthedocs.io](https://qupath.readthedocs.io)

For **help & support**, try [image.sc](https://forum.image.sc/tag/qupath) or the [links here](https://qupath.readthedocs.io/en/latest/docs/starting/help.html)

To **build QuPath from source** see [here](https://qupath.readthedocs.io/en/latest/docs/reference/building.html).

**If you find QuPath useful in work that you publish, please [_cite the publication_](https://qupath.readthedocs.io/en/latest/docs/intro/citing.html)!**

*QuPath is an academic project intended for research use only.*

*The software has been made freely available under the terms of the [GPLv3](https://github.com/qupath/qupath/blob/main/LICENSE) in the hope it is useful for this purpose, and to make analysis methods open and transparent.*

## Development & support

QuPath is being actively developed at the University of Edinburgh by:

* [Pete Bankhead](https://github.com/petebankhead) (creator)

* [Fiona Inglis](https://github.com/finglis)

* [Alan O'Callaghan](https://github.com/alanocallaghan)

* [Léo Leplat](https://github.com/Rylern)

* [Laura Nicolás-Sáenz](https://github.com/lauranicolass)

Past QuPath dev team members:

* Melvin Gelbard

* Mahdi Lamb

For all contributors, see [here](https://github.com/qupath/qupath/graphs/contributors).

This work is made possible in part thanks to funding from:

* [Wellcome Trust Technology Development Grant](https://wellcome.org/grant-funding/people-and-projects/grants-awarded/qupath-advanced-open-platform-next-generation) (2022-Present)

* [CZI Essential Open Source Software for Science, Cycle 4](https://chanzuckerberg.com/eoss/proposals/qupath-boosting-bioimage-analysis-for-users-developers/) (2022-Present)

* [CZI Essential Open Source Software for Science, Cycle 1](https://chanzuckerberg.com/eoss/proposals/qupath-open-source-bioimage-analysis-and-quantitative-pathology/) (2020-2022)

* Wellcome Trust / University of Edinburgh Institutional Strategic Support Fund (ISSF3) (2019-2020)

----

## Background

QuPath was first designed, implemented and documented by Pete Bankhead while at Queen's University Belfast, with additional code and testing by Jose Fernandez.

Versions up to v0.1.2 are copyright 2014-2016 The Queen's University of Belfast, Northern Ireland.

These were written as part of projects that received funding from:

* Invest Northern Ireland (RDO0712612)

* Cancer Research UK Accelerator (C11512/A20256)

![Image](https://raw.githubusercontent.com/wiki/qupath/qupath/images/qupath_demo.jpg)