QuPath

QuPath - Open Source Digital Pathology. 「QuPath -- 开源数字病理学」

Github stars Tracking Chart

QuPath

QuPath 是全幻灯片图像分析和数字病理的开源软件。

爱丁堡大学正在积极开发 QuPath,它提供了广泛的功能,包括:

  • 广泛的标注和可视化工具
  • IHC 和 H&E 分析的工作流程
  • 适用于常见任务的新颖算法,例如细胞分割、组织微阵列解排列
  • 交互式机器学习,例如用于细胞和纹理分类
  • 基于对象的分层数据模型,支持脚本
  • 可扩展性,添加新功能或对不同图像源的支持
  • 易于与其他工具集成,例如 MATLAB 和 ImageJ

总而言之,QuPath 旨在为研究人员提供一套新的工具,以一种对用户和开发人员都友好的方式帮助进行生物图像分析。

QuPath 是免费的开放源代码,使用 GPLv3。

要下载QuPath,请转到“最新版本”页面。

有关文档,请参见 QuPath Wiki

如需帮助和支持,请尝试 image.sc此处的链接

(First edition Part 1: vz edited at 2020.01.18)

Main metrics

Overview
Name With Ownerqupath/qupath
Primary LanguageJava
Program languageJava (Language Count: 7)
PlatformLinux, Mac, Windows
License:GNU General Public License v3.0
所有者活动
Created At2016-08-28 14:31:41
Pushed At2025-05-16 14:32:14
Last Commit At
Release Count46
Last Release Namev0.6.0-rc5 (Posted on )
First Release Namev0.0.1-beta (Posted on )
用户参与
Stargazers Count1.2k
Watchers Count55
Fork Count300
Commits Count4.6k
Has Issues Enabled
Issues Count853
Issue Open Count38
Pull Requests Count941
Pull Requests Open Count4
Pull Requests Close Count77
项目设置
Has Wiki Enabled
Is Archived
Is Fork
Is Locked
Is Mirror
Is Private

Image.sc forum

QuPath

QuPath is open source software for whole slide image analysis and digital pathology.

QuPath is being actively developed at the University of Edinburgh and offers a wide range of functionality, including:

  • extensive tools for annotation and visualization
  • workflows for both IHC and H&E analysis
  • novel algorithms for common tasks, e.g. cell segmentation, Tissue microarray dearraying
  • interactive machine learning, e.g. for cell and texture classification
  • an object-based hierarchical data model, with scripting support
  • extensibility, to add new features or support for different image sources
  • easy integration with other tools, e.g. MATLAB and ImageJ

All in all, QuPath aims to provide researchers with a new set of tools to help with bioimage analysis in a way that is both user- and developer-friendly.

QuPath is free and open source, using GPLv3.

To download QuPath, go to the Latest Releases page.

For documentation, see the QuPath Wiki

For help & support, try image.sc or the links here


Building QuPath with Gradle

Building software can be tricky, but hopefully this won't be at all - thanks to Gradle.

What you need is:

  • OpenJDK JDK 11 (or later)
  • JPackage (currently there is an early access build at jdk.java.net)
  • The QuPath source code (you can get it from GitHub with the Clone or download button)

You should then start a command prompt, find your way to the directory containing QuPath, and run

gradlew.bat createPackage -Ppackager=/full/path/to/jpackage.exe

for Windows, or

./gradlew createPackage -Ppackager=/full/path/to/jpackage

for MacOS and Linux.

This will download Gradle and all its dependencies, so may take a bit of time (and an internet connection) the first time you run it.

Afterwards, you should find QuPath inside the ./build/dist. You may then drag it to a more convenient location.

Congratulations! You've now built QuPath, and can run it as normal from now on... at least until there is another update, when you can repeat the (hopefully painless) process.

You can get Gradle itself from http://gradle.org -- but
in keeping with the Gradle guidelines, the Gradle Wrapper is included here. That makes things easier, and you don't need to download Gradle separately. Here's the Apache v2 license.

Libraries used within QuPath

To see a list of third-party open source libraries used within QuPath (generated automatically using Maven), see THIRD-PARTY.txt.

Full licenses and copyright notices for third-party dependencies are also included for each relevant submodule inside src/main/resources/licenses, and accessible from within within QUPath distributions under Help → License.


Background

QuPath versions up to v0.1.2 were created at Queen's University Belfast and released open source under the GPLv3.

Copyright 2014-2016 The Queen's University of Belfast, Northern Ireland

Image

Design, implementation & documentation

  • Pete Bankhead

Additional code & testing

  • Jose Fernandez

Group leaders

  • Prof Peter Hamilton
  • Prof Manuel Salto-Tellez

Project funding

The QuPath software has been developed as part of projects that have received funding from:

  • Invest Northern Ireland (RDO0712612)
  • Cancer Research UK Accelerator (C11512/A20256)