j-hudecek / qupath

Quantitative Pathology

QuPath

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

QuPath has been developed as a research tool at Queen's University Belfast. It 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 a version of QuPath to install, go to the Latest Releases page.

For documentation and more information, see the QuPath Wiki

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

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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)

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.

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Building QuPath with Gradle

To get the latest QuPath, you will need to build it yourself.

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

What you need is:

• A Java JDK (currently only version 8 works)
• The QuPath source code (you can get it from GitHub with the Clone or download button)

A brief search for java jdk 8 will most likely find the Oracle JDK. At the time or writing, the most recent version is 'Java SE Development Kit 8u161'. If you prefer OpenJDK then you will likely also need to install OpenJFX as well.

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

./gradlew.bat jfxNative

for Windows, or

./gradlew jfxNative

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/jfx/native. 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.