QuPath Warpy extension

This repo adds some support for nonlinear deformation and registration in QuPath, by using the ImgLib2 library.

Documentation

https://imagej.net/plugins/bdv/warpy/warpy

Installing

Download the latest qupath-extension-warpy-[version].zip file from releases. Unzip it, then and drag its contained files onto the main QuPath window.

If you haven't installed any extensions before, you'll be prompted to select a QuPath user directory. The extension will then be copied to a location inside that directory.

You might then need to restart QuPath (but not your computer).

Citing

https://doi.org/10.3389/fcomp.2021.780026

Building

You can build the QuPath Warpy extension from source with

gradlew clean build

The output will be under build/libs.

• clean removes anything old
• build builds the QuPath extension as a .jar file and adds it to libs