petebankhead/qupath-extension-warpy

ImgLib2 RealTransform brought to QuPath

QuPath Warpy extension

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

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

TODO

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