QuPath ABBA extension

This repo adds some support for the ABBA plugin in QuPath.

Installing

Download the latest zip release of this extension (releases), unzip it and drag the jar 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

If you use ABBA in your work, please cite the paper below, currently in pre-print:

Important

Chiaruttini, N., Castoldi, C. et al. ABBA, a novel tool for whole-brain mapping, reveals brain-wide differences in immediate early genes induction following learning. bioRxiv (2024).
https://doi.org/10.1101/2024.09.06.611625

Building

You can build the QuPath ABBA 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