QuPath ABBA extension

August 12, 2025 ยท View on GitHub

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

Installing

In QuPath 0.6, this extension should be installed via the QuPath BIOP catalog.

Don't forget to restart QuPath (but not your computer).

Citing

If you use ABBA in your work, please cite the paper below:

Important

Chiaruttini, N.; Castoldi, C.; Requie, L. et al. ABBA+BraiAn, an integrated suite for whole-brain mapping, reveals brain-wide differences in immediate-early genes induction upon learning. Cell Reports (2025).
https://doi.org/10.1016/j.celrep.2025.115876

Please do not forget to cite other tools you may use, such as DeepSlice, Brainglobe, QuPath...

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