This repository is now replaced by https://github.com/BIOP/abba_python
ABBA-Python
This repository demoes how to use ABBA with python by using PyImageJ and JPype.
For the documentation, please check the relevant sections within https://biop.github.io/ijp-imagetoatlas/.
DeepSlice
If you want to register mouse brain sections to the Allen Brain Atlas, ABBA-Python also includes DeepSlice, a powerful deep learning tool which can be used for automatic registration of coronal sections of mouse brains.
DeepSlice is completely independent from ABBA and has been developped by Harry Carey and colleagues. Please check its license and cite its preprint if you are using it.
DEEPSLICE IS INDEPENDENT FROM ABBA AND WAS NOT WRITTEN BY THE BIOP
But because of my lack of skills in dependency management in python, copying the code is the only way I found to make it run with ABBA.