ABBA is still in experimental phase. Expect bugs and do not expect backward compatibility when a more stable version will be released (all the code is versioned and stored in a worst case scenario, but do not count on it).
Aligning Big Brains & Atlases or ABBA for short, is a Fiji plugin which allows to register adult mouse brain serial sections to the adult mouse brain atlas by the Allen Institute.
It has been developed by the BioImaging & Optics Platform at EPFL. This page contains the documentation of ABBA (installation and usage). If you require additional help, please post your question on the image.sc forum and tag your question / issue with
qupath. If you have already installed ABBA, you can also click on
Help > Ask for help in the forum from the plugin.
If you want to test this plugin, you can download one of the following test dataset:
One animal, 85 serial sections, 3 fluorescent channels (DAPI - nuclei, FITC - autofluorescence, mCherry - labelled sparse cells)
One animal, 87 serial sections, 2 fluorescent channels (nuclei and autofluorescence)