Aligning Big Brains & Atlases


Documentation of the Aligning Big Brains & Atlases Fiji plugin.

View the Project on GitHub BIOP/ijp-imagetoatlas

[EXPERIMENTAL] ABBA - Aligning Big Brains & Atlases

A Fiji plugin for the registration of thin mouse brain slices to the 3D mouse Allen Brain atlas + QuPath associated tools.

:warning: 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 uses BigDataViewer and BigWarp for the display and on-the-fly computation of spline-transformed multiresolution images (typical output of Whole Slide Imaging).

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 forum and tag your question / issue with abba and fiji or 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:

Dataset 1, provided by Lucie Dixsaut, Johannes Gräff lab, EPFL

One animal, 85 serial sections, 3 fluorescent channels (DAPI - nuclei, FITC - autofluorescence, mCherry - labelled sparse cells)

Dataset 2, provided by Bianca A. Silva, Johannes Gräff lab, EPFL

One animal, 87 serial sections, 2 fluorescent channels (nuclei and autofluorescence)


Using ABBA

Developer documentation (In progress…)