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Aligning Big Brains & Atlases

The complete documentation of ABBA can be found here:

You can use ABBA by activating the PTBIOP update site, but more functionalities are acessible through other installation means. Check the full documentation for instructions.

ABBA - Aligning Big Brains & Atlases

Aligning Big Brains & Atlases or ABBA for short, is a Fiji plugin which allows to register thin serial sections to several atlases, in coronal, sagittal and horizontal orientations.

Within Fiji, you have access to the 3D mouse Allen Brain atlas, and the Waxholm Space Atlas of the Sprague Dawley Rat Brain. With ABBA-Python, you can access all BrainGlobe atlases.

ABBA is typically used in conjunction with QuPath: a QuPath project can serve as an input for ABBA, and the registration results can be imported back into QuPath for downstream processing.

ABBA 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 reference documentation of ABBA. If you require additional help, please check the troubleshooting section at the bottom of this page.


You will find the complete documentation in