Coregistration of data from imaged brains unto a brain atlas is one step to establish significance and legitimize differences in the densities/distributions of objects such as cells in the brain between separate channels or experimental cohorts. In this method, I provide a free, simple, and largely automated pipeline to coregister and analyze 3D mouse brain data using the tool ABBA, a free coregistration platform developed by Nicolas Chiaruttini, as well as some python scripts and ImageJ macros which I have developed. This protocol will go over preprocessing steps to prepare your image for import into ABBA as a serial, multi-channel .tiff image. It will provide instructions and tips on using ABBA to coregister 3D brains. Finally, it will explain a pipeline using python and the free imaging software ‘ImageJ’ to automatically obtain region specific information for all regions simultaneously, such as cell counts, cell densities, and a normalized, robust clustering factor that can safely be compared between heterogenous images, and provides a method for obtaining significance differences in regions between two cohorts regions based on the extracted information.
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Liam McLaughlin (2024) studied this question.
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