Trouble aligning flattened brains to CCFv3

Technical
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1

Hi everyone,

I’m currently using the ABBA pipeline to align whole-brain images to the Allen Brain Atlas (CCFv3). However, because my mice had a metal head-fixed pedestal for behavioral experiments, the brain appears to be compressed and flattened, especially in the brainstem region. This makes alignment very challenging.

I’m concerned that making too many manual adjustments might introduce inaccuracies. Do you have any suggestions on how to handle this issue? For example, should I consider aligning my slices to a flattened atlas, or is there a specific step within the current pipeline that I should adjust to improve the results?

Any advice or shared experience would be greatly appreciated.

Thank you!

2

Hello, thanks for your question. I’m not very familiar with ABBA (we typically use ANTs for our registration). From a read-through of the documentation, there may be a few ways to troubleshoot. Could you give me some information about the nature of the compression/flattening and the resulting alignment? For example, is the compression localized to one hemisphere or localized to a few slices?

In terms of manual adjustment, could you give me additional information on your manual affine transform step? Does the compressed brain roughly align with CCFv3 before nonlinear registration?

Thanks,

Ashwin