Mapping to a coronal P14 mouse brain atlas/space

Technical
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Hello brain mapping community,
I am looking to register IHC expression data from coronal sections to a P14 (3D) reference atlas. I would like to use stereotaxic coordinates so I can also register my images to the Mouse Brain Connectivity Atlas/expression data. Has anyone attempted to do this either of these things with success? As the Allen Developing mouse atlas has only an unannotated coronal P14 nissl atlas I was thinking of attempting to register the P14 nissl coronal sections to the P56 coronal atlas or the 3D atlas to create an annotated coronal P14 reference space/atlas. Has anyone tried this before?

I quite like the WholeBrain registration platform as I am comfortable coding in R, but very new/not savvy at python/python notebooks. I fear I may need to learn quickly to perform the above tasks. Any help or direction would be very much appreciated.

2

Hi Penelope,

We have not attempted to do this as you’ve described. One of our experts did raise some hesitation about this approach given the continued growth of the brain between P14 and P56, but we have not studied this in depth.

Best wishes for your research,
Tyler

3

Thank you very much for your reply Tyler. Would it be possible for me to email said expert with a couple questions, or does he/she prefer not to be contacted? Also, I imagine this is the same reason why no one has attempted this approach with the P29 Nissl images?

All the best,
Penny