I am trying to do a study about variability in mice brains, and was wondering if there was a way to check which brains have been annotated. The only one that I have seen that has been coronally sectioned and annotated was P56. When I would try using the download SVG option of the API for any brains found on the experimental section when I looked for coronally sliced brains that included certain regions, I would only get a blank image back. Is there any database for coronally sectioned mice brains that have also been annotated? Or is P56 the only one like that?
Thanks for your question! See the response below from one of our investigators, Lydia Ng:
The only mouse brains we have SVGs are reference atlases.
If you want to access other reference atlases I would start here:
Atlas Drawings and Ontologies - Allen Brain Atlas API (brain-map.org)
Otherwise, we don’t annotate experiment data.
If you are doing a variability study you might be interested in “CCF Applications and Resources” part of this paper Redirecting
and associated github repos
GitHub - AllenInstitute/3D-atlas-reverse-mapping: This repository contains a Jupyter Notebook that demonstrates the reverse mapping of the 3D atlas onto an imaged section.
Also this AllenInstitute/CCF_Tutorial (github.com)