Mouse brain volume from software

Technical
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1

Hi everyone,

First of all, I want to express my gratitude for the incredible work that has gone into creating the Allen Brain Map. The resources and tools provided are truly invaluable. Thank you!

I’ve been exploring the website, software, and forum and came across this visualization:

Screenshot 2025-02-28 162715
Screenshot 2025-02-28 162715590×418 23.9 KB

I assume this model exists as a 3D file (e.g., CAD or .stl). It would be extremely helpful for my research to have access to this file to create a 3D scientific visualization.

I understand there may be ways to use .nrrd data to generate a 3D file. However, the process seems to require expensive software that I currently do not have access to.

Could you please let me know if this specific model is available for download or if there are alternative ways to obtain it? Any guidance or recommendations would be greatly appreciated.

Thank you again for your amazing work, and I look forward to your response.

Best regards,
Natt

1 Like
2

Hi @Natt,
Thank you for your kind words and your question.

We have the related mesh files available as part of the allensdk:

from allensdk.core.mouse_connectivity_cache import MouseConnectivityCache
mcc = MouseConnectivityCache(resolution=10)
verts, norms, face_verts, face_normals = mcc.get_structure_mesh(node['id'])

Please let me know if this gives you what you were looking for.

3

Hi Sven,

Thank you very much for your help! I missed this info.

Best regards,
Natt