Is there a 3D mouse brain volume available? How would I access this data?
Yes indeed there is. The question is whether you are looking for a visualization application (BrainExplorer: http://connectivity.brain-map.org/3d-viewer?v=1) or the computational framework (via AllenSDK). If the latter, PM or email me and I will get you set up with the basics.
If you just want the files and can handle .nrrd, you can find 3D average mouse brain template volume here:
http://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/average_template/
The annotation volume is here:
The suffixes (10, 25, 50, 100) are isotropic resolution in microns. The annotation volume contains 32 bit structure IDs which come from the ‘id’ property here:
http://api.brain-map.org/api/v2/data/Structure/query.json?criteria=[graph_id$eq1]&num_rows=1500
perfect, thanks!
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