Mouse brain volume



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: 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:

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:[graph_id$eq1]&num_rows=1500


perfect, thanks!