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:
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: