The Allen Brain Institute publishes some really nice gene expression and fibre tracing maps.
Sadly, their API is beyond weird. I have managed to download some data which I believe is their template, but it’s in 1D and basically I would need to reconstruct the NIfTI from that. They do provide instructions on how to do it: http://help.brain-map.org/display/mousebrain/API#API-3DReferenceModels
I am wondering:
- Am I doing this all wrong, is there maybe a way to download their data in NIfTI or other 3d data formats?
- Has the parser for this 1D data structure been implemented in some python package already? What about a parser for their hierarchical annotation?
- If I go ahead and write this myself - what would be a nice place to contribute it to? nibabel?