Hi there. I’m reaching out to see how one would go about referencing the allen space to identify the brain regions at various coordinates in the atlas space.
Thanks!
To clarify, this would be within the mouse brain space.
I would recommend getting started with these:
CCFv3 Highlights: Getting Started - Technical - Allen Brain Map Community Forum (brain-map.org)
Did you manage to do this? I want to do the same thing
For more context, start with the links @lydian recommended. You could also review this API page: API - Allen Mouse Brain Atlas
Your specific question has come up a few times, and this is the solution I use:
- Download and unzip this: http://download.alleninstitute.org/informatics-archive/current-release/mouse_annotation/P56_Mouse_gridAnnotation.zip
- Matlab code for what you want to do is in the link above
- If you’d prefer R code:
fn2 = (folder where you unzipped grid annotation data)
annot = readBin(fn2,what="int",n=159326,size=4)"/energy.raw"),what="double",n=159326,size=4) - (I think this is the same as the “template” from here: mouse_connectivity)
And again, if this doesn’t work, see the links above 
.