My goal is to figure out the brain structure that each grid belongs to.
I have downloaded the expression grid data following the instruction in “http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data”. The label of brain structure seems to be somewhere else.
So I used the SDK following the demo in “http://alleninstitute.github.io/AllenSDK/_static/examples/nb/reference_space.html#Downloading-an-annotation-volume”. But the grid expression data is in 200um unit and the reference map is 100um at most. Also the orientation is different. I am thinking about resizing the reference map and aligning them myself. But this seems error-prone. Is there a reference map specifically for the ISH data that I failed to find?
Any help will be appreciated.