How to acquire the structure label for the expression grid data?

transcriptomics
how-to
#1

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.

#2

I have figured it out. There is a link to download the grid annotation: http://download.alleninstitute.org/informatics-archive/current-release/mouse_annotation/P56_Mouse_gridAnnotation.zip. Should have read more carefully in the API page.

1 Like
#3

Glad you found what you needed! We’d love to hear how your work is going and hope you share results or publications here, when they are ready! :+1:t4: