Relationship between injection coordinates in data portal and sdk

Technical
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Hi,

The injection coordinate in the data portal (e.g.:https://connectivity.brain-map.org/projection/experiment/113226232) is in mm and relative to Bregma while the data downloaded using allensdk.core.mouse_connectivity_cache.MouseConnectivityCache.get_structure_unionizes are using a different coordinate system. How do I convert bregma coordinates to the sdk system? What is the bregma coordinate in the reference atlas?

Thanks!

2

I just realized I can get the coordinates of the injection looking at the annotation where the field “is_injection” is equal 1. Should have thought about it!

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Hi @robertooooo,

Thanks for posting, and glad you found the solution. You also might be interested in reading a previous post about Bregma:

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