CCF v3 Anatomy: finding structure annotation ids


I have downloaded the mouse brain template and the annotation files, but I was wondering where I could find the data for understanding the labels of each brain structure in the annotation file.


Hi Momo

This page gives information on retrieving structure information:'s+Structure+Graph

Note that the Adult Mouse Brain atlas is structure graph id = 1

Best regards,

Hi Wayne,

Thank you for your reply! Is there any csv file that includes the structure names along with the structure IDs?


Our API does not provide a csv file. An Internet search will probably provide a number of options for converting a JSON file to CSV though. This is one that I found just now:

Hi Momo,

You can use Brainglobe’s AtlasAPI download and use the Allen Atlas in Python. The API has easy commands to display a list of all brain regions and a view of their hierarchical organization (both of which can easily be exported to .csv or any other format)


Hi @Momo,

You might be interested in a thread that contains links and references to other data mapping tools developed by the community, here:

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Thanks, I’ll check that out!


Thank you, I’ll take a look at them!