CCF v3 Anatomy: finding structure annotation ids

Technical
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1

Hi,

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.

Best,
Momo

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Density and orientation data
2

Hi Momo

This page gives information on retrieving structure information: http://help.brain-map.org/display/api/Downloading+an+Ontology's+Structure+Graph

Note that the Adult Mouse Brain atlas is structure graph id = 1
http://api.brain-map.org/api/v2/structure_graph_download/1.json

Best regards,
Wayne

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3

Hi Wayne,

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

Momo

4

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: https://www.convertcsv.com/json-to-csv.htm

5

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)

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6

Hi @Momo,

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

https://community.brain-map.org/t/mouse-brain-reference-atlases-mapping-your-own-data/

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7

Thanks, I’ll check that out!

Momo

8

Thank you, I’ll take a look at them!

Momo