Retrieving the volume of mouse brain structures with allensdk

Technical
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1

Hi
I have a dataset of cell counts that was generated using the mouse brain atlas’ segmentation. I want to normalize the counts using the structures’ volume in the atlas. I am trying to use the sdk in python to retrieve the volumes, but I cannot find out how to do so, in the documentation or using chat GPT.
I so far have gotten information about structures using the ontologies api, like so:

oa = OntologiesApi()

structure_tree_data = oa.get_structures(structure_graph_ids=[1])

Which gotten me entries like:

{‘acronym’: ‘FRP6a’,
‘atlas_id’: None,
‘color_hex_triplet’: ‘268F45’,
‘depth’: 7,
‘failed’: False,
‘failed_facet’: 734881840,
‘graph_id’: 1,
‘graph_order’: 10,
‘hemisphere_id’: 3,
‘id’: 526157196,
‘name’: ‘Frontal pole, layer 6a’,
‘neuro_name_structure_id’: None,
‘neuro_name_structure_id_path’: None,
‘ontology_id’: 1,
‘parent_structure_id’: 184,
‘safe_name’: ‘Frontal pole layer 6a’,
‘sphinx_id’: 11,
‘st_level’: 11,
‘structure_id_path’: ,
‘structure_name_facet’: 1215326494,
‘weight’: 8690},

But there does no seem to be information about the volume, and I could not find a description of the meaning of all the keys in the entries in the documentation.

Is this possible through the sdk? Am I using the right api? Where do I find the volumes if not in there?

Thank you

2

Hello,

Thank you for your question and for using the mouse brain atlas! You can find instructions and a link to example code describing how to obtain volumes here:
https://allensdk.readthedocs.io/en/latest/reference_space.html#annotation-volumes
Please let me know if this is not what you’re looking for and I’m happy to see how else we can help.

Thanks,
Ray

3

Thanks for the help! I was not able to find a way to get what I needed there, but I found out that the volumes I was looking for were in the supplementary data of the atlas paper https://doi.org/10.1016/j.cell.2020.04.007

Julien