Getting structure masks for fine substructures

Technical
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1

Hi there,

The Allen atlas has fine substructures for some regions (e.g. subregions of SCig, here).

I can find the structure ids associated with them, for example with the below code

scm_sub_acronyms = ['SCig-a',  'SCdg']
fine_substructures = structure_tree.get_structures_by_acronym(scm_sub_acronyms)

However, there are not structure masks for these fine substructures available on this page. I.e. structure_494.nrrd is not listed.

Hence, when I run the below I get an error

for i, s in enumerate(fine_substructures, start=1):
    mask, _ = mcc.get_structure_mask(s['id'])

The error tells me

HTTPError: 404 Client Error: Not Found for url: https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/structure_masks/structure_masks_50/structure_494.nrrd

Are there structure masks available for these fine substructures elsewhere? Or is there any alternative means of creating them?

494 is not present at 10um resolution in the annotation volumes for the 2017 or 2022 CCF

https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2022/annotation_10.nrrd

https://download.alleninstitute.org/informatics-archive/current-release/mouse_ccf/annotation/ccf_2017/annotation_10.nrrd

Thanks

2

The Allen Atlas (ARA) has lots of regions that aren’t in the CCF.

3

Thanks. If that’s the case, is there any way to download the ARA masks, or create them?

4

This team was working on aligning the original ARA’s compartments into the CCF space - they have a fun web viewer that allows you to download 3D meshes of the finer compartments.

I never found a great way to work it into any of my workflows. Maybe one day!

5

I can’t seem to download the structures as a mask - the meshes don’t work for what I need, but thankyou for the tip.

Can anyone at the Allen help with this question?