Investigate and create neuropil mask code

AllenInstitute / AllenSDK

code for reading and processing Allen Institute for Brain Science data

https://allensdk.readthedocs.io/en/latest/

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Investigate and create neuropil mask code #2571

Open morriscb opened 1 year ago

morriscb commented 1 year ago

Related to #2565, Investigate how neuropil masks are created in the neuropil subtraction (or potentially earlier processing). Recreate masks for release as part of the ROI data (cell_specimen_table).

[x] Interface with the science team regarding what we expect the masks to look like. Masks are not currently saved anywhere.
[x] Find the mask creation in the processing code.

morriscb commented 1 year ago

Looks like this bit of code is what is need to create the neuropil masks. From this, it looks like to create masks for a given roi you need: All ROI masks/locations within that imaging plane; the motion border. From there you can recreate the neuropil mask for each ROI in a given experiment.