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AllenInstitute / OpenScopeNWB

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NWB files currently contain CCF area but not layer #53

Closed Ahad-Allen closed 2 years ago

Ahad-Allen commented 2 years ago

Currently, the location info for each probe in the nwb files indicates the area of the brain the probe is in, e.g. VISp, but not the layer (e.g. VISp2

jeromelecoq commented 2 years ago

Hyeyoung needs it within a month

jeromelecoq commented 2 years ago

@Ahad-Allen explain the fix here.

Ahad-Allen commented 2 years ago

Not yet implemented but I believe this is because the numbers associated with each area get filtered out before being input into the nwb files during the write_nwb module. I will investigate and confirm today.

Ahad-Allen commented 2 years ago

This is correct. This specific line in ecephys modules is doing this: numbers = re.findall(r'\d+', structure_acronym)

Ahad-Allen commented 2 years ago

This should be resolved with the latest commit for conversions. WIll confirm when looking at the data with Carter

Ahad-Allen commented 2 years ago

Layers seem to be correct now! I can regen the appropriate files when the image_path changes are done.

jeromelecoq commented 2 years ago

@Ahad-Allen will provide commit number here

Ahad-Allen commented 2 years ago

Resolved with 13a1267844b7630908b3eb41868613c9356a2909