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IBL TODO: Confirm atlas locations #67

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CodyCBakerPhD opened this issue Sep 13, 2024 · 1 comment
Open

IBL TODO: Confirm atlas locations #67

CodyCBakerPhD opened this issue Sep 13, 2024 · 1 comment
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@CodyCBakerPhD
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In both the electrode table and the units table

It has been noted some inconsistencies in anatomical values

Maybe it's a bug in the code, maybe it was an old issue in the source data

Need to figure out

Ecephys:

self.recording_extractor.set_property(key="ibl_x", values=ibl_coords[:, 0])
self.recording_extractor.set_property(key="ibl_y", values=ibl_coords[:, 1])
self.recording_extractor.set_property(key="ibl_z", values=ibl_coords[:, 2])
self.recording_extractor.set_property( # SpikeInterface refers to this as 'brain_area'
key="brain_area", values=list(channels["acronym"]) # NeuroConv remaps to 'location', a required field
) # Acronyms are symmetric, do not differentiate hemisphere
self.recording_extractor.set_property(
key="beryl_location",
values=list(brain_regions.id2acronym(atlas_id=channels["atlas_id"], mapping="Beryl")),
)
self.recording_extractor.set_property(
key="cosmos_location",
values=list(brain_regions.id2acronym(atlas_id=channels["atlas_id"], mapping="Cosmos")),
)

Units: https://github.com/catalystneuro/IBL-to-nwb/blob/main/ibl_to_nwb/datainterfaces/iblsortingextractor.py#L88-L89

@CodyCBakerPhD
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@grg2rsr It would be great to finally get a concrete example of this reported mismatch so we can reproduce

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