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flatironinstitute / dendro-old

Analyze neuroscience data in the cloud
https://flatironinstitute.github.io/dendro-docs/
Apache License 2.0
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Pre-validation of NWB electrodes location for SI sorters Apps #33

Open luiztauffer opened 1 year ago

luiztauffer commented 1 year ago

@magland Should we include electrodes location data as a pre-validation step for SI-based sorters? I just encountered an error during job execution due to a NWB file not having valid electrodes location information, this looks like a cheap validation to make and it would be very helpful.

We could have something similar to what already exists for electrical_series_path, but with electrode_table columns as options for location.

@alejoe91 it looks like in SI nwbextractor this info is hardcoded to be fetched from rel_x , rel_y and rel_z columns. Can we make this flexible?

magland commented 1 year ago

@luiztauffer that's a good idea

In pc-spike-sorting I use x, y, z and then fall back to rel_x, rel_y, rel_z. I agree this should be configurable somehow.

https://github.com/scratchrealm/pc-spike-sorting/blob/1c5250faf5219f056b266436c94fc14fc794a990/kilosort3/NwbRecording.py#L33-L51