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This is originally reported by Scott Bolkan from the Princeton BRAINCoGS group.
the root source however i think is that SpikeGLX release 2023-02-02 onward has removed snsShankMap from the neuropixels/imec meta data (it's now replaced with snsGeomMap). i think some code in the datajoint ephys element looks for snsShankMap in order to create configuration files for spikesorting with kilosort. for example, my newly acquired neuropixels 2.0 data with the latest SpikeGLX fails in the follow princeton-u19 ephys pipeline:
File "/home/u19prod@pu.win.princeton.edu/miniconda3/envs/U19-pipeline_python_env/lib/python3.9/site-packages/element_array_ephys/ephys_precluster.py", line 187, in make
for shank, shank_col, shank_row, _ in spikeglx_meta.shankmap['data']]
TypeError: 'NoneType' object is not subscriptable
Jennifer Colonell has shared code for adding snsGeomMap fields to ap.meta files acquired in older versions of SpikeGLX here
The text was updated successfully, but these errors were encountered:
Feature Request
Problem
This is originally reported by Scott Bolkan from the Princeton BRAINCoGS group.
The text was updated successfully, but these errors were encountered: