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AllenInstitute / ecephys_spike_sorting

Modules for processing extracellular electrophysiology data from Neuropixels probes
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in KS2.5 channel_map.npy is now a row vector #55

Closed LaurenzMuessig closed 3 years ago

LaurenzMuessig commented 4 years ago

Hi,

Just to let you know that I noticed in the new kilosort 2.5 'channel_map.npy' is a row vector instead of a column vector. This crashes the kilosort_postprocessing for me (l.58 in 'postprocessing.py'). You might want to add a line that forces the channel_map to a column vector.

Cheers

Laurenz

jsiegle commented 4 years ago

Thanks for the heads up! Will get this updated soon.

LaurenzMuessig commented 4 years ago

No worries. Great to hear you guys are making the pipeline compatible with KS2.5 and phy although it seems to work fine for me already if the channel_map is in the right format (I only use the post-processing modules though). PS: also KS2.5 now outputs a 'cluster_group.tsv' which is just a copy of 'cluster_KSLabel.tsv' - I have to remove that before running your pipeline, presumably because the headers don't match with the cluster_group.tsv that the ecephys pipeline expects.

Cheers