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HELP: Spike sorting on 4-shank Neuropixels 2.0
Apologies if this has already been reported but I couldnt find anything.
In the lab we are recording with 4-shank Neuropixels 2.0 using all shanks. We are kilosorting the data but noticed that the probe layout that comes by default when installing kilosort (NP2_kilosortChanMap.mat) appears to have only 1 shank. We are assuming this is for the single-shank version of Neuropixels 2.0. Regardless, there seems to be neurons on all 384 channels which are spread across 4 shanks.
Our question is, does the fact that the geometry file have a single affect the kilosorting? We assume so but we wanted to double check. Do we have to create our own geometry file for 4-shank Neuropixels 2.0? Are there any available .mat files that have multi-shank Neuropixels 2.0 geometries.
Thank you!
Yes, you need to create your own probe layout for a 4-shank probe. For Neuropixels, you can use the tool here to export from a spikeglx .meta file: https://github.com/jenniferColonell/SGLXMetaToCoords. You can also check the Kilosort4 documentation for instructions on creating a custom probe file: https://kilosort.readthedocs.io/en/latest/tutorials/make_probe.html.
