Spike_sorting

Due to the high channel count and the need to consider information from many adjacent channels in the sorting of each spike, many existing spike sorting algorithms are insufficient or unusable for data produced by Neuropixels probes.

Automatic spike sorting

Kilosort is an automatic spike sorting algorithm developed for Neuropixels probes that can process the data quickly and accurately. Find the code for Kilosort here, a paper about how Kilosort 1.0 works here, and more information on Kilosort 2.5 here. Kilosort outperformed other tested algorithms in an objective comparison.

A channel map file for using Neuropixels data with Kilosort (if the data were recorded with SpikeGLX, at least) can be found here in this repository.

Manual revision of automatic results

Phy is a gui for manually reviewing and modifying the results of the automatic algorithm. The template-gui has been developed for use with results produced by Kilosort.

See this documentation for a user-friendly guide to spike sorting Neuropixels data, and an example manual curation workflow.

Sorting quality metrics

See ecephys_spike_sorting from the Allen Institute and sortingQuality from the CortexLab for code to calculate some quality metrics, in python and matlab respectively.

Alternatives

Other software that may work well for Neuropixels data includes Spyking Circus and JRCLUST: Janelia Rocket Clust.