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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.
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 and a paper about how it works 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.
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.
Other software that may work well for Neuropixels data includes Spyking Circus and JRCLUST: Janelia Rocket Clust.
- About Neuropixels and probe types
- Configurations and selecting electrodes
- Equipment List and example setup
- Probe handling/mounting
- Chronic implants
- Probe sharpening
- Probe care
- Planning probe trajectories
- Acquisition software
- Referencing and Grounding
- Gain settings
- Filter settings
- Impedance testing
- Synchronization
- Multiple probes on one computer
- Light artifacts
- Troubleshooting
- Recommended preprocessing
- Spike sorting
- Spike sorting curation
- Other analysis methods, and tutorial for getting started with Neuropixels Phase3 data in matlab
- Identifying tracks in histology