Spike sorting curation - cortex-lab/neuropixels GitHub Wiki

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 see an example manual curation workflow here.

Quality metrics

Manual curation is inherently noisy and biased. Thankfully, most of manual curation can be automated with quality metrics, although we currently don't have any solutions to split or merge spikes automatically. Several toolboxes exist to compute these quality metrics:

• bombcell from the Carandini & Harris lab, in MATLAB. See the wiki.
• sortingQuality from Nick Steinmetz, in MATLAB.
• ecephys_spike_sorting from the Allen Institute, in Python.
• ibl brainbox metrics from the International Brain lab, in Python.