Spike sorting for large, dense electrode arrays

By Cyrille Rossant, Shabnam N. Kadir, Dan F. M. Goodman, John Schulman, M. Belluscio, Alexander S. Ecker, György Buzsáki, Kenneth D. Harris. Nature Neuroscience, 2015

788 citations recorded by the source corpus.

Developments in microfabrication technology have enabled the production of neural electrode arrays with hundreds of closely spaced recording sites, and electrodes with thousands of sites are under development. These probes in principle allow the simultaneous recording of very large numbers of neurons. However, use of this technology requires the development of techniques for decoding the spike times of the recorded neurons from the raw data captured from the probes. Here we present a set of tools to solve this problem, implemented in a suite of practical, user-friendly, open-source software. We validate these methods on data from the cortex, hippocampus and thalamus of rat, mouse, macaque and marmoset, demonstrating error rates as low as 5%.

Subfields: Cellular and Molecular Neuroscience, Cognitive Neuroscience, Electrical and Electronic Engineering

View Paper: https://www.semanticscholar.org/paper/01fee6f8238b9b54013fc76d6a530cba04059980

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Citations in the corpus

Spike sorting with Kilosort4 (2024, neutral): “Either ground-truth units, as acquired above, or manually curated units are used 6,14,45 .”
A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo (2018, methodology): “of electrodes in vitro and in vivo, because their computation time would increase exponentially with the number of electrodes (Rossant et al., 2016).”
Fast and accurate spike sorting of high-channel count probes with KiloSort (2016, methodology): “Final best results as well as the required number of matches are shown in Figure 3defg (KiloSort vs KlustaKwik 69% vs 60% units with scores above 0.9).”
Challenges and opportunities for large-scale electrophysiology with Neuropixels probes (2018, methodology): “Given this context, careful manual curation of the results of spike sorting algorithms is still critical, and public, open-source software packages have been developed to improve the efficiency of this process [53].”
Neuropixels 2.0: A miniaturized high-density probe for stable, long-term brain recordings (2020, result): “In a subset of recordings we compared these results to results obtained after manual curation of the output using Phy (Rossant et al., 2016).”
Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology (2017, methodology): “(4) Kwik is a deprecated HDF5-based format originally developed for the KlustaKwik suite of spike sorting tools [14].”