Kilosort: realtime spike-sorting for extracellular electrophysiology with hundreds of channels
By Marius Pachitariu, Nicholas A. Steinmetz, Shabnam N. Kadir, Matteo Carandini, Harris Kenneth D.. bioRxiv, 2016
668 citations recorded by the source corpus.
Advances in silicon probe technology mean that in vivo electrophysiological recordings from hundreds of channels will soon become commonplace. To interpret these recordings we need fast, scalable and accurate methods for spike sorting, whose output requires minimal time for manual curation. Here we introduce Kilosort, a spike sorting framework that meets these criteria, and show that it allows rapid and accurate sorting of large-scale in vivo data. Kilosort models the recorded voltage as a sum of template waveforms triggered on the spike times, allowing overlapping spikes to be identified and resolved. Rapid processing is achieved thanks to a novel low-dimensional approximation for the spatiotemporal distribution of each template, and to batch-based optimization on GPUs. A novel post-clustering merging step based on the continuity of the templates substantially reduces the requirement for subsequent manual curation operations. We compare Kilosort to an established algorithm on data obtained from 384-channel electrodes, and show superior performance, at much reduced processing times. Data from 384-channel electrode arrays can be processed in approximately realtime. Kilosort is an important step towards fully automated spike sorting of multichannel electrode recordings, and is freely available (github.com/cortex-lab/Kilosort).
Subfields: Cellular and Molecular Neuroscience, Cognitive Neuroscience, Electrical and Electronic Engineering
View Paper: https://www.semanticscholar.org/paper/6977fc2177b7d3b987ce29d7f97e9bbd1a92cc2a
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In Cellular and Molecular Neuroscience
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Citations in the corpus
- Spike sorting with Kilosort4 (2024, positive): “Either ground-truth units, as acquired above, or manually curated units are used 6,14,45 .”
- Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology (2017, methodology): “(2) The Binary Format saves continuous data as flat files of int16s, and is used by the spike sorting package Kilosort [12].”