P-sort: An open-source software for cerebellar neurophysiology

Ehsan Sedaghat-Nejad, Mohammad Amin Fakharian, Jay Pi, Paul Hage, Yoshiko Kojima, Robi Soetedjo, Shogo Ohmae, Javier F. Medina, Reza Shadmehr

Research output: Contribution to journalArticlepeer-review


Analysis of electrophysiological data from Purkinje cells (P-cells) of the cerebellum presents unique challenges to spike sorting. Complex spikes have waveforms that vary significantly from one event to the next, raising the problem of misidentification. Even when complex spikes are detected correctly, the simple spikes may belong to a different P-cell, raising the danger of misattribution. To address these identification and attribution problems, we wrote an open-source, semiautomated software called P-sort, and then tested it by analyzing data from P-cells recorded in three species: marmosets, macaques, and mice. Like other sorting software, P-sort relies on nonlinear dimensionality reduction to cluster spikes. However, it also uses the statistical relationship between simple and complex spikes to merge disparate clusters and split a single cluster. In comparison with expert manual curation, occasionally P-sort identified significantly more complex spikes, as well as prevented misattribution of clusters. Three existing automatic sorters performed less well, particularly for identification of complex spikes. To improve the development of analysis tools for the cerebellum, we provide labeled data for 313 recording sessions, as well as statistical characteristics of waveforms and firing patterns of P-cells in three species.

Original languageEnglish (US)
Pages (from-to)1055-1075
Number of pages21
JournalJournal of neurophysiology
Issue number4
StatePublished - Oct 2021

ASJC Scopus subject areas

  • Neuroscience(all)
  • Physiology


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