SpikeInterface, a unified framework for spike sorting

By Alessio Paolo Buccino, C. Hurwitz, Samuel Garcia, Jeremy F. Magland, Joshua H. Siegle, Roger Hurwitz, Matthias H Hennig. bioRxiv, 2019

324 citations recorded by the source corpus.

Given the importance of understanding single-neuron activity, much development has been directed towards improving the performance and automation of spike sorting. These developments, however, introduce new challenges, such as file format incompatibility and reduced interoperability, that hinder benchmarking and preclude reproducible analysis. To address these limitations, we developed SpikeInterface, a Python framework designed to unify preexisting spike sorting technologies into a single codebase and to standardize extracellular data file operations. With a few lines of code and regardless of the underlying data format, researchers can: run, compare, and benchmark most modern spike sorting algorithms; pre-process, post-process, and visualize extracellular datasets; validate, curate, and export sorting outputs; and more. In this paper, we provide an overview of SpikeInterface and, with applications to both real and simulated extracellular datasets, demonstrate how it can improve the accessibility, reliability, and reproducibility of spike sorting in preparation for the widespread use of large-scale electrophysiology.

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

View Paper: https://www.semanticscholar.org/paper/e51bf1e59e4b96777f33c7045a6d697f647dd65a

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