Efficient and reliable spike sorting from neural recordings with UMAP-based unsupervised nonlinear dimensionality reduction

Daniel Suárez-Barrera, Lucas Bayones, Norberto Encinas-Rodríguez, Sergio Parra, Viktor Monroy, Sebastián Pujalte, Bernardo Andrade-Ortega, Héctor Díaz, Manuel Alvarez, Antonio Zainos, Alessio Franci and Román Rossi-Pool

PLOS Biology, 2025, vol. 23, issue 11, 1-28

Abstract: Spike sorting is one of the cornerstones of extracellular electrophysiology. By leveraging advanced signal processing and data analysis techniques, spike sorting makes it possible to detect, isolate, and map single neuron spiking activity from both in vivo and in vitro extracellular electrophysiological recordings. A crucial step of any spike sorting pipeline is to reduce the dimensionality of the recorded spike waveform data. Reducing the dimensionality of the processed data is a near-universal practice, fundamentally motivated by the use of clustering algorithms responsible to detect, isolate, and sort the recorded putative neurons. In this paper, we propose and illustrate on both synthetic and experimental data that employing the nonlinear dimensionality reduction technique Uniform Manifold Approximation and Projection (UMAP) can drastically improve the performance, efficiency, robustness, and scalability of spike sorting pipelines without increasing their computational cost. We show how replacing the linear or ad hoc, expert-defined, supervised nonlinear dimensionality reduction methods commonly used in spike sorting pipelines by the unsupervised, mathematically grounded, nonlinear dimensionality reduction method provided by UMAP drastically increases the number of correctly sorted neurons, makes the identification of quieter, seldom spiking neurons more reliable, enables deeper and more precise explorations and analysis of the neural code, and paves new ways toward more efficient and end-to-end automatable spike sorting pipelines of large-scale extracellular neural recording as those produced by high-density multielectrode arrays.Spike sorting makes it possible to detect and isolate single-neuron spiking activity from extracellular electrophysiological recordings. This study shows that replacing traditional spike-sorting methods with UMAP, a nonlinear unsupervised approach, enhances spike sorting accuracy, efficiency, and scalability, enabling reliable detection of rarely spiking neurons and paving the way for automated analysis of large-scale electrophysiological data.

Date: 2025
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Persistent link: https://EconPapers.repec.org/RePEc:plo:pbio00:3003527

DOI: 10.1371/journal.pbio.3003527

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