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SpikeForest: reproducible web-facing ground-truth validation of automated neural spike sorters

View ORCID ProfileJeremy F. Magland, James J. Jun, Elizabeth Lovero, Alexander J. Morley, Cole L. Hurwitz, Alessio P. Buccino, Samuel Garcia, Alex H. Barnett
doi: https://doi.org/10.1101/2020.01.14.900688
Jeremy F. Magland
Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
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  • For correspondence: jmagland@flatironinstitute.org
James J. Jun
Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
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Elizabeth Lovero
Scientific Computing Core, Flatiron Institute, New York, NY, USA
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Alexander J. Morley
Medical Research Council Brain Network Dynamics Unit, University of Oxford, Oxford, United Kingdom
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Cole L. Hurwitz
School of Informatics, University of Edinburgh, United Kingdom
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Alessio P. Buccino
Centre for Integrative Neuroplasticity (CINPLA), University of Oslo, Oslo, Norway
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Samuel Garcia
Centre de Recherche en Neuroscience de Lyon, CNRS, Lyon, France
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Alex H. Barnett
Center for Computational Mathematics, Flatiron Institute, New York, NY, USA
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Abstract

Spike sorting is a crucial but time-intensive step in electrophysiological studies of neuronal activity. While there are many popular software packages for spike sorting, there is little consensus about which are the most accurate under different experimental conditions. SpikeForest is an open-source and reproducible software suite that benchmarks the performance of automated spike sorting algorithms across an extensive, curated database of electrophysiological recordings with ground truth, displaying results interactively on a continuously-updating website. With contributions from over a dozen participating laboratories, our database currently comprises 650 recordings (1.3 TB total size) with around 35,000 ground-truth units. These data include extracellular recordings paired with intracellular voltages, state-of-the-art simulated recordings, and hybrid synthetic datasets. Ten of the most frequently used modern spike sorting codes are wrapped under a common Python framework and evaluated on a compute cluster using an automated pipeline. SpikeForest validates and documents community progress in automated spike sorting, and guides neuroscientists to an optimal choice of sorter and parameters for a wide range of probes and brain regions.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted January 14, 2020.
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SpikeForest: reproducible web-facing ground-truth validation of automated neural spike sorters
Jeremy F. Magland, James J. Jun, Elizabeth Lovero, Alexander J. Morley, Cole L. Hurwitz, Alessio P. Buccino, Samuel Garcia, Alex H. Barnett
bioRxiv 2020.01.14.900688; doi: https://doi.org/10.1101/2020.01.14.900688
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SpikeForest: reproducible web-facing ground-truth validation of automated neural spike sorters
Jeremy F. Magland, James J. Jun, Elizabeth Lovero, Alexander J. Morley, Cole L. Hurwitz, Alessio P. Buccino, Samuel Garcia, Alex H. Barnett
bioRxiv 2020.01.14.900688; doi: https://doi.org/10.1101/2020.01.14.900688

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