A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo
- Institut de la Vision - INSERM URMS 968, France
- The Natural and Medical Sciences Institute, Germany
Abstract
In recent years, multielectrode arrays and large silicon probes have been developed to record simultaneously between hundreds and thousands of electrodes packed with a high density. However, they require novel methods to extract the spiking activity of large ensembles of neurons. Here we developed a new toolbox to sort spikes from these large-scale extracellular data. To validate our method, we performed simultaneous extracellular and loose patch recordings in rodents to obtain 'ground truth' data, where the solution to this sorting problem is known for one cell. The performance of our algorithm was always close to the best expected performance, over a broad range of signal to noise ratios, in vitro and in vivo. The algorithm is entirely parallelized and has been successfully tested on recordings with up to 4225 electrodes. Our toolbox thus offers a generic solution to sort accurately spikes for up to thousands of electrodes.
Data availability
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Ground-Truth data from silicon polytrodesDirectly available for download.
Article and author information
Author details
Christophe Gardella
Funding
Agence Nationale de la Recherche (TRAJECTORY)
- Olivier Marre
European Commission (ERC StG 309776)
- Jens Duebel
National Institutes of Health (U01NS090501)
- Olivier Marre
Foundation Fighting Blindness
- Serge Picaud
Agence Nationale de la Recherche (ANR-14-CE13-0003)
- Pierre Yger
Agence Nationale de la Recherche (ANR-10-LABX-65)
- Serge Picaud
European Commission (FP7-604102)
- Olivier Marre
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- David Kleinfeld, University of California, San Diego, United States
Ethics
Animal experimentation: Experiments were performed in accordance with institutional animal care standards, using protocol (#00847.02) of the Institut de la Vision (Agreement number A751202). The protocol was approved by the Charles Darwin ethic committee (CEEACD/N{degree sign}5)
Version history
- Received: December 20, 2017
- Accepted: March 19, 2018
- Accepted Manuscript published: March 20, 2018 (version 1)
- Version of Record published: April 9, 2018 (version 2)
Copyright
© 2018, Yger et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo
eLife 7:e34518.
https://doi.org/10.7554/eLife.34518
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