A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo

  1. Pierre Yger
  2. Giulia LB Spampinato
  3. Elric Esposito
  4. Baptiste Lefebvre
  5. Stéphane Deny
  6. Christophe Gardella
  7. Marcel Stimberg
  8. Florian Jetter
  9. Guenther Zeck
  10. Serge Picaud
  11. Jens Duebel
  12. Olivier Marre  Is a corresponding author
  1. Institut de la Vision - INSERM URMS 968, France
  2. 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

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Pierre Yger

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  2. Giulia LB Spampinato

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  3. Elric Esposito

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  4. Baptiste Lefebvre

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  5. Stéphane Deny

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  6. Christophe Gardella

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3204-9012
  7. Marcel Stimberg

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2648-4790
  8. Florian Jetter

    Neurophysics group, The Natural and Medical Sciences Institute, Reutlingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  9. Guenther Zeck

    Neurophysics group, The Natural and Medical Sciences Institute, Reutlingen, Germany
    Competing interests
    The authors declare that no competing interests exist.
  10. Serge Picaud

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  11. Jens Duebel

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    Competing interests
    The authors declare that no competing interests exist.
  12. Olivier Marre

    Physiology and Information Processing, Institut de la Vision - INSERM URMS 968, Paris, France
    For correspondence
    olivier.marre@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0090-6190

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.

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)

Reviewing Editor

  1. David Kleinfeld, University of California, San Diego, United States

Publication history

  1. Received: December 20, 2017
  2. Accepted: March 19, 2018
  3. Accepted Manuscript published: March 20, 2018 (version 1)
  4. 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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  1. Pierre Yger
  2. Giulia LB Spampinato
  3. Elric Esposito
  4. Baptiste Lefebvre
  5. Stéphane Deny
  6. Christophe Gardella
  7. Marcel Stimberg
  8. Florian Jetter
  9. Guenther Zeck
  10. Serge Picaud
  11. Jens Duebel
  12. Olivier Marre
(2018)
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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