1. Neuroscience
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State-dependent geometry of population activity in rat auditory cortex

  1. Dmitry Kobak
  2. Jose L Pardo-Vazquez  Is a corresponding author
  3. Mafalda Valente
  4. Christian K Machens
  5. Alfonso Renart  Is a corresponding author
  1. Champalimaud Centre for the Unknown, Portugal
Research Article
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Cite this article as: eLife 2019;8:e44526 doi: 10.7554/eLife.44526

Abstract

The accuracy of the neural code depends on the relative embedding of signal and noise in the activity of neural populations. Despite a wealth of theoretical work on population codes, there are few empirical characterisations of the high-dimensional signal and noise subspaces. We studied the geometry of population codes in the rat auditory cortex across brain states along the activation-inactivation continuum, using sounds varying in difference and mean level across the ears. As the cortex becomes more activated, single-hemisphere populations go from preferring contralateral loud sounds to a symmetric preference across lateralisations and intensities, gain-modulation effectively disappears, and the signal and noise subspaces become approximately orthogonal to each other and to the direction corresponding to global activity modulations. Level-invariant decoding of sound lateralisation also becomes possible in the active state. Our results provide an empirical foundation for the geometry and state-dependence of cortical population codes.

Data availability

The full Matlab code for the analysis is located at https://github.com/dkobak/a1geometry. We made the spike count data (spike counts for each neuron for each stimulus presentation from −50 ms to 150 ms in 50 ms bins) available in the same repository. This allows most of our figures to be reproduced. The complete dataset that was collected, including spike time data not analysed here, is available upon reasonable request to the corresponding author.

Article and author information

Author details

  1. Dmitry Kobak

    Champalimaud Neuroscience Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5639-7209
  2. Jose L Pardo-Vazquez

    Circuit Dynamics and Computation Laboratory, Champalimaud Centre for the Unknown, Lisboa, Portugal
    For correspondence
    jose.pardovazquez@neuro.fchampalimaud.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4623-2440
  3. Mafalda Valente

    Champalimaud Neuroscience Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
    Competing interests
    The authors declare that no competing interests exist.
  4. Christian K Machens

    Champalimaud Neuroscience Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1717-1562
  5. Alfonso Renart

    Champalimaud Neuroscience program, Champalimaud Centre for the Unknown, Lisboa, Portugal
    For correspondence
    alfonso.renart@neuro.fchampalimaud.org
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7916-9930

Funding

Fundacao Bial (389/14)

  • Dmitry Kobak

EU FP7 grant (ICT-2011-9-600925)

  • Alfonso Renart

German Ministry of Education and Research (FKZ 01GQ1601)

  • Dmitry Kobak

HFSP postdoctoral fellowship (LT 000442/2012)

  • Jose L Pardo-Vazquez

Fundacao para a Ciencia e a Tecnologia

  • Mafalda Valente

Champalimaud Foundation

  • Christian K Machens
  • Alfonso Renart

Simons Collaboration on the Global Brain (543009)

  • Christian K Machens

National Institutes of Health (U01 NS094288)

  • Christian K Machens

Marie Curie Career Integration Grant (PCIG11-GA-2012-322339)

  • Alfonso Renart

HFSP Young Investigator Award (RGY0089)

  • Alfonso Renart

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All procedures were carried out in accordance with European Union Directive 86/609/EEC and approved by Direçao-Geral de Veterinaria.

Reviewing Editor

  1. Emilio Salinas, Wake Forest School of Medicine, United States

Publication history

  1. Received: December 19, 2018
  2. Accepted: April 7, 2019
  3. Accepted Manuscript published: April 10, 2019 (version 1)
  4. Version of Record published: April 30, 2019 (version 2)

Copyright

© 2019, Kobak 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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