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Reproducibility of in-vivo electrophysiological measurements in mice

Laboratory International Brain, Kush Banga, Julius Benson, Jai Bhagat, Dan Biderman, Daniel Birman, Niccolò Bonacchi, Sebastian A Bruijns, Robert AA Campbell, Matteo Carandini, Gaëlle A Chapuis, View ORCID ProfileAnne K Churchland, View ORCID ProfileM Felicia Davatolhagh, Hyun Dong Lee, Mayo Faulkner, Berk Gerçek, Fei Hu, Julia Huntenburg, Cole Hurwitz, View ORCID ProfileAnup Khanal, Christopher Krasniak, View ORCID ProfileGuido T Meijer, Nathaniel J Miska, Zeinab Mohammadi, Jean-Paul Noel, Liam Paninski, Alejandro Pan-Vazquez, View ORCID ProfileNoam Roth, Michael Schartner, Karolina Socha, Nicholas A Steinmetz, Karel Svoboda, View ORCID ProfileMarsa Taheri, View ORCID ProfileAnne E Urai, Miles Wells, Steven J West, Matthew R Whiteway, Olivier Winter, Ilana B Witten
doi: https://doi.org/10.1101/2022.05.09.491042
1Max-Planck-Institute, Tübingen, Germany;
Kush Banga
7University College London, UK;
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Julius Benson
11New York University, NY, USA;
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Jai Bhagat
7University College London, UK;
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Dan Biderman
3Columbia University, NY, USA;
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Daniel Birman
4University of Washington, WA, USA;
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Niccolò Bonacchi
2Champalimaud Foundation, Lisbon, Portugal;
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Sebastian A Bruijns
1Max-Planck-Institute, Tübingen, Germany;
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Robert AA Campbell
13Sainsbury Wellcome Center, London, UK;
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Matteo Carandini
7University College London, UK;
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Gaëlle A Chapuis
5University of Geneva, Switzerland;
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Anne K Churchland
6University of California Los Angeles, USA;
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  • For correspondence: anne.churchland@internationalbrainlab.org
M Felicia Davatolhagh
6University of California Los Angeles, USA;
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Hyun Dong Lee
3Columbia University, NY, USA;
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Mayo Faulkner
7University College London, UK;
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Berk Gerçek
5University of Geneva, Switzerland;
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Fei Hu
9University of California, Berkeley, USA;
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Julia Huntenburg
2Champalimaud Foundation, Lisbon, Portugal;
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Cole Hurwitz
3Columbia University, NY, USA;
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Anup Khanal
6University of California Los Angeles, USA;
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Christopher Krasniak
10Cold Spring Harbor Laboratory, NY, USA;
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Guido T Meijer
2Champalimaud Foundation, Lisbon, Portugal;
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Nathaniel J Miska
7University College London, UK;
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Zeinab Mohammadi
12Princeton University, NJ, USA;
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Jean-Paul Noel
11New York University, NY, USA;
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Liam Paninski
3Columbia University, NY, USA;
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Alejandro Pan-Vazquez
12Princeton University, NJ, USA;
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Noam Roth
4University of Washington, WA, USA;
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Michael Schartner
2Champalimaud Foundation, Lisbon, Portugal;
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Karolina Socha
7University College London, UK;
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Nicholas A Steinmetz
4University of Washington, WA, USA;
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Karel Svoboda
14Allen Institute for Neural Dynamics WA, USA
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Marsa Taheri
6University of California Los Angeles, USA;
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Anne E Urai
8Leiden University, The Netherlands;
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Miles Wells
7University College London, UK;
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Steven J West
7University College London, UK;
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Matthew R Whiteway
3Columbia University, NY, USA;
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Olivier Winter
2Champalimaud Foundation, Lisbon, Portugal;
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Ilana B Witten
12Princeton University, NJ, USA;
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Abstract

Understanding whole-brain-scale electrophysiological recordings relies on the collective work of many labs. Because two labs recording from the same region can reach different conclusions, it is critical to quantify and control features that hinder reproducibility. To address this, we formed a multi-lab collaboration using a shared, open-source behavioral task and experimental apparatus. Experimenters in ten laboratories repeatedly targeted Neuropixels probes to the same location (spanning secondary visual areas, hippocampus, and thalamus) in mice making decisions. After applying quality-control criteria, we found that neuronal yield, firing rates, spike amplitudes, and task-modulated neuronal activity were largely reproducible across laboratories. To quantify variance in neural activity explained by task variables, we developed a multi-task neural network model, and found that within- and between-lab random effects captured by this model were comparable. Our results demonstrate that across-lab standardization can produce reproducible results from large-scale Neuropixels recordings. Our dataset, code, and protocols are openly accessible.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Updated author list and figures/content (e.g., added RIGOR guidelines).

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 18, 2023.
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Reproducibility of in-vivo electrophysiological measurements in mice
Laboratory International Brain, Kush Banga, Julius Benson, Jai Bhagat, Dan Biderman, Daniel Birman, Niccolò Bonacchi, Sebastian A Bruijns, Robert AA Campbell, Matteo Carandini, Gaëlle A Chapuis, Anne K Churchland, M Felicia Davatolhagh, Hyun Dong Lee, Mayo Faulkner, Berk Gerçek, Fei Hu, Julia Huntenburg, Cole Hurwitz, Anup Khanal, Christopher Krasniak, Guido T Meijer, Nathaniel J Miska, Zeinab Mohammadi, Jean-Paul Noel, Liam Paninski, Alejandro Pan-Vazquez, Noam Roth, Michael Schartner, Karolina Socha, Nicholas A Steinmetz, Karel Svoboda, Marsa Taheri, Anne E Urai, Miles Wells, Steven J West, Matthew R Whiteway, Olivier Winter, Ilana B Witten
bioRxiv 2022.05.09.491042; doi: https://doi.org/10.1101/2022.05.09.491042
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Reproducibility of in-vivo electrophysiological measurements in mice
Laboratory International Brain, Kush Banga, Julius Benson, Jai Bhagat, Dan Biderman, Daniel Birman, Niccolò Bonacchi, Sebastian A Bruijns, Robert AA Campbell, Matteo Carandini, Gaëlle A Chapuis, Anne K Churchland, M Felicia Davatolhagh, Hyun Dong Lee, Mayo Faulkner, Berk Gerçek, Fei Hu, Julia Huntenburg, Cole Hurwitz, Anup Khanal, Christopher Krasniak, Guido T Meijer, Nathaniel J Miska, Zeinab Mohammadi, Jean-Paul Noel, Liam Paninski, Alejandro Pan-Vazquez, Noam Roth, Michael Schartner, Karolina Socha, Nicholas A Steinmetz, Karel Svoboda, Marsa Taheri, Anne E Urai, Miles Wells, Steven J West, Matthew R Whiteway, Olivier Winter, Ilana B Witten
bioRxiv 2022.05.09.491042; doi: https://doi.org/10.1101/2022.05.09.491042

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