. 2023 Mar;20(3):403-407.

doi: 10.1038/s41592-022-01742-6. Epub 2023 Mar 2.

A modular architecture for organizing, processing and sharing neurophysiology data

International Brain Laboratory; Niccolò Bonacchi¹, Gaelle A Chapuis^{2

3}, Anne K Churchland⁴, Eric E J DeWitt¹, Mayo Faulkner², Kenneth D Harris⁵, Julia M Huntenburg⁶, Max Hunter², Inês C Laranjeira¹, Cyrille Rossant², Maho Sasaki⁷, Michael M Schartner¹, Shan Shen⁷, Nicholas A Steinmetz⁸, Edgar Y Walker⁷, Steven J West⁹, Olivier Winter¹, Miles J Wells²

Collaborators, Affiliations

Collaborators

International Brain Laboratory:
Luigi Acerbi, Valeria Aguillon-Rodriguez, Mandana Ahmadi, Jaweria Amjad, Dora Angelaki, Jaime Arlandis, Zoe C Ashwood, Kush Banga, Hailey Barrell, Hannah M Bayer, Julius Benson, Brandon Benson, Jai Bhagat, Daniel Birman, Kcenia Bougrova, Julien Boussard, Sebastian A Bruijns, Matteo Carandini, Joana Catarino, Fanny Cazettes, Yang Dan, Felicia Davatolagh, Peter Dayan, Sophie Denève, Ling Liang Dong, Tatiana Engel, Michele Fabbri, Ila Fiete, Charles Findling, Laura Freitas-Silva, Surya Ganguli, Berk Gercek, Naureen Ghani, Ivan Gordeliy, Laura M Haetzel, Michael Hausser, Naoki Hiratani, Sonja Hofer, Fei Hu, Felix Huber, Cole Hurwitz, Anup Khanal, Christopher S Krasniak, Sanjukta Krishnagopal, Michael Krumin, Christopher Langdon, Peter Latham, Petrina Lau, Hyun Lee, Ari Liu, Zachary F Mainen, Hernando Martinez Vergara, Conor Mcgrory, Brenna McMannon, Guido T Meijer, Maxwell Melin, Leenoy Meshulam, Nathaniel J Miska, Catalin Mitelut, Zeinab Mohammadi, Thomas Mrsic-Flogel, Masayoshi Murakami, Jean-Paul Noel, Kai Nylund, Alex Pan Vazquez, Liam Paninski, Alberto Pezzotta, Samuel Picard, Jonathan W Pillow, Alexandre Pouget, Noam Roth, Nicholas A Roy, Kamron Saniee, Rylan Schaeffer, Yanliang Shi, Karolina Z Socha, Cristian Soitu, Karel Svoboda, Marsa Taheri, Charline Tessereau, Anne E Urai, Erdem Varol, Miles J Wells, Matthew R Whiteway, Charles Windolf, Ilana Witten, Lauren E Wool, Anthony M Zador

Affiliations

¹ Champalimaud Center for the Unknown, Lisboa, Portugal.
² Institute of Neurology, University College London, London, UK.
³ Department of Basic Neuroscience, University of Geneva, Geneva, Switzerland.
⁴ Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA.
⁵ Institute of Neurology, University College London, London, UK. kenneth.harris@ucl.ac.uk.
⁶ Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
⁷ DataJoint, Houston, TX, USA.
⁸ Department of Biological Structure, University of Washington, Seattle, WA, USA.
⁹ Sainsbury-Wellcome Centre, University College London, London, UK.

PMID: 36864199
PMCID: PMC7614641
DOI: 10.1038/s41592-022-01742-6

A modular architecture for organizing, processing and sharing neurophysiology data

International Brain Laboratory et al. Nat Methods. 2023 Mar.

. 2023 Mar;20(3):403-407.

doi: 10.1038/s41592-022-01742-6. Epub 2023 Mar 2.

Authors

Collaborators

International Brain Laboratory:
Luigi Acerbi, Valeria Aguillon-Rodriguez, Mandana Ahmadi, Jaweria Amjad, Dora Angelaki, Jaime Arlandis, Zoe C Ashwood, Kush Banga, Hailey Barrell, Hannah M Bayer, Julius Benson, Brandon Benson, Jai Bhagat, Daniel Birman, Kcenia Bougrova, Julien Boussard, Sebastian A Bruijns, Matteo Carandini, Joana Catarino, Fanny Cazettes, Yang Dan, Felicia Davatolagh, Peter Dayan, Sophie Denève, Ling Liang Dong, Tatiana Engel, Michele Fabbri, Ila Fiete, Charles Findling, Laura Freitas-Silva, Surya Ganguli, Berk Gercek, Naureen Ghani, Ivan Gordeliy, Laura M Haetzel, Michael Hausser, Naoki Hiratani, Sonja Hofer, Fei Hu, Felix Huber, Cole Hurwitz, Anup Khanal, Christopher S Krasniak, Sanjukta Krishnagopal, Michael Krumin, Christopher Langdon, Peter Latham, Petrina Lau, Hyun Lee, Ari Liu, Zachary F Mainen, Hernando Martinez Vergara, Conor Mcgrory, Brenna McMannon, Guido T Meijer, Maxwell Melin, Leenoy Meshulam, Nathaniel J Miska, Catalin Mitelut, Zeinab Mohammadi, Thomas Mrsic-Flogel, Masayoshi Murakami, Jean-Paul Noel, Kai Nylund, Alex Pan Vazquez, Liam Paninski, Alberto Pezzotta, Samuel Picard, Jonathan W Pillow, Alexandre Pouget, Noam Roth, Nicholas A Roy, Kamron Saniee, Rylan Schaeffer, Yanliang Shi, Karolina Z Socha, Cristian Soitu, Karel Svoboda, Marsa Taheri, Charline Tessereau, Anne E Urai, Erdem Varol, Miles J Wells, Matthew R Whiteway, Charles Windolf, Ilana Witten, Lauren E Wool, Anthony M Zador

Affiliations

¹ Champalimaud Center for the Unknown, Lisboa, Portugal.
² Institute of Neurology, University College London, London, UK.
³ Department of Basic Neuroscience, University of Geneva, Geneva, Switzerland.
⁴ Department of Neurobiology, University of California, Los Angeles, Los Angeles, CA, USA.
⁵ Institute of Neurology, University College London, London, UK. kenneth.harris@ucl.ac.uk.
⁶ Max Planck Institute for Biological Cybernetics, Tübingen, Germany.
⁷ DataJoint, Houston, TX, USA.
⁸ Department of Biological Structure, University of Washington, Seattle, WA, USA.
⁹ Sainsbury-Wellcome Centre, University College London, London, UK.

PMID: 36864199
PMCID: PMC7614641
DOI: 10.1038/s41592-022-01742-6

Abstract

We describe an architecture for organizing, integrating and sharing neurophysiology data within a single laboratory or across a group of collaborators. It comprises a database linking data files to metadata and electronic laboratory notes; a module collecting data from multiple laboratories into one location; a protocol for searching and sharing data and a module for automatic analyses that populates a website. These modules can be used together or individually, by single laboratories or worldwide collaborations.

PubMed Disclaimer

Conflict of interest statement

Competing Interests

The authors declare the following competing interests: E.Y.W. hold equity ownership in VathesLLC which provides development and consulting for the framework (DataJoint) described in this work. The remaining authors declare no competing interests

Figures

**Figure 1**
IBL data architecture. The “Alyx” database links colony management and electronic lab notebook metadata to experimental data files on a lab data server. Data from multiple labs are integrated on a central server, and distributed job management coordinates pre-processing on lab servers. Data are accessed via the Open Neurophysiology Environment (ONE) protocol, with adaptors for Neurodata Without Borders (NWB)^, and DataJoint, which also performs pipelined analyses for automatic display on a website.

See this image and copyright information in PMC

References

1. The International Brain Laboratory et al. Standardized and reproducible measurement of decision-making in mice. eLife. 2021;10:e63711. - PMC - PubMed
1. Pachitariu M, et al. Suite2p: beyond 10,000 neurons with standard two-photon microscopy. bioRxiv. 2017:061507. doi: 10.1101/061507. - DOI
1. Mathis A, et al. DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nat Neurosci. 2018;21:1281–1289. - PubMed
1. Giovannucci A, et al. CaImAn an open source tool for scalable calcium imaging data analysis. eLife. 2019;8:e38173. - PMC - PubMed
1. Vogelstein JT, et al. Fast nonnegative deconvolution for spike train inference from population calcium imaging. J Neurophysiol. 2010;104:3691–704. - PMC - PubMed

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A modular architecture for organizing, processing and sharing neurophysiology data

Collaborators

Affiliations

A modular architecture for organizing, processing and sharing neurophysiology data

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources