Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy

View ORCID ProfileMichael W. Reimann, View ORCID ProfileSirio Bolaños-Puchet, View ORCID ProfileJean-Denis Courcol, View ORCID ProfileDaniela Egas Santander, View ORCID ProfileAlexis Arnaudon, Benoît Coste, Fabien Delalondre, View ORCID ProfileThomas Delemontex, View ORCID ProfileAdrien Devresse, Hugo Dictus, Alexander Dietz, View ORCID ProfileAndrás Ecker, View ORCID ProfileCyrille Favreau, View ORCID ProfileGianluca Ficarelli, View ORCID ProfileMike Gevaert, View ORCID ProfileJoni Herttuainen, View ORCID ProfileJames B. Isbister, View ORCID ProfileLida Kanari, Daniel Keller, View ORCID ProfileJames King, View ORCID ProfilePramod Kumbhar, View ORCID ProfileSamuel Lapere, View ORCID ProfileJānis Lazovskis, View ORCID ProfileHuanxiang Lu, Nicolas Ninin, Fernando Pereira, View ORCID ProfileJudit Planas, View ORCID ProfileChristoph Pokorny, View ORCID ProfileJuan Luis Riquelme, View ORCID ProfileArmando Romani, View ORCID ProfileYing Shi, View ORCID ProfileJason P. Smith, Vishal Sood, Mohit Srivastava, View ORCID ProfileWerner Van Geit, View ORCID ProfileLiesbeth Vanherpe, View ORCID ProfileMatthias Wolf, View ORCID ProfileRan Levi, View ORCID ProfileKathryn Hess, Felix Schürmann, View ORCID ProfileEilif B. Muller, View ORCID ProfileSrikanth Ramaswamy, View ORCID ProfileHenry Markram
doi: https://doi.org/10.1101/2022.08.11.503144
Michael W. Reimann
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Michael W. Reimann
  • For correspondence: michael.reimann@epfl.ch
Sirio Bolaños-Puchet
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sirio Bolaños-Puchet
Jean-Denis Courcol
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jean-Denis Courcol
Daniela Egas Santander
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Daniela Egas Santander
Alexis Arnaudon
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Alexis Arnaudon
Benoît Coste
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fabien Delalondre
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Thomas Delemontex
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Thomas Delemontex
Adrien Devresse
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Adrien Devresse
Hugo Dictus
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alexander Dietz
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
András Ecker
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for András Ecker
Cyrille Favreau
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Cyrille Favreau
Gianluca Ficarelli
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Gianluca Ficarelli
Mike Gevaert
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Mike Gevaert
Joni Herttuainen
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Joni Herttuainen
James B. Isbister
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for James B. Isbister
Lida Kanari
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Lida Kanari
Daniel Keller
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
James King
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for James King
Pramod Kumbhar
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Pramod Kumbhar
Samuel Lapere
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Samuel Lapere
Jānis Lazovskis
3Riga Business School, Riga Technical University, Riga, Latvia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jānis Lazovskis
Huanxiang Lu
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Huanxiang Lu
Nicolas Ninin
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fernando Pereira
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Judit Planas
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Judit Planas
Christoph Pokorny
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christoph Pokorny
Juan Luis Riquelme
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Juan Luis Riquelme
Armando Romani
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Armando Romani
Ying Shi
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ying Shi
Jason P. Smith
4Nottingham Trent University, Nottingham, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jason P. Smith
Vishal Sood
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mohit Srivastava
5ELKH-University of Debrecen, Neuroscience Research Group, Hungary
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Werner Van Geit
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Werner Van Geit
Liesbeth Vanherpe
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Liesbeth Vanherpe
Matthias Wolf
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Matthias Wolf
Ran Levi
6University of Aberdeen, Aberdeen, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Ran Levi
Kathryn Hess
7Laboratory for Topology and Neuroscience (UPHESS), Brain Mind Institute, School of Life Sciences, École polytechnique fédérale de Lausanne (EPFL), Lausanne, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Kathryn Hess
Felix Schürmann
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Eilif B. Muller
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Eilif B. Muller
Srikanth Ramaswamy
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
2Neural Circuits Laboratory, Newcastle University, UK
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Srikanth Ramaswamy
  • For correspondence: michael.reimann@epfl.ch
Henry Markram
1Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL), Campus Biotech, Geneva, Switzerland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Henry Markram
  • For correspondence: michael.reimann@epfl.ch
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Data/Code
  • Preview PDF
Loading

Abstract

The function of the neocortex is fundamentally determined by its repeating microcircuit motif, but also by its rich, interregional connectivity. We present a data-driven computational model of the anatomy of non-barrel primary somatosensory cortex of juvenile rat, integrating whole-brain scale data while providing cellular and subcellular specificity. The model consists of 4.2 million morphologically detailed neurons, placed in a digital brain atlas. They are connected by 14.2 billion synapses, comprising local, long-range and extrinsic connectivity. We delineated the limits of determining connectivity from anatomy, finding that it reproduces the targeting of PV+ and VIP+ interneurons only with explicitly added specificity, but the one of Sst+ neurons even without. Globally, connectivity was characterized by local clusters tied together through hub neurons in layer 5, demonstrating how local and interegional connectivity are complicit, inseparable networks. A 211,712 neuron subvolume of the model has been made freely and openly available to the community.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵8 Co-lead authors

  • ↵9 Co-senior authors

  • Tightened the manuscript. Added new results comparing the model to electron microscopy.

  • https://zenodo.org/record/6906785

  • https://doi.org/10.5281/zenodo.6906785

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
Back to top
PreviousNext
Posted July 29, 2023.
Download PDF
Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy
Michael W. Reimann, Sirio Bolaños-Puchet, Jean-Denis Courcol, Daniela Egas Santander, Alexis Arnaudon, Benoît Coste, Fabien Delalondre, Thomas Delemontex, Adrien Devresse, Hugo Dictus, Alexander Dietz, András Ecker, Cyrille Favreau, Gianluca Ficarelli, Mike Gevaert, Joni Herttuainen, James B. Isbister, Lida Kanari, Daniel Keller, James King, Pramod Kumbhar, Samuel Lapere, Jānis Lazovskis, Huanxiang Lu, Nicolas Ninin, Fernando Pereira, Judit Planas, Christoph Pokorny, Juan Luis Riquelme, Armando Romani, Ying Shi, Jason P. Smith, Vishal Sood, Mohit Srivastava, Werner Van Geit, Liesbeth Vanherpe, Matthias Wolf, Ran Levi, Kathryn Hess, Felix Schürmann, Eilif B. Muller, Srikanth Ramaswamy, Henry Markram
bioRxiv 2022.08.11.503144; doi: https://doi.org/10.1101/2022.08.11.503144
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy
Michael W. Reimann, Sirio Bolaños-Puchet, Jean-Denis Courcol, Daniela Egas Santander, Alexis Arnaudon, Benoît Coste, Fabien Delalondre, Thomas Delemontex, Adrien Devresse, Hugo Dictus, Alexander Dietz, András Ecker, Cyrille Favreau, Gianluca Ficarelli, Mike Gevaert, Joni Herttuainen, James B. Isbister, Lida Kanari, Daniel Keller, James King, Pramod Kumbhar, Samuel Lapere, Jānis Lazovskis, Huanxiang Lu, Nicolas Ninin, Fernando Pereira, Judit Planas, Christoph Pokorny, Juan Luis Riquelme, Armando Romani, Ying Shi, Jason P. Smith, Vishal Sood, Mohit Srivastava, Werner Van Geit, Liesbeth Vanherpe, Matthias Wolf, Ran Levi, Kathryn Hess, Felix Schürmann, Eilif B. Muller, Srikanth Ramaswamy, Henry Markram
bioRxiv 2022.08.11.503144; doi: https://doi.org/10.1101/2022.08.11.503144

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Neuroscience
Subject Areas
All Articles
  • Animal Behavior and Cognition (4654)
  • Biochemistry (10299)
  • Bioengineering (7614)
  • Bioinformatics (26189)
  • Biophysics (13446)
  • Cancer Biology (10620)
  • Cell Biology (15333)
  • Clinical Trials (138)
  • Developmental Biology (8452)
  • Ecology (12754)
  • Epidemiology (2067)
  • Evolutionary Biology (16763)
  • Genetics (11356)
  • Genomics (15400)
  • Immunology (10548)
  • Microbiology (25041)
  • Molecular Biology (10152)
  • Neuroscience (54096)
  • Paleontology (398)
  • Pathology (1655)
  • Pharmacology and Toxicology (2877)
  • Physiology (4314)
  • Plant Biology (9196)
  • Scientific Communication and Education (1579)
  • Synthetic Biology (2541)
  • Systems Biology (6752)
  • Zoology (1452)