Reconstruction and Simulation of Neocortical Microcircuitry

doi:10.1016/j.cell.2015.09.029

. 2015 Oct 8;163(2):456-92.

doi: 10.1016/j.cell.2015.09.029.

Reconstruction and Simulation of Neocortical Microcircuitry

Henry Markram¹, Eilif Muller², Srikanth Ramaswamy², Michael W Reimann², Marwan Abdellah², Carlos Aguado Sanchez², Anastasia Ailamaki³, Lidia Alonso-Nanclares⁴, Nicolas Antille², Selim Arsever², Guy Antoine Atenekeng Kahou², Thomas K Berger⁵, Ahmet Bilgili², Nenad Buncic², Athanassia Chalimourda², Giuseppe Chindemi², Jean-Denis Courcol², Fabien Delalondre², Vincent Delattre⁵, Shaul Druckmann⁶, Raphael Dumusc², James Dynes², Stefan Eilemann², Eyal Gal⁷, Michael Emiel Gevaert², Jean-Pierre Ghobril⁵, Albert Gidon⁸, Joe W Graham², Anirudh Gupta⁵, Valentin Haenel², Etay Hay⁹, Thomas Heinis¹⁰, Juan B Hernando¹¹, Michael Hines¹², Lida Kanari², Daniel Keller², John Kenyon², Georges Khazen², Yihwa Kim², James G King², Zoltan Kisvarday¹³, Pramod Kumbhar², Sébastien Lasserre¹⁴, Jean-Vincent Le Bé⁵, Bruno R C Magalhães², Angel Merchán-Pérez⁴, Julie Meystre⁵, Benjamin Roy Morrice², Jeffrey Muller², Alberto Muñoz-Céspedes⁴, Shruti Muralidhar⁵, Keerthan Muthurasa², Daniel Nachbaur², Taylor H Newton², Max Nolte², Aleksandr Ovcharenko², Juan Palacios², Luis Pastor¹⁵, Rodrigo Perin⁵, Rajnish Ranjan¹⁶, Imad Riachi², José-Rodrigo Rodríguez⁴, Juan Luis Riquelme², Christian Rössert², Konstantinos Sfyrakis², Ying Shi¹⁶, Julian C Shillcock², Gilad Silberberg¹⁷, Ricardo Silva², Farhan Tauheed¹⁸, Martin Telefont², Maria Toledo-Rodriguez¹⁹, Thomas Tränkler², Werner Van Geit², Jafet Villafranca Díaz², Richard Walker², Yun Wang²⁰, Stefano M Zaninetta², Javier DeFelipe⁴, Sean L Hill², Idan Segev⁹, Felix Schürmann²

Affiliations

¹ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Laboratory of Neural Microcircuitry, Brain Mind Institute, EPFL, 1015 Lausanne, Switzerland. Electronic address: henry.markram@epfl.ch.
² Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland.
³ Data-Intensive Applications and Systems Lab, EPFL, 1015 Lausanne, Switzerland.
⁴ Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain; Instituto Cajal (CSIC) and CIBERNED, 28002 Madrid, Spain.
⁵ Laboratory of Neural Microcircuitry, Brain Mind Institute, EPFL, 1015 Lausanne, Switzerland.
⁶ The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
⁷ The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
⁸ Department of Neurobiology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
⁹ Department of Neurobiology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
¹⁰ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Data-Intensive Applications and Systems Lab, EPFL, 1015 Lausanne, Switzerland; Imperial College London, London SW7 2AZ, UK.
¹¹ CeSViMa, Centro de Supercomputación y Visualización de Madrid, Universidad Politécnica de Madrid, 28223 Madrid, Spain.
¹² Department of Neurobiology, Yale University, New Haven, CT 06510 USA.
¹³ MTA-Debreceni Egyetem, Neuroscience Research Group, 4032 Debrecen, Hungary.
¹⁴ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Laboratoire d'informatique et de visualisation, EPFL, 1015 Lausanne, Switzerland.
¹⁵ Modeling and Virtual Reality Group, Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain.
¹⁶ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Laboratory of Neural Microcircuitry, Brain Mind Institute, EPFL, 1015 Lausanne, Switzerland.
¹⁷ Department of Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden.
¹⁸ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Data-Intensive Applications and Systems Lab, EPFL, 1015 Lausanne, Switzerland.
¹⁹ School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom.
²⁰ Key Laboratory of Visual Science and National Ministry of Health, School of Optometry and Opthalmology, Wenzhou Medical College, Wenzhou 325003, China; Caritas St. Elizabeth's Medical Center, Genesys Research Institute, Tufts University, Boston, MA 02111, USA.

PMID: 26451489
DOI: 10.1016/j.cell.2015.09.029

Free article

Reconstruction and Simulation of Neocortical Microcircuitry

Henry Markram et al. Cell. 2015.

Free article

. 2015 Oct 8;163(2):456-92.

doi: 10.1016/j.cell.2015.09.029.

Authors

Affiliations

¹ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Laboratory of Neural Microcircuitry, Brain Mind Institute, EPFL, 1015 Lausanne, Switzerland. Electronic address: henry.markram@epfl.ch.
² Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland.
³ Data-Intensive Applications and Systems Lab, EPFL, 1015 Lausanne, Switzerland.
⁴ Laboratorio Cajal de Circuitos Corticales, Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, 28223 Madrid, Spain; Instituto Cajal (CSIC) and CIBERNED, 28002 Madrid, Spain.
⁵ Laboratory of Neural Microcircuitry, Brain Mind Institute, EPFL, 1015 Lausanne, Switzerland.
⁶ The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
⁷ The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
⁸ Department of Neurobiology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
⁹ Department of Neurobiology, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
¹⁰ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Data-Intensive Applications and Systems Lab, EPFL, 1015 Lausanne, Switzerland; Imperial College London, London SW7 2AZ, UK.
¹¹ CeSViMa, Centro de Supercomputación y Visualización de Madrid, Universidad Politécnica de Madrid, 28223 Madrid, Spain.
¹² Department of Neurobiology, Yale University, New Haven, CT 06510 USA.
¹³ MTA-Debreceni Egyetem, Neuroscience Research Group, 4032 Debrecen, Hungary.
¹⁴ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Laboratoire d'informatique et de visualisation, EPFL, 1015 Lausanne, Switzerland.
¹⁵ Modeling and Virtual Reality Group, Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain.
¹⁶ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Laboratory of Neural Microcircuitry, Brain Mind Institute, EPFL, 1015 Lausanne, Switzerland.
¹⁷ Department of Neuroscience, Karolinska Institutet, Stockholm 17177, Sweden.
¹⁸ Blue Brain Project, École polytechnique fédérale de Lausanne (EPFL) Biotech Campus, 1202 Geneva, Switzerland; Data-Intensive Applications and Systems Lab, EPFL, 1015 Lausanne, Switzerland.
¹⁹ School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom.
²⁰ Key Laboratory of Visual Science and National Ministry of Health, School of Optometry and Opthalmology, Wenzhou Medical College, Wenzhou 325003, China; Caritas St. Elizabeth's Medical Center, Genesys Research Institute, Tufts University, Boston, MA 02111, USA.

PMID: 26451489
DOI: 10.1016/j.cell.2015.09.029

Abstract

We present a first-draft digital reconstruction of the microcircuitry of somatosensory cortex of juvenile rat. The reconstruction uses cellular and synaptic organizing principles to algorithmically reconstruct detailed anatomy and physiology from sparse experimental data. An objective anatomical method defines a neocortical volume of 0.29 ± 0.01 mm(3) containing ~31,000 neurons, and patch-clamp studies identify 55 layer-specific morphological and 207 morpho-electrical neuron subtypes. When digitally reconstructed neurons are positioned in the volume and synapse formation is restricted to biological bouton densities and numbers of synapses per connection, their overlapping arbors form ~8 million connections with ~37 million synapses. Simulations reproduce an array of in vitro and in vivo experiments without parameter tuning. Additionally, we find a spectrum of network states with a sharp transition from synchronous to asynchronous activity, modulated by physiological mechanisms. The spectrum of network states, dynamically reconfigured around this transition, supports diverse information processing strategies.

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A Biological Imitation Game.
Koch C, Buice MA. Koch C, et al. Cell. 2015 Oct 8;163(2):277-80. doi: 10.1016/j.cell.2015.09.045. Cell. 2015. PMID: 26451478 Review.

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Reconstruction and Simulation of Neocortical Microcircuitry

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Reconstruction and Simulation of Neocortical Microcircuitry

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