Reconstruction and Simulation of Neocortical Microcircuitry

Henry Markram; Eilif Muller; Srikanth Ramaswamy; Michael W. Reimann; Marwan Abdellah; Carlos Aguado Sanchez; Anastasia Ailamaki; Lidia Alonso-Nanclares; Nicolas Antille; Selim Arsever; Guy Antoine Atenekeng Kahou; Thomas K. Berger; Ahmet Bilgili; Nenad Buncic; Athanassia Chalimourda; Giuseppe Chindemi; Jean Denis Courcol; Fabien Delalondre; Vincent Delattre; Shaul Druckmann; Raphael Dumusc; James Dynes; Stefan Eilemann; Eyal Gal; Michael Emiel Gevaert; Jean Pierre Ghobril; Albert Gidon; Joe W. Graham; Anirudh Gupta; Valentin Haenel; Etay Hay; Thomas Heinis; Juan B. Hernando; Michael Hines; Lida Kanari; Daniel Keller; John Kenyon; Georges Khazen; Yihwa Kim; James G. King; Zoltan Kisvarday; Pramod Kumbhar; Sébastien Lasserre; Jean Vincent Le Bé; Bruno R.C. Magalhães; Angel Merchán-Pérez; Julie Meystre; Benjamin Roy Morrice; Jeffrey Muller; Alberto Muñoz-Céspedes; Shruti Muralidhar; Keerthan Muthurasa; Daniel Nachbaur; Taylor H. Newton; Max Nolte; Aleksandr Ovcharenko; Juan Palacios; Luis Pastor; Rodrigo Perin; Rajnish Ranjan; Imad Riachi; José Rodrigo Rodríguez; Juan Luis Riquelme; Christian Rössert; Konstantinos Sfyrakis; Ying Shi; Julian C. Shillcock; Gilad Silberberg; Ricardo Silva; Farhan Tauheed; Martin Telefont; Maria Toledo-Rodriguez; Thomas Tränkler; Werner Van Geit; Jafet Villafranca Díaz; Richard Walker; Yun Wang; Stefano M. Zaninetta; Javier Defelipe; Sean L. Hill; Idan Segev; Felix Schürmann

doi:10.1016/j.cell.2015.09.029

Reconstruction and Simulation of Neocortical Microcircuitry

Henry Markram^*, Eilif Muller, Srikanth Ramaswamy, Michael W. Reimann, Marwan Abdellah, Carlos Aguado Sanchez, Anastasia Ailamaki, Lidia Alonso-Nanclares, Nicolas Antille, Selim Arsever, Guy Antoine Atenekeng Kahou, Thomas K. Berger, Ahmet Bilgili, Nenad Buncic, Athanassia Chalimourda, Giuseppe Chindemi, Jean Denis Courcol, Fabien Delalondre, Vincent Delattre, Shaul DruckmannRaphael Dumusc, James Dynes, Stefan Eilemann, Eyal Gal, Michael Emiel Gevaert, Jean Pierre Ghobril, Albert Gidon, Joe W. Graham, Anirudh Gupta, Valentin Haenel, Etay Hay, Thomas Heinis, Juan B. Hernando, Michael Hines, Lida Kanari, Daniel Keller, John Kenyon, Georges Khazen, Yihwa Kim, James G. King, Zoltan Kisvarday, Pramod Kumbhar, Sébastien Lasserre, Jean Vincent Le Bé, Bruno R.C. Magalhães, Angel Merchán-Pérez, Julie Meystre, Benjamin Roy Morrice, Jeffrey Muller, Alberto Muñoz-Céspedes, Shruti Muralidhar, Keerthan Muthurasa, Daniel Nachbaur, Taylor H. Newton, Max Nolte, Aleksandr Ovcharenko, Juan Palacios, Luis Pastor, Rodrigo Perin, Rajnish Ranjan, Imad Riachi, José Rodrigo Rodríguez, Juan Luis Riquelme, Christian Rössert, Konstantinos Sfyrakis, Ying Shi, Julian C. Shillcock, Gilad Silberberg, Ricardo Silva, Farhan Tauheed, Martin Telefont, Maria Toledo-Rodriguez, Thomas Tränkler, Werner Van Geit, Jafet Villafranca Díaz, Richard Walker, Yun Wang, Stefano M. Zaninetta, Javier Defelipe, Sean L. Hill, Idan Segev, Felix Schürmann

^*Corresponding author for this work

Alexander Silberman Institute of Life Sciences

Research output: Contribution to journal › Article › peer-review

986 Scopus citations

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 mm³ 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.

Original language	English
Pages (from-to)	456-492
Number of pages	37
Journal	Cell
Volume	163
Issue number	2
DOIs	https://doi.org/10.1016/j.cell.2015.09.029
State	Published - 8 Oct 2015

Bibliographical note

Publisher Copyright:
© 2015 Elsevier Inc.

Access to Document

10.1016/j.cell.2015.09.029

Cite this

Markram, H., Muller, E., Ramaswamy, S., Reimann, M. W., Abdellah, M., Sanchez, C. A., Ailamaki, A., Alonso-Nanclares, L., Antille, N., Arsever, S., Kahou, G. A. A., Berger, T. K., Bilgili, A., Buncic, N., Chalimourda, A., Chindemi, G., Courcol, J. D., Delalondre, F., Delattre, V., ... Schürmann, F. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell, 163(2), 456-492. https://doi.org/10.1016/j.cell.2015.09.029

@article{db8be55213b74970b101bd4bc1e0cce1,

title = "Reconstruction and Simulation of Neocortical Microcircuitry",

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 mm3 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.",

author = "Henry Markram and Eilif Muller and Srikanth Ramaswamy and Reimann, {Michael W.} and Marwan Abdellah and Sanchez, {Carlos Aguado} and Anastasia Ailamaki and Lidia Alonso-Nanclares and Nicolas Antille and Selim Arsever and Kahou, {Guy Antoine Atenekeng} and Berger, {Thomas K.} and Ahmet Bilgili and Nenad Buncic and Athanassia Chalimourda and Giuseppe Chindemi and Courcol, {Jean Denis} and Fabien Delalondre and Vincent Delattre and Shaul Druckmann and Raphael Dumusc and James Dynes and Stefan Eilemann and Eyal Gal and Gevaert, {Michael Emiel} and Ghobril, {Jean Pierre} and Albert Gidon and Graham, {Joe W.} and Anirudh Gupta and Valentin Haenel and Etay Hay and Thomas Heinis and Hernando, {Juan B.} and Michael Hines and Lida Kanari and Daniel Keller and John Kenyon and Georges Khazen and Yihwa Kim and King, {James G.} and Zoltan Kisvarday and Pramod Kumbhar and S{\'e}bastien Lasserre and {Le B{\'e}}, {Jean Vincent} and Magalh{\~a}es, {Bruno R.C.} and Angel Merch{\'a}n-P{\'e}rez and Julie Meystre and Morrice, {Benjamin Roy} and Jeffrey Muller and Alberto Mu{\~n}oz-C{\'e}spedes and Shruti Muralidhar and Keerthan Muthurasa and Daniel Nachbaur and Newton, {Taylor H.} and Max Nolte and Aleksandr Ovcharenko and Juan Palacios and Luis Pastor and Rodrigo Perin and Rajnish Ranjan and Imad Riachi and Rodr{\'i}guez, {Jos{\'e} Rodrigo} and Riquelme, {Juan Luis} and Christian R{\"o}ssert and Konstantinos Sfyrakis and Ying Shi and Shillcock, {Julian C.} and Gilad Silberberg and Ricardo Silva and Farhan Tauheed and Martin Telefont and Maria Toledo-Rodriguez and Thomas Tr{\"a}nkler and {Van Geit}, Werner and D{\'i}az, {Jafet Villafranca} and Richard Walker and Yun Wang and Zaninetta, {Stefano M.} and Javier Defelipe and Hill, {Sean L.} and Idan Segev and Felix Sch{\"u}rmann",

note = "Publisher Copyright: {\textcopyright} 2015 Elsevier Inc.",

year = "2015",

month = oct,

day = "8",

doi = "10.1016/j.cell.2015.09.029",

language = "אנגלית",

volume = "163",

pages = "456--492",

journal = "Cell",

issn = "0092-8674",

publisher = "Elsevier B.V.",

number = "2",

}

Markram, H, Muller, E, Ramaswamy, S, Reimann, MW, Abdellah, M, Sanchez, CA, Ailamaki, A, Alonso-Nanclares, L, Antille, N, Arsever, S, Kahou, GAA, Berger, TK, Bilgili, A, Buncic, N, Chalimourda, A, Chindemi, G, Courcol, JD, Delalondre, F, Delattre, V, Druckmann, S, Dumusc, R, Dynes, J, Eilemann, S, Gal, E, Gevaert, ME, Ghobril, JP, Gidon, A, Graham, JW, Gupta, A, Haenel, V, Hay, E, Heinis, T, Hernando, JB, Hines, M, Kanari, L, Keller, D, Kenyon, J, Khazen, G, Kim, Y, King, JG, Kisvarday, Z, Kumbhar, P, Lasserre, S, Le Bé, JV, Magalhães, BRC, Merchán-Pérez, A, Meystre, J, Morrice, BR, Muller, J, Muñoz-Céspedes, A, Muralidhar, S, Muthurasa, K, Nachbaur, D, Newton, TH, Nolte, M, Ovcharenko, A, Palacios, J, Pastor, L, Perin, R, Ranjan, R, Riachi, I, Rodríguez, JR, Riquelme, JL, Rössert, C, Sfyrakis, K, Shi, Y, Shillcock, JC, Silberberg, G, Silva, R, Tauheed, F, Telefont, M, Toledo-Rodriguez, M, Tränkler, T, Van Geit, W, Díaz, JV, Walker, R, Wang, Y, Zaninetta, SM, Defelipe, J, Hill, SL, Segev, I & Schürmann, F 2015, 'Reconstruction and Simulation of Neocortical Microcircuitry', Cell, vol. 163, no. 2, pp. 456-492. https://doi.org/10.1016/j.cell.2015.09.029

TY - JOUR

T1 - Reconstruction and Simulation of Neocortical Microcircuitry

AU - Markram, Henry

AU - Muller, Eilif

AU - Ramaswamy, Srikanth

AU - Reimann, Michael W.

AU - Abdellah, Marwan

AU - Sanchez, Carlos Aguado

AU - Ailamaki, Anastasia

AU - Alonso-Nanclares, Lidia

AU - Antille, Nicolas

AU - Arsever, Selim

AU - Kahou, Guy Antoine Atenekeng

AU - Berger, Thomas K.

AU - Bilgili, Ahmet

AU - Buncic, Nenad

AU - Chalimourda, Athanassia

AU - Chindemi, Giuseppe

AU - Courcol, Jean Denis

AU - Delalondre, Fabien

AU - Delattre, Vincent

AU - Druckmann, Shaul

AU - Dumusc, Raphael

AU - Dynes, James

AU - Eilemann, Stefan

AU - Gal, Eyal

AU - Gevaert, Michael Emiel

AU - Ghobril, Jean Pierre

AU - Gidon, Albert

AU - Graham, Joe W.

AU - Gupta, Anirudh

AU - Haenel, Valentin

AU - Hay, Etay

AU - Heinis, Thomas

AU - Hernando, Juan B.

AU - Hines, Michael

AU - Kanari, Lida

AU - Keller, Daniel

AU - Kenyon, John

AU - Khazen, Georges

AU - Kim, Yihwa

AU - King, James G.

AU - Kisvarday, Zoltan

AU - Kumbhar, Pramod

AU - Lasserre, Sébastien

AU - Le Bé, Jean Vincent

AU - Magalhães, Bruno R.C.

AU - Merchán-Pérez, Angel

AU - Meystre, Julie

AU - Morrice, Benjamin Roy

AU - Muller, Jeffrey

AU - Muñoz-Céspedes, Alberto

AU - Muralidhar, Shruti

AU - Muthurasa, Keerthan

AU - Nachbaur, Daniel

AU - Newton, Taylor H.

AU - Nolte, Max

AU - Ovcharenko, Aleksandr

AU - Palacios, Juan

AU - Pastor, Luis

AU - Perin, Rodrigo

AU - Ranjan, Rajnish

AU - Riachi, Imad

AU - Rodríguez, José Rodrigo

AU - Riquelme, Juan Luis

AU - Rössert, Christian

AU - Sfyrakis, Konstantinos

AU - Shi, Ying

AU - Shillcock, Julian C.

AU - Silberberg, Gilad

AU - Silva, Ricardo

AU - Tauheed, Farhan

AU - Telefont, Martin

AU - Toledo-Rodriguez, Maria

AU - Tränkler, Thomas

AU - Van Geit, Werner

AU - Díaz, Jafet Villafranca

AU - Walker, Richard

AU - Wang, Yun

AU - Zaninetta, Stefano M.

AU - Defelipe, Javier

AU - Hill, Sean L.

AU - Segev, Idan

AU - Schürmann, Felix

PY - 2015/10/8

Y1 - 2015/10/8

N2 - 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 mm3 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.

AB - 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 mm3 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.

UR - http://www.scopus.com/inward/record.url?scp=84943612722&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2015.09.029

DO - 10.1016/j.cell.2015.09.029

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 26451489

AN - SCOPUS:84943612722

SN - 0092-8674

VL - 163

SP - 456

EP - 492

JO - Cell

JF - Cell

IS - 2

ER -

Reconstruction and Simulation of Neocortical Microcircuitry

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this