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; Jᾱnis 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; Henry Markram; Srikanth Ramaswamy

doi:10.7554/elife.99688.2

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

Michael W Reimann^* (Corresponding Author), 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 KingPramod Kumbhar, Samuel Lapere, Jᾱnis 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, Henry Markram, Srikanth Ramaswamy

^*Corresponding author for this work

Mathematical Science

École Polytechnique Fédérale de Lausanne

Research output: Working paper › Preprint

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, mid-range and extrinsic connectivity. We delineated the limits of determining connectivity from neuron morphology and placement, finding that it reproduces targeting by Sst+ neurons, but requires additional specificity to reproduce targeting by PV+ and VIP+ interneurons. 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. The model is suitable for simulation-based studies, and a 211,712 neuron subvolume is made openly available to the community.

Original language	English
Publisher	eLife Sciences Publications
Volume	13
DOIs	https://doi.org/10.7554/elife.99688.2
Publication status	E-pub ahead of print - 24 Nov 2024

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10.7554/elife.99688.2Licence: CC BY

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Reimann, M. W., Bolaños-Puchet, S., Courcol, J.-D., Egas Santander, D., Arnaudon, A., Coste, B., Delalondre, F., Delemontex, T., Devresse, A., Dictus, H., Dietz, A., Ecker, A., Favreau, C., Ficarelli, G., Gevaert, M., Herttuainen, J., Isbister, J. B., Kanari, L., Keller, D., ... Ramaswamy, S. (2024). Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy. eLife Sciences Publications. Advance online publication. https://doi.org/10.7554/elife.99688.2

Reimann, MW, Bolaños-Puchet, S, Courcol, J-D, Egas Santander, D, Arnaudon, A, Coste, B, Delalondre, F, Delemontex, T, Devresse, A, Dictus, H, Dietz, A, Ecker, A, Favreau, C, Ficarelli, G, Gevaert, M, Herttuainen, J, Isbister, JB, Kanari, L, Keller, D, King, J, Kumbhar, P, Lapere, S, Lazovskis, J, Lu, H, Ninin, N, Pereira, F, Planas, J, Pokorny, C, Riquelme, JL, Romani, A, Shi, Y, Smith, JP, Sood, V, Srivastava, M, Van Geit, W, Vanherpe, L, Wolf, M, Levi, R, Hess, K, Schürmann, F, Muller, EB, Markram, H & Ramaswamy, S 2024 'Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I: Anatomy' eLife Sciences Publications. https://doi.org/10.7554/elife.99688.2

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AU - Courcol, Jean-Denis

AU - Egas Santander, Daniela

AU - Arnaudon, Alexis

AU - Coste, Benoît

AU - Delalondre, Fabien

AU - Delemontex, Thomas

AU - Devresse, Adrien

AU - Dictus, Hugo

AU - Dietz, Alexander

AU - Ecker, András

AU - Favreau, Cyrille

AU - Ficarelli, Gianluca

AU - Gevaert, Mike

AU - Herttuainen, Joni

AU - Isbister, James B

AU - Kanari, Lida

AU - Keller, Daniel

AU - King, James

AU - Kumbhar, Pramod

AU - Lapere, Samuel

AU - Lazovskis, Jᾱnis

AU - Lu, Huanxiang

AU - Ninin, Nicolas

AU - Pereira, Fernando

AU - Planas, Judit

AU - Pokorny, Christoph

AU - Riquelme, Juan Luis

AU - Romani, Armando

AU - Shi, Ying

AU - Smith, Jason P

AU - Sood, Vishal

AU - Srivastava, Mohit

AU - Van Geit, Werner

AU - Vanherpe, Liesbeth

AU - Wolf, Matthias

AU - Levi, Ran

AU - Hess, Kathryn

AU - Schürmann, Felix

AU - Muller, Eilif B

AU - Markram, Henry

AU - Ramaswamy, Srikanth

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N2 - 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, mid-range and extrinsic connectivity. We delineated the limits of determining connectivity from neuron morphology and placement, finding that it reproduces targeting by Sst+ neurons, but requires additional specificity to reproduce targeting by PV+ and VIP+ interneurons. 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. The model is suitable for simulation-based studies, and a 211,712 neuron subvolume is made openly available to the community.

AB - 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, mid-range and extrinsic connectivity. We delineated the limits of determining connectivity from neuron morphology and placement, finding that it reproduces targeting by Sst+ neurons, but requires additional specificity to reproduce targeting by PV+ and VIP+ interneurons. 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. The model is suitable for simulation-based studies, and a 211,712 neuron subvolume is made openly available to the community.

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DO - 10.7554/elife.99688.2

M3 - Preprint

VL - 13

BT - Modeling and Simulation of Neocortical Micro- and Mesocircuitry. Part I

PB - eLife Sciences Publications

ER -

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

Abstract

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