Modeling and Simulation of Rat Non-Barrel Somatosensory Cortex. Part I: Modeling Anatomy

Michael 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 Gonzalo King; Pramod Kumbhar; Samuel Lapere; Jānis Lazovskis; Huanxiang Lu; Nicolas Ninin; Fernando Pereira; Judit Planas; Christoph Pokorny; Juan Luis Riquelme; Armando Romani

doi:10.7554/elife.99688.3

NeuroscienceeLifeJan 20, 2026

Peer-reviewed journal article

Modeling and Simulation of Rat Non-Barrel Somatosensory Cortex. Part I: Modeling Anatomy

Michael Reimann iD, Sirio Bolaños‐Puchet iD, Jean-Denis Courcol iD, Daniela Egas Santander iD, Alexis Arnaudon iD, Benoît Coste iD, Fabien Delalondre, Thomas Delemontex iD, Adrien Devresse iD, Hugo Dictus iD, Alexander Dietz iD, András Ecker iD, Cyrille Favreau iD, Gianluca Ficarelli iD, Mike Gevaert iD, Joni Herttuainen iD, James B. Isbister iD, Lida Kanari iD, Daniel Keller iD, James Gonzalo King iD, Pramod Kumbhar iD, Samuel Lapere iD, Jānis Lazovskis iD, Huanxiang Lu iD, Nicolas Ninin, , Srikanth Ramaswamy iD

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.

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