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

Reimann, M. W.; Bolanos Puchet, S.; Egas Santander, D.; Courcol, J.-D.; Arnaudon, A.; Coste, B.; Delemontex, T.; Devresse, A.; Dictus, H.; Dietz, A.; Ecker, A.; Favreau, C.; Ficarelli, G.; Gevaert, M.; Hernando, J. B.; Herttuainen, J.; Isbister, J. B.; Kanari, L.; Keller, D.; King, J. G.; Kumbhar, P.; Lapere, S.; Lazovskis, J.; Lu, H.; Ninin, N.; Pereira, F.; Planas, J.; Pokorny, C.; Riquelme, J. L.; Romani, A.; Shi, Y.; Smith, J. P.; Sood, V.; Srivastava, M.; Van Geit, W.; Vanherpe, L.; Wolf, M.; Levi, R.; Hess, K.; Schürmann, F.; Muller, E. B.; Ramaswamy, S.; Markram, H.

doi:10.1101/2022.08.11.503144

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bioRxiv · 10.1101/2022.08.11.503144

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

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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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Reimann, M. W., Bolanos Puchet, S., Egas Santander, D., Courcol, J.-D., Arnaudon, A., Coste, B., Delemontex, T., Devresse, A., Dictus, H., Dietz, A., Ecker, A., Favreau, C., Ficarelli, G., Gevaert, M., Hernando, J. B., Herttuainen, J., Isbister, J. B., Kanari, L., Keller, D., King, J. G., Kumbhar, P., Lapere, S., Lazovskis, J., Lu, H., Ninin, N., Pereira, F., Planas, J., Pokorny, C., Riquelme, J. L., Romani, A., Shi, Y., Smith, J. P., Sood, V., Srivastava, M., Van Geit, W., Vanherpe, L., Wolf, M., Levi, R., Hess, K., Schürmann, F., Muller, E. B., Ramaswamy, S., Markram, H.. 2022-08-15. Modeling and Simulation of Rat Non-Barrel Somatosensory Cortex. Part I: Modeling Anatomy. https://doi.org/10.1101/2022.08.11.503144

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