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

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, long-range and extrinsic connectivity. We delineated the limits of determining connectivity from anatomy, finding that it reproduces the targeting of PV+ and VIP+ interneurons only with explicitly added specificity, but the one of Sst+ neurons even without. 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. A 211,712 neuron subvolume of the model has been made freely and openly available to the community.