Athanassia Chalimourda

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The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex

Henry Markram, Sean Lewis Hill, Eilif Benjamin Muller, Srikanth Ramaswamy, Michael Reimann, Daniel Keller, Werner Alfons Hilda Van Geit, James Gonzalo King, Marwan Muhammad Ahmed Abdellah, Lida Kanari, Julian Charles Shillcock, Ying Shi, Jean-Denis Georges Emile Courcol, Rajnish Ranjan, John Richard Walker, Michael Emiel Gevaert, Idan Segev, Yun Wang, Giuseppe Chindemi, Juan Bautista Hernando Vieites, Stefan Eilemann, Martin Telefont, Ahmet Bilgili, Guy Antoine Atenekeng Kahou, Nicolas Antille, Raphael Dumusc, Jeffrey Christopher Muller, Jafet Villafranca Diaz, Selim Arsever, Joseph William Graham, Athanassia Chalimourda, Stefano Zaninetta, Yury Brukau, Stanislaw Ryszard Adaszewski

We have established a multi-constraint, data-driven process to digitally reconstruct, and simulate prototypical neocortical microcircuitry, using sparse experimental data. We applied this process to reconstruct the microcircuitry of the somatosensory cortex in juvenile rat at the cellular and synaptic levels. The resulting reconstruction is broadly consistent with current knowledge about the neocortical microcircuit and provides an array of predictions on its structure and function. To engage the community in exploring, challenging, and refining the reconstruction, we have developed a collaborative, internet-accessible facility-the Neocortical Microcircuit Collaboration portal (NMC portal; https://bbp.epfl.ch/nmc-portal). The NMC portal allows users to access the experimental data used in the reconstruction process, download cellular and synaptic models, and analyze the predicted properties of the microcircuit: six layers, similar to 31,000 neurons, 55 morphological types, 11 electrical types, 207 morpho-electrical types, 1941 unique synaptic connection types between neurons of specific morphological types, predicted properties for the anatomy and physiology of similar to 40 million intrinsic synapses. It also provides data supporting comparison of the anatomy and physiology of the reconstructed microcircuit against results in the literature. The portal aims to catalyzee consensus on the cellular and synaptic organization of neocortical microcircuitry (ion channel, neuron and synapse types and distributions, connectivity, etc.). Community feedback will contribute to refined versions of the reconstruction to be released periodically. We consider that the reconstructions and the simulations they enable represent a major step in the development of in silica neuroscience.

Frontiers Research Foundation2015

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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 mm(3) containing similar to 31,000 neurons, and patch-clamp studies identify 55 layer-specific morphological and 207 morphoelectrical 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 similar to 8 million connections with similar to 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.

Elsevier2015