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Virtual Neurons Created by Blue Brain and the Allen Institute

The Allen Institute for Brain Science is releasing new, highly realistic computer models of neurons. The models were developed using tools and expertise from the Blue Brain Project.

The Allen Institute for Brain Science and the Blue Brain Project are deepening their collaboration. Today, the US-based Allen Institute is releasing a set of 40 computer models of neurons from the mouse visual cortex, created using tools developed by the Swiss-based Blue Brain Project at EPFL. Using Blue Brain technology, the researchers were able to reproduce the physiology and electrical activity of the neurons with an extremely high level of detail.

The Blue Brain Project is the simulation core of the Human Brain Project, a huge pan-European initiative. The scientific journal Cell recently published a long paper demonstrating the effectiveness of the Blue Brain Project’s modeling tools, focusing on the high accuracy and predictive power of the models and the discoveries they have already led to, including insight into the unexpected role of calcium. At the same time, the team has made these resources available to researchers around the world on a web-based platform.

“Our collaboration with the Allen Institute is an important step towards what we are striving to achieve,” said Eilif Muller, the leader of the Blue Brain Simulation group. “The goal is to provide the scientific community with simulation-based tools and techniques that can give us a better understanding of how neurons and neural networks function.”

The Allen Institute’s virtual neurons accurately reproduce the biophysical activity of their real counterparts. Modeling the activity of dendrites – treelike extensions of neurons through which they integrate input from other neurons – was especially realistic. “Combining the data, tools and knowledge from the world’s two largest neuroscience-oriented enterprises demonstrates the synergy that can be achieved by an Open Science policy, freely sharing all available data and metadata”, said Christoph Koch, President and Chief Scientific Officer of the Allen Institute for Brain Science. “Understanding the brain, here the nonlinear processing in cortical dendrites, is too difficult a task to accomplish in any other way.”

Image shows a virtual neuron.

A virtual neuron from the Blue Brain facility. Credit: EPFL.

For the Blue Brain Project researchers, this collaboration is just the first step. Now the project is in talks with other teams of researchers who would like to do the same. Sean Hill, a neuroscientist affiliated with EPFL, is delighted: “This is a watershed moment, when we can really have an impact: we’re a Swiss project that is central to a major European project; now we’re reaching out to the scientific community around the world.”

About this neuroscience research

Source: Lionel Pousaz – EPFL
Image Source: The image is credited to EPFL.
Original Research: Abstract for “Reconstruction and Simulation of Neocortical Microcircuitry” by Henry Markram, Eilif Muller, Srikanth Ramaswamy, Michael W. Reimann, Marwan Abdellah, Carlos Aguado Sanchez, Anastasia Ailamaki, Lidia Alonso-Nanclares, Nicolas Antille, Selim Arsever, Guy Antoine Atenekeng Kahou, Thomas K. Berger, Ahmet Bilgili, Nenad Buncic, Athanassia Chalimourda, Giuseppe Chindemi, Jean-Denis Courcol, Fabien Delalondre, Vincent Delattre, Shaul Druckmann, Raphael Dumusc, James Dynes, Stefan Eilemann, Eyal Gal, Michael Emiel Gevaert, Jean-Pierre Ghobril, Albert Gidon, Joe W. Graham, Anirudh Gupta, Valentin Haenel, Etay Hay, Thomas Heinis, Juan B. Hernando, Michael Hines, Lida Kanari, Daniel Keller, John Kenyon, Georges Khazen, Yihwa Kim, James G. King, Zoltan Kisvarday, Pramod Kumbhar, Sébastien Lasserre, Jean-Vincent Le Bé, Bruno R.C. Magalhães, Angel Merchán-Pérez, Julie Meystre, Benjamin Roy Morrice, Jeffrey Muller, Alberto Muñoz-Céspedes, Shruti Muralidhar, Keerthan Muthurasa, Daniel Nachbaur, Taylor H. Newton, Max Nolte, Aleksandr Ovcharenko, Juan Palacios, Luis Pastor, Rodrigo Perin, Rajnish Ranjan, Imad Riachi, José-Rodrigo Rodríguez, Juan Luis Riquelme, Christian Rössert, Konstantinos Sfyrakis, Ying Shi, Julian C. Shillcock, Gilad Silberberg, Ricardo Silva, Farhan Tauheed, Martin Telefont, Maria Toledo-Rodriguez, Thomas Tränkler, Werner Van Geit, Jafet Villafranca Díaz, Richard Walker, Yun Wang, Stefano M. Zaninetta, Javier DeFelipe, Sean L. Hill, Idan Segev, and Felix Schürmann in Cell. Published online October 2015 doi:10.1016/j.cell.2015.09.029


Abstract

Reconstruction and Simulation of Neocortical Microcircuitry

Highlights
•The Blue Brain Project digitally reconstructs and simulates a part of neocortex
•Interdependencies allow dense in silico reconstruction from sparse experimental data
•Simulations reproduce in vitro and in vivo experiments without parameter tuning
•The neocortex reconfigures to support diverse information processing strategies

Summary
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 mm3 containing ∼31,000 neurons, and patch-clamp studies identify 55 layer-specific morphological and 207 morpho-electrical 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 ∼8 million connections with ∼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.

“Reconstruction and Simulation of Neocortical Microcircuitry” by Henry Markram, Eilif Muller, Srikanth Ramaswamy, Michael W. Reimann, Marwan Abdellah, Carlos Aguado Sanchez, Anastasia Ailamaki, Lidia Alonso-Nanclares, Nicolas Antille, Selim Arsever, Guy Antoine Atenekeng Kahou, Thomas K. Berger, Ahmet Bilgili, Nenad Buncic, Athanassia Chalimourda, Giuseppe Chindemi, Jean-Denis Courcol, Fabien Delalondre, Vincent Delattre, Shaul Druckmann, Raphael Dumusc, James Dynes, Stefan Eilemann, Eyal Gal, Michael Emiel Gevaert, Jean-Pierre Ghobril, Albert Gidon, Joe W. Graham, Anirudh Gupta, Valentin Haenel, Etay Hay, Thomas Heinis, Juan B. Hernando, Michael Hines, Lida Kanari, Daniel Keller, John Kenyon, Georges Khazen, Yihwa Kim, James G. King, Zoltan Kisvarday, Pramod Kumbhar, Sébastien Lasserre, Jean-Vincent Le Bé, Bruno R.C. Magalhães, Angel Merchán-Pérez, Julie Meystre, Benjamin Roy Morrice, Jeffrey Muller, Alberto Muñoz-Céspedes, Shruti Muralidhar, Keerthan Muthurasa, Daniel Nachbaur, Taylor H. Newton, Max Nolte, Aleksandr Ovcharenko, Juan Palacios, Luis Pastor, Rodrigo Perin, Rajnish Ranjan, Imad Riachi, José-Rodrigo Rodríguez, Juan Luis Riquelme, Christian Rössert, Konstantinos Sfyrakis, Ying Shi, Julian C. Shillcock, Gilad Silberberg, Ricardo Silva, Farhan Tauheed, Martin Telefont, Maria Toledo-Rodriguez, Thomas Tränkler, Werner Van Geit, Jafet Villafranca Díaz, Richard Walker, Yun Wang, Stefano M. Zaninetta, Javier DeFelipe, Sean L. Hill, Idan Segev, and Felix Schürmann in Cell. Published online October 2015 doi:10.1016/j.cell.2015.09.029

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