Blue Brain and the Allen Institute created virtual neurons




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.

A virtual neuron from Blue Brain facility _EPFL

 A virtual neuron from Blue Brain facility©EPFL


⇐ cover image: A full column reconstruction of 217000 cells rendered with a voltage assigned colour-map at a particular point in a simulation ©Human 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.»

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.»

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Digital Reconstruction of Neocortical Microcircuitry

The Neocortical Microcircuit Collaboration Portal

This portal provides an online public resource of the Blue Brain Project’s first release of a digital reconstruction of the microcircuitry of juvenile Rat somatosensory cortex, access to experimental data sets used in the reconstruction, and the resulting models. The following functionality is provided through this portal to support community engagement to use and refine the reconstruction.

  • Neocortical Microcircuit – an interactive browser of the anatomical and physiological properties of the reconstructed microcircuit, which includes facts and figures, detailed analyses, simulation videos, model and data downloads.
  • Literature Consistency – a database of published experimental papers that were used either to constrain parameters of the reconstruction directly, or against which the reconstruction was assessed to be quantitatively or qualitatively consistent. This is intended to be an active list that can be discussed and extended by the community.
  • Videos – a collection of computer generated visualizations of in silico experiments.
  • Images – a collection of images illustrating the various steps in the reconstruction process.
  • Experimental Data – experimental data sets used in the reconstruction process.
  • Tools – tools and documentation for reconstructing, simulating and analyzing the reconstruction.  
  • Downloads – downloadable models from the reconstruction.

A quick guide to navigating the portal

Glossary of terms, and abbreviations

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  • Reference paper (limited access)



Reconstruction and Simulation of Neocortical Microcircuitry





• 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


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.

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Blue Brain Project

The Blue Brain Project is an attempt to reverse engineer the human brain and recreate it at the cellular level inside a computer simulation. The project was founded in May 2005 by Henry Markram at the EPFL in Lausanne, Switzerland. Goals of the project are to gain a complete understanding of the brain and to enable better and faster development of brain disease treatments.

The research involves studying slices of living brain tissue using microscopes and patch clampelectrodes. Data is collected about all the many different neuron types. This data is used to build biologically realistic models of neurons and networks of neurons in the cerebral cortex. The simulations are carried out on a Blue Gene supercomputer built by IBM. Hence the name «Blue Brain». The simulation software is based around Michael Hines‘s NEURON, together with other custom-built components.

As of August 2012 the largest simulations are of mesocircuits containing around 100 cortical columns(image above right). Such simulations involve approximately 1 million neurons and 1 billion synapses. This is about the same scale as that of a honey bee brain. It is hoped that a rat brain neocortical simulation (~21 million neurons) will be achieved by the end of 2014. A full human brain simulation (86 billion neurons) should be possible by 2023 provided sufficient funding is received.

Cortical mesocircuit simulation_Artificial Brains