Blue Brain Team Discovers a Multi-Dimensional Universe in Brain Networks

12 June 2017

In a paper published today, a team of scientists led by the Blue Brain Project have used a sophisticated type of mathematics in a way that it has never been used before in neuroscience.

The team have uncovered a universe of multi-dimensional geometrical structures and spaces within the networks of the brain.

This research, published in Frontiers in Computational Neuroscience, has significant implications for our understanding of the brain.

Click here for the Frontiers blog

 

Topology in neuroscience The image attempts to illustrate something that can not be imaged – a universe of multi-dimensional structures and spaces. On the left is a digital copy of a part of the neocortex, the most evolved part of the brain. On the right are shapes of different sizes and geometries in an attempt to represent structures ranging from 1D to 7D and beyond. The “black-hole” in the middle is used to symbolise a complex x of multi-dimensional spaces, or cavities. Blue Brain Project / EPFL © 2005 – 2017. All rights reserved

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Rich cell-type-specific network topology in neocortical microcircuitry

5 June 2017

Uncovering structural regularities and architectural topologies of cortical circuitry is vital for understanding neural computations.

In a paper published in Nature Neuroscience, the group of Idan Segev of the Hebrew University of Jerusalem in collaboration with the Cells & Circuits team in the Simulation Neuroscience Division of the Blue Brain, and Tel Aviv University identified a rich cell-type-specific network topology in neocortical microcircuitry. The systematic approach presented in the paper has enabled interpretation of microconnectomics ‘big data’, and provided several experimentally testable predictions.

Click here to read the paper.

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Blue Brain wins major award of supercomputing time from DOE

A Blue Brain team, led by Eilif Muller, has won a major award of supercomputing time, from the DOE’s prestigious Incite Leadership Computing Program. The award gives the team an unprecedented opportunity to simulate synaptic plasticity—the process through which brain activity shapes synaptic connections. The study -  which will build on Blue Brain’s recently published reconstruction of neural microcircuitry - it will focus on the impact of plasticity on the detailed organization and functioning of neural networks. The results  will provide insights, not just to neuroscientists but also to technologists, seeking to implement brain-like learning mechanisms in software and hardware. To see the Incite Announcement click here.

 

Blue Brain Project releases Open Source Software providing model parameter optimization for neuroscientists

The Allen Brain Institute recently used Blue Brain modelling and optimization tools to model neurons from mouse visual cortex (see news below). Now other neuroscientists can use Blue Brain tools to optimize their own models. The Blue Brain Project has just released the BlueBrain Python Optimization Library (BlueOptPy) - an extensible open source framework for data-driven model parameter optimisation that wraps and standardises several existing open-source tools. The library includes methods for setting up small- and large-scale optimizations on a broad range of compute platforms - from laptops to large cloud-based compute infrastructures. The code can be downloaded here. A preprint describing the library is available here.

 

Allen Brain Institute collaborates with Blue Brain Project to model neurons from mouse visual cortex

On March 3, 2016, the US-based Allen Institute released a set of 40 computer models of neurons from the mouse visual cortex, created using tools developed by the Blue Brain Project. 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. For further details click here.

 

Digitizing and Simulating Neural Tissue Reveals Mechanisms Underlying Diverse Brain States 

The Blue Brain Project, the simulation core of the Human Brain Project, has completed a first draft computer reconstruction of a piece of the neocortex. The electrical behavior of the virtual brain tissue was simulated on supercomputers and found to match the behavior observed in a number of experiments on the brain. Further simulations revealed novel insights into the functioning of the neocortex. This first step towards the digital reconstruction and simulation of the brain is published in Cell.

 

Web portal provides access to data and models used in reconstruction 

The Blue Brain Project has announced the opening of the Neocortical Microcircuit Collaboration Portal (NMC-Portal). The NMC portal allows researchers with access to the Internet, to access the experimental data used in the reconstruction, to download cellular and synaptic models, and to analyze the predicted properties of the microcircuit It also provides data supporting comparison of the anatomy and physiology of the reconstructed microcircuit against results in the literature. The aim is to catalyse community efforts to understand the cellular and synaptic organization of neocortical microcircuitry (ion channels and their densities, neuron types and their distributions across layers, connectivity between neurons, synapse types, synaptic properties etc.).. Future periodic releases will incorporate results from these efforts. To read more about the portal click here. To access the portal itself click here.

 

Algorithm to predict connectivity in neural microcircuits

A paper published today describes a mathematical algorithm that predicts the location of nearly 40 million synapses formed between the neurons in a small block of brain tissue about 100’000 times larger than has ever been analyzed with electron microscopy. The algorithm uses millions of times less experimental data than would normally be needed using purely experimental methods. The algorithm was developed as part of the Blue Brain Project’s mission to digitally reconstruct the biological detail of the brain and is a companion paper to the team's paper on the Reconstruction and Simulation of Neocortical Microcircuitry.  

 

Blue Brain Team Selected to Participate in Argonne Early Science Programme 

The Blue Brain Project's High Performance Computing Team (HPC)  has been selected by the Argonne Leadership Computing Facility (ALCF) to participate in the 2-year Theta Early Science Program. This program will target the porting and optimization at large scale of our CoreNeuron scientific application on ALCF next leadership-class supercomputer prototype, Theta. This opportunity will allow the HPC team developers to collaborate with Intel, Cray and ALCF HPC specialists to drive the development of CoreNeuron to support 4 challenging scientific use cases: (a) The analysis of the electrical activity of the mouse brain Somatosensory Cortex, (b) The study of Synaptic Plasticity phenomenon in a mouse brain, (c) The building and simulations of a full mouse brain model and (d) The study of the activity and plasticity of a mouse brain model when embedded into a simulated body interacting within its environment. 

 

In Silico Imaging of Fluorescent Brain Models

The Blue Brain Project visualization team has recently published an article on the modeling and simulation of brain imaging with light sheet fluorescence microscope (LSFM) on a physically plausible basis. This model reflects the light propagation in the optical setup of the LSFM using Monte Carlo rendering taking into account the physics of geometric optics. It can accurately render synthetic optical sections that are comparable to realistic ones produced by the LSFM. This in silico LSFM will be potentially employed for validating the reconstructed tissue models from microscopic imaging stacks.

 

Launch of Sino-Swiss Laboratory for Data Intensive Neuroscience

EPFL and the Chinese Academy of Sciences will collaborate on Neuroinformatics platforms, Data and Knowledge integration, algorithms for Brain Reconstruction and Brain Atlas platforms.

 

Upcoming Workshops

NEST User Workshop, 20-22 April 2015 in Geneva and Connectomics School, 9-16 May 2015, Florence.

 

A Simulated Mouse Brain

Neurorobotics engineers from the Human Brain Project (HBP) have recently taken the first steps towards building a "virtual mouse" by placing a simplified computer model of the mouse brain into a virtual mouse body.

 

Neural Simulations Hint at the Origin of Brain Waves

Sean Hill explains how computer models of individual neurons are being assembled into neural circuits that produce electrical signals akin to brain waves.

BMI Research Day 2014

The organizers of the BMI Research Day are happy to announce the program of the 2nd BMI Research Day 2014. The event takes place on June 11th and will start at 11:50 in EPFL (SV1717A / SV Lobby).

 

Un super-ordinateur permettant de simuler le cerveau d'une souris vient d'être créé

Grâce a lui, les chercheurs de l'EPFL pourront reproduire, en trois dimensions, les 70 millions de neurones d'un cerveau de souris >>.

 

Neural simulations hint at the origin of brain waves

For almost a century, scientists have been studying brain waves to learn about mental health and the way we think >>.