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Blue Brain Project

Blue Brain Project

A Swiss brain research initiative with the goal of the Blue Brain Project is to build biologically detailed digital reconstructions and simulations of the rodent and human brain.

The Blue Brain Project is a Swiss brain research initiative with the goal of the Blue Brain Project is to build biologically detailed digital reconstructions and simulations of the rodent and human brain. The Blue Brain Project is located at École polytechnique fédérale de Lausanne (EPFL) and is led by founder and director Professor Henry Markram. Blue Brain builds supercomputer-based simulations and reconstructions for the purpose of understanding brain structure and function.



3D mouse brain atlas

The first digital 3D atlas including every cell in the mouse brain with information about cell types, numbers and positions in all 737 brain regions. Information is integrated from thousands of whole brain tissue stains into an interactive and updatable online resource. The resource can be used for analysis an and modelling of specific brain areas. Prior to this atlas cell numbers were only available for 4% of mouse brain regions, and estimates varied by as much as three-fold. Lead author in the publication in which the Cell Alas was described, Csaba Erö, and colleagues used imaging data available from the Allen Institute for Brain Science, combined with other anatomical studies to construct the atlas. Navigating the Cell Atlas is likened to navigating Google Earth. The Cell Atlas is freely available.



Classification of neurons



The Blue Brain Project developed a mathematical algorithm to objectively classify the shapes of neurons in the brain. This will work towards developing a standardized taxonomy of all cells in the brain, which will aid researchers in comparing data. The team for this project, lead by Lida Kanari, developed an algorithm to distinguish different shapes of pyramidal cells which are the most common type of neuron in the neocortex. The algorithm was developed in collaboration with Professors Kathryn Hess (EPFL) and Ran Levi (University of Aberdeen). Tools from algebraic topology, the mathematics of shape, connectivity and emergence of global structure from local constraints, were applied to the project. 



Pyramidal cells are tree-like, making up 80% of the neurons in the neocortex that act like antennas collecting information from other neurons in the brain. Pyramidal cell are excitatory and send waves of electrical activity through the network when people perceive, act and feel. Up until this project, there had been no consensus among scientists on the types of pyramidal neurons. The Blue Brain study provided objective classification of 17 types of pyramidal cells in the rat somatosensory cortex. The study helped settle a long-standing debate on whether cell-types are discrete or continuous morphological variations of each other. 



Timeline

2019

Objective Morphological Classification of Neocortical Pyramidal Cells

An algorithm was developed using algebraic topology and dendritic arborization to provide objective classification of pyramidal cells into 17 types. Previously there was no consensus on the number of morphologically different types of pyramidal cells. 

November 28, 2018

A Cell Atlas for the Mouse Brain

A 3D cell atlas for the whole mouse brain. The atlas provides the densities and positions of all excitatory and inhibitory neurons, astrocytes, oligodendrocytes, and microglia in each of the 737 brain regions defined in the Allen Mouse Brain Atlas (AMBA).

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