EPFL launches interactive 3D atlas of mouse brain

Blue Brain Project leader Henry Markram presenting a brain in 2016. Keystone

Researchers from the Blue Brain Project in Lausanne have announced the unveiling of their ‘Cell Atlas’, a 3D, interactive, constantly-evolving simulation of a mouse brain.


“Like going from hand-drawn maps to digitized versions of satellite images of cities and geographical features – allowing us to navigate the brain the way Google Earth allows us to navigate the earth,” was how one researcher described it.

The Blue Brain Cell Atlas, by integrating data from thousands of brain tissue stainings over five years, offers the first ever digital 3D atlas of every cell, in all 737 regions, of the mouse brain.

A press release by Lausanne’s Federal Institute of Technology EPFL, where the Blue Brain Project is based, described the development as “a major step toward a full simulation of the rodent brain” that will also potentially “massively” accelerate progress in human brain science.

+ More on the background to the brain research happening in Lausanne

“Knowing the circuit components and how they are arranged is an essential starting point for modelling the brain – just as demographic data are essential for modelling a country,” said lead author and atlas creator Csaba Erö.

The project goes further than previous mapping attempts in that it doesn't just consist of stacks of brain slices, but gathers all available data into numbers and positions for every known cell in the brain in the form of a digitally navigable atlas.

It is also the first atlas that is “dynamic”, EPFL states: that is, as researchers discover more about the rodent brain, they can contribute to improvising the atlas by inserting their findings – something that the authors are keen to encourage.

The Atlas, which can be explored here, was published in the Frontiers in Computational Neuroscience journal.

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