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Navigating the brain

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  • Blue Brain Cell Atlas is first digital 3D cell atlas of the whole mouse brain
  • Users can interact with all neurons and glia in all 737 areas of the mouse brain
  • Digitally navigable atlas will continue to be updated with new findings

The first digital 3D atlas of every cell in the mouse brain provides neuroscientists with previously unavailable information on major cell types, numbers, and positions in all 737 brain regions. The comprehensive atlas has the potential to massively accelerate progress in brain science.

<strong>The first digital 3D atlas</strong> of every cell in the mouse brain is high-resolution, searchable, annotated and user-friendly—and fills a huge gap in existing knowledge. Courtesy Blue Brain Project/EPFL ©2005 – 2018. All rights reserved.

Released by EPFL's Blue Brain Project, the Blue Brain Cell Atlas integrates data from thousands of whole brain tissue stains into a comprehensive, interactive online resource that can continuously be updated with new findings. This groundbreaking digital atlas can be used for analyzing and further modeling specific brain areas, and is a major step toward a full simulation of the rodent brain.

Like 'going from hand-drawn maps to Google Earth,' the Blue Brain Cell Atlas allows anyone to visualize every region in the mouse brain, cell by cell.

"Despite vast numbers of studies over the past century, cell numbers were still only available for 4% of mouse brain regions—and these estimates often varied by as much as three-fold," says Blue Brain Project founder and director, Henry Markram. "The Cell Atlas solves this problem by presenting the best estimates for even the smallest-known region of the mouse brain."

"Knowing the circuit components and how they are arranged is also an essential starting point for modeling the brain - just as demographic data are essential for modeling a country, for example," explains lead author and creator of the Cell Atlas, Csaba Erö.

From image to atlas. The Blue Brain Cell Atlas relies on images of stained brain slices collected and prepared by the Allen Institute for Brain Science. The Blue Brain project combines this valuable data with other studies to calculate and validate the major types and positions of cells in each area of the mouse brain. Courtesy Allen Institute.

Previous brain atlases consist of stacks of images of stained brain slices. Some show precise cell positions for the entire brain, while others show particular cell types—but none turns this valuable data into numbers and positions of all the cells in the brain in the form of a digitally navigable atlas.

This revolutionary step took five years of carefully collecting and integrating thousands of stainings of brain tissue. Erö and colleagues relied mostly on imaging data made available from the Allen Institute for Brain Science.

The data was then combined with a large number of other anatomical studies to calculate and validate the major types, numbers, and positions of cells in each area of the mouse brain—including all the regions where cell data was never obtained before.

"Our Cell Atlas is 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," says Blue Brain Section Manager, Marc-Oliver Gewaltig.

"It's 3D, it's high resolution, it's searchable, it's navigable, it's annotated, it's user-friendly -- and it fills a huge gap in our knowledge of 96% of the mouse's brain regions."

<strong>Virtual fidelity.</strong> A side-by-side view of the original Nissl stained slice (l) and its virtual counterpart (r), in coronal view. Both show similar structures and correlate quite well despite the generated cells being displayed as simple spheres of uniform size. Courtesy Blue Brain Project/EPFL ©2005 – 2018. All rights reserved.Freely available online, the Blue Brain Cell Atlas allows users to visualize all 737 brain regions and the cells they contain, and to download the region with their numbers and locations.

The Atlas distinguishes excitatory, inhibitory, and some other types of neurons—as well as major types of non-neuronal cells called glia, which insulate and protect neurons. These data are important for researchers trying to understand the structure and function of different brain regions or for building functional models of specific brain regions.

"It is also a great teaching aid: you can choose to display just the regions of interest and navigate through these down to the scale of individual cells, which are color-coded by the type of their morphology," adds Gewaltig.

The Blue Brain Cell Atlas is also the first brain atlas that is dynamic—allowing researchers to contribute to and improve the atlas with new data.

"We can now move collaboratively towards the ground truth of what is inside the mouse brain," explains Markram.

"Our message to brain researchers everywhere is: try it, use it, add data to it.”

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Read the original article on Frontiers Science News.

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