Neuroscientists Create First Ever 3D 'Whole Human Brain' Map [VIDEO]

Published on June 21st, 2013 | by

June 21st, 2013 by

3D brain
photo credit: CLIPAREA l Custom media via

An international consortium of neuroscientists has completed a ten year effort in high-resolution “brain mapping” and created the most detailed map of a whole human brain ever produced.

The complete 3D brain atlas is constituted from over 20,000 trillion bytes (terabytes) of data (more data than could be handled by any computer ten years ago). Not surprisingly, the atlas is named ‘Big Brain’, and it reveals the underlying (microscopic) neurological details of a 65-yeal old woman’s brain. The atlas will help brain scientists clarify important brain structures revealed by earlier brain-mapping efforts — it may even redefine those structures and lead to important new insights.

Big Brain is a core project of the Human Brain Project (HBP) which is a ten-year long European effort to create a “supercomputer simulation of the human brain.” A more detailed mapping of neuronal clustering — such as provided by Big Brainwill help the group establish realistic parameters for the planned, final simulation. The atlas project was led by Katrin Amunts, a neuroscientist from the Heinrich Heine University Dusseldorf in Germany.

How to Make, and Use, Your Big Brain

The process of making Big Brain began in the usual way for brain anatomy studies: the brain of the dead woman was removed, cleaned, encased in paraffin wax and sectioned — 7,400 times to be precise — with the ultra-thin slices then imaged by a powerful microscope. This step alone took over 1,000 hours and generated a trillion bytes of data.

The final step took the longest time: supercomputers in Germany and Canada spent the last ten years reconstructing the whole brain from these 7,400 slices, after correcting for small tears and wrinkles in the thinner-than-a-human-hair brain slices.

The human brain is composed of highly-varied, many-sized and interconnected networks of neurons which are rather densely packed within its many lobes and structures. The atlas reveals the variable, spatial distribution of these heterogeneous networks as they spread out over the cerebral cortex and other brain areas. It is believe that these differences in neural density (the “neural clustering”) and distribution indicate distinct brain function areas, or units.

The Big Brain atlas achieves a 20 micron resolution (20 millionths of a meter) which is enough to see individual neurons and some of their details like the soma (the main part of of a nerve cell from which dendritic, “tree-like”, branchings protrude to receive incoming signals). Previous brain maps made from whole brain scans were only able to achieve a resolution of one millimeter — barely enough to see even a single neuron in many brain areas.

Watch this awesome video of the computer reconstruction of the individual brain sections to create the 3D whole brain map (article continues below):

“This completely changes the game in terms of our ability to discriminate very fine structural and physiological properties of the human brain,” said fellow researcher Alan Evans, a neurologist at the Montreal Neurological Institute at McGill University in Canada, at a press conference on 19 June.

Big Brain will serve as a reference atlas for the improvement other data sets and their respective brain maps. Next up: a collaboration with the Allen Brian Institute in Seattle, Washington, which will see the linking up of their two databases (the Allen Brain project is a full mapping, with network annotations, of the mouse brain). The team also plans to publicly release the full data set on-line in the near future and is already working on “brain number 2.”

The neuroscience team published their results today (June 21, 2013) in the journal Science. Learn more about the supercomputer simulation of the human brain.

Some source material for this post came from the Sci Am article ‘Whole Human Brain Mapped in 3D by Helen Shen and Nature magazine.

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