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Brain Anatomy Gets 3-D, High-Resolution Makeover

Megan Scudellari

A digital reconstruction of a human brain shows neurological structures at microscopic detail. How will neuroscientists use this new tool? Find out...

In medical schools and neuroscience laboratories around the world, researchers use maps and diagrams of the human brain to teach the fine anatomy of the cerebral cortex. One of the most popular of these is a diagram drawn by German neurologist Korbinian Brodmann back in 1909, detailing the cellular composition of 52 areas in the brain.

Researchers use a special tool called a mcirotome to cut sections from a brain preserved in paraffin wax into tiny slivers 20-micrometers thick. Source: Amunts, Zilles, Evans et al.

This week, an international team of researchers unveiled a brain model for the 21st century: BigBrain, a 3-D digital reconstruction of the human brain with a resolution of 20 microns in 3 directions, finer than the width of a human hair and 50 times more detailed than any other anatomical brain map currently available (1).

“It’s only recently that anatomic approaches have become popular again,” said Peter Sterns, a senior editor at Science who oversaw the publication of the paper, at a press conference on Wednesday. “Researchers have begun to realize that without a really deep knowledge of structures involved, we will never have an understanding of the data being produced by many of these other techniques.”

“BigBrain is the first ever brain model in 3-D that really presents a realistic human brain with all the cells and all the structures,” said study co-author Karl Zilles, a neuroscientist at the University of Düsseldorf and Research Center Jülich in Germany.

The model is the product of over 1000 hours of labor simply to collect the data, according to the authors. The brain of a 65-year-old woman was sliced into 7404 sections, each only 20 microns thick—like a flimsy piece of plastic Saran Wrap. Each section was then mounted on a slide, stained to visualize cellular structures, and scanned into a computer. Then that data was digitally reassembled into a 3-D object, including both manual and digital repairs to fix image defects such as rips, tears, folds, and distortions.

The final reconstruction is on the order of a terabyte of data, said lead author Alan Evans of McGill University in Montreal, Canada, whose team produced software tools to allow researchers to explore the data. “It is the equivalent of something over 100 times larger than a typical MRI [scan] volume.”

“We can now answer questions that can not be addressed using previous brain models because they require resolution at the cellular level,” said Zilles. The new resolution is powerful enough to visualize individual large neurons, such as those 120 micrometers in diameter. Researchers will also be able to use the new atlas as a scaffold to pile on additional data of their own, such as the distribution of receptors in the brain, to learn more about brain function and dysfunction, said Zilles.

“It is a common basis for scientific discussions because everybody can work with this brain model and we can speak about the same basic findings,” he said.

The BigBrain is free and publically available to the research community.


1. Amunts, K., C. Lepage, L. Borgeat, H. Mohlberg, T. Dickscheid, M.-Ã. Rousseau, S. Bludau, P.-L. Bazin, L. B. Lewis, A.-M. Oros-Peusquens, et al. 2013. BigBrain: An Ultrahigh-Resolution 3D human brain model. Science 340(6139):1472-1475.

Keywords:  nueroscience