Tech by VICE

Katrin Amunts is Making a Digital Atlas of the Human Brain

The celebrated German neuroscientist has spent her career pioneering the 3D reconstruction of the human brain.

by Daniel Oberhaus
Feb 3 2017, 8:19pm

Image: Electra Sinclair

Humans of the Year

The last decade has been a big one for neuroscience. Many of the large breakthroughs—from understanding how schizophrenic brains regenerate to how psychoactive drugs work on the brain—were only possible thanks to equally impressive advances in neuroimaging technology. In this respect, the European Union's Human Brain Project is in a league of its own.

The Human Brain Project is a decade-long initiative focused on a variety of different platforms related to human neuroscience, but at its core is BigBrain, the most detailed 3D atlas of the human brain ever created. BigBrain will allow researchers to better investigate telltale signs of neurological disease and the way drugs interact with diseased brains, paving the way for drastically improved diagnosis and treatment.

At the helm of the BigBrain project is Katrin Amunts, the 54-year-old director of the Institute of Neuroscience and Medicine at the Jülich Research Center in Germany. Amunts' career as a neuroscientist began in 1989 when she received her doctorate from the Institute of Brain Research in Moscow, but according to her, she has been fascinated by the brain for much longer.

"My interest [in neuroscience] had already started during my studies in the second or third grade," Amunts told Motherboard. "I found that neuroscience was the most interesting and cool topic that I had."

Amunts was born and raised in Eastern Germany and during the cold war the majority of her higher education took place in Russia. At the start of her career, she focused on researching the cellular structure of children with cerebral palsy. When the wall came down in 1989, she moved to Düsseldorf in Western Germany and her fascination with the architecture of the brain took on a broader scope as she became involved with early brain-mapping efforts in the 1990s.

Katrin Amunts with Joachim Gauck, president of Germany. Image courtesy of Katrin Amunts

These efforts would eventually culminate in BigBrain, which in 2013 became the most detailed 3D map of the brain ever created. Prior to BigBrain, the most sensitive magnetic resonance imaging systems could only give a spatial resolution of about 1 millimeter, far too large for cellular resolution. BigBrain blew this previous resolution out of the water by offering an ultra-high resolution 3D model of the brain at a scale of 20 micrometers—still a little larger than cellular scale, but barely so.

The 3D model created by BigBrain was based on the brain of a 65-year old male which was cut into 7400 sections of 20 micrometer thickness. These sections were then stained to show different cell bodies and then scanned to give a digital image of about 13,000 by 11,000 pixels.

This feat of neuroimaging was impressive in 2013, but now Amunts and her colleagues are working on an even more impressive task.

"My hope is that we are going to even higher resolution," said Amunts. "With a resolution of one micrometer, we can image and analyze every cell in the human brain and have a cellular model of the human brain in the next few years."

The supercomputers behind the BigBrain project. Image: Jülich Supercomputing Center

As Amunts points out, this demand is a large one. Scanning over 7000 sections of the brain at that high of a resolution takes months, and at the end of it all she and her colleagues are left with upwards of 8 petabytes of data to filter through and then use to reconstruct a 3D model of the brain. To do this, the BigBrain project has partnered with the Jülich Supercomputing Center to facilitate this process.

"I think to approach the human brain like this is simply not possible in one leap or even in one country because the complexity is so high," said Amunts. "To bridge all these different scales, to combine them and extract information of how these scales can be translated to each other, this is only feasible in a very large effort [and] the Human Brain Project makes achieving these goals possible. We are now running with this full speed and this is what I like most."