Method for making brain transparent may open scientific frontier

Scientists have created a way to make a human brain transparent, enabling them to take deep three-dimensional tours through the mysterious organ and trace its circuitry down to the molecular level.

The recipe for transforming cadaver brains into see-through research tools stands to accelerate investigations of Alzheimer’s disease, schizophrenia and a host of other brain maladies, and already has led to a significant insight into the peculiar characteristics of neurons associated with Down syndrome and autism.


The advance, published online Wednesday by the journal Nature, was described by scientists as “transformative” and just plain “cool.” It involves washing away the fat that normally obscures the view of cells and replacing it with a see-through gel to hold everything in place.

“This feat of chemical engineering promises to transform the way we study the brain’s anatomy and how disease changes it,” said Dr. Thomas R. Insel, director of the National Institute of Mental Health, which funded the research conducted at Stanford University.


The technique also could be applied to other organs and structures, making it useful for cancer research and other fields, according to the Stanford scientists who developed it.

In much the same way that advanced telescopes flooded astronomers with data that led to such discoveries as the existence of dark energy, the transparent brain model may push neuroscience into an era marked by rapid advances, experts said.

No longer will researchers have to choose between examining brain tissue one minuscule slice at a time or using larger-scale techniques that can’t detect the finest roots of the organ’s circuitry. As an added benefit, the finite supply of brain tissue, some of it stewing in jars for years, now can be subjected to multiple tests that won’t ruin the samples.

The result: Enormous amounts of data are likely to be unleashed in a field that President Obama has identified as the next frontier in science.


The Stanford team of engineers, neuroscientists, psychiatrists and computer experts aimed to break down stubborn barriers that made it extremely difficult to “see” inside the brain.

The first impediment was the brain’s structure itself, held together by a lattice of lipids. Those fats are excellent for transmitting electrical impulses over the relatively long networks of the brain, but they wreak havoc on light.

Scientists wondered whether they could remove the fats and replace them with something that didn’t diffract as much light but preserved the brain’s structure. The task was somewhat akin to removing the binder from a casserole and replacing it with Jell-O.

“It wasn’t obvious, the strategy,” said Karl Deisseroth, the Stanford bioengineer who led the team. “A lot of things didn’t work. There were a lot of eureka moments in the lab.”


Similar attempts by other researchers to clear the fat out of brain tissue had run into many obstacles, Deisseroth said. For instance, some of the solvents that had been tried made it difficult for scientists to use the fluorescent stains they need to highlight cells and other structures. Such staining is a mainstay of microbiology.

It took six years to find a successful technique that used acrylamide, bisacrylamide and formaldehyde, among other ingredients. They called their method CLARITY (short for Clear Lipid-exchanged Anatomically Rigid Imaging/immunostaining-compatible Tissue hYdrogel).

Their success is apparent in a pair of photographs taken by the researchers. In one of them, an untreated mouse brain sitting in a petri dish atop a printed page partially obscures a block of text. After it was subjected to the CLARITY technique, the words of Santiago Ramon y Cajal, the father of neuroscience, become visible: “The brain is a world consisting of a number of unexplored continents and great stretches of unknown territory.”

The team experimented first with mouse brains, then tested their method on a portion of a brain from a human cadaver.

The result was a research tool that stands to be much more versatile than the traditional methods used to study brain tissue.

Today, researchers tracing the brain’s smallest physical structures slice the tissue into sections less than a millimeter thick, then stain each one and track the results from slice to slice. The process is painstaking, and when they’re done, the tissue can’t be used again for other experiments.

Those difficulties and the limited supply of human brain tissue forced researchers to do most of their experiments in mice, which is less than ideal for studying human maladies.

“Human tissue, that’s often very precious,” said Pavel Osten, a neuroscientist at Cold Springs Harbor Laboratory in Long Island, N.Y., who was not involved in the study. “And good human tissue is extremely precious.”

Now scientists have the potential to get more information from that precious resource. Using CLARITY, the Stanford team was able to probe the brain without taking it apart, do it at a high resolution and do it repeatedly.

“You can find out where your favorite neurotransmitter is, where your favorite gene is expressed,” Insel said. “That’s pretty cool.”

Deisseroth and his colleagues were eager to take their invention for a test-drive. They tried it out on a human brain that had belonged to someone who had autism and that had been preserved for six years.

They found a deeply buried neuron that “looped back on itself,” Deisseroth said. That strange bridging is not typical of a normal brain, and it resembles abnormalities associated with autism and Down syndrome.

Much more work would need to be done to explore the implications of that find, which also has been seen in animals, but “it’s not out of the question” that the structure is key to autism, said Deisseroth, who is trained in psychiatry as well as engineering.

As buzz about CLARITY’s success circulated through scientific circles in recent weeks, researchers have been contacting the Stanford lab, eager to analyze brain samples and tumor biopsies from other parts of the body, Deisseroth said.

In theory, the recipe for removing lipids from brain tissue could be used in all other human organs.

“Nothing about CLARITY is limited to the brain,” Deisseroth said.

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