Brains as Clear as Jell-O for Scientists to Explore

Scientists at Stanford University reported on Wednesday that they have made a whole mouse brain, and part of a human brain, transparent so that networks of neurons that receive and send information can be highlighted in stunning color and viewed in all their three-dimensional complexity without slicing up the organ.

Even more important, experts say, is that unlike earlier methods for making the tissue of brains and other organs transparent, the new process, called Clarity by its inventors, preserves the biochemistry of the brain so well that researchers can test it over and over again with chemicals that highlight specific structures and provide clues to past activity. The researchers say this process may help uncover the physical underpinnings of devastating mental disorders like schizophrenia, autism, post-traumatic stress disorder and others.

The work, reported on Wednesday in the journal Nature, is not part of the Obama administration’s recently announced initiative to probe the secrets of the brain, although the senior author on the paper, Dr. Karl Deisseroth at Stanford, was one of those involved in creating the initiative and is involved in planning its future.

Dr. Thomas Insel, director of the National Institute of Mental Health, which provided some of the financing for the research, described the new work as helping to build an anatomical “foundation” for the Obama initiative, which is meant to look at activity in the brain.

Dr. Insel added that the technique works in a human brain that has been in formalin, a preservative, for years, which means that long-saved human brains may be studied. “Frankly,” he said, “that is spectacular.”

Kwanghun Chung, the primary author on the paper, and Dr. Deisseroth worked with a team at Stanford for years to get the technique right. Dr. Deisseroth, known for developing another powerful technique, called optogenetics, that allows the use of light to switch specific brain activity on and off, said Clarity could have a broader impact than optogenetics. “It’s really one of the most exciting things we’ve done,” he said, with potential applications in neuroscience and beyond.

“I think it’s great,” said Dr. Clay Reid, a senior investigator at the Allen Institute for Brain Science in Seattle, who was not involved in the work. “One of the very difficult challenges has been making the brain, which is opaque, clear enough so that you can see deep into it.” This technique, he said, makes brains “extremely clear” and preserves most of the brain chemistry. “It has it all,” he said.

In the mid-2000s, a team led by Dr. Jeff Lichtman at Harvard developed a process called Brainbow to breed mice that are genetically altered to make their brain neurons fluoresce in many different colors. The new technique would allow whole brains of those mice with their rainbow neurons to be preserved and studied.

“I’m quite excited to try this,” Dr. Lichtman said.

There are several ways to make tissue transparent. The key to the new technique is a substance called a hydrogel, a material that is mostly water held together by larger molecules to give it some solidity.

Dr. Chung said the hydrogel forms a kind of mesh that permeates the brain and connects to most of the molecules, but not to the lipids, which include fats and some other substances. The brain is then put in a soapy solution and an electric current is applied, which drives the solution through the brain, washing out the lipids. Once they are out, the brain is transparent, and its biochemistry is intact, so it may be infused with chemicals, like antibody molecules that also have a dye attached, that show fine details of its structure and previous activity.

Techniques like this, said Dr. Insel, “should give us a much more precise picture of what is happening in the brains of people who have schizophrenia, autism, post-traumatic stress disorder, bipolar disorder and depression.”

The tricky part was getting the right combination of temperature, electricity and solution. And it was very tricky indeed, said Dr. Chung. Over the course of years spent trying to make it work, he said, “I burned and melted more than a hundred brains.”

But with the paper’s publication, the recipe is now available to anyone who wants to use it, and, he said, “I think it will be relatively easy.”

The technique has its limits, of course. Dr. Chung said more work needed to be done before it could be applied to a whole human brain, because a human’s brain is so much larger than a mouse’s, and has more lipids.

Dr. Chung said he planned to start his own lab soon and to work on refining the technology. But he pointed out that it is already known that it works on all tissue, not just brains, and can be used to look for structures other than nerve cells. On his laboratory bench, he said, “I have a transparent liver, lungs and heart.”

Dr. Reid agreed that Clarity had applications in many fields. “It could permeate biology,” he said.

This article has been revised to reflect the following correction:

Correction: April 10, 2013

An earlier version of this article misstated Dr. Clay Reid’s work with Dr. Jeff Lichtman of Harvard. Dr. Reid was involved in Dr. Lichtman’s Connectome Project, not on the Brainbow team.