New Imaging Technique Turns Brain Transparent [VIDEO]

Image credit: Chung et al
Image credit: Chung et al

Since the dawn of 20th Century anatomical science, if you wanted to “see” inside an organ, like the brain, you had to remove it, wash it, freeze it, then section it (slice it into thin sections) and stain it for viewing under a microscope. This thin-sectioning or slicing was necessary because a large portion of an organ’s structure is composed of fatty molecules called lipids. Lipids are crucial structural molecules. They are also rather opaque and tend to scatter light, making visualization of internal compartments and processes next to impossible.

If one was more ambitious, one could try to reconstruct the organ by compiling individual images of the sections. Computers made this latter effort more feasible, but even so, the act of sectioning the organ damaged its tissue, and, reconstructing the whole (after slicing and dicing it) was a cumbersome endeavor, to say the least.

But there’s a new imaging technique in town, and its name is CLARITY. The remarkable imaging technique — developed by Stanford University researchers Kwanghun Chung and Karl Deisseroth — strips away an organ’s lipid molecules while leaving everything else (e.g., proteins) in place. This allows for what the researchers call “intact molecular interrogation”.

The CLARITY technique actually renders the organ structure (here, the hippocampus of a mouse brain) almost fully transparent, or nearly invisible. But, with some clever fluorescent molecule “tagging” (or immuno-labeling or staining), key structures (like neurons) can be readily visualized. The result is a mouse brain that you can see through, and actually “travel” through with the aid of 3D computer animation software.

How to Make a Brain Invisible (and Then Visible Again)

The reader may recall that lipids are important structural molecules; they are what hold everything together. If one were to simply, somehow, remove all the lipids from an organ, it would mostly disintegrate into a blob of bio-jelly. This fact has been a major obstacle to past attempts at making organs transparent (such as the ‘Scale’ technique developed by Japanese researchers in recent years).

The CLARITY technique works by immersing the mouse brain into a pool of formaldehyde and acrylamide. The formaldehyde enables important cellular structures to attach themselves to the acrylamide. The acrylamide, when heated, turns into a “nano-porous hydrogel”. Then, using another technique borrowed from gene sequencing science called electrophoresis, an electrical current is applied to the structure which causes anything not attached (like the lipids) to fall away, clearing the tissue and turning it transparent.

Importantly, all other crucial structures like dendrites, axons, organelles, mitochondria, proteins, neurotransmitters, and even DNA are retained in their proper places. In this way the structural integrity of the organ is fully preserved.

And finally, using various staining and fluorescent molecule labeling techniques, a three-dimensional network of hydrophilic polymers” or meshwork structure can be beautifully highlighted and observed in situ. What’s more, the immuno-staining can be removed (“de-staining”), as needed, and replaced with other imaging molecules (e.g., auto-fluorescent or photo-activatable protein dyes).

With the new CLARITY technique, scientists have achieved a long-sought goal: obtaining “high-resolution information about a complex system, while maintaining the global perspective needed to understand system function.”

This breakthrough imaging technique was first made public — presented as a 3D “fly-through” video of the mouse hippocampus — during a press conference at the annual Science/AAAS convention in Boston this past February — wowing all in attendance.

Watch this astounding video (by Chung et al) “fly-through” of a mouse hippocampus made possible by the new CLARITY technique and some nifty 3D animation software (article continues below):

Quoting from the paper abstract (Chung et al ; see link below for full abstract):

“…CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.”

The research was published under the title ‘Structural and molecular interrogation of intact biological systems’ in the on-line version of Nature (more videos can be found at the above link).

Some source material came from the article: Scientists can now turn brains invisible by Robert T. Gonzalez

Photos and video by Chung et al via

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