[ExI] Making brains transparent for HD brain imaging

[Stuart LaForge]

I just happened upon this Nature article from 2013 that blew me away  
and certainly has implications for cryonics and uploading. The highly  
recommended video shows off an incredible new brain imaging technique  
called CLARITY that uses detergents and a hydrogel to make entire  
brains transparent to light microscopes, allowing unprecedentedly  
detailed connectome mappings:

https://www.nature.com/news/see-through-brains-clarify-connections-1.12768

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A chemical treatment that turns whole organs transparent offers a big  
boost to the field of ‘connectomics’ — the push to map the brain’s  
fiendishly complicated wiring. Scientists could use the technique to  
view large networks of neurons with unprecedented ease and accuracy.  
The technology also opens up new research avenues for old brains that  
were saved from patients and healthy donors.

“This is probably one of the most important advances for doing  
neuroanatomy in decades,” says Thomas Insel, director of the US  
National Institute of Mental Health in Bethesda, Maryland, which  
funded part of the work. Existing technology allows scientists to see  
neurons and their connections in microscopic detail — but only across  
tiny slivers of tissue. Researchers must reconstruct three-dimensional  
data from images of these thin slices. Aligning hundreds or even  
thousands of these snapshots to map long-range projections of nerve  
cells is laborious and error-prone, rendering fine-grain analysis of  
whole brains practically impossible.

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The new method instead allows researchers to see directly into  
optically transparent whole brains or thick blocks of brain tissue.  
Called CLARITY, it was devised by Karl Deisseroth and his team at  
Stanford University in California. “You can get right down to the fine  
structure of the system while not losing the big picture,” says  
Deisseroth, who adds that his group is in the process of rendering an  
entire human brain transparent.

The technique, published online in Nature on 10 April, turns the brain  
transparent using the detergent SDS, which strips away lipids that  
normally block the passage of light  (K. Chung et al. Nature  
http://dx.doi.org/10.1038/nature12107; 2013). Other groups have tried  
to clarify brains in the past, but many lipid-extraction techniques  
dissolve proteins and thus make it harder to identify different types  
of neurons. Deisseroth’s group solved this problem by first infusing  
the brain with acryl­amide, which binds proteins, nucleic acids and  
other biomolecules. When the acrylamide is heated, it polymerizes and  
forms a tissue-wide mesh that secures the molecules. The resulting  
brain–hydrogel hybrid showed only 8% protein loss after lipid  
extraction, compared to 41% with existing methods.

Applying CLARITY to whole mouse brains, the researchers viewed  
fluorescently labelled neurons in areas ranging from outer layers of  
the cortex to deep structures such as the thalamus. They also traced  
individual nerve fibres through 0.5-millimetre-thick slabs of  
formalin-preserved autopsied human brain — orders of magnitude thicker  
than slices currently imaged.


Kwanghun Chung & Karl Deisseroth, HHMI/Stanford Univ.

Neurons in an intact mouse hippocampus visualized using CLARITY and  
fluorescent labelling.

Expand
“The work is spectacular. The results are unlike anything else in the  
field,” says Van Wedeen, a neuroscientist at the Massachusetts General  
Hospital in Boston and a lead investigator on the US National  
Institutes of Health’s Human Connectome Project (HCP), which aims to  
chart the brain’s neuronal communication networks. The new technique,  
he says, could reveal important cellular details that would complement  
data on large-scale neuronal pathways that he and his colleagues are  
mapping in the HCP’s 1,200 healthy participants using magnetic  
resonance imaging.

Francine Benes, director of the Harvard Brain Tissue Resource Center  
at McLean Hospital in Belmont, Massachusetts, says that more tests are  
needed to assess whether the lipid-clearing treatment alters or  
damages the fundamental structure of brain tissue. But she and others  
predict that CLARITY will pave the way for studies on healthy brain  
wiring, and on brain disorders and ageing.

Researchers could, for example, compare circuitry in banked tissue  
from people with neurological diseases and from controls whose brains  
were healthy. Such studies in living people are impossible, because  
most neuron-tracing methods require genetic engineering or injection  
of dye in living animals. Scientists might also revisit the many  
specimens in repositories that have been difficult to analyse because  
human brains are so large.

The hydrogel–tissue hybrid formed by CLARITY — stiffer and more  
chemically stable than untreated tissue — might also turn delicate and  
rare disease specimens into re­usable resources, Deisseroth says. One  
could, in effect, create a library of brains that different  
researchers check out, study and then return.
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This was way back in 2013. These days they are making whole mice  
transparent. How did I (we?) miss this?

Stuart LaForge