The Brain: Now You See It, Soon You Won’t

A post mortem brain is a white, fatty, opaque, three-pound mass. Traditionally scientists have looked inside it by cutting the brain into thin slices, but the relationships and connections of the tens of billions of neurons are then almost impossible to reconstruct.   What if we could strip away the fat and study the details of the wiring and the location of specific proteins, in three dimensions? An NIH funded team at Stanford University has done just that, developing a breakthrough method for unmasking the brain.

Using a chemical cocktail, they infuse the brain with a hydrogel that locks in the brain’s form and structure in a type of matrix. Then the fatty layer that coats each nerve cell is stripped away, leaving a transparent brain (check out the transparent mouse brain below). The hydrogel prevents the brain from disintegrating into a puddle once the fat is gone.

Photo on the left shows an opaque mouse brain. Photo on the right (after CLARITY) shows a nearly transparent mouse brain.

Caption: CLARITY transforms a mouse brain at left into a transparent but still intact brain at right. Shown superimposed over a quote from the great Spanish neuroanatomist Ramon y Cajal.
Credit: Kwanghun Chung and Karl Deisseroth, Howard Hughes Medical Institute/Stanford University

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