Currently, to see brain tissue under a microscope, neuroscientists have to slice it into slivers about the thickness of a human hair, so that light can pass through. To analyze an entire mouse brain this way — a process that Dr. Lichtman’s lab is attempting, but that is nowhere near finished — the organ needs to be divided into roughly a hundred slices, each of which must be passed under a microscope for a snapshot of its cells.

Not only is the process labor-intensive, but the slices of brain can get distorted, and small bits of tissue can get lost. These hard-to-avoid errors can turn the snapshots into deformed puzzle pieces that can’t easily be fitted together into a wiring diagram.

A mouse brain that has been clarified with Scale, on the other hand, is clear enough without thin-slicing, and could be imaged in three big chunks, avoiding these problems, according to Dr. Miyawaki. Because it clarifies tissue without removing water, the solution sustains genetically introduced cell labels — used to differentiate one neuron from the next — in a wet environment like the one in which they originally evolved. The labels are made of proteins that come from jellyfish and corals.

According to Dr. Miyawaki, Scale works much better on young brains than on older ones, which are filled with more hard connective tissue that doesn’t absorb the solution as readily.

So far, Dr. Miyawaki and his team have used the solution only on dead tissue. The next step, he said, is to come up with a formulation that works on living tissue, though for now that is a distant goal.

Scale is not difficult to make: It is a cheap mixture of urea (found in urine and fertilizer), glycerol and detergent. While he and a colleague hold the patent on it, Dr. Miyawaki included the complete recipe in his recently published article and hopes that labs around the world will start using it for brain mapping.

Neuroscientists can’t answer important questions about the brain until they have a map of the neuronal circuit, Dr. Miyawaki said, adding, “and there are many, many important questions.”