The Funky Physics of Turning an Animal Transparent

Biology labs use a new chemical called Scale to turn specimens transparent, so they can look into them. The result makes a mouse embryo (pictured) look like a Gummi bear.
Discovered last year by researchers at Japan’s Riken Brain Science Institute, Scale is made from compounds commonly found in the biology lab, like urea and the detergent Triton X. Scale’s low cost means it can be used much more widely than previously developed sample-clearing agents, and it allows scientists to see deeper into tissue than ever before. The discovery enabled the Riken team to produce some of the most detailed maps of brain neurons ever published.

An article at DISCOVER magazine looks at the physics of light and explains how transparent molecules are different from opaque molecules. Which leaves me to wonder how scientists can see what they are looking for if it all turns transparent -and could making a specimen transparent change it so much that what you find is rendered meaningless? Link -via Not Exactly Rocket Science

(Image credit: Riken)

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In this study, the authors are looking primarily for fluorescent proteins, and the article says that "Scale renders mouse brain and embryos transparent while completely preserving fluorescent signals from labeled cells."

It seem like the goal here is to be able to take a mutant mouse that expresses a fluorescent protein in some subset of cells, crack its neck, take out its brain, put it in a solution of Scale, and then use a confocal microscope to create a 3D reconstruction of the distribution of the fluorescent protein. That's pretty cool...
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Oddly enough, how they achieve transparency reminds me of how the invisible man became invisible in the book.

Something along the lines of drinking a potion that gives everything the same reflective index.

I looked for the excerpt but Google could not find it so all my options are exhausted.
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As an aside - I always wondered how the Invisible Man was supposed to see.

The eyes work by using (absorbing) light energy to trigger neuron signalling to the brain. If light is travelling right THROUGH (or being bent around) the retinas, it isn't being absorbed, so isn't triggering the nerves.

Therefore the Invisible Man would be blind!
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If I remember correctly one of the things about the invisible man that wasn't invisible were his retinas. While it has been a long time since I have read it I believe the trial cat subject had the same problem. It was one of the several drawbacks that he had not thought through, such as digestion.
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