The Eye-Opening Discovery of See-Through Brains

Neuroscientists are one step closer to science-fiction with the newest brain-imaging technique called CLARITY.

Developed by Karl Deisseroth and his team of scientists at Stanford University, and published in April, CLARITY is a ground-breaking protocol which renders a brain transparent to light, enabling scientists to make 3D computer models of the neuron networks inside of it.Until now, brains had to be cut up into very thin slices, or sections, to be studied this closely.

“To study the [brain’s] structure, it’s a lot easier if you don’t have to chop it up and put it back together.”

This technique has many limitations, firstly because the slicing could damage parts of the tissue, but also because cutting a brain into slices makes it harder to study as a whole.“You could slice up a sample an try to reconstruct it, but that is very time-consuming and it’s very prone to errors,” said Fabian Peters, a PhD student at University College London. “To study the structure, it’s a lot easier if you don’t have to chop it up and put it back together.”

The method used by CLARITY is called tissue clearing, which has been around for over 40 years, but this protocol is very different in that it injects the brain with a polymer, a transparent plastic, and the liquids and fat in the brain are then flushed out using an electric current.

“Most questions of connectivity can only be answered in 3D,” said Mr Fabian. He is part of one of the first research projects testing the new technique in the United Kingdom. “At this point, we wanted to see whether the tissues we’re interested in can be cleared and that can actually be done within two days, which we are very happy with,” he said.

He explains that the next step would be to stain the structures they are interested in – to inject chemicals into the studied brain, which will color certain parts of it – and see if what they observe using CLARITY corresponds to what they see in sections.


Some things still need to be worked out, though. For now, mice brains can be observed in their entirety, but human brains, being too large, must be cut into smaller chunks. Additionally, the technique being new, it is hard to know exactly how well preserved the brain really is, and how much of it is damaged in the process, according to Mr Peters.

Scientists also have to deal with large amounts of data – maybe too much, according to Mr Peters. He said: “You do produce a hell of a lot of data. For a lot of questions, it may not even be desirable to get a whole brain,” he adds that it is much harder to analyse.

CLARITY enables research to be done in many areas, including pathological conditions such as autism, Alzheimer’s disease, multiple sclerosis or even cancer, said Razan Abdel-Hadi, also studying neuroscience at UCL.

With the BRAIN initiative announced last April by United-States President Barack Obama, aimed at mapping the entire human brain, many innovations and discoveries are to be expected in neuroscience in the years to come.