“Clarifying” Neural Circuitry: A New Technique to Image the Brain


By: Daniel Hass, 1st year PhD student in the Neuroscience Program

brain-functions-1orm1qfThe brain is complicated.

There are hundreds of structures, layers, and cell types interacting with each other in complex ways in order for us to perform simple tasks, such as maintaining heart beat or moving a finger.  Much of this complexity comes from the trillions of connections between brain cells.  These connections are not only the basis for movement and perception, but also for thought and behavior.

A significant portion of neuroscience research is devoted towards mapping the connections between different areas of the brain.  In fact, this is an area of research that has seen an increase in funding due to President Obama’s BRAIN initiative. If we know how neurons (brain cells) are wired, we may be able to determine what is different in the brains of individuals with neurological disorders such as autism, schizophrenia, and bipolar disorder.

This is a pretty tall order for neuroscientists, and it is likely going to be years before the first human “connectome,” or map of all the neuronal connections in a human brain, is published.

The greatest roadblock of all, of course, is that the brain is 3-dimensional.

Some scientists, led by Dr. Dmitri Chklovskii, are currently attempting to build a 3-D diagram of a brain by cutting up the fruit fly medulla (a region in the brainstem), staining them, and reconstructing them using computer programs.


3D reconstruction of a fruit fly medulla.

Although time-consuming and difficult, these 3-D reconstructions of these brain sections are quite beautiful.

Another significant roadblock is that brains are opaque.  To you, my brain would look like a ball of tan mush (because that’s what it is—maybe other people’s look nicer).  This makes it very difficult to view internal connections.

Recently, efforts to solve this problem have yielded an experimental solution (quite literally) that will make brains clear.  Once a brain is clear, current techniques can be used to detect proteins, single neurons, or entire networks of neurons.

This system is called CLARITY (short for “Clear, Lipid-exchanged, Anatomically Rigid, Imaging/immunostaining compatible, Tissue hYdrogel”).  CLARITY takes advantage of the lipids (fats) that compose our cell membranes. First, experimenters preserve the molecular structure of the brain with chemicals like formaldehyde.  Next, they can perfuse a hydrogel (gel-like polymer containing water) throughout the brain that breaks down these lipids.  After clearing the hydrogel, scientists have a clear, intact 3D brain.


Mouse brain before and after CLARITY.

These experiments can be used to answer questions such as “Where is this protein in the brain?” or “What is connected to this neuron?”. The above image is an example of CLARITY where the Deisseroth lab was able to detect the expression of multiple proteins at once in the area of the brain devoted to memory formation called the hippocampus. See some amazing examples of some more science done by the Deisseroth lab here.

Theoretically, this technique could be used in any organ system.  The brain just happens to be the system with the most complex network of cellular connections.

Not many labs have adopted this technique yet.  It’s too recent, and human brains are not always in abundant supply.  However, in the next few years, we will likely see a surge in the number of labs using this technique to see how specific neurological pathways change, especially in cadaver tissue of individuals with Autism Spectrum Disorders, Parkinson’s Disease, and other neurological disorders.

Interestingly, both CLARITY and another recent technique called optogenetics were developed in the lab of Dr. Karl Deisseroth at Stanford. For those of you interested in learning more about imaging techniques, he will be the keynote speaker at the Penn State Hershey Neuroscience Retreat on Saturday, March 29th.


Mouse hippocampus using the CLARITY technique.

Both CLARITY and optogenetics are useful brain mapping tools that may lead us towards the creation of a map of all of the connections in the human brain, allowing us to finally gain a structural understanding of the many neurological disorders out there.

It is an exciting time to be in neuroscience.

Chung, K., et al. (2013). “Structural and molecular interrogation of intact biological systems.” Nature 497(7449): 332-337.

Takemura, S. Y., et al. (2013). “A visual motion detection circuit suggested by Drosophila connectomics.” Nature 500(7461): 175-181.

Images courtesy of the Deisseroth lab and Dmitri Chklovskii

2 thoughts on ““Clarifying” Neural Circuitry: A New Technique to Image the Brain

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