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We live in a three dimensional world.  X, Y and Z are the coordinates that define the space in which we occupy and are the boundaries that define the natural world.  Nature has learned to take full advantage of this space and has created beautiful three-dimensional structures that fill every dimension to the fullest.  Below is a photograph from one of my favorite photographers, Ansel Adams.  This photo has an amazing composition, perfect exposure and lighting, and the artistic touch of a master photographer.  And although this is a wonderfully beautiful photo, one must admit that something is lost when you try to view such a beautiful three-dimensional structure in a two-dimensional image.  The expansiveness of its branches and how they extend radially from the trunk, the fine details of each individual leaf and the way that the tree gently sways in the breeze are lost when flattened into a single image.

Figure 1: “Oak Tree, Sunrise” Ansel Adams

Neuroscientists have struggled with these same problems for decades. The brain, like this oak tree, is a complex three-dimensional structure that has been optimized to process information in a three-dimensional world. Likewise, there is a vast amount of knowledge that can be gained from knowing the three-dimensional structure of neurons within the brain and how this structure may be altered in disease. Unfortunately, the physics of optics and microscopes have made it very difficult to interrogate the three-dimensional connectivity of neurons in a completely intact brain.  As a result, scientists typically make very thin brain slices (around 0.4 mm!) that can be mounted on a microscope slide and then imaged with highly sophisticated microscopes. Figure 2 shows an image of a neuron that was taken using this method. Like the oak tree, this picture holds a lot of information about the structure and biology of the neuron, but there is also a lot of lost three-dimensional information. There is much that neuroscientists can learn from two-dimensional images of the brain, but in order to truly understand how neurons communicate within it, scientists must know the three-dimensional connectivity.

Figure 2: GFP expressing neuron in the dentate gyrus of the hippocampus

In the past few decades, new microscopy techniques such as “confocal” and “two-photon” microscopy, combined with advanced computer algorithms have started to unveil the three-dimensional structure of the brain, and on Wednesday we will post an infographic that describes these microscopy techniques. However, a recent report published in Nature by Karl Deisseroth’s lab at Stanford University, has developed new bio-engineering techniques that may solve many of the problems that have hindered three-dimensional understanding of the brain using current microscopy techniques.

CLARITY is a new technique for processing brain tissue that turns opaque brain tissue completely clear!  Below (Figure 3) is a before and after image of a mouse brain that has been treated with the CLARITY process. In short, CLARITY works by creating a hydrogel lattice that secures all of the proteins in the brain. Then, all of the lipids can be removed without altering the protein structures. Since the lipid bilayers of neurons and other cells are mainly responsible for making the brain impermeable to light, removing them leaves the brain nearly completely transparent!

Clarity Brain
Figure 3: The CLARITY procedure completely removes lipids in the brain, making it transparent.

With CLARITY, the Deisseroth lab was able to use standard microscopy techniques to image the three-dimesnsional neuronal connectivity in a completely intact mouse brain!  Finally, the Deisseroth lab was able to apply the CLARITY technique to a small piece of brain tissue from an autistic human and was able to image the three-dimensional connectivity of its neurons.  Even with this preliminary study, the researchers found the same abnormal connectivity that had been seen in animal models of autism.The CLARITY technique has the potential to completely revolutionize the whole field of neuroscience and biomedical research in general!  One wonders what amazing photographs Ansel Adams may have taken with a technique like this.



References: Chung et al. Structural and molecular interrogation of intact biological systems. Nature. 2013. DOI: 10.1038/nature12107

Images adapted from


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