For decades, researchers' understanding of brain structure and function has remained fragmented due to difficulties integrating observations and insights at the levels of individual brain cells, neural circuits and systems-level information processing. Now a new research protocol promises to help overcome this barrier by allowing scientists to visualize the brain across multiple scales.

As described in a newly published scientific report DARPA-funded performers have developed a new protocol that incorporates two major technological advances that enable more efficient application of the CLARITY method to study brain tissue.

CLARITY uses a chemical process to transform intact biological tissue into a hybrid of tissue and hydrogel, a transparent material that keeps three-dimensional tissue structure intact during preservation.

This process enables detailed exploration and analysis of the fine biological and molecular structure of the entire brain. The new protocol still involves hydrogel formation but improves upon the approach by reducing the risk of damaging the preserved brain tissue, which is especially important when working with irreplaceable human brain samples.

The second improvement has to do with how the tissue is imaged. Under the original CLARITY protocol, the imaging process was relatively slow-not a problem for smaller animal brains but a single human brain would take approximately 80 years to complete. The new protocol incorporates a method called light-sheet microscopy that greatly accelerates the imaging process so that visualizing an entire human brain would only take about 220 days.

The new methods were developed with support from DARPA's Neuro Function, Activity, Structure, and Technology (Neuro-FAST) program by the same Stanford University research team that created the original CLARITY technique.

It is described in detail in a paper in Nature Protocols (http://bit.ly/1nRiIW1) - the first paper with DARPA funding to be published in a peer-reviewed scientific journal under President Obama's brain initiative.

The Neuro-FAST program has as its goal the development of new neurotechnologies to enable unprecedented visualization and decoding of brain activity. DARPA is interested in CLARITY for its potential to reveal principles fundamental to the understanding of neural systems. Neuro-FAST intends to more fully leverage the CLARITY method by integrating new discoveries in genetics, optical recording technologies and brain-computer interfaces, with the goal of better understanding how brain processes work.

"For as long as neuroscience has existed as a field, researchers have been limited in their ability to understand the total brain because they haven't had the tools to measure all the critical details of neural circuits," said Justin Sanchez, DARPA program manager.

"DARPA is working to build out the neurotechnological toolkit to speed the rate of discovery and innovation."

DARPA's planned investment in the Neuro-FAST program is up to $30 million over four years.