New Era of rapid Brain Imaging allows brain imaging and understanding of interactions at the cellular level across the brain

Detailed high resolution brain imaging has been made one hundred times faster. Stanford University researchers who developed the new method CLARITY to see the brain in greater detail said that it could mark a new era of rapid brain imaging, allowing researchers to see in much greater detail not only how parts of the brain interact on a cellular level but also to better understand those interactions across the entire brain.

Cellular structure and neuron firing

It allows for three-dimensional visualization that is both granular and wide enough to encompass the entire brain. Said Sanchez, “Traditionally, with the optogenetic technique, you really don’t have the structure to go along with the activation. That’s why the Neuro-FAST program is so exciting.”

DARPA Neuro-FAST project builds off of the recently developed CLARITY process, as well as recent discoveries in genetics, optical recordings, and brain-computer interfaces. By combining all four areas, Neuro-FAST seeks to allow researchers to individually identify specific cell types, register the connections between organizations of neurons, and track their firing activity using optical methods in awake, behaving subjects. Neuro-FAST researchers must overcome the dual challenges of achieving single-neuron resolution while simultaneously being able to analyze activity from large numbers of neurons to acquire detailed modeling of the dynamic wiring of neural circuits that cause behavior. Such models would then be coupled with brain activity in real-time to better understand how brain processes work. Neuro-FAST envisions development of novel optical methods to enable the necessary recording.

The data generated by this process would be unlike any previously produced by the neuroscience community and would feed a growing body of knowledge about brain function and form. In addition to fundamental rodent research already underway, Neuro-FAST will expand the processes to non-human primate brains and whole-organ human tissue samples from existing repositories to create a deep understanding across higher-order mammals.

If successful, Neuro-FAST will support pioneering research into brain function over a wide range of spatial and temporal scales to better characterize and mitigate threats to the human brain and facilitate development of brain-in-the loop systems to accelerate and improve functional behaviors.

Nature Protocols – Advanced CLARITY for rapid and high-resolution imaging of intact tissues.

CLARITY is a method for chemical transformation of intact biological tissues into a hydrogel-tissue hybrid, which becomes amenable to interrogation with light and macromolecular labels while retaining fine structure and native biological molecules. This emerging accessibility of information from large intact samples has created both new opportunities and new challenges. Here we describe protocols spanning multiple dimensions of the CLARITY workflow, ranging from simple, reliable and efficient lipid removal without electrophoretic instrumentation (passive CLARITY) to optimized objectives and integration with light-sheet optics (CLARITY-optimized light-sheet microscopy (COLM)) for accelerating data collection from clarified samples by several orders of magnitude while maintaining or increasing quality and resolution. The entire protocol takes from 7–28 d to complete for an adult mouse brain, including hydrogel embedding, full lipid removal, whole-brain antibody staining (which, if needed, accounts for 7–10 of the days), and whole-brain high-resolution imaging; timing within this window depends on the choice of lipid removal options, on the size of the tissue, and on the number and type of immunostaining rounds performed. This protocol has been successfully applied to the study of adult mouse, adult zebrafish and adult human brains, and it may find many other applications in the structural and molecular analysis of large assembled biological systems.

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