Scientists Achieve Rapid Whole-Brain Imaging with Single Cell Resolution

An intensive effort has been made, particularly in the brain, to determine how neural activity is converted into consciousness and other complicated brain activities. A new high-throughput technology called CUBIC (clear, unobstructed brain imaging cocktails and computational analysis) appears to be a giant leap forward, as it offers unprecedented rapid whole-brain imaging at single cell resolution with a straightforward protocol to clear and make the brain sample transparent based on the use of amino-alcohols.

A key problem of systems biology is determining how phenomena at the cellular scale correlate with activity at the organism level. One example of the technologies that may provide better understanding of these phenomena is whole-brain imaging at single-cell resolution. This imaging typically involves preparing a highly transparent sample that minimizes light scattering and then imaging neurons tagged with fluorescent probes at different slices to generate a three-dimensional (3D) representation. However, limitations in current techniques prevent comprehensive study of the relationship. The project’s findings were published April 24, 2014, in the journal Cell.


In combination with light sheet fluorescence microscopy, CUBIC was evaluated for rapid imaging of a number of mammalian systems, such as mouse and primate, demonstrating its scalability for brains of different size. Moreover, it was used to acquire new spatial-temporal details of gene expression patterns in the hypothalamic circadian rhythm center. Moreover, by combining images captured from opposite directions, CUBIC enables whole brain imaging and direct comparison of brains in diverse environmental settings.

CUBIC tackles a number of obstacles compared with earlier strategies. One is the clearing and transparency protocol, which involves serially immersing fixed tissues into just two reagents for a comparatively short time. Second, CUBIC is compatible with many fluorescent probes because of low quenching, which allows for probes with longer wavelengths and lessens concern for scattering when whole brain imaging, while at the same time provides multicolor imaging. Lastly, it is highly reproducible and scalable. Whereas other approaches have achieved some of these abilities, CUBIC is the first to accomplish it all.

CUBIC provides data on earlier unattainable 3D gene expression profiles and neural networks at the systems level. Because of its rapid and high-throughput imaging, CUBIC offers an amazing opportunity to study localized effects of genomic editing. It also is expected to identify neural connections at the whole brain level. Last author Dr. Hiroki Ueda, from RIKEN (Saitama, Japan) is excited about further applications to even larger mammalian systems. “In the near future, we would like to apply CUBIC technology to whole-body imaging at single cell resolution.”

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