Understanding the relationship between cellular phenomena and activity at the organism level has been difficult, particularly where the brain is concerned. Whole-brain imaging at single-cell resolution could help. As scientists aim to clarify how neural activity translates into consciousness and other complex brain activities, a team from the Riken Quantitative Biology Center and other Japanese research institutions has developed a solution. Comparative analysis of whole-brain image. Courtesy of Riken. A new high-throughput method called CUBIC (Clear, Unobstructed Brain Imaging Cocktails and Computational Analysis) allows for rapid whole-brain imaging at single-cell resolution. Such imaging traditionally involves preparation of a highly transparent brain sample that minimizes light scattering, and then imaging of neurons tagged with fluorescent probes to produce a 3-D representation. With the new technique, which is a “simple and efficient method involving the immersion of brain samples in chemical mixtures,” the sample is cleared and made transparent with the use of amino alcohols. This enables rapid whole-brain imaging with single-photon excitation microscopy. Also using light sheet fluorescence microscopy, CUBIC has acquired new spatial-temporal details of gene expression patterns in the hypothalamic circadian rhythm center of the brain in mice and primates. Combining images taken from opposite directions, the technique enables whole-brain imaging as well as direct comparison of brains in different environmental conditions. CUBIC can be used with fluorescent probes, the researchers said, as low quenching allows longer wavelengths and also reduces concern about scattering, while at the same time inviting multi-color imaging. The method is highly reproducible and scalable, researchers said. Information about 3-D gene expression profiles and neural networks at the systems level has been previously unattainable. CUBIC’s imaging now allows analysis of localized effects of genomic editing, and may also be able to identify neural connections at the whole-brain level or beyond. “In the near future, we would like to apply CUBIC technology to whole-body imaging at single-cell resolution,” said Hiroki Ueda of the Riken Center for Developmental Biology. The research is published in Cell. (doi: 10.1016/j.cell.2014.03.042) For more information, visit: www.riken.jp/en