Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis

• Published in: Cell 2014-04, Vol.157 (3), p.726-739
• Main Authors: Susaki, Etsuo A., Tainaka, Kazuki, Perrin, Dimitri, Kishino, Fumiaki, Tawara, Takehiro, Watanabe, Tomonobu M., Yokoyama, Chihiro, Onoe, Hirotaka, Eguchi, Megumi, Yamaguchi, Shun, Abe, Takaya, Kiyonari, Hiroshi, Shimizu, Yoshihiro, Miyawaki, Atsushi, Yokota, Hideo, Ueda, Hiroki R.
• Format: Article
• Language: English
• Subjects: Animals; Brain - cytology; Callithrix; Indicators and Reagents - chemistry; Mice; Microscopy - methods; Neuroimaging - methods
• ISSN: 0092-8674; 1097-4172
• DOI: 10.1016/j.cell.2014.03.042

Systems-level identification and analysis of cellular circuits in the brain will require the development of whole-brain imaging with single-cell resolution. To this end, we performed comprehensive chemical screening to develop a whole-brain clearing and imaging method, termed CUBIC (clear, unobstructed brain imaging cocktails and computational analysis). CUBIC is a simple and efficient method involving the immersion of brain samples in chemical mixtures containing aminoalcohols, which enables rapid whole-brain imaging with single-photon excitation microscopy. CUBIC is applicable to multicolor imaging of fluorescent proteins or immunostained samples in adult brains and is scalable from a primate brain to subcellular structures. We also developed a whole-brain cell-nuclear counterstaining protocol and a computational image analysis pipeline that, together with CUBIC reagents, enable the visualization and quantification of neural activities induced by environmental stimulation. CUBIC enables time-course expression profiling of whole adult brains with single-cell resolution. [Display omitted] •Simple and efficient brain-clearing reagents and image informatics were developed•CUBIC is applicable to imaging of fluorescent proteins in adult brains and 3D-IHC•The CUBIC method is scalable from a primate brain to subcellular structures•CUBIC enables whole-brain imaging with single-cell resolution CUBIC enables rapid whole-brain imaging with single-photon excitation microscopy and scaling from subcellular structures to a primate brain.