title: Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis.
abstract: 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.
authors.affiliation: Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Systems Biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
authors.forename: Etsuo A
authors.initials: EA
authors.lastname: Susaki
authors.affiliation: Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Tainaka
authors.affiliation: Laboratory for Systems Biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Perrin
authors.affiliation: Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Fumiaki
authors.initials: F
authors.lastname: Kishino
authors.affiliation: Image Processing Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
authors.forename: Takehiro
authors.initials: T
authors.lastname: Tawara
authors.affiliation: Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center, OLABB, Osaka University, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
authors.forename: Tomonobu M
authors.initials: TM
authors.lastname: Watanabe
authors.affiliation: Bio-Function Imaging Team, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe City, Hyogo 650-0047, Japan.
authors.forename: Chihiro
authors.initials: C
authors.lastname: Yokoyama
authors.affiliation: Bio-Function Imaging Team, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe City, Hyogo 650-0047, Japan.
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Onoe
authors.affiliation: Division of Morphological Neuroscience, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu City, Gifu 501-1194, Japan.
authors.forename: Megumi
authors.initials: M
authors.lastname: Eguchi
authors.affiliation: Division of Morphological Neuroscience, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu City, Gifu 501-1194, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
authors.forename: Shun
authors.initials: S
authors.lastname: Yamaguchi
authors.affiliation: Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Takaya
authors.initials: T
authors.lastname: Abe
authors.affiliation: Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Kiyonari
authors.affiliation: Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Shimizu
authors.affiliation: Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Miyawaki
authors.affiliation: Image Processing Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
authors.forename: Hideo
authors.initials: H
authors.lastname: Yokota
authors.affiliation: Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Laboratory for Systems Biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan; Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan. Electronic address: uedah-tky@umin.ac.jp.
authors.forename: Hiroki R
authors.initials: HR
authors.lastname: Ueda
mesh_terms: D000818:Animals; D001921:Brain / Q000166:cytology; D002144:Callithrix; D007202:Indicators and Reagents / Q000737:chemistry; D051379:Mice; D008853:Microscopy / Q000379:methods; D059906:Neuroimaging / Q000379:methods*
chemical_list: D007202:Indicators and Reagents