Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis

Etsuo A Susaki; Kazuki Tainaka; Dimitri Perrin; Fumiaki Kishino; Takehiro Tawara; Tomonobu M Watanabe; Chihiro Yokoyama; Hirotaka Onoe; Megumi Eguchi; Shun Yamaguchi; Takaya Abe; Hiroshi Kiyonari; Yoshihiro Shimizu; Atsushi Miyawaki; Hideo Yokota; Hiroki R Ueda

doi:10.1016/j.cell.2014.03.042

Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis

Cell. 2014 Apr 24;157(3):726-39. doi: 10.1016/j.cell.2014.03.042. Epub 2014 Apr 17.

Authors

Etsuo A Susaki¹, Kazuki Tainaka², Dimitri Perrin³, Fumiaki Kishino⁴, Takehiro Tawara⁵, Tomonobu M Watanabe⁶, Chihiro Yokoyama⁷, Hirotaka Onoe⁷, Megumi Eguchi⁸, Shun Yamaguchi⁹, Takaya Abe¹⁰, Hiroshi Kiyonari¹⁰, Yoshihiro Shimizu¹¹, Atsushi Miyawaki¹², Hideo Yokota⁵, Hiroki R Ueda¹³

Affiliations

¹ 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.
² 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.
³ Laboratory for Systems Biology, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
⁴ Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
⁵ Image Processing Research Team, RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
⁶ Laboratory for Comprehensive Bioimaging, RIKEN Quantitative Biology Center, OLABB, Osaka University, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
⁷ Bio-Function Imaging Team, RIKEN Center for Life Science Technologies, 6-7-3 Minatojima-minamimachi, Chuo-ku, Kobe City, Hyogo 650-0047, Japan.
⁸ Division of Morphological Neuroscience, Gifu University Graduate School of Medicine, 1-1 Yanagido, Gifu City, Gifu 501-1194, Japan.
⁹ 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.
¹⁰ Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
¹¹ Laboratory for Cell-Free Protein Synthesis, RIKEN Quantitative Biology Center, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
¹² Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
¹³ 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.

PMID: 24746791
DOI: 10.1016/j.cell.2014.03.042

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Brain / cytology
Callithrix
Indicators and Reagents / chemistry
Mice
Microscopy / methods
Neuroimaging / methods*

Substances

Indicators and Reagents