title: Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.
abstract: Here we describe a protocol for advanced CUBIC (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis). The CUBIC protocol enables simple and efficient organ clearing, rapid imaging by light-sheet microscopy and quantitative imaging analysis of multiple samples. The organ or body is cleared by immersion for 1-14 d, with the exact time required dependent on the sample type and the experimental purposes. A single imaging set can be completed in 30-60 min. Image processing and analysis can take <1 d, but it is dependent on the number of samples in the data set. The CUBIC clearing protocol can process multiple samples simultaneously. We previously used CUBIC to image whole-brain neural activities at single-cell resolution using Arc-dVenus transgenic (Tg) mice. CUBIC informatics calculated the Venus signal subtraction, comparing different brains at a whole-organ scale. These protocols provide a platform for organism-level systems biology by comprehensively detecting cells in a whole organ or body.
authors.affiliation: Department of Systems Pharmacology, The University of Tokyo, Tokyo, Japan.|Japan Agency for Medical Research and Development (AMED) - Core Research for Evolutionary Science and Technology (CREST), AMED, Tokyo, Japan.|Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), Osaka, Japan.
authors.forename: Etsuo A
authors.initials: EA
authors.lastname: Susaki
authors.affiliation: Department of Systems Pharmacology, The University of Tokyo, Tokyo, Japan.|Japan Agency for Medical Research and Development (AMED) - Core Research for Evolutionary Science and Technology (CREST), AMED, Tokyo, Japan.|Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), Osaka, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Tainaka
authors.affiliation: School of Electrical Engineering and Computer Science, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
authors.forename: Dimitri
authors.initials: D
authors.lastname: Perrin
authors.affiliation: Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), Osaka, Japan.
authors.forename: Hiroko
authors.initials: H
authors.lastname: Yukinaga
authors.affiliation: Department of Systems Pharmacology, The University of Tokyo, Tokyo, Japan.|Japan Agency for Medical Research and Development (AMED) - Core Research for Evolutionary Science and Technology (CREST), AMED, Tokyo, Japan.|Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.|PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Ibaraki, Japan.
authors.forename: Akihiro
authors.initials: A
authors.lastname: Kuno
authors.affiliation: Department of Systems Pharmacology, The University of Tokyo, Tokyo, Japan.|Japan Agency for Medical Research and Development (AMED) - Core Research for Evolutionary Science and Technology (CREST), AMED, Tokyo, Japan.|Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), Osaka, Japan.
authors.forename: Hiroki R
authors.initials: HR
authors.lastname: Ueda
mesh_terms: D000818:Animals; D001921:Brain / Q000473:pathology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D051379:Mice; D008853:Microscopy / Q000379:methods*; D061848:Optical Imaging / Q000379:methods*; D010336:Pathology / Q000379:methods*