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Nat Protoc. 2015 Nov;10(11):1709-27. doi: 10.1038/nprot.2015.085. Epub 2015 Oct 8.

Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging.

Susaki EA1,2,3, Tainaka K1,2,3, Perrin D4, Yukinaga H3, Kuno A1,2,5,6, Ueda HR1,2,3.

Author information

1
Department of Systems Pharmacology, The University of Tokyo, Tokyo, Japan.
2
Japan Agency for Medical Research and Development (AMED) - Core Research for Evolutionary Science and Technology (CREST), AMED, Tokyo, Japan.
3
Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center (QBiC), Osaka, Japan.
4
School of Electrical Engineering and Computer Science, Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Queensland, Australia.
5
Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan.
6
PhD Program in Human Biology, School of Integrative and Global Majors, University of Tsukuba, Ibaraki, Japan.

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.

PMID:
26448360
DOI:
10.1038/nprot.2015.085
[Indexed for MEDLINE]

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