Our CUBIC tissue clearing reagent is an excellent example of a hydrophilic tissue clearing reagent. By virtue of its exceptional cleaning, protein preservation, and safety properties, it enables whole-organ 3D imaging at single-cell resolution using fluorescent microscopy.

CUBIC Tissue Clearing Procedure

Products

CUBICStars offers a series of CUBIC tissue clearing reagents through direct sales. Please contact us if you intend to use these products.

*CUBIC tissue clearing reagents have been commercialized under license from RIKEN, Japan

  • CSCR001 CUBIC-L hydrophilic tissue delipidation and decolorization reagent
  • CSCR002 CUBIC-R hydrophilic tissue RI matching reagent
  • CSCR003 CUBIC-P hydrophilic tissue decolorization reagent (for perfusion)
  • CSCR004 CUBIC-B hydrophilic bone clearing (decalcification) reagent
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Protocols & Examples

Basic clearing protocol (for whole mouse organ)

The clearing by only two successive steps of sample immersion into CUBIC reagents:

  • CUBIC-L: reagent for delipidation and decolorization
  • CUBIC-R: reagent for refractive index matching

Bone tissue clearing protocol

The clearing adapted for hard tissues containing calcium:

  • CUBIC-B: reagent for decalcification

Whole body clearing protocol

The cleaning boosted by the addition of a powerful decolorization reagent:

  • CUBIC-P: reagent for perfusion-based decolorization

References

Original articles

Susaki EA, Tainaka K, Perrin D, et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell. 2014 157(3):726-39.

Tainaka K, Kubota SI, et al. Whole-body imaging with single-cell resolution by tissue decolorization. Cell. 2014 159(4):911-24.

Tainaka K, Murakami TC, et al. Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents. Cell Rep. 2018 24(8):2196-2210.e9.

Murakami TC, et al. A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing. Nat Neurosci. 2018 21(4):625-637.

Susaki EA, et al. Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues. Nat Commun. 2020 11(1):1982.

Mano T, et al. CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping. Cell Rep Methods. 2021 1(2):100038.

Protocols

Susaki EA, Tainaka K, Perrin D, et al. Advanced CUBIC protocols for whole-brain and whole-body clearing and imaging. Nat Protoc. 2015 10(11):1709-27.

Matsumoto K, et al. Advanced CUBIC tissue clearing for whole-organ cell profiling. Nat Protoc. 2019 14(12):3506-3537.

Reviews

Susaki EA, Ueda HR. Whole-body and Whole-Organ Clearing and Imaging Techniques with Single-Cell Resolution: Toward Organism-Level Systems Biology in Mammals. Cell Chem Biol. 2016 23(1):137-157.

Tainaka K, Kuno A, Kubota SI, Murakami T, Ueda HR. Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling. Annu Rev Cell Dev Biol. 2016 32:713-741.

Ueda HR, et al. Tissue clearing and its applications in neuroscience. Nat Rev Neurosci. 2020 21(2):61-79.

Ueda HR, et al. Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy. Neuron. 2020 106(3):369-387.

Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW. TISSUE CLEARING. Nat Rev Methods Primers. 2021 1(1):84.