open access

Vol 81, No 1 (2022)
Review article
Submitted: 2020-11-19
Accepted: 2021-01-08
Published online: 2021-02-09
Get Citation

CLARITY techniques based tissue clearing: types and differences

Z. Guo1, Y. Zheng2, Y. Zhang1
DOI: 10.5603/FM.a2021.0012
·
Pubmed: 33577077
·
Folia Morphol 2022;81(1):1-12.
Affiliations
  1. Department of General Surgery, Hepatic-biliary-pancreatic Institute, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China
  2. Department of Plastic Surgery, Lanzhou University Second Hospital, Lanzhou University, Lanzhou, China

open access

Vol 81, No 1 (2022)
REVIEW ARTICLES
Submitted: 2020-11-19
Accepted: 2021-01-08
Published online: 2021-02-09

Abstract

CLARITY is a tissue imaging technique that uses hydrogel embedded tissue to remove lipids while maintaining the intactness of protein and tissue fine structure. CLARITY has been widely used in the field of three-dimensional reconstruction of intact tissues and biomolecular information analysis, which enhances the ability to obtain biological structural and molecular information from intact systems. Therefore, many modified tissue clearing methods based on CLARITY have emerged. However, the variety and complexity of modified CLARITY techniques, as well as such challenges as low tissue clearing efficiency, tissue damage, and expensive experimental equipment significantly limited popular application. This review systematically summarises the progress of CLARITY techniques from the perspective of tissue clearing and classifies them into active CLARITY, passive CLARITY, and the method of merging active CLARITY with passive CLARITY according to different tissue clearing methods, which helps researchers to select a suitable tissue clearing method for the experimental samples more quickly and effectively based on balancing the removal speed and tissue transparency of different tissue clearing methods. In addition, combing through the advantage and highlighting the limitations of CLARITY techniques may be beneficial for the ideas building of different research and enlighten to improve the details of the techniques.

Abstract

CLARITY is a tissue imaging technique that uses hydrogel embedded tissue to remove lipids while maintaining the intactness of protein and tissue fine structure. CLARITY has been widely used in the field of three-dimensional reconstruction of intact tissues and biomolecular information analysis, which enhances the ability to obtain biological structural and molecular information from intact systems. Therefore, many modified tissue clearing methods based on CLARITY have emerged. However, the variety and complexity of modified CLARITY techniques, as well as such challenges as low tissue clearing efficiency, tissue damage, and expensive experimental equipment significantly limited popular application. This review systematically summarises the progress of CLARITY techniques from the perspective of tissue clearing and classifies them into active CLARITY, passive CLARITY, and the method of merging active CLARITY with passive CLARITY according to different tissue clearing methods, which helps researchers to select a suitable tissue clearing method for the experimental samples more quickly and effectively based on balancing the removal speed and tissue transparency of different tissue clearing methods. In addition, combing through the advantage and highlighting the limitations of CLARITY techniques may be beneficial for the ideas building of different research and enlighten to improve the details of the techniques.

Get Citation

Keywords

CLARITY, three-dimensional imaging, tissue clearing, lipid removal, electrophoresis, brain, histology

About this article
Title

CLARITY techniques based tissue clearing: types and differences

Journal

Folia Morphologica

Issue

Vol 81, No 1 (2022)

Article type

Review article

Pages

1-12

Published online

2021-02-09

Page views

1290

Article views/downloads

1010

DOI

10.5603/FM.a2021.0012

Pubmed

33577077

Bibliographic record

Folia Morphol 2022;81(1):1-12.

Keywords

CLARITY
three-dimensional imaging
tissue clearing
lipid removal
electrophoresis
brain
histology

Authors

Z. Guo
Y. Zheng
Y. Zhang

References (54)
  1. Ando K, Laborde Q, Lazar A, et al. Inside Alzheimer brain with CLARITY: senile plaques, neurofibrillary tangles and axons in 3-D. Acta Neuropathol. 2014; 128(3): 457–459.
  2. Choi J, Lee E, Kim JH, et al. FxClear, a free-hydrogel electrophoretic tissue clearing method for rapid de-lipidation of tissues with high preservation of immunoreactivity. Exp Neurobiol. 2019; 28(3): 436–445.
  3. Chung K, Wallace J, Kim SY, et al. Structural and molecular interrogation of intact biological systems. Nature. 2013; 497(7449): 332–337.
  4. DePas WH, Starwalt-Lee R, Van Sambeek L, et al. Exposing the three-dimensional biogeography and metabolic states of pathogens in cystic fibrosis sputum via hydrogel embedding, clearing, and rRNA labeling. mBio. 2016; 7(5).
  5. Dodt HU, Leischner U, Schierloh A, et al. Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain. Nat Methods. 2007; 4(4): 331–336.
  6. Du H, Hou P, Wang L, et al. Modified CLARITY achieving faster and better intact mouse brain clearing and immunostaining. Sci Rep. 2019; 9(1): 10571.
  7. El-Sherbiny IM, Yacoub MH. Hydrogel scaffolds for tissue engineering: Progress and challenges. Glob Cardiol Sci Pract. 2013; 2013(3): 316–342.
  8. Epp JR, Niibori Y, Liz Hsiang HL, et al. Optimization of CLARITY for clearing whole-brain and other intact organs. eNeuro. 2015; 2(3).
  9. Ertürk A, Becker K, Jährling N, et al. Three-dimensional imaging of solvent-cleared organs using 3DISCO. Nat Protoc. 2012; 7(11): 1983–1995.
  10. Ertürk A, Bradke F. High-resolution imaging of entire organs by 3-dimensional imaging of solvent cleared organs (3DISCO). Exp Neurol. 2013; 242: 57–64.
  11. Ertürk A, Mauch CP, Hellal F, et al. Three-dimensional imaging of the unsectioned adult spinal cord to assess axon regeneration and glial responses after injury. Nat Med. 2011; 18(1): 166–171.
  12. Feng Yi, Cui P, Lu X, et al. CLARITY reveals dynamics of ovarian follicular architecture and vasculature in three-dimensions. Sci Rep. 2017; 7: 44810.
  13. Gage GJ, Kipke DR, Shain W. Whole animal perfusion fixation for rodents. J Vis Exp. 2012(65).
  14. Gradinaru V, Treweek J, Overton K, et al. Hydrogel-Tissue chemistry: principles and applications. Annu Rev Biophys. 2018; 47: 355–376.
  15. Greenbaum A, Chan KY, Dobreva T, et al. Bone CLARITY: Clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow. Sci Transl Med. 2017; 9(387).
  16. Hama H, Hioki H, Namiki K, et al. ScaleS: an optical clearing palette for biological imaging. Nat Neurosci. 2015; 18(10): 1518–1529.
  17. Hama H, Kurokawa H, Kawano H, et al. Scale: a chemical approach for fluorescence imaging and reconstruction of transparent mouse brain. Nat Neurosci. 2011; 14(11): 1481–1488.
  18. Humphrey JD, Dufresne ER, Schwartz MA. Mechanotransduction and extracellular matrix homeostasis. Nat Rev Mol Cell Biol. 2014; 15(12): 802–812.
  19. Ke MT, Fujimoto S, Imai T. SeeDB: a simple and morphology-preserving optical clearing agent for neuronal circuit reconstruction. Nat Neurosci. 2013; 16(8): 1154–1161.
  20. Kim JH, Jang MJ, Choi J, et al. Optimizing tissue-clearing conditions based on analysis of the critical factors affecting tissue-clearing procedures. Sci Rep. 2018; 8(1): 12815.
  21. Kim SY, Cho JH, Murray E, et al. Stochastic electrotransport selectively enhances the transport of highly electromobile molecules. Proc Natl Acad Sci U S A. 2015; 112(46): E6274–E6283.
  22. Kim SY, Chung K, Deisseroth K. Light microscopy mapping of connections in the intact brain. Trends Cogn Sci. 2013; 17(12): 596–599.
  23. Lai HM, Liu AK, Ng WL, et al. Rationalisation and validation of an acrylamide-free procedure in three-dimensional histological imaging. PLoS One. 2016; 11(6): e0158628.
  24. Lee E, Choi J, Jo Y, et al. ACT-PRESTO: Rapid and consistent tissue clearing and labeling method for 3-dimensional (3D) imaging. Sci Rep. 2016; 6: 18631.
  25. Lee H, Park JH, Seo I, et al. Improved application of the electrophoretic tissue clearing technology, CLARITY, to intact solid organs including brain, pancreas, liver, kidney, lung, and intestine. BMC Dev Biol. 2014; 14: 48.
  26. Liu AKL, Hurry MED, Ng OTW, et al. Bringing CLARITY to the human brain: visualization of Lewy pathology in three dimensions. Neuropathol Appl Neurobiol. 2016; 42(6): 573–587.
  27. Liu AKL, Lai HM, Chang RCC, et al. Free of acrylamide sodium dodecyl sulphate (SDS)-based tissue clearing (FASTClear): a novel protocol of tissue clearing for three-dimensional visualization of human brain tissues. Neuropathol Appl Neurobiol. 2017; 43(4): 346–351.
  28. Mano T, Albanese A, Dodt HU, et al. Whole-Brain analysis of cells and circuits by tissue clearing and light-sheet microscopy. J Neurosci. 2018; 38(44): 9330–9337.
  29. Mao Z, Zhu D, Hu Y, et al. Influence of alcohols on the optical clearing effect of skin in vitro. J Biomed Opt. 2008; 13(2): 021104.
  30. Murray E, Cho JH, Goodwin D, et al. Simple, scalable proteomic imaging for high-dimensional profiling of intact systems. Cell. 2015; 163(6): 1500–1514.
  31. Palmer WM, Martin AP, Flynn JR, et al. PEA-CLARITY: 3D molecular imaging of whole plant organs. Sci Rep. 2015; 5: 13492.
  32. Parra SG, Chia TH, Zinter JP, et al. Multiphoton microscopy of cleared mouse organs. J Biomed Opt. 2010; 15(3): 036017.
  33. Poguzhelskaya E, Artamonov D, Bolshakova A, et al. Simplified method to perform CLARITY imaging. Mol Neurodegener. 2014; 9: 19.
  34. Renier N, Wu Z, Simon DJ, et al. iDISCO: a simple, rapid method to immunolabel large tissue samples for volume imaging. Cell. 2014; 159(4): 896–910.
  35. Rocha MD, Düring DN, Bethge P, et al. Tissue clearing and light sheet microscopy: imaging the unsectioned adult zebra finch brain at cellular resolution. Front Neuroanat. 2019; 13: 13.
  36. Spence RD, Kurth F, Itoh N, et al. Bringing CLARITY to gray matter atrophy. Neuroimage. 2014; 101: 625–632.
  37. Sung K, Ding Y, Ma J, et al. Simplified three-dimensional tissue clearing and incorporation of colorimetric phenotyping. Sci Rep. 2016; 6: 30736.
  38. 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): 726–739.
  39. 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.
  40. Syková E, Nicholson C. Diffusion in brain extracellular space. Physiol Rev. 2008; 88(4): 1277–1340.
  41. Tainaka K, Kuno A, Kubota SI, et al. Chemical principles in tissue clearing and staining protocols for whole-body cell profiling. Annu Rev Cell Dev Biol. 2016; 32: 713–741.
  42. Treweek JB, Chan KY, Flytzanis NC, et al. Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping. Nat Protoc. 2015; 10(11): 1860–1896.
  43. Ueda HR, Ertürk A, Chung K, et al. Tissue clearing and its applications in neuroscience. Nat Rev Neurosci. 2020; 21(2): 61–79.
  44. Vigouroux RJ, Belle M, Chédotal A. Neuroscience in the third dimension: shedding new light on the brain with tissue clearing. Mol Brain. 2017; 10(1): 33.
  45. Wang J, Zhang Y, Xu TH, et al. An innovative transparent cranial window based on skull optical clearing. Laser Physics Letters. 2012; 9(6): 469–473.
  46. Wen X, Mao Z, Han Z, et al. In vivo skin optical clearing by glycerol solutions: mechanism. J Biophotonics. 2010; 3(1-2): 44–52.
  47. Wen X, Tuchin VV, Luo Q, et al. Controling the scattering of intralipid by using optical clearing agents. Phys Med Biol. 2009; 54(22): 6917–6930.
  48. Woo J, Kang H, Lee EY, et al. Investigation of PRDM7 and PRDM12 expression pattern during mouse embryonic development by using a modified passive clearing technique. Biochem Biophys Res Commun. 2020; 524(2): 346–353.
  49. Woo J, Lee EY, Park HS, et al. Novel passive clearing methods for the rapid production of optical transparency in whole CNS tissue. J Vis Exp. 2018(135).
  50. Woo J, Lee M, Seo JM, et al. Optimization of the optical transparency of rodent tissues by modified PACT-based passive clearing. Exp Mol Med. 2016; 48(12): e274.
  51. Xu Na, Tamadon A, Liu Y, et al. Fast free-of-acrylamide clearing tissue (FACT)-an optimized new protocol for rapid, high-resolution imaging of three-dimensional brain tissue. Sci Rep. 2017; 7(1): 9895.
  52. Yang B, Treweek JB, Kulkarni RP, et al. Single-cell phenotyping within transparent intact tissue through whole-body clearing. Cell. 2014; 158(4): 945–958.
  53. Zhu D, Larin KV, Luo Q, et al. Recent progress in tissue optical clearing. Laser Photon Rev. 2013; 7(5): 732–757.
  54. Zhu X, Xia Y, Wang X, et al. Optical brain imaging: a powerful tool for neuroscience. Neurosci Bull. 2017; 33(1): 95–102.

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