Optical Clearing and Tissue Imaging

  • Luís Manuel Couto Oliveira
  • Valery Victorovich Tuchin
Part of the SpringerBriefs in Physics book series (SpringerBriefs in Physics)


Imaging methods are a powerful tool for diagnostic purposes. In this chapter, the most important light-imaging methods, their advantages, and drawbacks are described. The advantages of radiation-free light-based imaging methods relative to traditional radiation methods, such as X-ray, magnetic resonance, or positron emission imaging, are indicated, and the recent advances to improve probing depth, contrast, and resolution in thick tissues are demonstrated. Some historical aspects and recent improvements in light-imaging methods, such as optical coherence tomography, speckle-imaging, second harmonic generation, or light-sheet microscopies, are presented. Due to the recent combination of optical immersion clearing with light-based imaging methods, several studies have been reported, where high-quality images and 3D reconstruction have been obtained for various tissues, providing an alternative to traditional histology or histopathology methods. The purpose of optical clearing is to reduce light scattering, but tissue clearing is obtained through three mechanisms: tissue dehydration, refractive index matching, and protein dissociation. This last mechanism leads to a reduction in the intensity of protein fluorescence, which can be a disadvantage in fluorescence imaging methods. The selection of certain clearing protocols that minimizes or eliminates protein dissociation has been made by some researchers, and a review of such literature is made in the various sections of this chapter.


Radiation-free imaging Fluorescence Contrast improvement Subcellular resolution Improved probing depth Optimized clearing protocols 


  1. 1.
    M. Li, Developing a Technique for Combining Light and Ultrasound for Deep Tissue Imaging (MS thesis), Sweden: Lund University, 2018Google Scholar
  2. 2.
    E.A. Genina, A.N. Bashkatov, V.V. Tuchin, Tissue optical immersion clearing. Expert Rev. Med. Devices 7(6), 825–842 (2010)CrossRefGoogle Scholar
  3. 3.
    V.V. Tuchin, Optical Clearing of Tissues and Blood (SPIE Press, Bellingham, WA, 2006)Google Scholar
  4. 4.
    L. Oliveira, M.I. Carvalho, E.M. Nogueira, V.V. Tuchin, Diffusion characteristics of ethylene glycol in skeletal muscle. J. Biomed. Opt. 20(5), 051019 (2015)ADSCrossRefGoogle Scholar
  5. 5.
    D.S. Richardson, J.W. Lichtman, Clarifying tissue clearing. Cell 162, 246–257 (2015)CrossRefGoogle Scholar
  6. 6.
    P.S. Tsai, P. Blinder, B.J. Migliori, J. Neev, Y. Jin, J.A. Squier, D. Kleinfeld, Plasma-mediated ablation: an optical tool for submicrometer surgery on neuronal and vascular systems. Curr. Opin. Biotech. 20, 90–99 (2009)CrossRefGoogle Scholar
  7. 7.
    S. Carvalho, N. Gueiral, E. Nogueira, R. Henrique, L. Oliveira, V.V. Tuchin, Comparative study of the optical properties of colon mucosa and colon precancerous polyps between 400 and 1000 nm, in Dynamics and Fluctuations in Biomedical Photonics XIV, ed. by V.V. Tuchin, K.V. Larin, M.J. Leahy, R.K. Wang. Proc. SPIE 10063, 100631L (2017)CrossRefGoogle Scholar
  8. 8.
    H. Duong, M. Han, A multispectral LED array for the reduction of background autofluorescence in brain tissue. J. Neurosci. Methods 220, 46–54 (2013)CrossRefGoogle Scholar
  9. 9.
    B. Clancy, L.J. Cauller, Reduction of background autofluorescence in brain sections following immersion in sodium borohydride. J. Neurosci. Methods 83, 97–102 (1998)CrossRefGoogle Scholar
  10. 10.
    T. Zimmermann, Spectral imaging and linear unmixing in light microscopy. Adv. Biochem. Eng. Biotechnol. 95, 245–265 (2005)Google Scholar
  11. 11.
    A.Y. Sdobnov, V.V. Tuchin, J. Lademann, M.E. Darvin, Confocal Raman microscopy supported by optical clearing treatment of the skin – influence on collagen hydration. J. Phys. D Appl. Phys. 50(28), 285401 (2017)CrossRefGoogle Scholar
  12. 12.
    A.Y. Sdobnov, M.E. Darvin, J. Lademann, V.V. Tuchin, A comparative study of ex vivo skin optical clearing using two-photon microscopy. J. Biophotonics 10(9), 1115–1123 (2017)CrossRefGoogle Scholar
  13. 13.
    A.Y. Sdobnov, M.E. Darvin, J. Schleusener, J. Lademann, V.V. Tuchin, Hydrogen bound water profiles in the skin influenced by optical clearing molecular agents-quantitative analysis using confocal Raman microscopy. J. Biophotonics 12(5), e201800283 (2019)CrossRefGoogle Scholar
  14. 14.
    A.Y. Sdobnov, M.E. Darvin, E.A. Genina, A.N. Bashkatov, J. Lademan, V.V. Tuchin, Recent progress in tissue optical clearing for spectroscopic application. Spectrochim. Acta Part A: Mol. Biomol. Spectrosc. 197, 216–229 (2018)ADSCrossRefGoogle Scholar
  15. 15.
    A.Y. Sdobnov, J. Lademann, M.E. Darvin, V.V. Tuchin, Methods for optical skin clearing in molecular optical imaging in dermatology. Biochem. 84(S1), 144–158 (2019)Google Scholar
  16. 16.
    D. Huang, E.A. Swanson, C.P. Lin, J.S. Schuman, W.G. Stinson, W. Chang, M.R. Hee, T. Flotte, K. Gregory, C.A. Puliafito, J.G. Fujimoto, Optical coherence tomography. Science 254, 1178–1181 (1991)ADSCrossRefGoogle Scholar
  17. 17.
    A.F. Fercher, K. Mengedoht, W. Werner, Eye-length measurement by interferometry with partially coherent light. Opt. Lett. 13(3), 186–188 (1988)ADSCrossRefGoogle Scholar
  18. 18.
    W. Drexler, J. G. Fujimoto (eds.), Optical Coherence Tomography: Technology and Applications, 2nd edn. (Springer International Publishing Switzerland, Cham, 2015)Google Scholar
  19. 19.
    V.V. Tuchin, Tissue Optics – Light Scattering Methods and Instruments for Medical Diagnostics, 3rd edn. (SPIE Press, Bellingham, WA, 2015)CrossRefGoogle Scholar
  20. 20.
  21. 21.
    A.F. Fercher, Optical coherence tomography. J. Biomed. Opt. 1, 157–173 (1996)ADSCrossRefGoogle Scholar
  22. 22.
    E.A. Genina, A.N. Bashkatov, M.D. Kozintseva, V.V. Tuchin, OCT study of optical clearing of muscle tissue in vitro with 40% glucose solution. Opt. Spect. 120(1), 27–35 (2016)ADSCrossRefGoogle Scholar
  23. 23.
    Y.M. Liew, R.A. McLaughlin, F.M. Wood, D.D. Sampson, Reduction of image artifacts in three-dimensional optical coherence tomography of skin in vivo. J. Biomed. Opt. 16(11), 116018 (2011)ADSCrossRefGoogle Scholar
  24. 24.
    E.A. Genina, A.N. Bashkatov, Y.P. Sinichkin, I.Y. Yanina, V.V. Tuchin, Optical clearing of biological tissues: prospects of application in medical diagnostics and phototherapy. J. Biomed. Phot. Eng. 1(1), 22–58 (2015)CrossRefGoogle Scholar
  25. 25.
    R.K. Wang, V.V. Tuchin, Optical coherence tomography. Light scattering and imaging enhancement, Chapter 16, in Handbook of Coherent-Domain Optical Methods: Biomedical Diagnostics, Environmental Monitoring, and Material Science, ed. by V. V. Tuchin, vol. 2, 2nd edn., (Springer, New York, NY, 2013), p. 665CrossRefGoogle Scholar
  26. 26.
    A.N. Bashkatov, E.A. Genina, V.I. Kochubey, V.V. Tuchin, Optical properties of human sclera in spectral range 370-2500 nm. Opt. Spectr. 109(2), 197–204 (2010)ADSCrossRefGoogle Scholar
  27. 27.
    A.N. Bashkatov, E.A. Genina, V.I. Kochubey, V.V. Tuchin, Optical properties of human skin, subcutaneous and mucous tissues in the wavelength range from 400 to 2000 nm. J. Phys. D Appl. Phys. 38(15), 2543–2555 (2005)ADSCrossRefGoogle Scholar
  28. 28.
    A.N. Bashkatov, E.A. Genina, M.D. Kozintseva, V.I. Kochubey, S.Y. Gorofkov, V.V. Tuchin, Optical properties of peritoneal biological tissues in the spectral range of 350-2500 nm. Opt. Spectr. 120(1), 1–8 (2016)ADSCrossRefGoogle Scholar
  29. 29.
    I. Carneiro, S. Carvalho, R. Henrique, L.M. Oliveira, V.V. Tuchin, Optical properties of colorectal muscle in visible/NIR range, in Biophotonics: Photonic Solutions for Better Health Care VI, ed. by J. Popp, V.V. Tuchin, F.S. Pavone. Proc. SPIE 10685, 106853D (2018)Google Scholar
  30. 30.
    A.N. Bashkatov, E.A. Genina, V.V. Tuchin, Optical properties of skin, subcutaneous and muscle tissues: a review. J. Innov. Opt. Health Sci. 4(1), 9–38 (2011)CrossRefGoogle Scholar
  31. 31.
    M.G. Ghosn, V.V. Tuchin, K.V. Larin, Nondestructive quantification of analyte diffusion in cornea and sclera using optical coherence tomography. Invest. Ophthalmol. Vis. Sci. 48(6), 2726–2733 (2007)CrossRefGoogle Scholar
  32. 32.
    A.N. Bashkatov, E.A. Genina, V.V. Tuchin, Measurement of glucose diffusion coefficients in human tissues, Chapter 19, in Handbook of Optical Sensing of Glucose in Biological Fluids and Tissues, ed. by V. V. Tuchin, (Taylor & Francis Group LLC, CRC Press, Boca Raton, FL, 2009), pp. 587–621Google Scholar
  33. 33.
    M.G. Ghosn, E.F. Carbajal, N.A. Befrui, V.V. Tuchin, K.V. Larin, Differential permeability rate and percent clearing of glucose in different regions in rabbit sclera. J. Biomed. Opt. 13(2), 021110 (2008)ADSCrossRefGoogle Scholar
  34. 34.
    X. Guo, G. Wu, H. Wei, X. Deng, H. Yang, Y. Ji, Y. He, Z. Guo, S. Xie, H. Zhong, Q. Zhao, Z. Zhu, Quantification of glucose diffusion in human lung tissues by using Fourier domain optical coherence tomography. Potochem. Photobiol. 88, 311–316 (2012)CrossRefGoogle Scholar
  35. 35.
    K.V. Larin, M.G. Ghosn, A.N. Bashkatov, E.A. Genina, N.A. Trunina, V.V. Tuchin, Optical clearing for OCT image enhancement and in-depth monitoring of molecular diffusion. IEEE J. Sel. Top. Quant. Elect. 18(3), 1244–1259 (2012)ADSCrossRefGoogle Scholar
  36. 36.
    R. Wang, V.V. Tuchin, Enhance light penetration in tissue for high resolution optical imaging techniques by the use of biocompatible chemical agents. J. X ray Sci. Tech. 10, 167–176 (2002)Google Scholar
  37. 37.
    R.K. Wang, J.B. Elder, Propylene glycol as a contrasting agent for optical coherence tomography to image gastrointestinal tissues. Lasers Surg. Med. 30, 201–208 (2002)CrossRefGoogle Scholar
  38. 38.
    L. Pires, V. Demidov, I.A. Vitkin, V. Bagnato, C. Kurachi, B.C. Wilson, Optical clearing of melanoma in vivo: characterization by diffuse reflectance spectroscopy and optical coherence tomography. J. Biomed. Opt. 21(8), 081210 (2016)ADSCrossRefGoogle Scholar
  39. 39.
    Z. Zhu, G. Wu, H. Wei, H. Yang, Y. He, S. Xie, Q. Zhao, X. Guo, Investigation of the permeability and optical clearing ability of different analytes in human normal and cancerous breast tissues by spectral domain OCT. J. Biophotonics 5(7), 536–543 (2012)CrossRefGoogle Scholar
  40. 40.
    H. Xiong, Z. Guo, C. Zeng, L. Wang, Y. He, S. Liu, Application off hyperosmotic agent to determine gastric cancer with optical coherence tomography ex vivo in mice. J. Biomed. Opt. 14(2), 024029 (2009)ADSCrossRefGoogle Scholar
  41. 41.
    H.Q. Zhong, Z.Y. Guo, H.J. Wei, J.L. Si, L. Guo, Q.L. Zhao, C.C. Zheng, H.L. Xiong, Y.H. He, S.H. Liu, Enhancement of permeability of glycerol with ultrasound in human normal and cancer breast tissues in vitro using optical coherence tomography. Laser Phys. Lett. 7(5), 388–395 (2010)ADSCrossRefGoogle Scholar
  42. 42.
    E.A. Genina, A.N. Bashkatov, O.V. Semyachkina-Glushkovskaya, V.V. Tuchin, Optical clearing of cranial bone by multicomponent immersion solutions and cerebral venous blood flow visualization. Izv. Saratov Univ. (N. S.), Ser. Phys. 17, 98–110 (2017)Google Scholar
  43. 43.
    H. Zhong, Z. Guo, H. Wei, L. Uo, C. Wang, Y. He, H. Xiong, S. Liu, Synergistic effect of ultrasound and thiazone-PEG 400 on human skin optical clearing in vivo. Photochem. Photobiol. 86, 732–737 (2010)CrossRefGoogle Scholar
  44. 44.
    E.A. Genina, A.N. Bashkatov, E.A. Kolesnikova, M.V. Basko, G.S. Terentyuk, V.V. Tuchin, Optical coherence tomography monitoring of enhanced skin optical clearing in rats in vivo. J. Biomed. Opt. 19(2), 021109 (2014)ADSCrossRefGoogle Scholar
  45. 45.
    W. Feng, R. Shi, N. Ma, D.K. Tuchina, V.V. Tuchin, D. Zhu, Skin optical clearing potential of disaccharides. J. Biomed. Opt. 21(8), 081207 (2016)ADSCrossRefGoogle Scholar
  46. 46.
    L. Guo, R. Shi, C. Zhang, D. Zhu, Z. Ding, P. Li, Optical coherence tomography angiography offers comprehensive evaluation of skin optical clearing in vivo by quantifying optical properties and blood flow imaging simultaneously. J. Biomed. Opt. 21(8), 081202 (2016)ADSCrossRefGoogle Scholar
  47. 47.
    N.S. Ksenofontova, E.A. Genina, A.N. Bashkatov, G.S. Terentyuk, V.V. Tuchin, OCT study of skin optical clearing with preliminary laser ablation of epidermis. J. Biomed. Phot. Eng. 3(2), 020307 (2017)CrossRefGoogle Scholar
  48. 48.
    O. Zhernovaya, V.V. Tuchin, M.J. Leahy, Enhancement of OCT imaging by blood optical clearing in vessels – a feasibility study. Photon. Lasers Med. 5(2), 151–159 (2016)CrossRefGoogle Scholar
  49. 49.
    A. Bykov, T. Hautala, M. Kinnunen, A. Popov, S. Karhula, S. Saarakkala, M.T. Nieminen, V.V. Tuchin, I. Meglinski, Imaging of subchondral bone by optical coherence tomography upon optical clearing of articular cartilage. J. Biophotonics 9(3), 270–275 (2016)CrossRefGoogle Scholar
  50. 50.
    C.H. Liu, M. Singh, J. Li, Z. Han, C. Wu, S. Wang, R. Idugboe, R. Raghunathan, E.N. Sobol, V.V. Tuchin, M. Twa, K.V. Larin, Quantitative assessment of hyaline cartilage elasticity during optical clearing using optical coherence elastography. Med. Technol. Med 7, 44–51 (2015)Google Scholar
  51. 51.
    A.F. Peña, A. Doronin, V.V. Tuchin, I. Meglinski, Monitoring of interaction of low-frequency electric field with biological tissues upon optical clearing with optical coherence tomography. J. Biomed. Opt. 19(8), 086002 (2014)ADSCrossRefGoogle Scholar
  52. 52.
  53. 53.
    I.V. Meglinski, A.N. Bashkatov, E.A. Genina, D.Y. Churmakov, V.V. Tuchin, The enhancement of confocal images of tissues at bulk optical immersion. Laser Phys. 13(1), 65–69 (2003)Google Scholar
  54. 54.
    I.V. Meglinski, A.N. Bashkatov, E.A. Genina, D.Y. Churmakov, V.V. Tuchin, Study of the possibility of increasing the probing depth by the method of reflection confocal microscopy upon immersion clearing of near-surface human skin layers. Quant. Elect. 32(10), 875–882 (2002)ADSCrossRefGoogle Scholar
  55. 55.
    R. Dickie, R.M. Bachoo, M.A. Rupnick, S.M. Dallabrida, G.M. Deloid, J. Lai, R.A. DePinho, R.A. Rogers, Three-dimensional visualization of microvessel architecture of whole-mount tissue by confocal microscopy. Microvasc. Res. 72, 20–26 (2006)CrossRefGoogle Scholar
  56. 56.
    A.-S. Chiang, Y.-C. Liu, S.-L. Chiu, S.-H. Hu, C.-Y. Huang, C.-H. Hsieh, Three-dimensional mapping of brain neuropils in the cockroach Diploptera punctate. J. Comp. Neurol. 440, 1–11 (2001)CrossRefGoogle Scholar
  57. 57.
    A.J. Moy, B.V. Capulong, R.B. Saager, M.P. Wiersma, P.C. Lo, A.J. Durkin, B. Choi, Optical properties of mouse brain tissue after optical clearing with FocusClear. J. Biomed. Opt. 20(9), 095010 (2015)ADSCrossRefGoogle Scholar
  58. 58.
    Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, S.-C. Tang, Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution. Gastroenterology 137, 453–465 (2009)CrossRefGoogle Scholar
  59. 59.
    Y. Aoyagi, R. Kawakami, H. Osanai, T. Hibi, T. Nemoto, A rapid optical clearing protocol using 2,2′-thiodiethanol for microscopic observation of fixed mouse brain. PLoS One 10(1), e0116280 (2015)CrossRefGoogle Scholar
  60. 60.
    I. Costantini, J.-P. Ghobril, A.P. Di Giovanna, A.L.A. Mascaro, L. Silvestri, M.C. Müllenbroich, L. Onofri, V. Conti, F. Vanzi, L. Sacconi, R. Guerrini, H. Markram, G. Lannelo, F.S. Pavone, A versatile clearing agent for multi-modal brain imaging. Sci. Rep. 5, 9808 (2015)CrossRefGoogle Scholar
  61. 61.
    J. Hasegawa, Y. Sakamoto, S. Nakagami, M. Aida, S. Sawa, S. Matsunaga, Three-dimensional imaging of plant organs using a simple and rapid transparency technique. Plant Cell Physiol. 57(3), 462–472 (2016)CrossRefGoogle Scholar
  62. 62.
    T.J. Musielak, D. Slane, C. Liebig, M. Bayer, A versatile optical clearing protocol for deep tissue imaging of fluorescent proteins in Arabidopsis thaliana. PLoS One 11(8), e0161107 (2016)CrossRefGoogle Scholar
  63. 63.
    W. Li, R.N. Germain, M.Y. Gerner, Multiplex, quantitative cellular analysis in large tissue volumes with clearing-enhanced 3D microscopy (Ce3D). Proc. Natl. Sci. Acad. U S A 114(35), E7321–E7330 (2017)CrossRefGoogle Scholar
  64. 64.
    Online supporting information appendix to reference 64. Accessed 5 Apr 2019
  65. 65.
    R. Samatham, K.G. Phillips, S.L. Jacques, Assessment of optical clearing agents using reflectance-mode confocal scanning laser microscopy. J. Innov. Opt. Health Sci. 3, 183–188 (2010)CrossRefGoogle Scholar
  66. 66.
    C.P. Neu, T. Novak, K.F. Gilliland, P. Marshall, S. Calve, Optical clearing in collagen- and proteoglycan-rich osteochondral tissues. Osteoarthr. Cartil. 23, 405–413 (2015)CrossRefGoogle Scholar
  67. 67.
    M. Pende, K. Becker, M. Wanis, S. Saghafi, R. Kaur, C. Hahn, N. Pende, M. Foroughipour, T. Hummel, H.-U. Dodt, High-resolution ultramicroscopy of the developing and adult nervous system in optically cleared Drosophila melanogaster. Nat. Commun. 9, 4731 (2018)ADSCrossRefGoogle Scholar
  68. 68.
    H. Hama, H. Hioki, K. Namiki, T. Hoshida, H. Kurokawa, F. Ishidate, T. Kaneko, T. Akagi, T. Saito, T. Saido, A. Miyawaki, ScaleS: an optical clearing palette for biological imaging. Nat. Neurosci. 18(10), 1518–1529 (2015)CrossRefGoogle Scholar
  69. 69.
    L. Liu, A. Liu, W. Xiao, R. Li, X. Hu, L. Chen, Volumetric fluorescence imaging combined with modified optical clearing Alzheimer’s disease pathology, in 2018 Asia Communications and Photonics Conference (ACP), Hangzhou, (IEEE, New York, NY, 2018), pp. 1–3. Scholar
  70. 70.
    A.F. Fercher, J.D. Briers, Flow visualization by means of single-exposure speckle photography. Opt. Commun. 37(5), 326–330 (1981)ADSCrossRefGoogle Scholar
  71. 71.
    J.D. Briers, Laser Doppler, speckle and related techniques for blood perfusion mapping and imaging. Physiol. Meas. 22, 35–66 (2001)CrossRefGoogle Scholar
  72. 72.
    A.K. Dunn, H. Bolay, M.A. Moskowitz, D.A. Boas, Dynamic imaging of cerebral blood flow using laser speckle. J. Cereb. Blood Flow Metab. 21, 195–201 (2001)CrossRefGoogle Scholar
  73. 73.
    A.K. Dunn, Laser speckle contrast imaging of cerebral blood flow. Ann. Biomed. Eng. 40, 367–377 (2012)CrossRefGoogle Scholar
  74. 74.
    D. Briers, D.D. Duncan, E. Hirst, S.J. Kirkpatrick, M. Larsson, W. Steenbergen, T. Stromberg, O.B. Thompson, Laser speckle contrast imaging: theoretical and practical limitations. J. Biomed. Opt. 18(6), 066018 (2013)ADSCrossRefGoogle Scholar
  75. 75.
    I. Sigal, R. Gad, A.M. Caravaca-Aguirre, Y. Atchia, D.B. Conkey, R. Piestun, O. Levi, Laser speckle contrast imaging with extended depth of field for in-vivo tissue imaging. Biomed. Opt. Express 5(1), 123–135 (2014)CrossRefGoogle Scholar
  76. 76.
    A.N. Bashkatov, K.V. Berezin, K.N. Dvoretskiy, M.L. Chernavina, E.A. Genina, V.D. Genin, V.I. Kochubey, E.N. Lazareva, A.B. Pravdin, M.E. Shvachkina, P.A. Timoshina, D.K. Tuchina, D.D. Yakovlev, D.A. Yakovlev, I.Y. Yanina, O.S. Zhernovaya, V.V. Tuchin, Measurement of tissue optical properties in the context of tissue optical clearing. J. Biomed. Opt. 23(9), 091416 (2018)ADSCrossRefGoogle Scholar
  77. 77.
    J. Wang, D. Zhu, Switchable skin window induced by optical clearing method for dermal blood flow imaging. J. Biomed. Opt. 18(6), 061209 (2013)ADSCrossRefGoogle Scholar
  78. 78.
    Q. Luo, C. Jiang, P. Li, H. Cheng, Z. Wang, Z. Wang, V.V. Tuchin, Laser speckle imaging of cerebral blood flow, Chapter 5, in Coherent-Domain Optical Methods: Biomedical Diagnostics, Environmental Monitoring and Material Science, ed. by V. V. Tuchin, vol. 1, 2nd edn., (Springer, New York, NY, 2013), pp. 167–212CrossRefGoogle Scholar
  79. 79.
    E.I. Galanzha, V.V. Tuchin, A.V. Solovieva, T.V. Stepanova, Q. Luo, H. Cheng, Skin backreflectance and microvascular system functioning at the action of osmotic agents. J. Phys. D Appl. Phys. 36, 1739–1746 (2003)ADSCrossRefGoogle Scholar
  80. 80.
    D. Zhu, J. Zhang, H. Cui, Z. Mao, P. Li, Q. Luo, Short-term and long-term effects of optical clearing agents on blood vessels in chick chorioallantoic membrane. J. Biomed. Opt. 13(2), 021106 (2008)ADSCrossRefGoogle Scholar
  81. 81.
    D. Zhu, J. Wang, Z. Zhi, X. Wen, Q. Luo, Imaging dermal blood flow through the intact rat skin with an optical clearing method. J. Biomed. Opt. 15(2), 026008 (2010)ADSCrossRefGoogle Scholar
  82. 82.
    R. Shi, M. Chen, V.V. Tuchin, D. Zhu, Accessing to arteriovenous blood flow dynamics response using combined laser speckle contrast imaging and skin optical clearing. Biomed. Opt. Express 6(6), 1977–1989 (2015)CrossRefGoogle Scholar
  83. 83.
    Z. Mao, X. Wen, J. Wang, D. Zhu, The biocompatibility of the dermal injection of glycerol in vivo to achieve optical clearing. Proc. SPIE 7519, 75191N (2009)ADSCrossRefGoogle Scholar
  84. 84.
    W. Feng, R. Shi, C. Zhang, S. Liu, T. Yu, D. Zhu, Visualization of skin microvascular dysfunction of type 1 diabetic mice using in vivo skin optical clearing method. J. Biomed. Opt. 24(3), 031003 (2019)ADSGoogle Scholar
  85. 85.
    J. Wang, Y. Zhang, T.H. Xu, Q.M. Luo, D. Zhu, An innovative transparent cranial window based on skull optical clearing. Laser Phys. Lett. 9(6), 469–473 (2012)ADSCrossRefGoogle Scholar
  86. 86.
    P.A. Timoshina, A.B. Bucharskaya, D.A. Alexandrov, V.V. Tuchin, Study of blood microcirculation of pancreas in rats with alloxan diabetes by laser speckle contrast imaging. J. Biomed. Phot. Eng. 3(2), 020301 (2017)CrossRefGoogle Scholar
  87. 87.
    P.A. Timoshina, E.M. Zinchenko, D.K. Tuchina, M.M. Sagatova, O.V. Semyachkina-Glushkovskaya, V.V. Tuchin, Laser speckle contrast imaging of cerebral blood flow of newborn mice at optical clearing. Proc. SPIE 10336, 1033610 (2017)CrossRefGoogle Scholar
  88. 88.
    P.A. Timoshina, A.B. Bucharskaya, N.A. Navolokin, V.V. Tuchin, Speckle-contrast imaging of pathological tissue microhemodynamics at optical clearing, in Dynamics and Fluctuations in Biomedical Photonics XVI. Proc. SPIE 10877, 108770Z (2019). Scholar
  89. 89.
    D. Abookasis, T. Moshe, Feasibility study of hidden flow imaging based on laser speckle technique using multiperspectives contrast images. Opt. Lasers Eng. 62, 38–45 (2014)CrossRefGoogle Scholar
  90. 90.
    D. Abookasis, T. Moshe, Reconstruction enhancement of hidden objects using multiple speckle contrast projections and optical clearing agents. Opt. Commun. 400, 58–64 (2013)ADSCrossRefGoogle Scholar
  91. 91.
    T. Moshe, M.A. Firer, D. Abookasis, Object reconstruction in scattering medium using multiple elliptical polarized speckle contrast projections and optical clearing agents. Opt. Lasers Eng. 68, 172–179 (2015)CrossRefGoogle Scholar
  92. 92.
    J. Wang, N. Ma, R. Shi, Y. Zhang, T. Yu, D. Zhu, Sugar-induced skin optical clearing: from molecular dynamics simulation to experimental demonstration. IEEE J Sel. Top. Quant. Elect. 20(2), 7101007 (2014)Google Scholar
  93. 93.
    I. Freund, M. Deutsch, Second-harmonic microscopy of biological tissue. Opt. Lett. 11(2), 94–96 (1986)ADSCrossRefGoogle Scholar
  94. 94.
    P.J. Campagnola, C.Y. Dong, Second harmonic generation microscopy: principles and applications to disease diagnosis. Laser Phot. Rev. 5(1), 13–26 (2011)ADSCrossRefGoogle Scholar
  95. 95.
    P. Campagnola, H.A. Clark, W.A. Mohler, A. Lewis, L.M. Loew, Second-harmonic imaging microscopy of living cells. J. Biomed. Opt. 6(3), 277–286 (2001)ADSCrossRefGoogle Scholar
  96. 96.
    X. Chen, O. Nadiarynkh, S. Plotnikov, P.J. Campagnola, Second harmonic generation microscopy for quantitative analysis of collagen fibrillar structure. Nat. Protoc. 7(4), 654–669 (2012)CrossRefGoogle Scholar
  97. 97.
    O. Nadiarnykh, P.J. Campagnola, SHG and optical clearing, in Second Harmonic Generation Imaging, ed. by F. S. Pavone, P. J. Campagnola, (CRC Press, Boca Raton, FL, 2014), pp. 169–189Google Scholar
  98. 98.
    R. LaComb, O. Nadiarnykh, S. Carey, P.J. Campagnola, Quantitative second harmonic generation imaging and modeling of the optical clearing mechanism in striated muscle and tendon. J. Biomed. Opt. 13(2), 021109 (2008)ADSCrossRefGoogle Scholar
  99. 99.
    A.T. Yeh, B. Choi, J.S. Nelson, B.J. Tromberg, Reversible dissociation of collagen in tissues. J. Invest. Dermatol. 121, 1332–1335 (2003)CrossRefGoogle Scholar
  100. 100.
    N.G. Khlebtsov, I.L. Maksimova, V.V. Tuchin, L. Wang, Introduction to light scattering by biological objects, Chapter 1, in Handbook of Optical Biomedical Diagnosis, ed. by V. V. Tuchin, vol. PM107, (SPIE Press, Bellingham, WA, 2002), pp. 31–167Google Scholar
  101. 101.
    T. Yasui, Y. Tohno, T. Araki, Characterization of collagen orientation in human dermis by two-dimensional second-harmonic-generation polarimetry. J. Biomed. Opt. 9(2), 259–264 (2004)ADSCrossRefGoogle Scholar
  102. 102.
    S. Plotnikov, V. Juneja, A.B. Isaacson, W.A. Mohler, P.J. Campagnola, Optical clearing for improved contrast in second harmonic generation imaging of skeletal muscle. Biophys. J. 90, 328–339 (2006)ADSCrossRefGoogle Scholar
  103. 103.
    A. Milgroom, E. Ralston, Clearing skeletal muscle with CLARITY for light microscopy imaging. Cell Biol. Int. 40(4), 478–483 (2016)CrossRefGoogle Scholar
  104. 104.
    E. Olson, M.J. Levene, R. Torres, Multiphoton microscopy with clearing for three dimensional histology of kidney biopsies. Biomed. Opt. Express 7(8), 3089–3096 (2016)CrossRefGoogle Scholar
  105. 105.
    L. Richardson, G. Vargas, T. Brown, L. Ochoa, J. Trivedi, M. Kacerovský, M. Lappas, R. Menon, Redefining 3Dimensional placental membrane microarchitecture using multiphoton microscopy and optical clearing. Placenta 53, 66–75 (2017)CrossRefGoogle Scholar
  106. 106.
    L.F. Ochoa, A. Kholodnykh, P. Villarreal, B. Tian, R. Pal, A.N. Freiberg, A.R. Brasier, M. Motamedi, G. Vargas, Imaging of murine whole lung fibrosis by large Scale 3D microscopy aided by tissue optical clearing. Sci. Rep. 8, 13348 (2018)ADSCrossRefGoogle Scholar
  107. 107.
    C. Zhang, W. Feng, Y. Zhao, T. Yu, P. Li, T. Xu, Q. Luo, D. Zhu, A large, switchable optical clearing skull window for cerebrovascular imaging. Theranostics 8(10), 2696–2708 (2018)CrossRefGoogle Scholar
  108. 108.
    D. Jing, S. Zhang, W. Luo, X. Gao, Y. Men, C. Ma, X. Liu, Y. Yi, A. Budge, B.O. Zhou, Z. Zhao, Q. Yuan, J.Q. Feng, L. Gao, W.-P. Ge, H. Zhao, Tissue clearing of both hard and soft tissue organs with the PEGASOS method. Cell Res. 2(8), 803–818 (2018)CrossRefGoogle Scholar
  109. 109.
    E.A. Susaki, H.R. Ueda, Whole-body and whole-organ clearing and imaging techniques with single-cell resolution: toward organism-level systems biology in mammals. Cell Chem. Biol. 23(1), 137–157 (2016)CrossRefGoogle Scholar
  110. 110.
    P.J. Keller, M.B. Ahrens, Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy. Neuron 85(3), 462–483 (2015)CrossRefGoogle Scholar
  111. 111.
    P.J. Keller, H.-U. Dodt, Light sheet microscopy of living or cleared specimens. Curr. Opin. Neurobiol. 22(1), 138–143 (2012)CrossRefGoogle Scholar
  112. 112.
    P. Osten, T.W. Margrie, Mapping brain circuitry with a light microscope. Nat. Methods 10, 515–523 (2013)CrossRefGoogle Scholar
  113. 113.
    R. Tomer, L. Ye, B. Hsueh, K. Deisseroth, Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nat. Protoc. 9, 1682–1697 (2014)CrossRefGoogle Scholar
  114. 114.
    J.M. Girkin, M.T. Carvalho, The light-sheet revolution. J. Opt. 20, 053002 (2018)ADSCrossRefGoogle Scholar
  115. 115.
    A.H. Voie, D.H. Burns, F.A. Spelman, Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens. J. Microsc. 170(3), 229–236 (1993)CrossRefGoogle Scholar
  116. 116.
    J. Huisken, J. Swoger, F. Del Bene, J. Wittbrodt, E.H.K. Stelzer, Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305(5686), 1007–1009 (2004)ADSCrossRefGoogle Scholar
  117. 117.
    The first commercial ultramicroscope. Accessed 21 Mar 2019
  118. 118.
    P.A. Santi, Light sheet fluorescence microscopy: a review. J. Histochem. Cytochem. 59(2), 129–138 (2011)CrossRefGoogle Scholar
  119. 119.
    L. Silvestri, A. Bria, L. Sacconi, G. Iannello, F.S. Pavone, Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain. Opt. Express 20(18), 20582–20598 (2012)ADSCrossRefGoogle Scholar
  120. 120.
    B. Lloyd-Lewis, F.M. Davis, O.B. Harris, J.R. Hitchcock, F.C. Lourenço, M. Pasche, C.J. Watson, Imaging the mammary gland and mammary tumours in 3D: optical tissue clearing and immunofluorescence methods. Breast Cancer Res. 18(1), 127 (2016)CrossRefGoogle Scholar
  121. 121.
    A. Greenbaum, K.Y. Chan, T. Dobreva, D. Brown, D.H. Balani, R. Boyce, H.M. Kronenberg, H.J. McBride, V. Gradinaru, Bone CLARITY: clearing, imaging, and computational analysis of osteoprogenitors within intact bone marrow. Sci. Transl. Med. 9(387), eaah6518 (2017)CrossRefGoogle Scholar
  122. 122.
    J.N. Singh, T.M. Nowlin, G.J. Seedorf, S.H. Abman, D.P. Shepherd, Quantifying three-dimensional rodent retina vascular development using optical tissue clearing and light-sheet microscopy. J. Biomed. Opt. 22(7), 076011 (2017)ADSCrossRefGoogle Scholar
  123. 123.
    Y. Henning, C. Osadnik, E.P. Malkemper, EyeCi: optical clearing and imaging of immunolabeled mouse eyes using light-sheet microscopy. Exp. Eye Res. 180, 137–145 (2019)CrossRefGoogle Scholar
  124. 124.
    A.P. Di Giovanna, A. Tibo, L. Silvestri, M.C. Müllenbroich, I. Costantini, A.L. Mascaro, L. Sacconi, P. Frasconi, F.S. Pavone, Whole-brain vasculature reconstruction at the single capilary level. Sci. Rep. 8, 12573 (2018)ADSCrossRefGoogle Scholar
  125. 125.
    M.C. Müllenbroich, L. Silvestri, A.P. Di Giovanna, G. Mazzamuto, I. Costantini, L. Sacconi, F.S. Pavone, High-fidelity imaging in brain-wide structural studies using light-sheet microscopy. eNeuro 5(6), ENEURO.0124-18.2018 (2018)CrossRefGoogle Scholar
  126. 126.
    N. Renier, E.L. Adams, C. Kirst, Z. Wu, R. Azevedo, J. Kohl, A.E. Autry, L. Kadiri, K.U. Venkataraju, Y. Zhou, V.X. Wang, C.Y. Tang, O. Olsen, C. Dulac, P. Osten, M. Tessier-Lavigne, Mapping of brain activity by automated volume analysis of immediate early genes. Cell 165, 1789–1802 (2016)CrossRefGoogle Scholar
  127. 127.
    M.D. Rocha, D.N. Düring, P. Bethge, F.F. Voigt, S. Hildebrand, F. Helmchen, A. Pfeifer, R.H.R. Hahnloser, M. Gahr, Tissue clearing and light-sheet microscopy: imaging the unsectioned adult zebra finch brain at cellular resolution. Front. Neuroanat. 13, 13 (2019)CrossRefGoogle Scholar
  128. 128.
    J. Bürgers, I. Pavlova, J.E. Rodriguez-Gatica, C. Henneberger, M. Oeller, J.A. Ruland, J.P. Siebrasse, U. Kubitscheck, M.K. Schwarz, Light-sheet fluorescence expansion microscopy: fast mapping of neural circuits at super resolution. Neurophotonics 6(1), 015005 (2019)CrossRefGoogle Scholar

Copyright information

© The Author(s), under exclusive license to Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Luís Manuel Couto Oliveira
    • 1
  • Valery Victorovich Tuchin
    • 2
    • 3
    • 4
    • 5
  1. 1.Physics Department and Center for Innovation in Engineering and Industrial TechnologyPolytechnic Institute of Porto – School of EngineeringPortoPortugal
  2. 2.Department of Optics and BiophotonicsSaratov State UniversitySaratovRussia
  3. 3.Institute of Precision Mechanics and Control of the RASSaratovRussia
  4. 4.Bach Institute of BiochemistryResearch Center of Biotechnology of the RASMoscowRussia
  5. 5.Tomsk State University, Tomsk & ITMO UniversitySt. PetersburgRussia

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