Handbook of Tissue Optical Clearing

Valery V. Tuchin, Dan Zhu, Elina A. Genina

Preface............................................................................................................................................................................................. ix

Acknowledgments..........................................................................................................................................................................xiii

Editors............................................................................................................................................................................................. xv

Contributors..................................................................................................................................................................................xvii

Part I Basic principles of tissue optical clearing

1. Tissue optical clearing mechanisms...................................................................................................................................... 3

Tingting Yu, Dan Zhu, Luís Oliveira, Elina A. Genina, Alexey N. Bashkatov, and Valery V. Tuchin

2. Tissue optical clearing for Mueller matrix microscopy.................................................................................................... 31

Nan Zeng, Honghui He, Valery V. Tuchin, and Hui Ma

3. Traditional and innovative optical clearing agents........................................................................................................... 67

Elina A. Genina, Vadim D. Genin, Jingtan Zhu, Alexey N. Bashkatov, Dan Zhu, and Valery V. Tuchin

4. Chemical enhancers for improving tissue optical clearing efficacy................................................................................. 93

Dan Zhu, Yanmei Liang, Xingde Li, and Valery V. Tuchin

5. Human skin autofluorescence and optical clearing......................................................................................................... 109

Walter Blondel, Marine Amouroux, Sergey M. Zaytsev, Elina A. Genina, Victor Colas, Christian Daul,

Alexander B. Pravdin, and Valery V. Tuchin

6. Molecular modeling of post-diffusion phase of optical clearing of biological tissues.................................................. 127

Kirill V. Berezin, Konstantin N. Dvoretskiy, Maria L. Chernavina, Anatoly M. Likhter, and Valery V. Tuchin

7. Refractive index measurements of tissue and blood components and OCAs in a wide spectral range......................141

Ekaterina N. Lazareva, Luís Oliveira, Irina Yu. Yanina, Nikita V. Chernomyrdin, Guzel R. Musina,

Daria K. Tuchina, Alexey N. Bashkatov, Kirill I. Zaytsev, and Valery V. Tuchin

8. Water migration at skin optical clearing...........................................................................................................................167

Anton Yu. Sdobnov, Johannes Schleusener, Jürgen Lademann, Valery V. Tuchin, and Maxim E. Darvin

9. Optical and mechanical properties of cartilage during optical clearing...................................................................... 185

Yulia M. Alexandrovskaya, Olga I. Baum, Vladimir Yu. Zaitsev, Alexander A. Sovetsky, Alexander L. Matveyev,

Lev A. Matveev, Kirill V. Larin, Emil N. Sobol, and Valery V. Tuchin

10. Compression optical clearing............................................................................................................................................. 199

Olga A. Zyuryukina and Yury P. Sinichkin

Part II Tissue optical clearing method for biology (3D imaging)

11. Optical clearing for multiscale tissues and the quantitative evaluation of clearing methods in mouse organs..............221

Tingting Yu, Jianyi Xu, and Dan Zhu

12. Ultrafast aqueous clearing methods for 3D imaging....................................................................................................... 239

Tingting Yu, Jingtan Zhu, and Dan Zhu

13. Challenges and opportunities in hydrophilic tissue clearing methods.......................................................................... 257

Etsuo A. Susaki and Hiroki R. Ueda

14. Combination of tissue optical clearing and 3D fluorescence microscopy for high-throughput imaging

of entire organs and organisms ......................................................................................................................................... 277

Peng Fei and Chunyu Fang

15. Endogenous fluorescence preservation from solvent-based optical clearing................................................................ 297

Tingting Yu, Yisong Qi, and Dan Zhu

16. Progress in ex situ tissue optical clearing – shifting immuno-oncology to the third dimension..................................315

Paweł Matryba, Leszek Kaczmarek, and Jakub Gołąb

Part III Towards in vivo tissue optical clearing

17. In vivo skin optical clearing methods for blood flow and cell imaging.......................................................................... 333

Dongyu Li, Wei Feng, Rui Shi, and Dan Zhu

18. In vivo skull optical clearing for imaging cortical neuron and vascular structure and function................................351

Dongyu Li, Yanjie Zhao, Chao Zhang, and Dan Zhu

19. In vivo skin optical clearing in humans............................................................................................................................. 369

Elina A. Genina, Alexey N. Bashkatov, Vladimir P. Zharov, and Valery V. Tuchin

20. Optical clearing of blood and tissues using blood components...................................................................................... 383

Olga S. Zhernovaya, Elina A. Genina, Valery V. Tuchin, and Alexey N. Bashkatov

21. Blood and lymph flow imaging at optical clearing........................................................................................................... 393

Polina A. Dyachenko (Timoshina), Arkady S. Abdurashitov, Oxana V. Semyachkina-Glushkovskaya,

and Valery V. Tuchin

Part IV Combination of tissue optical clearing and optical

imaging/spectroscopy for diagnostics

22. Optical clearing aided photoacoustic imaging in vivo......................................................................................................411

Yong Zhou and Lihong V. Wang

23. Enhancement of contrast in photoacoustic – fluorescence tomography and cytometry using

optical clearing and contrast agents...................................................................................................................................419

Julijana Cvjetinovic, Daniil V. Nozdriukhin, Maksim Mokrousov, Alexander Novikov, Marina V. Novoselova,

Valery V. Tuchin, and Dmitry A. Gorin

24. Tissue optical clearing in the terahertz range.................................................................................................................. 445

Olga A. Smolyanskaya, Kirill I. Zaytsev, Irina N. Dolganova, Guzel R. Musina, Daria K. Tuchina,

Maxim M. Nazarov, Alexander P. Shkurinov, and Valery V. Tuchin

25. Magnetic resonance imaging study of diamagnetic and paramagnetic agents for optical clearing

of tumor-specific fluorescent signal in vivo....................................................................................................................... 459

Alexei A. Bogdanov Jr., Natalia I. Kazachkina, Victoria V. Zherdeva, Irina G. Meerovich, Daria K. Tuchina,

Ilya D. Solovyev, Alexander P. Savitsky, and Valery V. Tuchin

26. Use of optical clearing and index matching agents to enhance the imaging of caries, lesions,

and internal structures in teeth using optical coherence tomography and SWIR imaging........................................ 471

Daniel Fried

27. Optical clearing of adipose tissue...................................................................................................................................... 487

Irina Yu. Yanina, Yohei Tanikawa, Daria K. Tuchina, Polina A. Dyachenko (Timoshina), Yasunobu Iga,

Shinichi Takimoto, Elina A. Genina, Alexey N. Bashkatov, Georgy S. Terentyuk, Nikita A. Navolokin,

Alla B. Bucharskaya, Galina N. Maslyakova, and Valery V. Tuchin

28. Diabetes mellitus-induced alterations of tissue optical properties, optical clearing efficiency,

and molecular diffusivity.....................................................................................................................................................517

Daria K. Tuchina and Valery V. Tuchin

29. Tissue optical clearing for in vivo detection and imaging diabetes induced changes in cells,

vascular structure, and function....................................................................................................................................... 539

Dongyu Li, Wei Feng, Rui Shi, Valery V. Tuchin, and Dan Zhu

30. Light operation on cortex through optical clearing skull window................................................................................. 557

Dongyu Li, Chao Zhang, Oxana Glushkovskaya, Yanjie Zhao, and Dan Zhu

31. The role of optical clearing to enhance the applications of in vivo OCT and photodynamic therapy:

Towards PDT of pigmented melanomas and beyond...................................................................................................... 569

Layla Pires, Michelle Barreto Requena, Valentin Demidov, Ana Gabriela Salvio,

I. Alex Vitkin, Brian C. Wilson, and Cristina Kurachi

32. Combination of tissue optical clearing and OCT for tumor diagnosis via permeability

coefficient measurements.................................................................................................................................................... 577

Qingliang Zhao

33. Optical clearing for cancer diagnostics and monitoring................................................................................................. 597

Luís M. Oliveira and Valery V. Tuchin

34. Contrast enhancement and tissue differentiation in optical coherence tomography

with mechanical compression............................................................................................................................................ 607

Pavel D. Agrba and Mikhail Yu. Kirillin

35. Measurement of the dermal beta-carotene in the context of multimodal optical clearing..........................................619

Mohammad Ali Ansari and Valery V. Tuchin

36. Optical clearing and molecular diffusivity of hard and soft oral tissues...................................................................... 629

Alexey A. Selifonov and Valery V. Tuchin

37. Optical clearing and Raman spectroscopy: In vivo applications................................................................................... 647

Qingyu Lin, Ekaterina N. Lazareva, Vyacheslav I. Kochubey, Yixiang Duan, and Valery V. Tuchin

Index............................................................................................................................................................................................. 655