Handbook of Tissue Optical Clearing

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

The book—subtitled “New Prospects in Optical Imaging”—is unique in bringing together a number of diverse tissue optical clearing (TOC) topics, such as 3D imaging and the combination of TOC and optical imaging/spectroscopy for diagnostics, and presenting it all at a level suitable for graduate students in biophysics and engineering. This task is accomplished with an emphasis on both methodology and applications. I found the description of these basic biophotonics techniques particularly detailed and interesting. Although written by more than 100 contributors, the style of the book is generally clear and fluent.Review by Christian Brosseau, Optica Fellow and professor of physics, Université de Bretagne Occidentale, Brest, France, June 2022.

• Preface............................................................................................................................................................................................. ixAcknowledgments..........................................................................................................................................................................xiiiEditors............................................................................................................................................................................................. xvContributors..................................................................................................................................................................................xviiPart I Basic principles of tissue optical clearing1. Tissue optical clearing mechanisms...................................................................................................................................... 3Tingting Yu, Dan Zhu, Luís Oliveira, Elina A. Genina, Alexey N. Bashkatov, and Valery V. Tuchin2. Tissue optical clearing for Mueller matrix microscopy.................................................................................................... 31Nan Zeng, Honghui He, Valery V. Tuchin, and Hui Ma3. Traditional and innovative optical clearing agents........................................................................................................... 67Elina A. Genina, Vadim D. Genin, Jingtan Zhu, Alexey N. Bashkatov, Dan Zhu, and Valery V. Tuchin4. Chemical enhancers for improving tissue optical clearing efficacy................................................................................. 93Dan Zhu, Yanmei Liang, Xingde Li, and Valery V. Tuchin5. Human skin autofluorescence and optical clearing......................................................................................................... 109Walter Blondel, Marine Amouroux, Sergey M. Zaytsev, Elina A. Genina, Victor Colas, Christian Daul,Alexander B. Pravdin, and Valery V. Tuchin6. Molecular modeling of post-diffusion phase of optical clearing of biological tissues.................................................. 127Kirill V. Berezin, Konstantin N. Dvoretskiy, Maria L. Chernavina, Anatoly M. Likhter, and Valery V. Tuchin7. Refractive index measurements of tissue and blood components and OCAs in a wide spectral range......................141Ekaterina 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. Tuchin8. Water migration at skin optical clearing...........................................................................................................................167Anton Yu. Sdobnov, Johannes Schleusener, Jürgen Lademann, Valery V. Tuchin, and Maxim E. Darvin9. Optical and mechanical properties of cartilage during optical clearing...................................................................... 185Yulia 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. Tuchin10. Compression optical clearing............................................................................................................................................. 199Olga A. Zyuryukina and Yury P. SinichkinPart 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..............221Tingting Yu, Jianyi Xu, and Dan Zhu12. Ultrafast aqueous clearing methods for 3D imaging....................................................................................................... 239Tingting Yu, Jingtan Zhu, and Dan Zhu13. Challenges and opportunities in hydrophilic tissue clearing methods.......................................................................... 257Etsuo A. Susaki and Hiroki R. Ueda14. Combination of tissue optical clearing and 3D fluorescence microscopy for high-throughput imagingof entire organs and organisms ......................................................................................................................................... 277Peng Fei and Chunyu Fang15. Endogenous fluorescence preservation from solvent-based optical clearing................................................................ 297Tingting Yu, Yisong Qi, and Dan Zhu16. Progress in ex situ tissue optical clearing – shifting immuno-oncology to the third dimension..................................315Paweł Matryba, Leszek Kaczmarek, and Jakub GołąbPart III Towards in vivo tissue optical clearing17. In vivo skin optical clearing methods for blood flow and cell imaging.......................................................................... 333Dongyu Li, Wei Feng, Rui Shi, and Dan Zhu18. In vivo skull optical clearing for imaging cortical neuron and vascular structure and function................................351Dongyu Li, Yanjie Zhao, Chao Zhang, and Dan Zhu19. In vivo skin optical clearing in humans............................................................................................................................. 369Elina A. Genina, Alexey N. Bashkatov, Vladimir P. Zharov, and Valery V. Tuchin20. Optical clearing of blood and tissues using blood components...................................................................................... 383Olga S. Zhernovaya, Elina A. Genina, Valery V. Tuchin, and Alexey N. Bashkatov21. Blood and lymph flow imaging at optical clearing........................................................................................................... 393Polina A. Dyachenko (Timoshina), Arkady S. Abdurashitov, Oxana V. Semyachkina-Glushkovskaya,and Valery V. TuchinPart IV Combination of tissue optical clearing and opticalimaging/spectroscopy for diagnostics22. Optical clearing aided photoacoustic imaging in vivo......................................................................................................411Yong Zhou and Lihong V. Wang23. Enhancement of contrast in photoacoustic – fluorescence tomography and cytometry usingoptical clearing and contrast agents...................................................................................................................................419Julijana Cvjetinovic, Daniil V. Nozdriukhin, Maksim Mokrousov, Alexander Novikov, Marina V. Novoselova,Valery V. Tuchin, and Dmitry A. Gorin24. Tissue optical clearing in the terahertz range.................................................................................................................. 445Olga A. Smolyanskaya, Kirill I. Zaytsev, Irina N. Dolganova, Guzel R. Musina, Daria K. Tuchina,Maxim M. Nazarov, Alexander P. Shkurinov, and Valery V. Tuchin25. Magnetic resonance imaging study of diamagnetic and paramagnetic agents for optical clearingof tumor-specific fluorescent signal in vivo....................................................................................................................... 459Alexei A. Bogdanov Jr., Natalia I. Kazachkina, Victoria V. Zherdeva, Irina G. Meerovich, Daria K. Tuchina,Ilya D. Solovyev, Alexander P. Savitsky, and Valery V. Tuchin26. 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........................................ 471Daniel Fried27. Optical clearing of adipose tissue...................................................................................................................................... 487Irina 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. Tuchin28. Diabetes mellitus-induced alterations of tissue optical properties, optical clearing efficiency,and molecular diffusivity.....................................................................................................................................................517Daria K. Tuchina and Valery V. Tuchin29. Tissue optical clearing for in vivo detection and imaging diabetes induced changes in cells,vascular structure, and function....................................................................................................................................... 539Dongyu Li, Wei Feng, Rui Shi, Valery V. Tuchin, and Dan Zhu30. Light operation on cortex through optical clearing skull window................................................................................. 557Dongyu Li, Chao Zhang, Oxana Glushkovskaya, Yanjie Zhao, and Dan Zhu31. The role of optical clearing to enhance the applications of in vivo OCT and photodynamic therapy:Towards PDT of pigmented melanomas and beyond...................................................................................................... 569Layla Pires, Michelle Barreto Requena, Valentin Demidov, Ana Gabriela Salvio,I. Alex Vitkin, Brian C. Wilson, and Cristina Kurachi32. Combination of tissue optical clearing and OCT for tumor diagnosis via permeabilitycoefficient measurements.................................................................................................................................................... 577Qingliang Zhao33. Optical clearing for cancer diagnostics and monitoring................................................................................................. 597Luís M. Oliveira and Valery V. Tuchin34. Contrast enhancement and tissue differentiation in optical coherence tomographywith mechanical compression............................................................................................................................................ 607Pavel D. Agrba and Mikhail Yu. Kirillin35. Measurement of the dermal beta-carotene in the context of multimodal optical clearing..........................................619Mohammad Ali Ansari and Valery V. Tuchin36. Optical clearing and molecular diffusivity of hard and soft oral tissues...................................................................... 629Alexey A. Selifonov and Valery V. Tuchin37. Optical clearing and Raman spectroscopy: In vivo applications................................................................................... 647Qingyu Lin, Ekaterina N. Lazareva, Vyacheslav I. Kochubey, Yixiang Duan, and Valery V. TuchinIndex............................................................................................................................................................................................. 655