Yun, S. H. & Kwok, S. J. J. Light in diagnosis, therapy and surgery. Nat. Biomed. Eng. 1, 0008 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lichtman, J. W. & Conchello, J.-A. Fluorescence microscopy. Nat. Methods 2, 910–919 (2005).

Article  CAS  PubMed  Google Scholar 

Valdastri, P., Simi, M. & Webster, R. J. 3rd Advanced technologies for gastrointestinal endoscopy. Annu. Rev. Biomed. Eng. 14, 397–429 (2012).

Article  CAS  PubMed  Google Scholar 

Boas, D. A. & Dunn, A. K. Laser speckle contrast imaging in biomedical optics. J. Biomed. Opt. 15, 011109 (2010).

Article  PubMed  PubMed Central  Google Scholar 

Song, G., Jelly, E. T., Chu, K. K., Kendall, W. Y. & Wax, A. A review of low-cost and portable optical coherence tomography. Prog. Biomed. Eng. 3, 032002 (2021).

Article  Google Scholar 

Cho, S.-W. et al. Sounding out the dynamics: a concise review of high-speed photoacoustic microscopy. J. Biomed. Opt. 29, S11521 (2024).

Article  PubMed  PubMed Central  Google Scholar 

McWade, M. A., Sanders, M. E., Broome, J. T., Solórzano, C. C. & Mahadevan-Jansen, A. Establishing the clinical utility of autofluorescence spectroscopy for parathyroid detection. Surgery 159, 193–202 (2016).

Article  PubMed  Google Scholar 

Cao, R., Wallrabe, H. & Periasamy, A. Multiphoton FLIM imaging of NAD(P)H and FAD with one excitation wavelength. J. Biomed. Opt. 25, 1–16 (2020).

Article  PubMed  Google Scholar 

Tan, Y., Lin, H. & Cheng, J.-X. Profiling single cancer cell metabolism via high-content SRS imaging with chemical sparsity. Sci. Adv. 9, eadg6061 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sun, H., Wang, S., Chen, J. & Yu, H. Label-free second harmonic generation imaging of cerebral vascular wall in local ischemia mouse model in vivo. Neuroscience 502, 10–24 (2022).

Article  CAS  PubMed  Google Scholar 

Wang, L., Jacques, S. L. & Zheng, L. MCML—Monte Carlo modeling of light transport in multi-layered tissues. Comput. Methods Prog. Biomed. 47, 131–146 (1995).

Article  CAS  Google Scholar 

Jacques, S. L. & Pogue, B. W. Tutorial on diffuse light transport. J. Biomed. Opt. 13, 041302 (2008).

Article  PubMed  Google Scholar 

Tuchin, V. Tissue optics and photonics: light-tissue interaction II. J. Biomed. Photonics Eng. 2, 030201 (2016).

Article  Google Scholar 

Bohren, C. F. & Huffman, D. R. Absorption and Scattering of Light by Small Particles (Wiley, 2008).

Hong, G., Antaris, A. L. & Dai, H. Near-infrared fluorophores for biomedical imaging. Nat. Biomed. Eng. 1, 0010 (2017).

Article  CAS  Google Scholar 

Xu, C., Nedergaard, M., Fowell, D. J., Friedl, P. & Ji, N. Multiphoton fluorescence microscopy for in vivo imaging. Cell 187, 4458–4487 (2024).

Article  CAS  PubMed  Google Scholar 

Schmidt, E. L. et al. Near-infrared II fluorescence imaging. Nat. Rev. Methods Prim. 4, 23 (2024).

Article  CAS  Google Scholar 

Ueda, H. R. et al. Tissue clearing and its applications in neuroscience. Nat. Rev. Neurosci. 21, 61–79 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ou, Z. et al. Achieving optical transparency in live animals with absorbing molecules. Science 385, eadm6869 (2024).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lucarini, V., Saarinen, J. J., Peiponen, K. -E. & Vartiainen, E. M. Kramers–Kronig Relations in Optical Materials Research (Springer, 2010).

Hecht, E. Optics (Pearson Education, 2001).

Boothe, T. et al. A tunable refractive index matching medium for live imaging cells, tissues and model organisms. eLife 6, e27240 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Oliveira, L. M. C. & Tuchin, V. V. The Optical Clearing Method: A New Tool for Clinical Practice and Biomedical Engineering (Springer, 2019).

Tuchin, V. V. Optical Clearing of Tissues and Blood (SPIE, 2005).

Talei Franzesi, G. et al. In vivo optical clearing of mammalian brain. Preprint at bioRxiv https://doi.org/10.1101/2024.09.05.611421 (2024).

König, J. in Colour Additives for Foods and Beverages (ed. Scotter, M. J.) 35–60 (Woodhead Publishing, 2015).

FAO Nutrition Meetings Report Series (Food and Agriculture Organization of the United Nations, World Health Organization, 1966).

Narawane, A. et al. Optical clearing with tartrazine enables deep transscleral imaging with optical coherence tomography. J. Biomed. Opt. 29, 120501 (2024).

CAS  PubMed  PubMed Central  Google Scholar 

Miller, D. et al. Enhanced penetration depth in optical coherence tomography and photoacoustic microscopy in vivo enabled by absorbing dye molecules. Optica 12, 24–30 (2025).

Article  CAS  Google Scholar 

Cai, R. et al. Whole-mouse clearing and imaging at the cellular level with vDISCO. Nat. Protoc. 18, 1197–1242 (2023).

Article  CAS  PubMed  Google Scholar 

Chung, K. et al. Structural and molecular interrogation of intact biological systems. Nature 497, 332–337 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Susaki, E. A. et al. Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. Cell 157, 726–739 (2014).

Article  CAS  PubMed  Google Scholar 

He, R. et al. Effects of optical clearing agents on noninvasive blood glucose monitoring with optical coherence tomography: a pilot study. J. Biomed. Opt. 17, 101513 (2012).

Article  PubMed  Google Scholar 

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

Article  CAS  PubMed  Google Scholar 

Feng, W., Liu, C.-J., Wang, L. & Zhang, C. An optical clearing imaging window: realization of mouse brain imaging and manipulation through scalp and skull. J. Cereb. Blood Flow. Metab. 43, 2105–2119 (2023).

Article  PubMed  PubMed Central  Google Scholar 

Inagaki, S. et al. Isotonic and minimally invasive optical clearing media for live cell imaging ex vivo and in vivo. Preprint at bioRxiv https://doi.org/10.1101/2024.09.13.612584 (2024).

Antaris, A. L. et al. A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging. Nat. Commun. 8, 15269 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Theer, P., Hasan, M. T. & Denk, W. Two-photon imaging to a depth of 1000 micron in living brains by use of a Ti:Al2O3 regenerative amplifier. Opt. Lett. 28, 1022–1024 (2003).

Article  CAS  PubMed  Google Scholar 

Horton, N. G. et al. In vivo three-photon microscopy of subcortical structures within an intact mouse brain. Nat. Photon. 7, 205–209 (2013).

Article  CAS  Google Scholar 

Costantini, I., Cicchi, R., Silvestri, L., Vanzi, F. & Pavone, F. S. In-vivo and ex-vivo optical clearing methods for biological tissues: review. Biomed. Opt. Express 10, 5251–5267 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Iijima, K., Oshima, T., Kawakami, R. & Nemoto, T. Optical clearing of living brains with MAGICAL to extend in vivo imaging. iScience 24, 101888 (2021).

Article  CAS  PubMed