Laboratory of Optical Bioimaging and Spectroscopy

Journal Publications


42. Fung A. A., Shi L**. “Mammalian cell and tissue imaging using Raman and coherent Raman microscopy”. WIREs Systems Biology and Medicine. 2020;e1501. , 2020.

41. Shi L.**, Gayen T., Budansky Y., Yoo K., Secor J., Harvey T., Harvey G., Shumyatsky P., Nolan D., and Alfano R. "Enhanced stimulated raman scattering of solvent due to anharmonic energy transfer from resonance raman solute molecules". Opt. Express 28, 21792-21804, 2020.

40. Shi L., Liu X.*, Shi L.*, Stinson H., Rowlette J., Kahl L., Evans C., Zheng C., Dietrich L., Min W. "Mid-infrared metabolic imaging with vibrational probes". Nature Methods 17, 844-851, 2020.

39. Mazhar SFB., Meyer H.J., Samuels T., Sharonov M., Shi L, Alfano R.R. “Explanation of the competition between O-and E-wave induced stimulated Raman and supercontinuum in calcite under ultrafast laser excitation”. Applied Optics 59 (17), 5252-5257, 2020.

38. Xiong H., Qian N., Zhao L., Shi L, Miao Y, Min W. “Background-free imaging of chemical bonds by a simple and robust frequency-modulated stimulated Raman scattering microscopy”. Optics Express 28 (10), 15663-15677, 2020.

37. Bendau E., Smith J., Zhang L., Ackerstaff E., Kruchevsky N., Wu B., Koutcher J. A., Alfano R. R. and Shi L.** Distinguishing Metastatic Triple Negative Breast Cancer from Non‐Metastatic Breast Cancer using SHG Imaging and Resonance Raman Spectroscopy". J. Biophotonics, 2020;e202000005, 2020 (**corresponding author)

36. Mamani S., Nolan D. A., Shi L., Alfano R. R. “Special classes of optical vector vortex beams are Majorana-like photons”. Optics Communications, 464, 125425, 2020.

35. Shumyatsky P., Shi L., Sordillo L. A., Budansky Y., Alfano R. R. “Comparison of continuous wave versus picosecond SRS and the resonance SRS effect”. Applied Optics 59 (3), 622-627, 2020.


34. Zhang L*, Shi L*, Shen Y*, Miao Y, Wei M, Qian N, Liu Y, Min W. “Spectral tracing of isotope deuterium for imaging glucose metabolism”. Nature Biomedical Engineering 3(5):402-413, 2019. (co-first author)

33. Wei M*, Shi L*, Shen Y, Zhao Z, Guzman A, Kaufman L, Wei L, Min W. “Volumetric chemical imaging by clearing-enhanced stimulated Raman scattering microscopy”. PNAS 116 (14): 6608-6617, 2019. (co-first author)

32. Zhou Y., Liu C., Wu B.,Yu X., Cheng G., Zhu K., Wang K., Zhang C., Zhao M., Zong R., Zhang L., Shi L., Alfano R. R. Optical biopsy identification and grading of gliomas using label-free visible resonance Raman spectroscopy, J. of Biomedical Optics, 24(9), 095001, 2019.

31. Liu C., Wu B., Sordillo L., Boydston-White S., Sriramoju V., Zhang C., Beckman H., Zhang L., Pei Z., Shi L., Alfano R. R. "A pilot study for distinguishing basal cell carcinoma from normal human skin tissues using visible resonance Raman spectroscopy". J Cancer Metastasis Treat; 5:4, 2019.


30. Zhou Y, Liu C, Wu B, Zhang C, Yu X, Cheng G, Chen H, Li S, Liang Q, Zhang M, Zhu K, Shi L, and Alfano R. R. "Molecular biomarkers characterization for human brain glioma grading using visible resonance Raman spectroscopy". APL Photonics 3, 120802, 2018.

29. Shi L*, Zheng C*, Shen Y, Chen Z, Silveira E, Zhang L, Wei M, Liu C, De Sena-Tomas C, Targoff K, Min W. “Optical imaging of metabolic dynamics in animals”. Nature Communications, 9, 2995, 2018.

28. Shi L, Shen Y, and Min W. “Visualizing protein synthesis in mice with in vivo labeling of deuterated amino acids using vibrational imaging”. APL Photonics 3, 092401, 2018.

27. Long R, Zhang L, Shi L, Shen Y, Hu F, Zeng C. and Min W. “Two-color vibrational imaging of glucose metabolism by stimulated Raman scattering”. Chemical Communications 152-155, 2018.

26. Mamani S, Shi L, Ahmed T, Karnik R, Rodríguez‐Contreras A, Nolan D. and Alfano R. R. “Transmission of classically entangled beams through mouse brain tissue”. J. Biophotonics. 11(12):e201800096, 2018.

25. Lu L, Shi L, Secor J, Alfano R. R. "Resonance Raman scattering of β-carotene solution excited by visible laser beams into second singlet state". J. Photochem. Photobiol. B 179:18-22, 2018.


24. Shen Y, Zhao Z, Zhang L, Shi L, Shahriar S, Chan R, Paolo G, Min W. “Metabolic activity induces membrane phase separation in endoplasmic reticulum”. PNAS 114(51):13394-13399, 2017.

23. Sordillo DC, Sordillo LA, Sordillo PP, Shi L, Alfano RR. "Short wavelength infrared optical windows for evaluation of benign and malignant tissues". J. Biomed. Opt. 22(4):45002, 2017.

22. Shi L, Lindwasser L, Wang W, Rodríguez-Contreras A, and Alfano RR. “Propagation of Gaussian and Laguerre Gaussian vortex beams through mouse brain tissue”. J. Biophotonics 10(12): 1756-1760, 2017.

21. Shi L, Lu L, Harvey G, Harvey T, Rodríguez-Contreras A, and Alfano RR. “Label-free fluorescence spectroscopy for detecting key biomolecules in brain tissue from a mouse model of Alzheimer’s disease”. Scientific Reports 7:2599, 2017.

20. Das B*, Shi L*, Budansky Y, Rodríguez-Contreras A, and Alfano RR. “Alzheimer mouse brain tissue measured by time resolved fluorescence spectroscopy using single- and multi-photon excitation of label free native molecules”. J. Biophotonics 11(1), 2017. (co-first author).


19. Shi L, Galvez E, and Alfano R. R. “Photon entanglement through brain tissue”. Scientific Reports 6:37714, 2016.

18. Liu C, Boydston-White S, Weisberg A, Wang W, Sordillo L, Perotte A, Tomaselli V, Sordillo P, Pei Z, Shi L, and Alfano RR. “Vulnerable atherosclerotic plaque detection by resonance Raman spectroscopy”, J. Biomed. Opt. 21 (12):127006, 2016.

17. Alfano RR, Milione G, Galvez E. J., Shi L. “Optical sources: A laser for complex spatial modes”. Nature Photonics 10 (5): 286-288, 2016.

16. Wang W, Gozali R, Shi L, and Alfano R. R. “Deep transmission of Laguerre-Gaussian vortex beams through turbid scattering media”. Opt. Lett. 41(9): 2069-72, 2016.

15. Shi L, Shumyatsky P, Rodríguez-Contreras A, Alfano R. R. “Terahertz spectra ofbrain tissue from a mouse model of Alzheimer disease”. J. Biomed. Opt. 21(1):015014-1, 2016.

14. Shi L, Sordillo LA, Rodríguez-Contreras A, Alfano R. R. “Transmission in near-infrared optical windows for deep brain imaging”. J. Biophotonics 9(1–2):38–43, 2016.


13. Shi L, Rodriguez-Contreras A, Alfano R. R. “Gaussian beam in two photon fluorescence imaging of rat brain microvessel”. J. Biomed. Opt. 19(12):126006, 2014.

12. Shi L, Palacio P, Badami J, Shin D, Zeng M, Cardoso L, Tu R, Fu B. M. “Quantification of transient increase of the blood-brain barrier permeability to macromolecules by optimized focused ultrasound combined with microbubbles”. Int. J. Nanomedicine. 9(1): 4437-48, 2014.

11. Shi L, Zeng M, Fu BM. “Temporal effects of vascular endothelial growth factor and 3,5-cyclic monophosphate on blood–brain barrier solute permeability in vivo”. J. Neurosci. Res. 92(12):1678-89, 2014.

10. Shi L, Rodriguez-Contreras A, Budansky Y, Pu Y, Nguyen T, Alfano R. R. “Deep two-photon microscopic imaging through brain tissue using the second singlet state from fluorescent agent chlorophyll α in spinach leaf”. J. Biomed. Opt. 19(6):066009, 2014.

9. Shi L. Book review of “Diagnostic Endoscopy”. J. Biomed. Opt. 19(4):049902-1. 2014.

8. Shi L, Zeng M, Sun Y, Fu B. M. “Quantification of blood-brain barrier solute permeability and brain transport by multiphoton microscopy”. J. Biomech. Eng. 136: 031005, 2014.

7. Rodríguez-Contreras A, Shi L, Fu B. M. “A method to make a craniotomy on the ventral skull of neonate rodents”. J. Vis. Exp. (87), e51350, 2014.

6. Islam SMZ, Gayen T, Tint N, Shi L, Seredych M, Bandosz T. J., and Alfano R. R. “The effects of fabrication temperature on current-voltage characteristics and energy efficiencies of quantum dot sensitized ZnOH-GO hybrid solar cells”. J. Appl. Phys. 116, 173102, 2014.

5. Islam SMZ, Gayen T, Tint N, Shi L, Seredych M, Bandosz T. J., Alfano R. R. “Hybrid solar cells of micro/meso-porous Zn(OH)2 and its graphite composites sensitized by CdSe quantum dots”. J. Photon. Energy. 4 (1):043098, 2014.


4. Pu Y, Shi L, Pratavieira S, Alfano R. R. “Two-Photon excitation microscopy using the second singlet state of fluorescent agents within the tissue optical window”. J. Appl. Phys. 114(15):153102-4, 2013.

3. Islam SMZ, Gayen T, Seredych M, Mabayoye O, Shi L, Bandosz TJ, and Alfano R. R. “Band gap energies of solar micro/meso-porous composites of zinc (hydr)oxide with graphite oxides”. J. Appl. Phys. 114 (4): 043522 - 6, 2013.

2. Islam SMZ, Gayen T, Das B, Shi L, Seredych M, Moussawi A, Bandosz TJ, Alfano R. R. “Time resolved fluorescence of Zn(OH)2 and it composite with graphite Oxide”. Opt. Lett. 38(13): 2227- 2229, 2013.

1. Islam SMZ, Gayen T, Moussawi A, Shi L, Seredych M, Bandosz TJ, Alfano R. R. “Structural and optical characterization of Zn(OH)2 and its composites with graphite oxides”. Opt. Lett. 38(6): 962- 964, 2013.


  1. Shi L, Alfano R. R. “Deep Imaging in Tissue and biomedical materials using Linear and Non-linear Optics” (1st Ed.). Pan Stanford Publishing, 2017. ISBN 9789814745888.

  2. Alfano R. R., Shi L. “Neurophotonics and Biomedical Spectroscopy” (1st Ed.). Elsevier Publishing, 2018. ISBN-13: 978-0323480673.


1. Shi L., Min W. “System, method and computer-accessible medium for use of heavy water as a probe for imaging metabolic activities”. U.S. Patent Docket No.: 300440.US.01 – 32883-280915 PATENT APPLICATION

2. Alfano R.R., Shi L. “Supercontinuum microscope for resonance and non-resonance enhanced linear and nonlinear time resolved microscope for tissue and materials”. U.S. Patent Appln No. 15409303, 2017.

3. Alfano R.R., Shi L. “Resonant Stimulated Raman Scattering Micrsocope”. U.S. Patent Application Number: 15904089 Application Date: 23.02.2018 Publication Number: 20180238738 Publication Date: 23.08.2018. Allowed.

4. Alfano R.R., Laura Sordillo, Yang Pu, Shi L. “Deep optical imaging of tissue with less scattering in the second, third and fourth NIR spectral windows using supercontinuum and other laser coherent light sources” Awarded patent Number: 10123705 Grant Date: 11/13/2018

5. Alfano R.R., Yang P., Shi L., Pratavieira S. “Method of deep tissue imaging using multi-photon excitation of a fluorophore”. Awarded patent number 10420471. 09/04/2019

6. Alfano R.R., Shi L., Budansky Y. “Continuous Diode Laser Stimulated Raman Gain/Loss Vibrational Microscope”. U.S. Patent Appln. No. 62/283,067. Awarded patent number 10433731, 10/08/2019

7. Alfano R.R., Yang P., Shi L., Pratavieira S. “Method of deep tissue imaging using multi-photon excitation of a fluorophore”. U.S. Patent Appln. No. 14/299,564 (filed June 9th, 2014) Attorney Docket No. 3064421 US01. Publication No. US 2014-0371582-A1, publication date: 12/18/2014.