Laboratory of Optical Bioimaging and Spectroscopy

Journal Publications

  1. 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)
  2. 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)
  3. 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 RR. "Molecular biomarkers characterization for human brain glioma grading using visible resonance Raman spectroscopy". APL Photonics 3, 120802, 2018.
  4. Shi L*, Zheng C*, Shen Y, Chen Z, Silveira E, Zhang L, Chang L, De Sena Tomas C, Targoff K, Min W. “Optical imaging of metabolic dynamics in animals”. Nature Communications, 9, 2995, 2018.
  5. 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.
  6. 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.
  7. Mamani S, Shi L, Ahmed T, Karnik R, Rodríguez‐Contreras A, Nolan D. and Alfano RR. “Transmission of classically entangled beams through mouse brain tissue”. J. Biophotonics. 11(12):e201800096, 2018.
  8. Lu L, Shi L, Secor J, Alfano RR. "Resonance Raman scattering of β-carotene solution excited by visible laser beams into second singlet state". J. Photochem. Photobiol. B 179:18-22, 2018.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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).
  14. Shi L, Galvez E, and Alfano RR. “Photon entanglement through brain tissue”. Scientific Reports 6:37714, 2016.
  15. 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.
  16. Alfano RR, Milione G, Galvez EJ, Shi L. “Optical sources: A laser for complex spatial modes”. Nature Photonics 10 (5): 286-288, 2016.
  17. Wang W, Gozali R, Shi L, and Alfano RR. “Deep transmission of Laguerre-Gaussian vortex beams through turbid scattering media”. Opt. Lett. 41(9): 2069-72, 2016.
  18. Shi L, Shumyatsky P, Rodríguez-Contreras A, Alfano RR. “Terahertz spectra ofbrain tissue from a mouse model of Alzheimer disease”. J. Biomed. Opt. 21(1):015014-1, 2016.
  19. Shi L, Sordillo LA, Rodríguez-Contreras A, Alfano RR. “Transmission in near-infrared optical windows for deep brain imaging”. J. Biophotonics 9(1–2):38–43, 2016.
  20. Shi L, Rodriguez-Contreras A, Alfano RR. “Gaussian beam in two photon fluorescence imaging of rat brain microvessel”. J. Biomed. Opt. 19(12):126006, 2014.
  21. Shi L, Palacio P, Badami J, Shin D, Zeng M, Cardoso L, Tu R, Fu BM. “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.
  22. 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.
  23. Shi L, Rodriguez-Contreras A, Budansky Y, Pu Y, Nguyen T, Alfano RR. “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.
  24. Shi L. Book review of “Diagnostic Endoscopy”. J. Biomed. Opt. 19(4):049902-1. 2014.
  25. Shi L, Zeng M, Sun Y, Fu BM. “Quantification of blood-brain barrier solute permeability and brain transport by multiphoton microscopy”. J. Biomech. Eng. 136: 031005, 2014.
  26. Rodríguez-Contreras A, Shi L, Fu BM. “A method to make a craniotomy on the ventral skull of neonate rodents”. J. Vis. Exp. (87), e51350, 2014.
  27. Islam SMZ, Gayen T, Tint N, Shi L, Seredych M, Bandosz TJ, and Alfano RR. “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.
  28. Islam SMZ, Gayen T, Tint N, Shi L, Seredych M, Bandosz TJ, Alfano RR. “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.
  29. Pu Y, Shi L, Pratavieira S, Alfano RR. “Two-Photon excitation of the second singlet (S2) state of fluorescent agents for deeper tissue microscope imaging”. J. Appl. Phys. 114(15):153102-4, 2013.
  30. Islam SMZ, Gayen T, Seredych M, Mabayoye O, Shi L, Bandosz TJ, and Alfano RR. “Band gap energies of solar micro/meso-porous composites of zinc (hydr)oxide with graphite oxides”. J. Appl. Phys. 114 (4): 043522 - 6, 2013.
  31. Islam SMZ, Gayen T, Das B, Shi L, Seredych M, Moussawi A, Bandosz TJ, Alfano RR. “Time resolved fluorescence of Zn(OH)2 and it composite with graphite Oxide”. Opt. Lett. 38(13): 2227- 2229, 2013.
  32. Islam SMZ, Gayen T, Moussawi A, Shi L, Seredych M, Bandosz TJ, Alfano RR. “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 RR. “Deep Imaging in Tissue and biomedical materials using Linear and Non-linear Optics” (1st Ed.). Pan Stanford Publishing, 2017. ISBN 9789814745888.
  2. Alfano RR, Shi L. “Neurophotonics and Biomedical Spectroscopy” (1st Ed.). Elesvier 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” Application Number: 15243165 Application Date: 22.08.2016 Publication Number: 20170049326 Publication Date: 23.02.2017 Grant Number: 10123705 Grant Date: 13.11.2018

5. Alfano R.R., Shi L.. “Linear and nonlinear optical microscopes using laser excitation in near-infrared spectral range 1550-1870 nm and 1950-2300nm for deep imaging in brain”. U.S. (filed on January 12, 2016).

6. 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.