DRAFT: This module has unpublished changes.
Peer-reviewed publications

J.T.C. Liu, A.K. Glaser, K. Bera, L.D. True, N.P. Reder, K.W. Eliceiri, and A. Madabhushi, “Harnessing the potential of nondestructive 3D pathology,” Nature Biomedical Engineering [in press]

A.K. Glaser, K.W. Bishop, L.A. Barner, R.B. Serafin, and J.T.C. Liu, “A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues,” bioRxiv preprint

L.A. Barner, A.K. Glaser, H. Huang, L.D. True, and J.T.C. Liu, “Multi-resolution open-top light-sheet microscopy to enable efficient 3D pathology workflows,” Biomed. Opt. Exp. 11, 6605 (2020)  [PDF]

R. Serafin, W. Xie, A.K. Glaser, and J.T.C. Liu, "FalseColor-Python: a rapid intensity-leveling and digital-staining package for fluorescence-based slide-free digital pathology," PLoS ONE 15, e0233198 (2020)  [PDF]

Y. Fujita, L. Wei, P.J. Cimino, J.T.C. Liu, and N. Sanai, “Video-mosaicked handheld dual-axis confocal microscopy of gliomas: an ex vivo feasibility study in humans,” Frontiers in Oncology, 10, 1674 (2020)  [PDF]

K.W. Bishop, A.K. Glaser, and J.T.C. Liu, “Performance trade-offs for single- and dual-objective light-sheet microscope designs,” Biomed. Opt. Exp. 11, 4627 (2020)  [PDF]

Y. Lee, G. Krishnan, N. Nishio, N.S. van den Berg, G. Lu, B.A. Martin, S. van Keulen, A.D. Colevas, S. Kapor, J.T.C. Liu, and E.L. Rosenthal, “Intraoperative fluorescence-guided surgery in head and neck squamous cell carcinoma,” Laryngoscope, early online [PDF]


C. Mao, M.Y. Lee, J. Jhan, A.R. Halpern, M.A. Woodworth, A.K. Glaser, T.J. Chozinski, L. Shin, J.W. Pippin, S.J. Shankland, J.T.C. Liu, and J.C. Vaughan, “Feature-rich covalent stains for super-resolution and cleared-tissue fluorescence microscopy,” Science Advances, 6, eaba4542 (2020)  [PDF]


C. Yin, L. Wei, K. Kose, A.K. Glaser, G. Peterson, M. Rajadhyaksha, and J.T.C. Liu, “Real-time video mosaicking to guide handheld in vivo microscopy,” J. Biophotonics, 13, e202000048 (2020)  [PDF]


L.A. Barner, A.K. Glaser, L.D. True, N.P. Reder, and J.T.C. Liu, "Solid immersion meniscus lens (SIMlens) for open-top light-sheet microscopy," 
Opt. Lett. 44, 4451 (2019) [PDF]

A.K. Glaser, N.P. Reder, Y. Chen, C. Yin, L. Wei, S. Kang, L.A. Barner, W. Xie, E.F. McCarty, C. Mao, A.R. Halpern, C.R. Stoltzfus, J.S. Daniels, M.Y. Gerner, P.R. Nicovich, J.C. Vaughan, L.D. True, and J.T.C. Liu, "Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues," Nature Communications 10, 2781 (2019) [PDF | Supplement and videos | PreLights commentary]


L. Wei, Y. Fujita, N. Sanai, and J.T.C. Liu, "Towards quantitative neurosurgical guidance with high-resolution microscopy of 5-aminolevulinic acid-induced protoporphyrin IX" (perspective review article) Frontiers in Oncology 9, 592 (2019) [PDF]


N.P. Reder, A.K. Glaser, E.F. McCarty, Y. Chen, L.D. True, and J.T.C. Liu, "Open-top light-sheet microscopy image atlas of prostate core needle biopsies," Arch. Pathol. Lab. Med. 143, 1069 (2019) [PDF]


C. Yin, L. Wei, S. Abeytunge, G. Peterson, M. Rajadhyaksha, and J.T.C. Liu, "Label-free in vivo pathology of human epithelia with a high-speed handheld dual-axis confocal microscope," J. Biomed. Opt. 24, 030501 (2019) [PDF]


S. Kang, X. Xu, E. Navarro; Y. Wang, J.T.C. Liu, and K.M. Tichauer, "Modeling the binding and diffusion of receptor-targeted nanoparticles topically applied on fresh tissue specimens," Physics in Medicine and Biology 64, 045013 (2019) [PDF]

Y. Chen, W. Xie, A.K. Glaser, N.P. Reder, C. Mao, S.M. Dintzis, J.C. Vaughan, and J.T.C. Liu, "Rapid pathology of lumpectomy margins with open-top light-sheet (OTLS) microscopy," Biomed. Opt. Exp. 10, 1257 (2019) [PDF]



W. Xie, Y. Chen, Y. Wang, L. Wei, C. Yin, A.K. Glaser, M.E. Fauver, E.J. Seibel, S.M. Dintzis, J.C. Vaughan, N.P. Reder and J.T.C. Liu, "Microscopy with ultraviolet surface excitation for wide-area pathology of breast surgical margins," J. Biomed. Opt. 24, 026501 (2019) [PDF]


L. Wei, C. Yin, Y. Fujita, N. Sanai, and J.T.C. Liu, "A handheld line-scanned dual-axis confocal microscope with pistoned MEMS actuation for flat-field fluorescence imaging," Opt. Lett. 44, 671 (2019) [PDF]

L. Wei, D.W. Roberts, N. Sanai, and J.T.C. Liu, "Visualization technologies for 5-ALA-based fluorescence-guided surgeries," J. Neuro-Oncology 141, 495 (2019) [PDF]

L. Wei, C. Yin, and J.T.C. Liu, "Dual-axis confocal microscopy for point-of-care pathology," IEEE J. Select. Topics Quantum Elect. 25 (2019) [PDF

R.M. Davis, J.L. Campbell, S. Burkitt, Z. Qiu, S. Kang, M. Mehraein, D. Miyasato, H. Salinas, J.T.C. Liu, and C. Zavaleta, "A Raman imaging approach using CD47 antibody-labeled SERS nanoparticles for identifying breast cancer and its potential to guide surgical resection," Nanomaterials 8, 953 (2018) [PDF]

A.K. Glaser, Y. Chen, C. Yin, L. Wei, L.A. Barner, N.P. Reder, and J.T.C. Liu, "Multidirectional digital scanned light-sheet microscopy enables uniform fluorescence excitation and contrast-enhanced imaging," Scientific Reports 8, 13878 (2018) [PDF]

M.A. Wall, B.M. Cossairt, and J.T.C. Liu, "Reaction-driven nucleation theory," J. Phys. Chem. C  (2018) [PDF]

 Y. Wang, Q. Yang, S. Kang, M.A. Wall, and J.T.C. Liu, "High-speed Raman-encoded molecular imaging of freshly excised tissue surfaces with topically applied SERRS nanoparticles," J. Biomed. Opt. 23, 046005 (2018) [PDF]

S. Kang, Y. Wang, X. Xu, E. Navarro, K.M. Tichauer, and J.T.C. Liu, "Microscopic investigation of topically applied nanoparticles for molecular imaging of fresh tissue surfaces," J. Biophotonics (2018) [PDF | Supplement]

Y. Wang, N.P. Reder, S. Kang, A.K. Glaser, and J.T.C. Liu, "Multiplexed Optical Imaging of Tumor-Directed Nanoparticles: A Review of Imaging Systems and Approaches," Nanotheranostics 1, 369 (2017) [PDF]




Y. Wang*, N.P. Reder*, S. Kang, A.K. Glaser, Q. Yang, M.A. Wall, S.H. Javid, S.M. Dintzis, and J.T.C. Liu, "Raman-encoded molecular imaging (REMI) with topically applied SERS nanoparticles for intraoperative guidance of lumpectomy," Cancer Research 77, 4506 (2017) [PDF | Supplement]   *equal contribution


A.K. Glaser*, N.P. Reder*, Y. Chen, E.F. McCarty, C. Yin, L. Wei, Y. Wang, L.D. True, and J.T.C. Liu, "Light-sheet microscopy for slide-free nondestructive pathology of large clinical specimens," Nature Biomedical Engineering 1, 0084 (2017)     *equal contribution

[PDF | Supplement and videos | "Behind the paper" blog | UW press release | KOMO news video | UW360 video"News and views" editorial in Nat Biomed Eng | Editor's choice in Sci Transl Med | Interview in thePathologist | Blog post by @NIHDirector Francis Collins]


 X. Xu, Y. Wang, J. Xiang, J.T.C. Liu, and K.M. Tichauer, "Rinsing paired-agent model (RPAM) to quantify cell-surface receptor concentrations in topical staining applications of thick tissues," Physics in Medicine and Biology 62, 5098 (2017) [download


L. Wei, Y. Chen, C. Yin, S. Borwege, N. Sanai, and J.T.C. Liu, "Optical-sectioning microscopy of protoporphyrin IX fluorescence in human gliomas: standardization and quantitative comparison with histology," J. Biomed. Opt. 22, 046005 (2017) [download]


Y. Chen, A.K. Glaser, and J.T.C. Liu, "Bessel-beam illumination in dual-axis confocal microscopy mitigates resolution degradation caused by refractive heterogeneities," J. Biophotonics 10, 68 (2017) [download]

S. Kang, Y. Wang, N.P. Reder, and J.T.C. Liu, "Multiplexed molecular imaging of biomarker-targeted SERS nanoparticles on fresh tissue specimens with channel-compressed spectrometry" PLoS ONE 11, e016473 (2016) [download]

Y. Wang, J.D. Doerksen, S. Kang, D. Walsh, Q. Yang, D. Hong, and J.T.C. Liu, "Multiplexed molecular imaging of fresh tissue surfaces enabled by convection-enhanced topical staining with SERS-coded nanoparticles, Small (2016) [download]

A.K. Glaser, Y. Chen, and J.T.C. Liu, "Fractal propagation method enables realistic optical microscopy simulations in biological tissues," Optica 3, 861 (2016) [download]

Y. Wang, S. Kang, A. Khan, G. Ruttner, S.Y. Leigh, M. Murray, S. Abeytunge, G. Peterson, M. Rajadhyaksha, S. Dintzis, S. Javid, and J.T.C. Liu, “Quantitative molecular phenotyping with topically applied SERS nanoparticles for intraoperative guidance of breast cancer lumpectomy,” Scientific Reports 6, 21242 (2016) [download]

A.K. Glaser, Y. Wang, and J.T.C. Liu, "Assessing the imaging performance of light sheet microscopies in highly scattering tissues," Biomed. Opt. Exp. 7, 454 (2016) [download]

C. Yin, A.K. Glaser, S.Y. Leigh, Y. Chen, Linpeng Wei, P.C.S. Pillai, M. Rosenberg, S. Abeytunge, G. Peterson, C. Glazowski, N. Sanai, M.J. Mandella, M. Rajadhyaksha, and J.T.C. Liu, “Miniature in vivo MEMS-based line-scanned dual-axis confocal microscope for point-of-care pathology,” Biomed. Opt. Exp. 7, 251 (2016)   [PDF]   
UW press release link

S. Kossatz, C. Brand, S. Gutiontov, J.T.C. Liu, N.Y. Lee, M. Gonen, W.A. Weber, and T. Reiner,” Detection and delineation of oral cancer with a PARP1 targeted optical imaging agent,” Scientific Reports 6, 21371 (2016) [download]

S.Y. Leigh, Y. Chen, and J.T.C. Liu, "Modulated-alignment dual-axis (MAD) confocal microscopy optimized for speed and contrast," IEEE Trans. Biomed. Eng. 63, 2119 (2016) [download]

Y. Wang, S. Kang, J. Doerksen, A.K. Glaser, and J.T.C. Liu, “Surgical guidance via multiplexed molecular imaging of fresh tissues labeled with SERS-coded nanoparticles,” IEEE J. Select. Topics Quantum Elect. 22 (2016) [download]

Y. Chen, D. Wang, A. Khan, Y. Wang, S. Borwege, N. Sanai, and J.T.C. Liu, "Video-rate in vivo fluorescence imaging with a line-scanned dual-axis confocal microscope," J. Biomed. Opt. 20, 106011 (2015) [download]

Y. Wang, S. Kang, A. Khan, P. Bao, and J.T.C. Liu, "In vivo multiplexed molecular imaging of esophageal cancer via spectral endoscopy of topically applied SERS nanoparticles," Biomed. Opt. Exp. 6, 3714 (2015)  [download]

K.M. Tichauer, Y. Wang, Brian W. Pogue, and J.T.C. Liu, "Quantitative in vivo cell-surface receptor imaging in oncology: kinetic modeling & paired-agent principles from nuclear medicine and optical imaging," Physics in Medicine and Biology 60, R239 (2015)  [download]

Y. Chen and J.T.C. Liu, "Characterizing the beam steering and distortion of Gaussian and Bessel beams focused in tissues with microscopic heterogeneities," Biomed. Opt. Exp. 6, 1318 (2015)  [download]

E. Garai, S. Sensarn, C.L. Zavaleta, N.O. Loewke, S. Rogalla, M.J. Mandella, S.A. Felt, S. Friedland, J.T.C. Liu, S.S. Gambhir, and C.H. Contag, “A real-time clinical endoscopic system for intraluminal multiplexed imaging of surface-enhanced raman scattering nanoparticles,” PLoS ONE 10, e0123185 (2015)  [download]

 L. Sinha*, Y. Wang*, C. Yang, A. Khan, J.G. Brankov, J.T.C. Liu, and K.M. Tichauer, "Quantification of the binding potential of cell-surface receptors in fresh excised specimens via dual-probe modeling of SERS nanoparticles," Scientific Reports 5, 8582 (2015)  [download]        *authors contributed equally

D. Meza, D. Wang, Y. Wang, S. Borwege, N. Sanai, and J.T.C. Liu, "Comparing high-resolution microscopy techniques for potential intraoperative use in guiding low-grade glioma resections," Lasers in Surgery and Medicine 47, 289 (2015)  [download]

D. Wang, D. Meza, Y. Wang, L. Gao, and J.T.C. Liu, "Sheet-scanned dual-axis confocal (SS-DAC) microscopy using Richardson-Lucy deconvolution," Opt. Lett. 39, 5431 (2014)  [download]

Y. Wang, A. Khan, S.Y. Leigh, D. Wang, Y. Chen, D. Meza, and J.T.C. Liu, "Comprehensive spectral endoscopy of topically applied SERS nanoparticles in the rat esophagus," Biomed. Opt. Exp. 5, 2883 (2014)  [download]

S.Y. Leigh, Y. Chen, and J.T.C. Liu, "Modulated-alignment dual-axis (MAD) confocal microscopy for deep optical sectioning in tissues," Biomed. Opt. Exp. 5, 1709 (2014)  [download

Y. Wang, A. Khan, M. Som; D. Wang, Y. Chen, S.Y. Leigh, D. Meza; P.Z. McVeigh, B.C. Wilson, and J.T.C. Liu, “Rapid ratiometric biomarker detection with topically applied SERS nanoparticles,” Technology 2, 1-15 (2014)  [download]

J.T.C. Liu, D. Meza, and N. Sanai, “Trends in fluorescence image-guided surgery for gliomas,” Neurosurgery 75, 61-71 (2014)  [download]

D. Wang, Y. Chen, Y. Wang, and J.T.C. Liu, “Comparison of line-scanned and point-scanned dual-axis confocal (DAC) microscope performance,” Opt. Lett. 38, 5280-5283 (2013)  [download]

Y. Chen and J.T.C. Liu, “Optimizing the performance of dual-axis confocal microscopes via Monte-Carlo scattering simulations and diffraction theory,” J. Biomed. Opt. 18, 066006 (2013)  [download]

C. Zavaleta, E. Garai, J.T.C. Liu, S. Sensarn, M.J. Mandella, D. Van de Sompel, S. Friedland, J. Van Dam, C.H. Contag, and S.S. Gambhir, “A Novel Raman-Based Endoscopic Imaging Tool for Multiplexed Molecular Imaging,” Proc. Natl. Acad. Sci. USA (2013)  [download]

S.Y. Leigh, M. Som, and J.T.C. Liu, "Method for assessing the reliability of molecular diagnostics based on multiplexed Raman-coded nanoparticles," PLoS ONE 8, e62084 (2013)  [download

D. Wang, Y. Chen, and J.T.C. Liu, "A liquid optical phantom with tissue-like heterogeneities for confocal microscopy," Biomed. Opt. Exp. 12, 3153-3160 (2012)  [download]

Y. Chen, D. Wang, and J.T.C. Liu, “Assessing the tissue-imaging performance of confocal microscope architectures via Monte-Carlo scattering simulations,” Opt. Lett. 37, 4495-4497 (2012)  [download].

D. Wang, S.Y. Leigh, Y. Chen, H. Haeberle, C.H. Contag, and J.T.C. Liu, “Microscopic delineation of medulloblastoma margins in a transgenic mouse model using a topically applied VEGFR-1 probe,” Translational Oncology 5, 408-414 (2012)  [download] - chosen as the cover article.  Stony Brook press release (with video).

S.Y. Leigh and J.T.C. Liu, “Multi-color miniature dual-axis confocal microscope for point-of-care pathology,” Opt. Lett. 37, 2430-2432 (2012)  [download]

H. Haeberle, J.T. Dudley, J.T.C. Liu, A. J. Butte, and C.H. Contag, “Identification of cell surface targets through meta-analysis of microarray data,” Neoplasia 14, 666-669 (2012)  [download]

W. Piyawattanametha, H. Ra, Z. Qiu, S. Friedland, J.T.C. Liu, K. Loewke, G.S. Kino, O. Solgaard, T.D. Wang, M.J. Mandella, and C.H. Contag, "In vivo near-infrared dual-axis confocal microendoscopy in the human lower gastrointestinal tract," J. Biomed. Opt. 17, 021102 (2012)  [download]

J.T.C. Liu, N.O. Loewke, M.J. Mandella, R.L. Levenson, J.M. Crawford, and C.H. Contag, “Point-of-care pathology with miniature microscopes,” Anal. Cell. Pathol. 34, 81-98 (2011)  [download] 

J.T.C. Liu, M.J. Mandella, N.O. Loewke, H. Ra, W. Piyawattanametha, H. Haeberle, O. Solgaard, G.S. Kino, and C.H. Contag, “Micromirror-scanned dual-axis confocal microscope utilizing a gradient-index relay lens for image-guidance during brain surgery,” J. Biomed. Opt. 15, 026029 (2010)  [download]

J.T.C. Liu, M.W. Helms, M.J. Mandella, J.M. Crawford, G.S. Kino, and C.H. Contag, “Quantifying cell-surface biomarker expression in thick tissues with ratiometric three-dimensional microscopy,” Biophys. J. 96, 2405-2414 (2009)  [download]

J.T.C. Liu, M.J. Mandella, J.M. Crawford, C.H. Contag, T.D. Wang, and G.S. Kino “Efficient rejection of scattered light enables deep optical sectioning in turbid media with low-NA optics in a dual-axis confocal architecture,” J. Biomed. Opt. 13, 034020 (2008)  [download]

T.D. Wang, S. Friedland, P. Sahbaie, R. Soetikno, P.L. Hsiung, J.T.C. Liu, J.M. Crawford, C.H. Contag, “Functional Imaging of Colonic Mucosa With a Fibered Confocal Microscope for Real-Time In Vivo Pathology,” Clin. Gastroenterol. and Hepatol. 5, 1300-1305 (2007)  [download]

J.T.C. Liu, M.J. Mandella, H. Ra, L.K. Wong, O. Solgaard, G.S. Kino, W. Piyawattanametha, C.H. Contag, and T.D. Wang, “Miniature near-infrared dual-axes confocal microscope utilizing a two-dimensional microelectromechanical systems scanner,” Opt. Lett. 32, 256-258 (2007)  [download]

G.B. Rieker, H. Li, X. Liu, J.T.C. Liu, J.B. Jeffries, R.K. Hanson, M.G. Allen, S.D. Wehe, P.A. Mulhall, H.S. Kindle, A. Kakuho, K.R. Sholes, T. Matsuura, and S. Takatani, "Rapid Measurements of Temperature and H2O Concentrations in IC Engines with a Spark Plug-Mounted Diode Laser Sensor," 31st Int. Symp. on Combustion, Heidelberg, Aug. 2006; in Proc. Comb. Inst 31, 3041-3049 (2007).

J.T.C. Liu, M.J. Mandella, J.M. Crawford, C.H. Contag, G.S. Kino, and T.D. Wang, “Dual-axes confocal reflectance microscope for distinguishing colonic neoplasia,” J. Biomed. Opt. 11, 054019 (2006)  [download]

J.T.C. Liu, G.B. Rieker, J.B. Jeffries, R.K. Hanson, M.R. Gruber, T. Mathur, and C.D. Carter,  "Near-infrared diode laser absorption diagnostic for temperature and water vapor in a scramjet combustor," Appl. Opt. 44, 6701-6711 (2005).

J.T.C. Liu, J.B. Jeffries and R.K. Hanson, "Large-Modulation-Depth 2f Spectroscopy with Diode Lasers for Rapid Temperature and Species Measurements in Gases with Blended and Broadened Spectra," Appl. Opt. 43, 6500-6509 (2004).

J.T.C. Liu, J.B. Jeffries and R.K. Hanson, "Wavelength Modulation Absorption Spectroscopy with 2f Detection using Multiplexed Diode Lasers for Rapid Temperature Measurements in Gaseous Flows," App. Phys. B 78, 503-511 (2004).

J.T.C. Liu, R.K. Hanson, and J.B. Jeffries, "High-sensitivity absorption diagnostic for NO2 using a blue diode laser," J. Quant. Spectrosc. and Radiat. Transfer 72, No. 5, 655-664 (2002).
DRAFT: This module has unpublished changes.