DRAFT: This module has unpublished changes.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


W. Xie, N.P. Reder, C. Koyuncu, P. Leo, S. Hawley, H. Huang, C. Mao, N. Postupna, S. Kang, R. Serafin, G. Gao, Q. Han, K.W. Bishop, L.A. Barner, P. Fu, J.L. Wright, C.D. Keene, J.C. Vaughan, A. Janowczyk, A.K. Glaser, A. Madabhushi, and J.T.C. Liu, "Prostate cancer risk stratification via non-destructive 3D pathology with deep learning-assisted gland analysis," Cancer Research [in press]. medRxiv preprint 

A.K. Glaser, K.W. Bishop, L.A. Barner, E.A. Susaki, S.I. Kubota, G. Gao, R.B. Serafin, P. Balaram, E. Turschak, P.R. Nicovich, H. Lai, L.A.G. Lucas, Y. Yi, E.K. Nichols, H. Huang, N.P. Reder, J.J. Wilson, R. Sivakumar, E. Shamskhou, C.R. Stoltzfus, X. Wei, A.K. Hempton, M. Pende, P. Murawala, H.U. Dodt, T. Imaizumi, J. Shendure, B.J. Beliveau, M.Y. Gerner, L. Xin, H. Zhao, L.D. True, R.C. Reid, J. Chandrashekar, H.R. Ueda, K. Svoboda, and J.T.C. Liu, “A hybrid open-top light-sheet microscope for multi-scale imaging of cleared tissues,” bioRxiv preprint [manuscript under revision]

M.Y. Lee, C. Mao, A.K. Glaser, M.A. Woodworth, J.T.C. Liu, and J.C. Vaughan, “FLARE: Fluorescent Labeling of Abundant Reactive Entities for Cleared Tissue and Super-Resolution Microscopy,” Nature Protocols [in press].

J.T.C. Liu, A.K. Glaser, K. Bera, L.D. True, N.P. Reder, K.W. Eliceiri, and A. Madabhushi, “Harnessing non-destructive 3D pathology,” Nature Biomedical Engineering (2021)  [PDF]

E.A. Blakeney, S. Kang, K. Henrikson, J.T.C. Liu, E.G. Seibel, J. Sprecher, N. Summerside, M.T. Vogel, B.K. Zierler, and J.D. Posner, “Implementation and evaluation of team science training for interdisciplinary teams in an engineering design program,” J. Clin. Transl. Sci. 5, e127 (2021)  [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, 131, 529 (2021) [PDF]


L. Horowitz, A. Rodriguez, A. Au-Yeung, K.W. Bishop, L.A. Barner, G. Mishra, A. Raman, P. Delgado, J.T.C. Liu, T. Gujral, M. Mehrabi, M. Yang, R. Pierce, and A. Folch, “Microdissected cuboids for microfluidic drug testing of intact tissues,” Lab Chip (2021) [PDF]

W. Xie, A.K. Glaser, F. Vakar-Lopez, J.L. Wright, N.P. Reder, J.T.C. Liu, and L.D. True, “Diagnosing 12 prostate needle cores within an hour of biopsy,” J. Biomed. Opt. 25, 126502 (2020)  [PDF]

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]


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.