Yi lab

Design and build imaging techniques to study life

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Assistant Prof, PI

PhD, Northwestern Univ.

BS, Tsinghua Univ.

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Lab Positions

We have openings for all levels of lab members: postdocs, PhD/MS and undergrad students. 

Apply JHU BME graduate program NOW.

Please reach out to us for more info. 

Wenjun Shao
Postdoc Fellow

PhD, Huazhong U of Sci & Tech (HUST)

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Yuli Wang
PhD student

BS, HuaZhong U of Sci and Tech


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Postdoc Fellow

PhD, Univ. of Oklahoma

Mengyuan Xue
JHU BME MS student

BS, BME, Washington U in St. Louis

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Zhengping Guan
Postdoc Fellow

PhD, National Univ. of Singapore

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Tony Pan
JHU BME UG student
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Yahui Wang, PhD

Current Position: Topcon US

Zhiyu Zhang, MS

Current Position: Shanghai

Weiye Song, PhD

Current Position: Shandong University, Professor

Lei Zhang, PhD

Current Position: Shantou Univ, Assis Prof

Libo Zhou, PhD

Current Position: Univ of Connecticut, Postdoc fellow

Xiaojun Xu, PhD

Current Position:

Sipei Fu, BS

Current Position: Broad Institute, Cambrige

Colby Kim, Undergrad

Current Position: Boston Univ, Boston

Wei Yi, PhD

Current Position: Shandong Univ, Instructor

Rongrong Liu, PhD

Current Position: Chicago



Light Sheet Microscopy

We design and implement various form of light sheet microscopy for observing life in 3D across different length scales from cells to whole body of small organisms.  Harnessing rich light-tissue interaction and advanced imaging technology, we aim to observe life in its native form in 3D in real time and reveal the connection among structure, function, genomics and phenotypes. 

Visible Light Optical Coherence Tomography

We pioneer visible light OCT for three distinct advantages.  First, the shorter wavelength in vis-OCT results in ultra-high image resolution.  Second, hemoglobin has strong absorption in the visible light rage, which allows oxygen sensing.  Third, the expansion of the wavelength range enhances the capability of elastic light spectroscopy, for detecting early structural changes in diseases.  By utilizing motion contrast, label-free microangiography down to single capillary can be achieved.

Imaging oxygen

Oxygen is essential to life. The importance of how human body reacts to oxygen change is recognized by the 2019 Nobel Prize in physiology and medicine.  We developed several cutting-edge techniques (label-free vis-OCT, phosphorescence oxygen sensor) to map oxygen in 3D to quantify the metabolic function of living tissue. 

Retinal and neuroimaging 

We develop retinal imaging techniques to quantify the vascular dysfunction, ultra-structural alterations for blinding pathologies (e.g. diabetic retinopathy, glaucoma, ad AMD).  As the retina shares many similarities with the cerebral cortex and yet has less neuronal cell types and simpler anatomy, the retina is an excellent target for studying neural circuitry and neurovascular coupling.

Crossing modalities with deep learning

Multimodal, multi-dimensional, real-time imaging generates large amount of data.  We are interested in using deep learning network to transform different imaging modalities, for example, transform label-free reflectance to immunofluorescent images, to ultimately eliminate the staining process.  Holistically, deep learning may hold advantage to identify hidden phenotypical features that is hard to perceive or quantitate using analytical model. 

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EN.580.489/689 Modern Optical Microscopy: Theory and Practice

Description: Modern optical microscopy is one of the most exciting frontiers in biomedical engineering.  It visualizes and studies the 3D complex structures of biological systems, by implementing and engineering the physics of light and optics.  This course will teach the fundamental theory in optical image formation, microscopy, propagation of light wave and Fourier optics.  The theoretical framework will be reinforced  through hand-on projects and labs.  By the end of the course, the students will know how to design and build their own advanced microscopes, such as light sheet microscopy for 3D imaging and reconstruction. 

Style: Lab/design style (50% in class lecture, and 50% lab).  The ratio will be scaled more towards lectures and discussion during COVID.  The emphasis is that the student learn the fundamental theory and practice by hands-on experiments.  Ideally, the lecture and lab should be well coordinated, such that the optical theory is reinforced in lab class.  The goal is that student will develop understanding of the optical physics, and be able to design and implement microscopy platforms. 

Prerequisites: Fourier analysis, Linear system, Linear algebra, Proficiency for Matlab programing 



64. Lei Tian, Brady Hunt, Muyinatu A Lediju Bell, Ji Yi, Jason T Smith, Marien Ochoa, Xavier Intes, Nicholas J Durr, "Deep learning in biomedical optics", Lasers in Surgery and Medicine, Lasers Surg Med, 53: 748-775, 2021

63. Shiyi Cheng, Sipei Fu, Yumi Mun Kim, Weiye Song, Yunzhe Li, Yujia Xue, Ji Yi, Lei Tian Single-cell cytometry via multiplexed fluorescence prediction by label-free reflectance microscopy", Sci Advances, Vol. 7, no. 3, eabe0431 2021. Pre-print version is here.

62. Wenjun Shao, Kivilcim Kilic, Wenqing Yin, Gregory Wirak, Xiaodan Qin, Hui Feng, David Boas, Christopher V Gabel, Ji Yi Wide field-of-view volumetric imaging by a mesoscopic scanning oblique plane microscopy with switchable objective lens", Quantitative Imaging in Medicine and Surgery (QMIS), vol 11, No 3, 2021. Pre-print version is here.

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61. Weiye Song, Wenjun Shao, Wei Yi, Rongrong Liu, Manishi Desai, Steven Ness, Ji Yi “Visible light optical coherence tomography angiography (vis-OCTA) and local microvascular retinal oximetry in human retina”, Biomed Opt Express, 11, 4037-4051. 2020  Preprint version is here .

59. Weiye Song, Alex Matlock, Sipei Fu, Xiaodan Qin, Hui Feng, Christopher V. Gabel, Lei Tian, Ji Yi “LED array reflectance microscopy for scattering-based multi-contrast imaging ”, Opt Lett. 45, 7, 2020
Codes and PCB design is here .

58. Alex Matlock, Anne Sentenac, Patrick C. Chaumet, Ji Yi, Lei Tian “Inverse scattering for reflection intensity phase microscopy”, Biomed Opt Express,11,2, 2020

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Preprint. Alex Matlock, Anne Sentenac, Patrick C. Chaumet, Ji Yi, Lei Tian “Inverse scattering for reflection intensity phase microscopy”, arXiv:1912.07709

57. Graham LC Spicer, Aya Eid, D Wangpraseurt, TD Swain, James A Winkelmann, J Yi, M Kühl, LA Marcelino, V Backman “Measuring light scattering and absorption in corals with Inverse Spectroscopic Optical Coherence Tomography (ISOCT): a new tool for non-invasive monitoring”, Sci. Rep. 9(1) 1-12, 2019

56. Rongrong Liu, Shiyi Cheng, Lei Tian, Ji Yi “Deep spectral learning for label-free optical imaging oximetry with uncertainty quantification”, Light Sci. Appl. 8, 102. 2019  Preprint version, bioRxiv 650259
Data and codes are open-sourced at Github.

54. Weiye Song, Sipei Fu, Shangshang Song, Sui Zhang, Lei Zhang, Steven Ness, Manishi Desai, Ji Yi “Longitudinal detection of retinal alteration by visible and near-infrared optical co-herence tomography (vnOCT) in a dexamethasone-induced ocular hypertension mouse model”, Neurophotonics, 6(4), 041103. 2019 Preprint version is here.

53. Hyunjoo Jean Lee, Lei Zhang, Sui Zhang, Ji Yi “Detection of Malignancy in Ocular Surface Lesions by Inverse Spectroscopic Optical Coherence Tomography and Two-Photon Autofluorescence”, Translational Vision Science & Technology 8 (3), 16-16, 2019

52. Rongrong Liu, Weiye Song, Vadim Backman, Ji Yi, “Quantitative quality-control metrics for in vivo oximetry in small vessels by visible light optical coherence tomography angiography”, Biomed. Opt. Express, 10 (2) 465-486, 2018

51. Rongrong Liu, James Winkelmann, Graham Spicer, Yunxiao Zhu, Aya Eid, Guillermo Ameer, Vadim Backman, Ji Yi, “Single capillary oximetry and tissue ultrastructural sensing by dual-band dual-scan inverse spectroscopic optical coherence tomography”, Light:Science & applications, (7) 57. 2018

50. Weiye Song, Libo Zhou, Sui Zhang, Steven Ness, Manishi Desai, Ji Yi, “Fiber-based visible and near infrared optical coherence tomography (vnOCT) enables quantitative elastic light scattering spectroscopy in human retina”, Biomed. Opt. Express, 9, 3464-3480. 2018

49. Weiye Song, Libo Zhou, Kevin Liu Kot, Huijie Fan, Jingyan Han, Ji Yi, “Measurement of Flow-Mediated Dilation of Mouse Femoral Artery in vivo by Optical Coherence Tomography”, Journal of Biophotonics, e201800053. 2018

47. James A. Winkelmann, Aya Eid, The-Quyen Nguyen, Thang Bui, Ji Yi, Vadim Backman, “In Vivo Broad-band Visible Light Optical Coherence Tomography Probe Enables Inverse Spectroscopic Analysis”, Opt Lett. 43, 619-622. 2018

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46. Lei Zhang*, Weiye Song*, Di Shao, Sui Zhang, Manishi Desai, Steven Ness, Sayon Roy, Ji Yi “Volumetric fluorescence retinal imaging in vivo over a 30-degree field of view by oblique scanning laser ophthalmoscopy (oSLO)”, Biomed. Opt. Express. 9(1), 25-40. 2017

44. Lei Zhang, Amalia Capilla1, Weiye Song, Gustavo Mostoslavsky, Ji Yi “Oblique scanning laser microscopy for simultaneously volumetric structural and molecular imaging using only one raster scan ”, Sci. Rep. 7: 8591, 2019

43. Rongrong Liu, Graham Spicer, Siyu Chen, HF Zhang, Ji Yi, Vadim Backman, “Theoretical model for optical oximetry at the capillary level: exploring hemoglobin oxygen saturation through backscattering of single red blood cells”, J. Biomed. Opt. 22(2), 025002, 2017

42. Wenzhong Liu, Shoujian Wang, Ji Yi, Kevin Zhang, Siyu Chen, Robert A. Linsenmeier, Christine M. Sorenson, Nader Sheibani, Hao F. Zhang, “Increased retinal oxygen metabolism precedes microvascular alterations in Type 1 diabetic mice”, IOVS, 58 (2), 981-989, 2017

41. Jisheng Xiao, Siyu Chen, Ji Yi, Hao F Zhang, Guillermo A Ameer, “A Cooperative Copper Metal–Organic Framework‐Hydrogel System Improves Wound Healing in Diabetes”, Adv. Funct. Mater., 27 (1), 1604872, 2017

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40. Wenli Wu, Andrew J Radosevich, Adam Eshein, Ji Yi, Lusik Cherkezyan, Hemant K Roy, Igal Szleifer, Vadim Backman, “Using electron microscopy to calculate optical properties of biological samples”, BOE, 7(11), 4749-4762, 2016

39. Ji Yi, Zhen Puyang, Liang Feng, Lian Duan, Peiji Liang, Vadim Backman, Xiaorong Liu, Hao F. Zhang, “Optical detection of early damage in retinal ganglion cells in a mouse model of partial optic nerve crush injury”, IOVS, 57 (13), 5665-5671, 2016

38. Biqin Dong, Siyu Chen, Fan Zhou, Christina Chan, Ji Yi, Hao F. Zhang, and Cheng Sun, “Real-time Functional Analysis of Inertial Microfluidic Devices via Spectral Domain Optical Coherence Tomography”, Scientific Reports, 6: 33250, 2016

37. Yunxiao Zhu, Ryan Hoshi, Siyu Chen, Ji Yi, Chongwen Duan, Robert D Galiano, Hao F Zhang,Guillermo A. Ameer, “Sustained release of stromal cell derived factor-1 from an antioxidant thermoresponsive hydrogel enhances dermal wound healing in diabetes”, Journal of Controlled Release, 238(28),114-122. 2016

36. Graham Spicer, Samira Azarin, Ji Yi; Scott Young, Ronald Ellis, Greta Bauer, Lonnie Shea, Vadim Backman, “Detection of extracellular matrix modification in cancer models with inverse spectroscopic optical coherence tomography”, Phys. Med. Biol. 61 6892. 2016

34. Siyu Chen, Xiao Shu, Ji Yi, Amani A. Fawzi, and Hao Zhang, “Dual-band Optical Coherence Tomography Using a Single Supercontinuum Laser Source”, JBO, 21(6), 066013. 2016

33. Ronil S. Shah*, Brian T. Soetikno*, Ji Yi, Wenzhong Liu, Dimitra Skondra, Hao F. Zhang, Amani A. Fawzi, “Visible-light Optical Coherence Tomography Angiography for Monitoring Laser-induced Choroidal Neovascularization in Mice”, IOVS, 57 (9), OCT86-OCT95. 2016

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32. Brian T. Soetikno, Ji Yi, Ronil Shah, Wenzhong Liu, Patryk Purta, Hao F Zhang, and Amani A. Fawzi, “Inner retinal oxygen metabolism in the 50/10 oxygen-induced retinopathy model”, Scientific Report,5,16752. 2015

31. Ji Yi, Yolanda Stypula-Cyrus, Catherine Blaha, Hemant K. Roy, and Vadim Backman, "Fractal characterization of chromatin decompaction in live cells", Biophys. J., 109(11) 2218–2226. 2015

30. Samira M. Azarin, Ji Yi, Robert M. Gower, Brian A. Aguado, Megan E. Sullivan, Ashley G. Goodman, Eric J. Jiang, Shreyas S. Rao, Yinying Ren, Susan L. Tucker, Vadim Backman, Jacqueline S. Jeruss, and Lonnie D Shea, "In vivo capture and label-free detection of early metastatic cells", Nat. Commun. 6:8094 doi: 10.1038/ncomms9094. 2015

29. Ji Yi*, Siyu Chen*, Xiao Shu*, Amani A. Fawzi, and Hao F. Zhang, “Human retinal imaging using visible-light optical coherence tomography guided by scanning laser ophthalmoscopy”, Biomed. Opt. Express 6, 3701-3713. 2015

28. Wenzhong Liu*, Ji Yi*, Siyu Chen, Shuliang Jiao, Hao F Zhang, “Measuring retinal blood flow in rats using Doppler optical coherence tomography without knowing eyeball axial length”, Med. Phys. 42, 5356. 2015

26. Ji Yi, Wenzhong Liu, Siyu Chen, Vadim Backman, Nader Sheibani, Amani A. Fawzi, Robert A. Linsenmeier, and Hao F. Zhang, “Visible light optical coherence tomography measures retinal oxygen metabolic response to systemic oxygenation”, Light: Science &Applications, 4, e334. 2015

25. Siyu Chen, Ji Yi, Wenzhong Liu, Vadim Backman, Hao F. Zhang, “Monte Carlo investigation of optical coherence tomography retinal oximetry”, IEEE Trans. Biomed. Eng., 62 (9) 2015

24. Ben E. Urban*, Ji Yi*, Siyu Chen*, Biqin Dong, Yongling Zhu, Steven H. DeVries, Vadim Backman, and Hao F. Zhang, “Super-resolution two-photon microscopy via scanning patterned illumination” , Physical Review E 91, 042703. 2015

23. Siyu Chen, Ji Yi, Biqin Dong, Cheng Sun, Patrick F Kiser, Thomas J Hope, Hao F Zhang, “Imaging endocervical mucus anatomy and dynamics in macaque female reproductive track using optical coherence tomography”, Quantitative Imaging in Medicine and Surgery, 5(1), 40–45. 2015

22. Hui Chen, Yan Zhao, Mingna Liu, Liang Feng, Zhen Puyang, Ji Yi, Peiji Liang, Hao F. Zhang, Jianhua Cang, John B. Troy, and Xiaorong Liu, “Progressive Degeneration of Retinal and Superior Collicular Functions in Mice With Sustained Ocular Hypertension”, IOVS, 56(3), 1971-1984. 2015

21. Ji Yi, Siyu Chen, Vadim Backman, Hao F. Zhang, “In vivo functional microangiography by visible light optical coherence tomography”, Biomedical Optics Express, 5(10), 3603-3612. 2014

20. Wei Song, Qing Wei, Wenzhong Liu, Tan Liu, Ji Yi, Nader Sheibani, Amani A. Fawzi, Robert A. Linsenmeier, Shuliang Jiao, Hao F. Zhang, “A combined method to quantify the retinal metabolic rate of oxygen using photoacoustic ophthalmoscopy and optical coherence tomography”, Scientific Report 4, 6525. 2014

19. Ben Urban, Ji Yi, Vladislav Yakovlev, and Hao F. Zhang, “Investigating femtosecond-laser induced two-photon photoacoustic generation”, Journal of Biomedical Optics 19(8), 085001. 2014

18. Ji Yi, Andrew J. Radosevich, Yolanda Stypula-Cyrus, Nikhil N. Mutyal, Samira Michelle Azarin, Elizabeth Horcher, Michael J. Goldberg; Laura K. Bianchi; Shailesh Bajaj; Hemant K. Roy; Vadim Backman, “Spatially-resolved optical and ultra-structural properties of colorectal and pancreatic field carcinogenesis observed by inverse spectroscopic optical coherence tomography,” Journal of Biomedical Optics 19, 036013. 2014

17. Kvar. C. L. Black, Tadas. S. Sileika, Ji Yi, R. Zhang, J. G. Rivera, and Phillip B. Messersmith, "Bacterial Killing by Light-Triggered Release of Silver from Biomimetic Metal Nanorods," Small 10, 169-178. 2014

16. J. D. Rogers*, A. J. Radosevich*, Ji Yi*, and V. Backman, "Modeling Light Scattering in Tissue as Continuous Random Media Using a Versatile Refractive Index Correlation Function," Selected Topics in Quantum Electronics, IEEE Journal of 20, 1-14. 2014

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15. A. J. Radosevich, N. N. Mutyal, Ji Yi, Y. Stypula-Cyrus, J. D. Rogers, M. J. Goldberg, L. K. Bianchi, S. Bajaj, H. K. Roy, and V. Backman, "Ultrastructural alterations in field carcinogenesis measured by enhanced backscattering spectroscopy," Journal of Biomedical Optics 18, 097002. 2013

14. Wenzhong Liu, Tan Liu, Wei Song, Ji Yi, and Hao F. Zhang, “Automatic retinal vessel segmentation based on active contours method in Doppler spectral-domain optical coherence tomography,” Journal of Biomedical Optics 18, 016002. 2013

13. Ji Yi, Qing Wei, Wenzhong Liu, Vadim Backman, and Hao F. Zhang, “Visible-light optical coherence tomography for retinal oximetry,” Optics Letters, 38(11), 1796-1798. 2013

12. Kvar CL Black, Ji Yi, José G. Rivera, Daria C. Zelasko-Leon, and Phillip B. Messersmith, "Polydopamine-enabled surface functionalization of gold nanorods for cancer cell-targeted imaging and photothermal therapy," Nanomedicine 8, 17-28. 2013

11. Ji Yi, Wenzhong Liu, Shuliang Jiao, and Hao F. Zhang, “Combining light and sound for retinal imaging,” SPIE Newsroom, DOI: 10.1117/2.1201303.004764. 2013

10. Ji Yi, Andrew J. Radosevich, Jeremy D. Rogers, Sam C.P. Norris, İlker R. Çapoğlu, Allen Taflove, and Vadim Backman, "Can OCT be sensitive to nanoscale structural alterations in biological tissue?," Optics Express 21, 9043-9059. 2013

9. Andrew J. Radosevich, J. D. Rogers, V. Turzhitsky, N. N. Mutyal, Ji Yi, H. K. Roy, V. Backman, "Polarized enhanced backscattering spectroscopy for characterization of biological tissues at subdiffusion length scales," Selected Topics in Quantum Electronics, IEEE Journal of 18, 1313-1325, 2012

8. Andrew J. Radosevich, Ji Yi, Jeremy D. Rogers, and Vadim Backman, "Structural length-scale sensitivities of reflectance measurements in continuous random media under the Born approximation," Optics Letters 37, 5220-5222. 2012

7. Ji Yi, Qing Wei, Hao F. Zhang, and Vadim Backman, "Structured interference optical coherence tomography," Optics Letters 37, 3048-3050. 2012

4. Andrew J Radosevich, Nikhil N Mutyal, Vladimir Turzhitsky, Jeremy D Rogers, Ji Yi, Allen Taflove, and Vadim Backman, “Measurement of the spatial backscattering impulse-response at short length scales with polarized enhanced backscattering”, Optics Letters 36, 4737-4739. 2011

2. Jianmin Gong, Ji Yi, Vladimir M. Turzhitsky, Kenji Muro, and Xu Li. "Characterization of malignant brain tumor using elastic light scattering spectroscopy," Disease Markers 25, 303-312. 2008

1. Xiaolei Song, Ji Yi, Jing Bai, "A parallel reconstruction scheme in fluorescence tomography based on contrast of independent inversed absorption properties," International Journal of Biomedical Imaging, 70839. 2006





Mengyuan Xue joined our group.  Welcome Mengyuan, and we are happy to have you joining us and looking forward to getting some great work done!

Aug 2021

Congrats to lab Alumni Dr. Weiye Song soon joining professorship in Shandong University. 

Yuli Wang joined the lab!  Welcome and we are excited to have you!

July 2021

We are honored to participate a newly funded NEI R01 (Zambidis) on using iPSC derived vascular progenitor for vascular regeneration and repair.  Our in vivo imaging technique would monitor the structural and functional responses.

Mar 2021

Collaborative R01 (Yi) with BU, UPenn is funded by NEI on 3D oxygen mapping in living retina! We are cracking down the oxygen perfusion function in the eye, and how it may translate in clinical cares.

Jan 2021

Dr. Yahui Wang joined our group.  Welcome Yahui!

Mar 2021

Collaborative work on "Single-cell cytometry via multiplexed fluorescence prediction by label-free reflectance microscopy".  Shout out to all the authors, and the hardworking UG students Sipei, and Colby!  NIH please fund this great project. 

Jan 2021

Wenjun's work on Wide FOV mesoscopic oblique plane microscopy is published!  We achieved a whooping ~5x6 mm volumetric imaging with low NA objectives. 

Dec 2020

Dr. Jingyu Wang is joining our group.  Welcome Jingyu!  

Sept 2020

Our paper "Visible light optical coherence tomography angiography (vis-OCTA) and local microvascular retinal oximetry in human retina" is top downloads on Biomed Opt Express in July.  We have 5 consecutive papers in monthly top download list! 

Sept 2020

Yi lab will be moving to Johns Hopkins University Biomedical Engineering department and Wilmer Eye Institute in July 2020.

Jan 2020

Our paper on high-speed volumetric fluorescein angiography in mice is among top downloads in BOE! We have 4 consecutive papers in monthly top download list. We are excited to further develop this new technique for human imaging .

Oct 2019




400 N. Broadway

Baltimore MD,  21231

Email: jiyi at jhu dot edu


For any inquiries and questions, please feel free to contact us or you are welcomed to visit us!