Publications

45.    High-Speed Optical Imaging with sCMOS Pixel Reassignment


Biagio Mandracchia*, Corey Zheng*, Suraj Rajendran, Wenhao Liu, Parvin Forghani, Chunhui Xu, Shu Jia

Nature Communications accepted in principle (2024) (*equal contribution) (open source)

44.    hydroSIM: Super-resolution speckle illumination microscopy with a hydrogel diffuser

Zijun Gao, Keyi Han, Xuanwen Hua, Wenhao Liu, Shu Jia

Biomedical Optics Express 15, 3574 (2024) (open source)

43.    Light-Field Flow Cytometry for High-Resolution, Volumetric, and Multiparametric 3D Single-Cell Analysis

Xuanwen Hua*, Keyi Han*, Biagio Mandracchia, Afsane Radmand, Wenhao Liu, Hyejin Kim, Zhou Yuan, Samuel M. Ehrlich, Kaitao Li, Corey Zheng, Jeonghwan Son, Aaron D. Silva Trenkle, Gabriel A. Kwong, Cheng Zhu, James E. Dahlman, Shu Jia

Nature Communications  15, 1975 (2024)  (*equal contribution) (open source)

42.    Cationic cholesterol-dependent LNP delivery to lung stem cells, the liver, and heart

Afsane Radmand, Hyejin Kim, Jared Beyersdorf, Curtis N. Dobrowolski, Ryan Zenhausern, Kalina Paunovska, Sebastian G. Huayamares, Xuanwen Hua, Keyi Han, David Loughrey, Marine Z. C. Hatit, Ada Del Cid, Huanzhen Ni, Aram Shajii, Andrea Li, Abinaya Muralidharan, Hannah E. Peck, Karen E. Tiegreen, Shu Jia, Philip J. Santangelo, and James E. Dahlman

Proceedings of the National Academy of Sciences  121, e2307801120 (2024) 

41.    OctoShaker: A Versatile Robotic Biomechanical Agitator for Cellular and Organoid Research

Yan Huang, Soojung Lee, Wenhao Liu, Shuichi Takayama, Shu Jia

Review of Scientific Instruments 94, 124104 (2023) (open source) 

40.    Three-Dimensional Multifocal Scanning Microscopy for Super-Resolution Cell and Tissue Imaging

  Kidan Tadesse, Keyi Han, Biagio Mandracchia, Kyungduck Yoon, Shu Jia

Optics Express 31, 38550-38559 (2023) (open source) 

39.    Optimal sparsity allows reliable system-aware restoration of fluorescence microscopy images

Biagio Mandracchia, Wenhao Liu, Xuanwen Hua, Parvin Forghani, Soojung Lee, Jessica Hou, Shuyi Nie, Chunhui Xu, Shu Jia

Science Advances 9, eadg9245 (2023) (cover story) (open source) (GT/Emory BME News)

38.    Volumetric Live-Cell Autofluorescence Imaging Using Fourier Light-Field Microscopy

Zhi Ling, Keyi Han, Wenhao Liu, Xuanwen Hua, Shu Jia

Biomedical Optics Express 14, 4237-4245 (2023)

37.    Simultaneous Multicolor Multifocal Scanning Microscopy

Kyungduck Yoon, Keyi Han, Kidan Tadesse, Biagio Mandracchia, Shu Jia

ACS Photonics 10, 3035-3041 (2023) (cover story)

36.    Implementation of miniaturized modular-array fluorescence microscopy for long-term live-cell imaging 

Qingyu Chen*, Jeonghwan Son*^, Shu Jia

Applied Optics  62, 2456-2461 (2023)  (*equal contribution, ^corresponding author)

35.    Portable Light-sheet Optofluidic Microscopy for 3D Fluorescence Imaging Flow Cytometry

Jeonghwan Son, Biagio Mandracchia, Aaron Silva Trenkle, Gabriel A. Kwong and Shu Jia

Lab on a Chip 23, 624 (2023) (cover story)

34.    3D Super-resolution Live-cell Imaging with Radial Symmetry and Fourier Light-field Microscopy  

Keyi Han, Xuanwen Hua, Vishwa Vasani, Ge-Ah R Kim, Wenhao Liu, Shuichi Takayama, Shu Jia

Biomedical Optics Express 13, 5574-5584 (2022)

33.    Raster-scanning Donut simplifies MINFLUX and provides alternative implementation on other scanning-based microscopes 

Xinzhu Xu, Shu Jia, Peng Xi

Light: Science & Applications  11, 293 (2022)

32.    Fourier Light-Field Imaging of Human Organoids with a Hybrid Point-Spread Function

Wenhao Liu, Ge-Ah R Kim, Shuichi Takayama, Shu Jia

Biosensors and Bioelectronics 208, 114201 (2022) (open source) (news article: 3D in a Snap )

31.    Three-Dimensional Light-Field Microendoscopy with a GRIN Lens Array 

Tara Urner*, Andrew Inman*, Ben Lapid*, Shu Jia

Biomedical Optics Express 13, 590-607 (2022) (*equal contribution) (open source)

30.    High-Resolution Fourier Light-Field Microscopy for Volumetric Multi-Color Live-Cell Imaging 

Xuanwen Hua*, Wenhao Liu*, Shu Jia

Optica 8, 614-620 (2021) (*equal contribution) (open source)

29.    wFLFM: Enhancing the resolution of Fourier light-field microscopy using a hybrid wide-field image 

Wenhao Liu, Shu Jia

Applied Physics Express 14, 012007 (2021) (Spotlight Article)

28.    Super-Resolution Optofluidic Scanning Microscopy

Biagio Mandracchia, Jeonghwan Son, Shu Jia

Lab on a Chip  21, 489-493 (2021) (cover story)  

27.    Miniaturized Modular-Array Fluorescence Microscopy

Jeonghwan Son, Biagio Mandracchia, Shu Jia

Biomedical Optics Express 11, 7221-7235 (2020) (open source)

26.    Airy-beam Tomographic Microscopy 

Jian Wang, Xuanwen Hua, Changliang Guo, Wenhao Liu, Shu Jia

Optica 7, 790 (2020) (open source)

25.    3D Light-Field Endoscopic Imaging Using a GRIN Lens Array 

Changliang Guo*, Tara Urner*, Shu Jia

Applied Physics Letters 116, 101105 (2020) (*equal contribution)

24.    Fast and Accurate sCMOS Noise Correction for Fluorescence Microscopy

Biagio Mandracchia, Xuanwen Hua, Changliang Guo, Jeonghwan Son, Tara Urner, Shu Jia

Nature Communications 11, 94 (2020) (open source) 

23.    Fourier Light-Field Microscopy

Changliang Guo*, Wenhao Liu*, Xuanwen Hua, Haoyu Li, Shu Jia 

Optics Express 27, 25573 (2019) (Editors' Pick) (*equal contribution) (open source 1) (open source 2)

22.    BSSE: An open-source image processing tool for miniaturized microscopy

Jeonghwan Son, Biagio Mandracchia, Michael D. Caponegro, Stella E. Tsirka, Shu Jia 

Optics Express 27, 17620 (2019) (open source)

21.    Depth-Extended, High-Resolution Fluorescence Microscopy: Whole-Cell Imaging with Double-Ring Phase (DRiP) Modulation

Xuanwen Hua, Changliang Guo, Jian Wang, Deborah Kim-Holzapfel, Bryce Schroeder, Wenhao Liu, Junhua Yuan, Jarrod French, Shu Jia

Biomedical Optics Express 10, 204 (2019)

20.    Fast, Volumetric Live-Cell Imaging Using High-Resolution Light-Field Microscopy  

Haoyu Li*, Changliang Guo*, Deborah Kim-Holzapfel, Weiyi Li, Yelena Altshuller, Bryce Shcroeder, Wenhao Liu, Yizhi Meng, Jarrod B. French, Ken-Ichi Takemaru, Michael A. Frohman, Shu Jia

Biomedical Optics Express 10, 29 (2019) (*equal contribution) (Inaugural Best Paper Prize)

19.    Example-Based Super-Resolution Fluorescence Microscopy

Shu Jia^, Boran Han, J. Nathan Kutz^

Scientific Reports 8, 5700 (2018) (^co-corresponding authors)

18. Blind Sparse Inpainting Reveals Cytoskeletal Filaments with Sub-Nyquist Localization

Yanhua Wang, Shu Jia, Hao Zhang, Doory Kim, Hazen Babcock, Xiaowei Zhuang, Leslie Ying

Optica 4, 1277 (2017)

17. Spatial and Spectral Imaging of Point-Spread Functions Using a Spatial Light Modulator

Sravan Munagavalasa*, Bryce Schroeder*, Xuanwen Hua and Shu Jia 

Optics Communications 404, 51 (2017) (*equal contribution)

16.   Engineering and Optimization of Quasi-nondiffracting Helicon-like Beams with an Evolutionary Algorithm

Bryce Schroeder, Zhen Zhu, Changliang Guo, Shu Jia

IEEE Photonics 9, 6101109 (2017) (open source)

15.   Volumetric Light-Field Encryption at the Microscopic Scale 

Haoyu Li*, Changliang Guo*, Inbarasan Muniraj, Bryce C. Schroeder, John T. Sheridan and Shu Jia

Scientific Reports 7, 40113 (2017) (*equal contribution) 

14.   Frequency Analysis of a Self-Bending Point Spread Function for 3D Localization-based Optical Microscopy

Bryce Schroeder and Shu Jia 

Optics Letters 40, 3189 (2015) 


Prior publications

13.   Super-Resolution Imaging with Airy Beams

Shu Jia and Xiaowei Zhuang,

Optics and Photonics News (Year Review in Optics) 25, 35 (2014)

12.   Isotropic 3D Super-resolution Imaging with a Self-bending Point Spread Function

Shu Jia, Joshua C. Vaughan and Xiaowei Zhuang,

Nature Photonics 8, 302 (2014)  

                - Nature Methods Highlight: A Curveball for Microscopists (Link)

11.   Ultra-bright Photoactivatable Fluorophores Created by Reductive Caging

         Joshua C. Vaughan, Shu Jia and Xiaowei Zhuang,

         Nature Methods 9, 1181 (2012)

10.  Rayleigh-Taylor Instability in Nonlinear Schrödinger Flow (Invited)

        Shu Jia, Mikko P. Haataja and Jason W. Fleischer,

        New Journal of Physics 14, 075009 (2012)

                - Focus issues: Bose Condensation Phenomena in Atomic and Solid State Physics

9.    Observation of the Kinetic Condensation of Classical Waves

       Can Sun, Shu Jia, Christopher Barsi, Sergio Rica, Antonio Picozzi and Jason W. Fleischer,

       Nature Physics 8, 471 (2012)

8.    Diffusion-trapped Airy Beams in Photorefractive Media

       Shu Jia, Joyce Lee, G. Siviloglou, D. Christodoulides and Jason W. Fleischer,

       Physical Review Letters 104, 253904 (2010)

7.    Nonlinear Light Propagation in Fractal Waveguide Arrays 

       Shu Jia and Jason W. Fleischer, 

       Optics Express 18, 14409 (2010)

6.    Nonlinear Light Propagation in Rotating Waveguide Arrays 

       Shu Jia and Jason W. Fleischer, 

       Physical Review A 79, 041804 (2009)

5.    Dispersive Shock Waves in Nonlinear Arrays 

       Shu Jia, Wenjie Wan and Jason W. Fleischer, 

       Physical Review Letters 99, 223901 (2007)

4.    Dispersive Superfluid-like Shock Waves in Nonlinear Optics 

       Wenjie Wan, Shu Jia and Jason W. Fleischer, 

       Nature Physics 3, 46 (2007)

3.    Forward Four-wave Mixing with Defocusing Nonlinearity 

       Shu Jia, Wenjie Wan and Jason W. Fleischer, 

       Optics Letters 32, 1668 (2007)

2.    Dispersion of square solid-core photonic bandgap fibers 

       Yi Ni, Lei Zhang, Shu Jia and Jiangde Peng, 

       Optics Express 12, 2825 (2004)

1.    A novel design for all-solid silica Bragg fiber with zero-dispersion wavelength at 1550 nm 

       Yi Ni, Lei Zhang, C. Gu, Shu Jia and Jiangde Peng, 

       Optics Express 12, 4602 (2004)


Book Chapter

Spatially Dispersive Shock Waves in Nonlinear Optics

Christopher Barsi, Wenjie Wan, Shu Jia and Jason W. Fleischer,

Springer Series in Optical Sciences - Nonlinear Photonics and Novel Optical Phenomena, Springer (2012)