publications

2025

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    The Role of Pretraining in High-Throughput Laminography Restoration
    Zijing Guo ,  Shiqi Xu ,  Kamyar Majlan ,  Zeyu Zhou ,  Moran Xu ,  Andriy Andreyev ,  Johannes Ruoff ,  and  Matthew Andrew
    Microscopy and Microanalysis, 2025
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  2. lightfield4d.jpg
    High-speed 4D fluorescence light field tomography of whole freely moving organisms
    Kevin C Zhou ,  Clare Cook ,  Archan Chakraborty ,  Jennifer Bagwell ,  Joakim Jönsson ,  Kyung Chul Lee ,  Xi Yang ,  Shiqi Xu ,  Ramana Balla ,  Kushal Kolar ,  and  others
    Optica, 2025
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    Beneath the surface: revealing deep-tissue blood flow in human subjects with massively parallelized diffuse correlation spectroscopy
    Lucas Kreiss ,  Melissa Wu ,  Michael Wayne ,  Shiqi Xu ,  Paul McKee ,  Derrick Dwamena ,  Kanghyun Kim ,  Kyung Chul Lee ,  Kyle R Cowdrick ,  Wenhui Liu ,  and  others
    Neurophotonics, 2025
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2024

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    Rapid 3D imaging at cellular resolution for digital cytopathology with a multi-camera array scanner (MCAS)
    Kanghyun Kim ,  Amey Chaware ,  Clare B Cook ,  Shiqi Xu ,  Monica Abdelmalak ,  Colin Cooke ,  Kevin C Zhou ,  Mark Harfouche ,  Paul Reamey ,  Veton Saliu ,  and  others
    npj Imaging, 2024
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  2. Self-supervised deep image restoration for x-ray computed laminographic tomography
    Shiqi Xu ,  Susan Candell ,  Tom Case ,  Aksel Goehnermeier ,  Jeffrey Irwin ,  Kamyar Majlan ,  Moshe Preil ,  Johannes Ruoff ,  Moran Xu ,  Faguo Yang ,  and  others
    In Developments in X-Ray Tomography XV , 2024
  3. X-ray reconstruction using synthetic prior image restoration, with application to noise and artefact removal
    Matthew Andrew ,  Andriy Andreyev ,  Faguo Yang ,  Moran Xu ,  and  Shiqi Xu
    In Developments in X-Ray Tomography XV , 2024
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    Anisotropic regularization for sparsely sampled and noise-robust Fourier ptychography
    Kyung Chul Lee ,  Hyesuk Chae ,  Shiqi Xu ,  Kyungwon Lee ,  Roarke Horstmeyer ,  Seung Ah Lee ,  and  Byung-Woo Hong
    Optics Express, 2024
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  5. tofu.png
    Tensorial tomographic Fourier Ptychography with applications to muscle tissue imaging
    Shiqi Xu ,  Xi Yang ,  Paul Ritter ,  Xiang Dai ,  Kyung Chul Lee ,  Lucas Kreiss ,  Kevin C Zhou ,  Kanghyun Kim ,  Amey Chaware ,  Jadee Neff ,  and  others
    Advanced Photonics, 2024
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  6. digistain_review.png
    Digital staining in optical microscopy using deep learning - a review
    Lucas Kreiss ,  Shaowei Jiang ,  Xiang Li ,  Shiqi Xu ,  Kevin C Zhou ,  Alexander Mühlberg ,  Kyung Chul Lee ,  Kanghyun Kim ,  Amey Chaware ,  Michael Ando ,  and  others
    PhotoniX, 2024
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2023

  1. kk_mcam_falcon.png
    Imaging across multiple spatial scales with the multi-camera array microscope
    Mark Harfouche ,  Kanghyun Kim ,  Kevin C Zhou ,  Pavan Chandra Konda ,  Sunanda Sharma ,  Eric E Thomson ,  Colin Cooke ,  Shiqi Xu ,  Lucas Kreiss ,  Amey Chaware ,  and  others
    Optica, 2023
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  2. mfast.png
    Multi-modal imaging using a cascaded microscope design
    Xi Yang ,  Mark Harfouche ,  Kevin C Zhou ,  Lucas Kreiss ,  Shiqi Xu ,  Pavan Chandra Konda ,  Kanghyun Kim ,  and  Roarke Horstmeyer
    Optics Letters, 2023
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2022

  1. ericelife.png
    Gigapixel imaging with a novel multi-camera array microscope
    Eric E Thomson ,  Mark Harfouche ,  Kanghyun Kim ,  Pavan C Konda ,  Catherine W Seitz ,  Colin Cooke ,  Shiqi Xu ,  Whitney S Jacobs ,  Robin Blazing ,  Yang Chen ,  and  others
    Elife, 2022
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  2. Optical imaging and spectroscopy for the study of the human brain: status report
    Hasan Ayaz ,  Wesley B Baker ,  Giles Blaney ,  David A Boas ,  Heather Bortfeld ,  Kenneth Brady ,  Joshua Brake ,  Sabrina Brigadoi ,  Erin M Buckley ,  Stefan A Carp ,  and  others
    Neurophotonics, 2022
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  3. covid_mil.png
    A multiple instance learning approach for detecting COVID-19 in peripheral blood smears
    Colin L Cooke ,  Kanghyun Kim ,  Shiqi Xu ,  Amey Chaware ,  Xing Yao ,  Xi Yang ,  Jadee Neff ,  Patricia Pittman ,  Chad McCall ,  Carolyn Glass ,  and  others
    PLOS Digital Health, 2022
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  4. t2dpc.png
    Tensorial tomographic differential phase-contrast microscopy
    Shiqi Xu ,  Xiang Dai ,  Xi Yang ,  Kevin C Zhou ,  Kanghyun Kim ,  Vinayak Pathak ,  Carolyn Glass ,  and  Roarke Horstmeyer
    In 2022 IEEE International Conference on Computational Photography (ICCP) , 2022
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    Transient motion classification through turbid volumes via parallelized single-photon detection and deep contrastive embedding
    Shiqi Xu ,  Wenhui Liu ,  Xi Yang ,  Joakim Jönsson ,  Ruobing Qian ,  Paul McKee ,  Kanghyun Kim ,  Pavan Chandra Konda ,  Kevin C Zhou ,  Lucas Kreiß ,  and  others
    Frontiers in neuroscience, 2022
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  6. pdci.png
    Imaging Dynamics Beneath Turbid Media via Parallelized Single-Photon Detection
    Shiqi Xu ,  Xi Yang ,  Wenhui Liu ,  Joakim Jönsson ,  Ruobing Qian ,  Pavan Chandra Konda ,  Kevin C Zhou ,  Lucas Kreiß ,  Haoqian Wang ,  Qionghai Dai ,  and  others
    Advanced Science, 2022
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  7. vfp2d.png
    Quantitative Jones matrix imaging using vectorial Fourier ptychography
    Shiqi Xu ,  Xiang Dai ,  Xi Yang ,  Kevin C Zhou ,  Carolyn Glass ,  Pavan Chandra Konda ,  and  Roarke Horstmeyer
    Biomedical optics express, 2022
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  8. overlap.png
    Increasing a microscope’s effective field of view via overlapped imaging and machine learning
    Xing Yao ,  Vinayak Pathak ,  Haoran Xi ,  Amey Chaware ,  Colin Cooke ,  Kanghyun Kim ,  Shiqi Xu ,  Yuting Li ,  Timothy Dunn ,  Pavan Chandra Konda ,  and  others
    Optics Express, 2022
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2021

  1. qfp.png
    Quantized Fourier ptychography with binary images from SPAD cameras
    Xi Yang ,  Pavan Chandra Konda ,  Shiqi Xu ,  Liheng Bian ,  and  Roarke Horstmeyer
    Photonics Research, 2021
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  2. pdcs_wenhui.png
    Fast and sensitive diffuse correlation spectroscopy with highly parallelized single photon detection
    Wenhui Liu ,  Ruobing Qian ,  Shiqi Xu ,  Pavan Chandra Konda ,  Joakim Jönsson ,  Mark Harfouche ,  Dawid Borycki ,  Colin Cooke ,  Edouard Berrocal ,  Qionghai Dai ,  and  others
    APL Photonics, 2021
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2020

  1. fp_review.png
    Fourier ptychography: current applications and future promises
    Pavan Chandra Konda ,  Lars Loetgering ,  Kevin C Zhou ,  Shiqi Xu ,  Andrew R Harvey ,  and  Roarke Horstmeyer
    Optics express, 2020
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  2. oct_colon.png
    Real-time colorectal cancer diagnosis using PR-OCT with deep learning
    Shiqi Xu ,  Yifeng Zeng ,  William C Chapman Jr ,  Shuying Li ,  Zahra Alipour ,  Heba Abdelal ,  Deyali Chatterjee ,  Matthew Mutch ,  and  Quing Zhu
    Theranostics, 2020
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2019

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    Improving DOT reconstruction with a Born iterative method and US-guided sparse regularization
    Shiqi Xu ,  KM Shihab Uddin ,  and  Quing Zhu
    Biomedical optics express, 2019
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  2. hela_fpm_sparse.png
    Regularized fourier ptychography using an online plug-and-play algorithm
    Yu Sun ,  Shiqi Xu ,  Yunzhe Li ,  Lei Tian ,  Brendt Wohlberg ,  and  Ulugbek S Kamilov
    In ICASSP 2019-2019 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP) , 2019
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