Publications
You can also find my publications on my Google Scholar profile.
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2026
9. Detection of non-invasive sexing of early chick embryos in intact eggs using laser speckle contrast imaging and deep neural networks
Simon Mahler*, Anika Arora*, Carol Readhead*, Siyuan Yin*, Surya Narayanan Hari, Ellie Wang, Cecilia I. Moxley, Abdullahi A. Adeboye, Zhenyu Dong, Haowen Zhou, Xi Chen, Marianne Bronner, Changhuei Yang
Plos One, 2026 (BibTex)
We integrated LSCI imaging with deep learning to investigate early-stage sex differentiation of chicken embryos from extraembryonic vascular patterns.
Simon Mahler*, Anika Arora*, Carol Readhead*, Siyuan Yin*, Surya Narayanan Hari, Ellie Wang, Cecilia I. Moxley, Abdullahi A. Adeboye, Zhenyu Dong, Haowen Zhou, Xi Chen, Marianne Bronner, Changhuei Yang
Plos One, 2026 (BibTex)
We integrated LSCI imaging with deep learning to investigate early-stage sex differentiation of chicken embryos from extraembryonic vascular patterns.
8. Digital defocus aberration interference for automated optical microscopy
Haowen Zhou*, Shi Zhao*, Yujie Fan, Zhenyu Dong, Oumeng Zhang, Viviana Gradinaru, Changhuei Yang
Nature Communications, 2026 (BibTex) [Project Page] [Code Link]
We recently observed a phenomenon that the digitally summed Fourier spectrum of two images acquired from two-angle illumination exhibits interference-like fringe modulation when the sample is out-of-focus. These digital fringes correlate directly with defocus through a physics-based relation. Based on this principle, we developed an automatic, efficient, and generalizable defocus detection method termed digital defocus aberration interference (DAbI).
Haowen Zhou*, Shi Zhao*, Yujie Fan, Zhenyu Dong, Oumeng Zhang, Viviana Gradinaru, Changhuei Yang
Nature Communications, 2026 (BibTex) [Project Page] [Code Link]
We recently observed a phenomenon that the digitally summed Fourier spectrum of two images acquired from two-angle illumination exhibits interference-like fringe modulation when the sample is out-of-focus. These digital fringes correlate directly with defocus through a physics-based relation. Based on this principle, we developed an automatic, efficient, and generalizable defocus detection method termed digital defocus aberration interference (DAbI).
2025
7. Analytic Fourier ptychotomography for aberration-free and high-resolution volumetric refractive index imaging
Zhenyu Dong*, Haowen Zhou*, Ruizhi Cao*, Oumeng Zhang, Shi Zhao, Panlang Lyu, Reinaldo E Alcalde, Changhuei Yang
Nature Communications, 2025 (BibTex) [Project Page] [Code Link]
We propose Analytic Fourier Ptychotomography (AFP), a computational microscopy technique that analytically reconstructs aberration-free, complex-valued 3D RI distributions without iterative optimization or axial scanning. We derived an analytic darkfield spectrum recovery and extension scheme to synthesize high-spatial-frequency information beyond the objective NA, achieving two-fold resolution enhancement in both lateral and axial dimensions.
Zhenyu Dong*, Haowen Zhou*, Ruizhi Cao*, Oumeng Zhang, Shi Zhao, Panlang Lyu, Reinaldo E Alcalde, Changhuei Yang
Nature Communications, 2025 (BibTex) [Project Page] [Code Link]
We propose Analytic Fourier Ptychotomography (AFP), a computational microscopy technique that analytically reconstructs aberration-free, complex-valued 3D RI distributions without iterative optimization or axial scanning. We derived an analytic darkfield spectrum recovery and extension scheme to synthesize high-spatial-frequency information beyond the objective NA, achieving two-fold resolution enhancement in both lateral and axial dimensions.
6. Rotational Memory Effect-Inspired Radon Domain Learning Empowers Image Transmission Through Multimode Fibers
Ninghe Liu, Lele Wang, Zhaofan He, Haoran Zhang, Zhenyu Dong, Dan Li, Ping Yan, Qirong Xiao
Laser & Photonics Reviews, 2025 (BibTex) [Code Link]
We developed RTMnet, a physics-guided cross-domain learning framework integrating the rotational memory effect, Radon transform, and Fourier neural operator for efficient image transmission through MMFs. RTMnet achieves high-fidelity reconstruction with an order-of-magnitude lower computational cost than conventional DNNs and generalizes to arbitrarily rotated images using only non-rotated training data.
Ninghe Liu, Lele Wang, Zhaofan He, Haoran Zhang, Zhenyu Dong, Dan Li, Ping Yan, Qirong Xiao
Laser & Photonics Reviews, 2025 (BibTex) [Code Link]
We developed RTMnet, a physics-guided cross-domain learning framework integrating the rotational memory effect, Radon transform, and Fourier neural operator for efficient image transmission through MMFs. RTMnet achieves high-fidelity reconstruction with an order-of-magnitude lower computational cost than conventional DNNs and generalizes to arbitrarily rotated images using only non-rotated training data.
5. Automated non-invasive laser speckle imaging of the chick heart rate and extraembryonic blood vessels and their response to Nifedipine and Amlodipine drugs
Carol Readhead*, Simon Mahler*, Zhenyu Dong, Yuki Sato, Changhuei Yang, Marianne E. Bronner
Developmental Biology, 2025 (BibTex)
We built an automated, incubator-integrated LSCI platform for longitudinal monitoring of embryonic heart rate, blood-flow dynamics, and vascular structures. We established its potential as a rapid, quantitative platform for screening cardiovascular drugs and assessing their effects on embryonic heart function.
Carol Readhead*, Simon Mahler*, Zhenyu Dong, Yuki Sato, Changhuei Yang, Marianne E. Bronner
Developmental Biology, 2025 (BibTex)
We built an automated, incubator-integrated LSCI platform for longitudinal monitoring of embryonic heart rate, blood-flow dynamics, and vascular structures. We established its potential as a rapid, quantitative platform for screening cardiovascular drugs and assessing their effects on embryonic heart function.
2024
4. Non-invasive laser speckle contrast imaging (LSCI) of extra-embryonic blood vessels in intact avian eggs at early developmental stages
Zhenyu Dong*, Simon Mahler*, Carol Readhead, Xi Chen, Maya Dickson, Marianne Bronner, Changhuei Yang
Biomedical Optics Express, 2024 Editor's Pick & Journal Cover (BibTex) [Code Link]
We built a non-invasive LSCI system for visualizing extra-embryonic blood vessels through intact avian eggs,enabling detection of vessels as small as ∼100 𝜇m in diameter. We improved temporal resolution for real-time and longitudinal monitoring of blood-flow dynamics and embryonic heart rate through intact eggshells. We further extended longitudinal vascular imaging to day 5 by developing a time-domain Fourier high-pass filtering method to suppress low-frequency artifacts from eggshell cracks and embryo body movements. We finally implemented a machine-learning framework with feature extraction to classify embryonic developmental stages from LSCI images, achieving 85% accuracy.
Zhenyu Dong*, Simon Mahler*, Carol Readhead, Xi Chen, Maya Dickson, Marianne Bronner, Changhuei Yang
Biomedical Optics Express, 2024 Editor's Pick & Journal Cover (BibTex) [Code Link]
We built a non-invasive LSCI system for visualizing extra-embryonic blood vessels through intact avian eggs,enabling detection of vessels as small as ∼100 𝜇m in diameter. We improved temporal resolution for real-time and longitudinal monitoring of blood-flow dynamics and embryonic heart rate through intact eggshells. We further extended longitudinal vascular imaging to day 5 by developing a time-domain Fourier high-pass filtering method to suppress low-frequency artifacts from eggshell cracks and embryo body movements. We finally implemented a machine-learning framework with feature extraction to classify embryonic developmental stages from LSCI images, achieving 85% accuracy.
2023
3. Single multimode fibre for in vivo light-field-encoded endoscopic imaging
Zhong Wen, Zhenyu Dong, Qilin Deng, Chenlei Pang, Clemens F. Kaminski, Xiaorong Xu, Huihui Yan, Liqiang Wang, Songguo Liu, Jianbin Tang, Wei Chen, Xu Liu, Qing Yang
Nature Photonics, 2023 (BibTex) [Media Coverage]
We developed STABLE, a bend-resistant 3D imaging method that enables MMF imaging under practical fiber deformations. We proposed a single-DMD scheme for simultaneous amplitude, phase, and polarization modulation of the fiber incident wavefront, enabling full-vector transmission-matrix (TM) measurement of long and bent MMFs and precise wavefront control at the fiber output. We implemented reflective guide stars as closed-loop feedback to identify the optimal fiber TM from a compact pre-calibrated TM library, enabling efficient compensation of bending-induced TM variations and stable imaging under fiber deformation. We demonstrated high-resolution in-vivo MMF endoscopic imaging of the gastrointestinal tract in living mice.
Zhong Wen, Zhenyu Dong, Qilin Deng, Chenlei Pang, Clemens F. Kaminski, Xiaorong Xu, Huihui Yan, Liqiang Wang, Songguo Liu, Jianbin Tang, Wei Chen, Xu Liu, Qing Yang
Nature Photonics, 2023 (BibTex) [Media Coverage]
We developed STABLE, a bend-resistant 3D imaging method that enables MMF imaging under practical fiber deformations. We proposed a single-DMD scheme for simultaneous amplitude, phase, and polarization modulation of the fiber incident wavefront, enabling full-vector transmission-matrix (TM) measurement of long and bent MMFs and precise wavefront control at the fiber output. We implemented reflective guide stars as closed-loop feedback to identify the optimal fiber TM from a compact pre-calibrated TM library, enabling efficient compensation of bending-induced TM variations and stable imaging under fiber deformation. We demonstrated high-resolution in-vivo MMF endoscopic imaging of the gastrointestinal tract in living mice.
2022
2. Spatially variant deblur and image enhancement in a single multimode fiber imaged by deep learning
Qilin Deng, Zhong Wen, Zhenyu Dong, Jianbin Tang, Wei Chen, Xu Liu, Qing Yang
Optics Letters, 2022 (BibTex) [Code Link]
We implemented a CNN-based framework to deblur and denoise MMF endoscopic images degraded by spatially varying PSFs, achieving 5-ms reconstruction and up to three orders of magnitude speed up over iterative methods.
Qilin Deng, Zhong Wen, Zhenyu Dong, Jianbin Tang, Wei Chen, Xu Liu, Qing Yang
Optics Letters, 2022 (BibTex) [Code Link]
We implemented a CNN-based framework to deblur and denoise MMF endoscopic images degraded by spatially varying PSFs, achieving 5-ms reconstruction and up to three orders of magnitude speed up over iterative methods.
1. A modulated sparse random matrix for high-resolution and high-speed 3D compressive imaging through a multimode fiber
Zhenyu Dong, Zhong Wen, Chenlei Pang, Liqiang Wang, Lan Wu, Xu Liu, Qing Yang
Science Bulletin, 2022 Journal Cover (BibTex)
We proposed a compressive-sensing approach for high-speed 3D imaging through MMFs, generating multiple 3D focal spots via wavefront modulation for volumetric scanning and reconstructing the 3D volume by solving the corresponding inverse problem. We demonstrated superior volumetric imaging performance of multi-focus 3D scanning over random-speckle illumination through MMFs. We achieved an eightfold improvement in imaging speed and demonstrated 3D fluorescence imaging of complex biological samples,including lung tissue slices and microbeads.
Zhenyu Dong, Zhong Wen, Chenlei Pang, Liqiang Wang, Lan Wu, Xu Liu, Qing Yang
Science Bulletin, 2022 Journal Cover (BibTex)
We proposed a compressive-sensing approach for high-speed 3D imaging through MMFs, generating multiple 3D focal spots via wavefront modulation for volumetric scanning and reconstructing the 3D volume by solving the corresponding inverse problem. We demonstrated superior volumetric imaging performance of multi-focus 3D scanning over random-speckle illumination through MMFs. We achieved an eightfold improvement in imaging speed and demonstrated 3D fluorescence imaging of complex biological samples,including lung tissue slices and microbeads.