Computational Fluorescence & Neural Imaging
Topics include: Computational fluorescence microscopy, miniature and distributed optics, light-field imaging, and neural imaging.
Dual-Mode Bio-CM²: Multimodal Computational Miniature Mesoscope for Fluorescence and Label-Free Imaging
Dual-Mode Bio-CM2: Multimodal Computational Miniature Mesoscope for Fluorescence and Label-Free Imaging
Qilin Deng, Guorong Hu, Bradley C. Rauscher, Marcelo Villafuerte, Bethany Weinberg, Zhixiong Chen, Hui Feng, Anna Devor, Martin Thunemann, and Lei Tian
bioRxiv, 2026.09.08.750281 (2026). Preprint.
Point Spread Function Engineering Using Implicit Neural Representations
Point Spread Function Engineering Using Implicit Neural Representations
Suet Ying Chan, Mitchell Gilmore, Qilin Deng, Guorong Hu, Joseph Greene, Ruipeng Guo, and Lei Tian
arXiv:2608.20277 (2026). Preprint.
Bio-CM²: Distributed computational optics for cortex-wide cellular imaging
Bio-CM2: Distributed computational optics for cortex-wide cellular imaging
Guorong Hu, Qilin Deng, Tianrui Qi, Zhixiong Chen, Bradley C. Rauscher, Nathan Chai, Daria Bogatova, Bethany Weinberg, Jesse Smith, Ian G. Davison, Martin Thunemann, Anna Devor, and Lei Tian
bioRxiv, 2026.07.27.740823 (2026). Preprint.
DeepFilters: Scattering-Aware Pupil Engineering with Learned Digital Filter Reconstruction for Extended Depth of Field Microscopy
DeepFilters: Scattering-Aware Pupil Engineering with Learned Digital Filter Reconstruction for Extended Depth of Field Microscopy
Joseph L. Greene, Suet Ying Chan, Qilin Deng, Jeffrey Alido, Alexandra Lion, Guorong Hu, Ruipeng Guo, Tongyu Li, Kivilcim Kiliç, Ian Davison, and Lei Tian
arXiv:2605.13619 (2026). Preprint.
Versatile high-speed volumetric imaging from microscopic to macroscopic scale by self-adaptive oblique plane microscopy
Versatile high-speed volumetric imaging from microscopic to macroscopic scale by self-adaptive oblique plane microscopy
Dominique Meyer, Grant Kroeschell, Xiankun Lu, Linh Hoang, Haochen Wang, Shuying Li, Yu Kang T Xu, Lei Tian, Jeff S Mumm, Dwight E Bergles, and Ji Yi
bioRxiv, 2025.12.16.694458 (2026). Preprint.
Physics-informed neural network for mapping vascular and tissue dynamics using laser speckle contrast imaging
Physics-informed neural network for mapping vascular and tissue dynamics using laser speckle contrast imaging
Shuying Li, Rockwell Tang, Bingxue Liu, Victoria Krepulec, Will Donovan, David Boas, Xiaojun Cheng, and Lei Tian
Neurophotonics, Vol. 13, Issue 3, 035012, 2026.
Coordinate-conditioned Deconvolution for Scalable Spatially Varying High-Throughput Imaging
Coordinate-conditioned Deconvolution for Scalable Spatially Varying High-Throughput Imaging
Qianwan Yang; Zhixiong Chen; Jiaqi Zhang; Ruipeng Guo; Guorong Hu; Lei Tian
IEEE Transactions on Computational Imaging 2026.
Dual-channel event microscopy for ultrafast biological imaging
Dual-channel event microscopy for ultrafast biological imaging
R. Guo, X. Pan, Q. Deng, A. Ahmed, Q. Yang, J. Greene, T. Li, S.Y. Chan, Z. Chen, G. Hu, H. Feng, & L. Tian
Proc. Natl. Acad. Sci. (PNAS) 123 (17) e2531386123
The neurovascular impulse response function differentially reflects intrinsic neuromodulation across cortical regions
The neurovascular impulse response function differentially reflects intrinsic neuromodulation across cortical regions
B. C. Rauscher, N. Fomin-Thunemann, S. Kura, P. R. Doran, P. D. Perez, K. Kılıç, E. A. Martin, D. Balog, N. X. Chai, F. A. Froio, P. F. Bloniasz, K. E. Herrema, R. P. Tang, S. G. Knudstrup, A. Garcia, J. X. Jiang, J. P. Gavornik, M. London, D. Kleinfeld, M. E. Hasselmo, L. D. Lewis, S. Sakadzic, L. Tian, G. Mishne, E. P. Stephen, M. Thunemann, D. A. Boas, and A. Devor
Nature Neuroscience 29, 1203–1211 (2026).
Whitened Score Diffusion: A Structured Prior for Imaging Inverse Problems
Whitened Score Diffusion: A Structured Prior for Imaging Inverse Problems
J Alido, T Li, Y Sun, L Tian
NeurIPS 2025.
⭑ Github Project
DeepVID v2: self-supervised denoising with decoupled spatiotemporal enhancement for low-photon voltage imaging
DeepVID v2: self-supervised denoising with decoupled spatiotemporal enhancement for low-photon voltage imaging
Chang Liu, Jiayu Lu, Yicun Wu, Xin Ye, Allison M. Ahrens, Jelena Platisa, Vincent A. Pieribone, Jerry L. Chen, Lei Tian
Neurophotonics, Vol. 11, Issue 4, 045007 (October 2024).
⭑ Github Project
EventLFM: event camera integrated Fourier light field microscopy for ultrafast 3D imaging
EventLFM: event camera integrated Fourier light field microscopy for ultrafast 3D imaging
Ruipeng Guo, Qianwan Yang, Andrew S. Chang, Guorong Hu, Joseph Greene, Christopher V. Gabel, Sixian You & Lei Tian
Light: Science & Applications 13: 144 (2024).
Wide-field, high-resolution reconstruction in computational multi-aperture miniscope using a Fourier neural network
Wide-field, high-resolution reconstruction in computational multi-aperture miniscope using a Fourier neural network
Qianwan Yang, Ruipeng Guo, Guorong Hu, Yujia Xue, Yunzhe Li, and Lei Tian
Optica Vol. 11, Issue 6, pp. 860-871 (2024).
⭑Github Project
HiLo microscopy with caustic illumination
HiLo microscopy with caustic illumination
Guorong Hu, Joseph Greene, Jiabei Zhu, Qianwan Yang, Shuqi Zheng, Yunzhe Li, Jeffrey Alido, Ruipeng Guo, Jerome Mertz, and Lei Tian
Biomedical Optics Express Vol. 15, Issue 7, pp. 4101-4110 (2024). ⭑ On the Cover
Robust single-shot 3D fluorescence imaging in scattering media with a simulator-trained neural network
Robust single-shot 3D fluorescence imaging in scattering media with a simulator-trained neural network
J. Alido, J. Greene, Y. Xue, G. Hu, Y. Li, K. Monk, B. DeBenedicts, I. Davison, L. Tian
Optics Express Vol. 32, Issue 4, pp. 6241-6257 (2024).
⭑Github Project
Pupil engineering for extended depth-of-field imaging in a fluorescence miniscope
Pupil engineering for extended depth-of-field imaging in a fluorescence miniscope
Joseph Greene, Yujia Xue, Jeffrey Alido, Alex Matlock, Guorong Hu, Kivilcim Kiliç, Ian Davison, Lei Tian
Neurophotonics, Vol. 10, Issue 4, 044302 (2023).
High-Speed Low-Light In Vivo Two-Photon Voltage Imaging of Large Neuronal Populations
High-Speed Low-Light In Vivo Two-Photon Voltage Imaging of Large Neuronal Populations
Jelena Platisa, Xin Ye, Allison M Ahrens, Chang Liu, Ichun A Chen, Ian G Davison, Lei Tian, Vincent A Pieribone, Jerry L Chen
Nature Methods 20, 1095–1103 (2023).
⭑Github Project
⭑ Spotlight: AI to the rescue of voltage imaging, Cell Reports Methods
3D Chemical Imaging by Fluorescence-detected Mid-Infrared Photothermal Fourier Light Field Microscopy
3D Chemical Imaging by Fluorescence-detected Mid-Infrared Photothermal Fourier Light Field Microscopy
Danchen Jia, Yi Zhang, Qianwan Yang, Yujia Xue, Yuying Tan, Zhongyue Guo, Meng Zhang, Lei Tian, Ji-Xin Cheng
Chem. Biomed. Imaging 2023, 1, 3, 260–267
Deep-learning-augmented Computational Miniature Mesoscope
Deep-learning-augmented Computational Miniature Mesoscope
Yujia Xue, Qianwan Yang, Guorong Hu, Kehan Guo, Lei Tian
Optica 9, 1009-1021 (2022)
Neurophotonic tools for microscopic measurements and manipulation: status report
Neurophotonic tools for microscopic measurements and manipulation: status report
Ahmed Abdelfattah, Sapna Ahuja, Taner Akkin, Srinivasa Rao Allu, David A. Boas, Joshua Brake, Erin M. Buckley, Robert E. Campbell, Anderson I. Chen, Xiaojun Cheng, Tomáš Cižmár, Irene Costantini, Massimo De Vittorio, Anna Devor, Patrick R. Doran, Mirna El Khatib, Valentina Emiliani, Natalie Fomin-Thunemann, Yeshaiahu Fainman, Tomás Fernández Alfonso, Christopher G. L. Ferri, Ariel Gilad, Xue Han, Andrew Harris, Elizabeth M. C. Hillman, Ute Hochgeschwender, Matthew G. Holt, Na Ji, Kivilcim Kiliç, Evelyn M. R. Lake, Lei Li, Tianqi Li, Philipp Mächler, Rickson C. Mesquita, Evan W. Miller, K.M. Naga Srinivas Nadella, U. Valentin Nägerl, Yusuke Nasu, Axel Nimmerjahn, Petra Ondrácková, Francesco S. Pavone, Citlali Perez Campos, Darcy S. Peterka, Filippo Pisano, Ferruccio Pisanello, Francesca Puppo, Bernardo L. Sabatini, Sanaz Sadegh, Sava Sakadžic, Shy Shoham, Sanaya N. Shroff, R. Angus Silver, Ruth R. Sims, Spencer L. Smith, Vivek J. Srinivasan, Martin Thunemann, Lei Tian, Lin Tian, Thomas Troxler, Antoine Valera, Alipasha Vaziri, Sergei A. Vinogradov, Flavia Vitale, Lihong V. Wang, Hana Uhlířová, Chris Xu, Changhuei Yang, Mu-Han Yang, Gary Yellen, Ofer Yizhar, Yongxin Zhao
Neurophotonics, 9(S1), 013001 (2022).
