Publications

Selected Journal Articles

1. Chen Li, Mani Ratnam Rai, Yehe Cai, H. Troy Ghashghaei, and Alon Greenbaum
   "Intelligent Beam Optimization for Light-Sheet Fluorescence Microscopy through Deep Learning"
   Intelligent Computing 3, 0095 (2024)

2. Yehe Cai, Xuying Zhang, Chen Li, H. Troy Ghashghaei, and Alon Greenbaum
   "COMBINe enables automated detection and classification of neurons and astrocytes in tissue-cleared mouse brains"
   Cell Reports Methods 3 (4) (2023)

3. Mani Ratnam Rai, Chen Li, H. Troy Ghashghaei, and Alon Greenbaum
   "Deep learning-based adaptive optics for light sheet fluorescence microscopy"
   Biomedical Optics Express 14 (6), 2905-2919 (2023)

4. Chen Li, Mani Ratnam Rai, H. Troy Ghashghaei, and Alon Greenbaum
   "Illumination angle correction during image acquisition in light-sheet fluorescence microscopy using deep learning"
   Biomedical Optics Express 13 (2), 888-901 (2022)

5. Mani Ratnam Rai, Chen Li, and Alon Greenbaum
   "Quantitative analysis of illumination and detection corrections in adaptive light sheet fluorescence microscopy"
   Biomedical Optics Express 13 (5), 2960-2974 (2022)

6. Adele Moatti, Chen Li, Sandeep Sivadanam, Yehe Cai, Jayne Ranta, Jorge A. Piedrahita, Alan G. Cheng, and Alon Greenbaum
   "Ontogeny of cellular organization and LGR5 expression in porcine cochlea revealed using tissue clearing and 3D imaging"
   iScience 25 (8) (2022)

7. Chen Li, Adele Moatti, Xuying Zhang, H. Troy Ghashghaei, and Alon Greenbaum
   "Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy"
   Biomedical Optics Express 12 (8), 5214-5226 (2021)

8. Adele Moatti, Yehe Cai, Chen Li, Tanner Sattler, Lauren Edwards, Jorge Piedrahita, Frances S. Ligler, and Alon Greenbaum
   "Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy"
   Biomedical Optics Express 11 (11), 6181-6196 (2020)

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Last updated: November 2025