Chen Li

College of Engineering

Works (10)

Updated: August 4th, 2025 07:28

2025 article

Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae

Cai, Y., Leitz-Najarian, G. M., Rosen, R., Hutson, K. A., Moatti, A., Li, C., … Greenbaum, A. (2025, June 18). IScience.

By: Y. Cai  n, G. Leitz-Najarian*, R. Rosen, K. Hutson *, A. Moatti n , C. Li n, D. Fitzpatrick *, A. Greenbaum n

topics (OpenAlex): Hearing Loss and Rehabilitation; Hearing, Cochlea, Tinnitus, Genetics; Structural Health Monitoring Techniques
Source: Web Of Science
Added: July 28, 2025

2023 article

COMBINe enables automated detection and classification of neurons and astrocytes in tissue-cleared mouse brains

Cai, Y., Zhang, X., Li, C., Ghashghaei, H. T., & Greenbaum, A. (2023, April 1). Cell Reports Methods.

By: Y. Cai  n, X. Zhang n, C. Li n, H. Ghashghaei n & A. Greenbaum n

MeSH headings : Animals; Mice; Astrocytes; Excipients; Microscopy, Fluorescence; Neurons; Prosencephalon
topics (OpenAlex): Cell Image Analysis Techniques; Single-cell and spatial transcriptomics; Advanced Fluorescence Microscopy Techniques
TL;DR: An automated workflow to map sparsely labeled neurons and astrocytes in genetically distinct mouse forebrains using mosaic analysis with double markers (MADM) is presented and the regional and subregional effects of MADM-based deletion of the epidermal growth factor receptor (EGFR) are quantitatively analyzed. (via Semantic Scholar)
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Source: Web Of Science
Added: May 30, 2023

2023 article

Deep learning-based adaptive optics for light sheet fluorescence microscopy

Rai, M. R., Li, C., Ghashghaei, H. T., & Greenbaum, A. (2023, May 19). Biomedical Optics Express.

By: M. Rai n, C. Li n, H. Ghashghaei n & A. Greenbaum n

topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; Optical Coherence Tomography Applications; Photoacoustic and Ultrasonic Imaging
TL;DR: It is shown that the application of correction using a deformable mirror greatly improves image quality and two conceptually different network architectures are compared; one that shares convolutional features and another that estimates each aberration independently. (via Semantic Scholar)
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Source: Web Of Science
Added: July 24, 2023

2023 article

Tissue clearing and three-dimensional imaging of the whole cochlea and vestibular system from multiple large-animal models

Moatti, A., Cai, Y., Li, C., Popowski, K. D., Cheng, K., Ligler, F. S., & Greenbaum, A. (2023, April 14). STAR Protocols.

By: A. Moatti n , Y. Cai  n, C. Li n, K. Popowski n , K. Cheng n, F. Ligler*, A. Greenbaum n

author keywords: imaged cochleae using open -source software.; several mm; larger animal inner; open -source software
topics (OpenAlex): Single-cell and spatial transcriptomics; Cell Image Analysis Techniques; Photoacoustic and Ultrasonic Imaging
TL;DR: A protocol that enables three-dimensional (3D) characterization of intact inner ears from large-animal models is presented and a pipeline to count hair cells in antibody-stained and 3D imaged cochleae using open-source software is detailed. (via Semantic Scholar)
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Source: Web Of Science
Added: September 5, 2023

2022 article

Illumination angle correction during image acquisition in light-sheet fluorescence microscopy using deep learning

Li, C., Rai, M. R., Ghashghaei, H. T., & Greenbaum, A. (2022, January 6). Biomedical Optics Express.

By: C. Li n, M. Rai n, H. Ghashghaei n & A. Greenbaum n

topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; Image Processing Techniques and Applications; Cell Image Analysis Techniques
TL;DR: This study provides a framework that can correct the angle of the light-sheet and improve the overall image quality in high-resolution LSFM 3D image acquisition. (via Semantic Scholar)
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Source: Web Of Science
Added: February 14, 2022

2022 article

Ontogeny of cellular organization and LGR5 expression in porcine cochlea revealed using tissue clearing and 3D imaging

Moatti, A., Li, C., Sivadanam, S., Cai, Y., Ranta, J., Piedrahita, J. A., … Greenbaum, A. (2022, June 30). IScience, Vol. 25.

By: A. Moatti n , C. Li n, S. Sivadanam  n, Y. Cai  n, J. Ranta n, J. Piedrahita n , A. Cheng *, F. Ligler n, A. Greenbaum n

topics (OpenAlex): Hearing, Cochlea, Tinnitus, Genetics; Molecular Biology Techniques and Applications; Bat Biology and Ecology Studies
TL;DR: Data reveal that hair cell organization, inner ear morphology, cellular cartography in the organ of Corti, and spatiotemporal expression of LGR5 are dynamic over developmental stages in a pattern not previously documented. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries
Added: December 19, 2022

2022 article

Quantitative analysis of illumination and detection corrections in adaptive light sheet fluorescence microscopy

Rai, M. R., Li, C., & Greenbaum, A. (2022, April 18). Biomedical Optics Express.

By: M. Rai n, C. Li n & A. Greenbaum n

topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; Cell Image Analysis Techniques; Photoacoustic and Ultrasonic Imaging
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Source: Web Of Science
Added: May 31, 2022

2021 article

Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy

Li, C., Moatti, A., Zhang, X., Ghashghaei, H. T., & Greenbaum, A. (2021, July 7). Biomedical Optics Express, Vol. 12, p. 5214.

By: C. Li n, A. Moatti n , X. Zhang n, H. Ghashghaei n & A. Greenbaum  n

topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; Image Processing Techniques and Applications; Cell Image Analysis Techniques
TL;DR: A deep learning-based autofocus framework that can estimate the position of the objective-lens focal plane relative to the light-sheet, based on two defocused images is presented, which outperforms or provides comparable results with the best traditional aut ofocus method on small and large image patches respectively. (via Semantic Scholar)
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Sources: Web Of Science, ORCID
Added: August 16, 2021

2021 article

Deep learning-based autofocus method enhances image quality in light-sheet fluorescence microscopy: publisher’s note

Li, C., Moatti, A., Zhang, X., Ghashghaei, H. T., & Greenbaum, A. (2021, December 8). Biomedical Optics Express.

By: C. Li n, A. Moatti n , X. Zhang n, H. Ghashghaei n & A. Greenbaum n

topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; Cell Image Analysis Techniques; Image Processing Techniques and Applications
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Source: Web Of Science
Added: January 10, 2022

2020 article

Three-dimensional imaging of intact porcine cochlea using tissue clearing and custom-built light-sheet microscopy

Moatti, A., Cai, Y., Li, C., Sattler, T., Edwards, L., Piedrahita, J., … Greenbaum, A. (2020, September 30). Biomedical Optics Express, Vol. 11, pp. 6181–6196.

By: A. Moatti n , Y. Cai  n, C. Li n, T. Sattler n, L. Edwards n , J. Piedrahita n , F. Ligler n, A. Greenbaum n

topics (OpenAlex): Advanced Fluorescence Microscopy Techniques; Cell Image Analysis Techniques; Photoacoustic and Ultrasonic Imaging
TL;DR: 3D microscopic analysis was performed on an intact cochlea of newborn and juvenile pigs with a volume up to ∼ 250 mm3 using the BoneClear tissue clearing technique, which renders the bone transparent, to support the growing effort to regenerate cochlear tissues and assist with basic research to advance cures for hearing impairments. (via Semantic Scholar)
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Sources: Web Of Science, NC State University Libraries, ORCID
Added: December 11, 2020

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