Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae
Summary: Tissue clearing and light-sheet fluorescence microscopy were applied for 3D profiling of intact cochleae. However, the spiral ganglion neurons (SGNs) remain relatively understudied compared to hair cells and supporting cells, especially in large animal models. Here, we: (1) introduced colla...
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| Language: | English |
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Elsevier
2025-07-01
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| Series: | iScience |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004225011903 |
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| author | Yuheng Cai Greta M. Leitz-Najarian Reuben Rosen Kendall A. Hutson Adele Moatti Chen Li Douglas C. Fitzpatrick Alon Greenbaum |
| author_facet | Yuheng Cai Greta M. Leitz-Najarian Reuben Rosen Kendall A. Hutson Adele Moatti Chen Li Douglas C. Fitzpatrick Alon Greenbaum |
| author_sort | Yuheng Cai |
| collection | DOAJ |
| description | Summary: Tissue clearing and light-sheet fluorescence microscopy were applied for 3D profiling of intact cochleae. However, the spiral ganglion neurons (SGNs) remain relatively understudied compared to hair cells and supporting cells, especially in large animal models. Here, we: (1) introduced collagenase treatment to the current protocol of tissue clearing to enhance uniform antibody staining of SGNs within the pig cochlea and (2) adopted a deep learning object detection model to locate and count SGNs in large 3D datasets via Spiner (Spiral ganglion neuron profiler). Using this approach, Type I SGNs in intact gerbil and pig cochleae were detected and counted in 3D, and Spiner counts were consistent with manual counts. We believe broad adaptation of the method will improve understanding of the SGN population and their role in hearing loss. Codes for a user-friendly web interface were provided for model running and fine-tuning, making it accessible to those without programming experience. |
| format | Article |
| id | doaj-art-a9772c38b2b14327aa93ed42b8522b68 |
| institution | DOAJ |
| issn | 2589-0042 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj-art-a9772c38b2b14327aa93ed42b8522b682025-08-20T03:17:27ZengElsevieriScience2589-00422025-07-0128711292910.1016/j.isci.2025.112929Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleaeYuheng Cai0Greta M. Leitz-Najarian1Reuben Rosen2Kendall A. Hutson3Adele Moatti4Chen Li5Douglas C. Fitzpatrick6Alon Greenbaum7Lampe Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USADepartment of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USALampe Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USADepartment of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USALampe Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA; Department of Otolaryngology-Head & Neck Surgery, University of Pittsburgh, Pittsburgh, PA 15213, USALampe Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USADepartment of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USALampe Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University, Raleigh, NC 27695, USA; Comparative Medicine Institute, North Carolina State University, Raleigh, NC 27695, USA; Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695, USA; Corresponding authorSummary: Tissue clearing and light-sheet fluorescence microscopy were applied for 3D profiling of intact cochleae. However, the spiral ganglion neurons (SGNs) remain relatively understudied compared to hair cells and supporting cells, especially in large animal models. Here, we: (1) introduced collagenase treatment to the current protocol of tissue clearing to enhance uniform antibody staining of SGNs within the pig cochlea and (2) adopted a deep learning object detection model to locate and count SGNs in large 3D datasets via Spiner (Spiral ganglion neuron profiler). Using this approach, Type I SGNs in intact gerbil and pig cochleae were detected and counted in 3D, and Spiner counts were consistent with manual counts. We believe broad adaptation of the method will improve understanding of the SGN population and their role in hearing loss. Codes for a user-friendly web interface were provided for model running and fine-tuning, making it accessible to those without programming experience.http://www.sciencedirect.com/science/article/pii/S2589004225011903Optical imagingCellular neuroscienceSensory neuroscience |
| spellingShingle | Yuheng Cai Greta M. Leitz-Najarian Reuben Rosen Kendall A. Hutson Adele Moatti Chen Li Douglas C. Fitzpatrick Alon Greenbaum Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae iScience Optical imaging Cellular neuroscience Sensory neuroscience |
| title | Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae |
| title_full | Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae |
| title_fullStr | Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae |
| title_full_unstemmed | Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae |
| title_short | Spiner, deep learning-based automated detection of spiral ganglion neurons in intact cochleae |
| title_sort | spiner deep learning based automated detection of spiral ganglion neurons in intact cochleae |
| topic | Optical imaging Cellular neuroscience Sensory neuroscience |
| url | http://www.sciencedirect.com/science/article/pii/S2589004225011903 |
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