Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning
The highly organized spatial arrangement of sensory hair cells in the organ of Corti is essential for inner ear function. Here, we report a new analytical pipeline, based on optical clearing of tissue, for the construction of a single-cell resolution map of the organ of Corti. A sorbitol-based optic...
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doaj-b00228e21e6f497eb7b69bec17f80f8e2021-05-05T17:19:58ZengeLife Sciences Publications LtdeLife2050-084X2019-01-01810.7554/eLife.40946Cellular cartography of the organ of Corti based on optical tissue clearing and machine learningShinji Urata0https://orcid.org/0000-0002-5947-6842Tadatsune Iida1Masamichi Yamamoto2Yu Mizushima3https://orcid.org/0000-0002-8184-4437Chisato Fujimoto4Yu Matsumoto5Tatsuya Yamasoba6Shigeo Okabe7https://orcid.org/0000-0003-1216-8890Department of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Otolaryngology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanDepartment of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanDepartment of Nephrology, Graduate School of Medicine, Kyoto University, Kyoto, JapanDepartment of Otolaryngology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanDepartment of Otolaryngology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanDepartment of Otolaryngology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanDepartment of Otolaryngology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanDepartment of Cellular Neurobiology, Graduate School of Medicine, The University of Tokyo, Tokyo, JapanThe highly organized spatial arrangement of sensory hair cells in the organ of Corti is essential for inner ear function. Here, we report a new analytical pipeline, based on optical clearing of tissue, for the construction of a single-cell resolution map of the organ of Corti. A sorbitol-based optical clearing method enabled imaging of the entire cochlea at subcellular resolution. High-fidelity detection and analysis of all hair cell positions along the entire longitudinal axis of the organ of Corti were performed automatically by machine learning–based pattern recognition. Application of this method to samples from young, adult, and noise-exposed mice extracted essential information regarding cellular pathology, including longitudinal and radial spatial characteristics of cell loss, implying that multiple mechanisms underlie clustered cell loss. Our method of cellular mapping is effective for system-level phenotyping of the organ of Corti under both physiological and pathological conditions.https://elifesciences.org/articles/40946organ of Cortioptical tissue clearinghair cellhearing losshard tissuemachine learning |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Shinji Urata Tadatsune Iida Masamichi Yamamoto Yu Mizushima Chisato Fujimoto Yu Matsumoto Tatsuya Yamasoba Shigeo Okabe |
spellingShingle |
Shinji Urata Tadatsune Iida Masamichi Yamamoto Yu Mizushima Chisato Fujimoto Yu Matsumoto Tatsuya Yamasoba Shigeo Okabe Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning eLife organ of Corti optical tissue clearing hair cell hearing loss hard tissue machine learning |
author_facet |
Shinji Urata Tadatsune Iida Masamichi Yamamoto Yu Mizushima Chisato Fujimoto Yu Matsumoto Tatsuya Yamasoba Shigeo Okabe |
author_sort |
Shinji Urata |
title |
Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning |
title_short |
Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning |
title_full |
Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning |
title_fullStr |
Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning |
title_full_unstemmed |
Cellular cartography of the organ of Corti based on optical tissue clearing and machine learning |
title_sort |
cellular cartography of the organ of corti based on optical tissue clearing and machine learning |
publisher |
eLife Sciences Publications Ltd |
series |
eLife |
issn |
2050-084X |
publishDate |
2019-01-01 |
description |
The highly organized spatial arrangement of sensory hair cells in the organ of Corti is essential for inner ear function. Here, we report a new analytical pipeline, based on optical clearing of tissue, for the construction of a single-cell resolution map of the organ of Corti. A sorbitol-based optical clearing method enabled imaging of the entire cochlea at subcellular resolution. High-fidelity detection and analysis of all hair cell positions along the entire longitudinal axis of the organ of Corti were performed automatically by machine learning–based pattern recognition. Application of this method to samples from young, adult, and noise-exposed mice extracted essential information regarding cellular pathology, including longitudinal and radial spatial characteristics of cell loss, implying that multiple mechanisms underlie clustered cell loss. Our method of cellular mapping is effective for system-level phenotyping of the organ of Corti under both physiological and pathological conditions. |
topic |
organ of Corti optical tissue clearing hair cell hearing loss hard tissue machine learning |
url |
https://elifesciences.org/articles/40946 |
work_keys_str_mv |
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