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...

Full description

Bibliographic Details
Main Authors: Shinji Urata, Tadatsune Iida, Masamichi Yamamoto, Yu Mizushima, Chisato Fujimoto, Yu Matsumoto, Tatsuya Yamasoba, Shigeo Okabe
Format: Article
Language:English
Published: eLife Sciences Publications Ltd 2019-01-01
Series:eLife
Subjects:
Online Access:https://elifesciences.org/articles/40946
id doaj-b00228e21e6f497eb7b69bec17f80f8e
record_format Article
spelling 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 AT shinjiurata cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
AT tadatsuneiida cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
AT masamichiyamamoto cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
AT yumizushima cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
AT chisatofujimoto cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
AT yumatsumoto cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
AT tatsuyayamasoba cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
AT shigeookabe cellularcartographyoftheorganofcortibasedonopticaltissueclearingandmachinelearning
_version_ 1721459346237292544