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InSegtCone: interactive segmentation of crystalline cones in compound eyes

BACKGROUND: Understanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography (micr...

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Autores principales: Tichit, Pierre, Zhou, Tunhe, Kjer, Hans Martin, Dahl, Vedrana Andersen, Dahl, Anders Bjorholm, Baird, Emily
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10127308/
https://www.ncbi.nlm.nih.gov/pubmed/37170292
http://dx.doi.org/10.1186/s40850-021-00101-w
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author Tichit, Pierre
Zhou, Tunhe
Kjer, Hans Martin
Dahl, Vedrana Andersen
Dahl, Anders Bjorholm
Baird, Emily
author_facet Tichit, Pierre
Zhou, Tunhe
Kjer, Hans Martin
Dahl, Vedrana Andersen
Dahl, Anders Bjorholm
Baird, Emily
author_sort Tichit, Pierre
collection PubMed
description BACKGROUND: Understanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography (micro-CT) is a promising high-throughput imaging technique that enables to reconstruct the 3D anatomy of eyes, but powerful tools are needed to perform fast conversions of anatomical reconstructions into functional eye models. RESULTS: We developed a computing method named InSegtCone to automatically segment the crystalline cones in the apposition compound eyes of arthropods. Here, we describe the full auto-segmentation process, showcase its application to three different insect compound eyes and evaluate its performance. The auto-segmentation could successfully label the full individual shapes of 60-80% of the crystalline cones and is about as accurate and 250 times faster than manual labelling of the individual cones. CONCLUSIONS: We believe that InSegtCone can be an important tool for peer scientists to measure the orientation, size and dynamics of crystalline cones, leading to the accurate optical modelling of the diversity of arthropod eyes with micro-CT. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40850-021-00101-w.
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spelling pubmed-101273082023-04-26 InSegtCone: interactive segmentation of crystalline cones in compound eyes Tichit, Pierre Zhou, Tunhe Kjer, Hans Martin Dahl, Vedrana Andersen Dahl, Anders Bjorholm Baird, Emily BMC Zool Methodology Article BACKGROUND: Understanding the diversity of eyes is crucial to unravel how different animals use vision to interact with their respective environments. To date, comparative studies of eye anatomy are scarce because they often involve time-consuming or inefficient methods. X-ray micro-tomography (micro-CT) is a promising high-throughput imaging technique that enables to reconstruct the 3D anatomy of eyes, but powerful tools are needed to perform fast conversions of anatomical reconstructions into functional eye models. RESULTS: We developed a computing method named InSegtCone to automatically segment the crystalline cones in the apposition compound eyes of arthropods. Here, we describe the full auto-segmentation process, showcase its application to three different insect compound eyes and evaluate its performance. The auto-segmentation could successfully label the full individual shapes of 60-80% of the crystalline cones and is about as accurate and 250 times faster than manual labelling of the individual cones. CONCLUSIONS: We believe that InSegtCone can be an important tool for peer scientists to measure the orientation, size and dynamics of crystalline cones, leading to the accurate optical modelling of the diversity of arthropod eyes with micro-CT. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40850-021-00101-w. BioMed Central 2022-02-04 /pmc/articles/PMC10127308/ /pubmed/37170292 http://dx.doi.org/10.1186/s40850-021-00101-w Text en © The Author(s) 2022, corrected publication 2022 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Methodology Article
Tichit, Pierre
Zhou, Tunhe
Kjer, Hans Martin
Dahl, Vedrana Andersen
Dahl, Anders Bjorholm
Baird, Emily
InSegtCone: interactive segmentation of crystalline cones in compound eyes
title InSegtCone: interactive segmentation of crystalline cones in compound eyes
title_full InSegtCone: interactive segmentation of crystalline cones in compound eyes
title_fullStr InSegtCone: interactive segmentation of crystalline cones in compound eyes
title_full_unstemmed InSegtCone: interactive segmentation of crystalline cones in compound eyes
title_short InSegtCone: interactive segmentation of crystalline cones in compound eyes
title_sort insegtcone: interactive segmentation of crystalline cones in compound eyes
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10127308/
https://www.ncbi.nlm.nih.gov/pubmed/37170292
http://dx.doi.org/10.1186/s40850-021-00101-w
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