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SEGMENT3D: A web-based application for collaborative segmentation of 3D images used in the shoot apical meristem

Spina, Thiago V. and Stegmaier, Johannes and Falcão, Alexandre X. and Meyerowitz, Elliot and Cunha, Alexandre (2018) SEGMENT3D: A web-based application for collaborative segmentation of 3D images used in the shoot apical meristem. In: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018). IEEE , Piscataway, NJ, pp. 391-395. ISBN 9781538636367. https://resolver.caltech.edu/CaltechAUTHORS:20190201-111653966

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Abstract

The quantitative analysis of 3D confocal microscopy images of the shoot apical meristem helps understanding the growth process of some plants. Cell segmentation in these images is crucial for computational plant analysis and many automated methods have been proposed. However, variations in signal intensity across the image mitigate the effectiveness of those approaches with no easy way for user correction. We propose a web-based collaborative 3D image segmentation application, SEGMENT3D, to leverage automatic segmentation results. The image is divided into 3D tiles that can be either segmented interactively from scratch or corrected from a pre-existing segmentation. Individual segmentation results per tile are then automatically merged via consensus analysis and then stitched to complete the segmentation for the entire image stack. SEGMENT3D is a comprehensive application that can be applied to other 3D imaging modalities and general objects. It also provides an easy way to create supervised data to advance segmentation using machine learning models.


Item Type:Book Section
Related URLs:
URLURL TypeDescription
https://doi.org/10.1109/isbi.2018.8363600DOIArticle
http://xplorestaging.ieee.org/ielx7/8359997/8363198/08363600.pdf?arnumber=8363600PublisherArticle
ORCID:
AuthorORCID
Stegmaier, Johannes0000-0003-4072-3759
Meyerowitz, Elliot0000-0003-4798-5153
Additional Information:© 2018 IEEE. We are grateful for funding by the São Paulo Research Foundation in projects 2016/11853-2, 2015/09446-7, and 2014/12236-1 (TS, AF), CNPq (AF), the Center for Advanced Methods in Biological Image Analsysis, Beckman Institute at Caltech (TS, JS, EM, AC), the German Research Foundation DFG in the project MI1315/4-1 (JS), the Howard Hughes Medical Institute (EM) and the Gordon and Betty Moore Foundation through grant GBMF3406 (EM, AC), and the Serrapilheira Institute in the project Serra-1708-16161 (TS).
Funders:
Funding AgencyGrant Number
Fundação de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP)2016/11853-2
Fundação de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP)2015/09446-7
Fundação de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP)2014/12236-1
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)UNSPECIFIED
Caltech Beckman InstituteUNSPECIFIED
Deutsche Forschungsgemeinschaft (DFG)MI1315/4-1
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Gordon and Betty Moore FoundationGBMF3406
Serrapilheira InstituteSerra-1708-16161
Subject Keywords:3D Image Segmentation, Shoot Apical Meristem, Web-based Tool, Collaborative Segmentation, Confocal Microscopy
Record Number:CaltechAUTHORS:20190201-111653966
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190201-111653966
Official Citation:T. V. Spina, J. Stegmaier, A. X. Falcão, E. Meyerowitz and A. Cunha, "SEGMENT3D: A web-based application for collaborative segmentation of 3D images used in the shoot apical meristem," 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018), Washington, DC, 2018, pp. 391-395. doi: 10.1109/ISBI.2018.8363600
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:92562
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:01 Feb 2019 22:34
Last Modified:03 Oct 2019 20:45

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