ArticlePLoS computational biology2015
Segmentation and tracking of adherens junctions in 3D for the analysis of epithelial tissue morphogenesis.
Article in PLoS computational biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 26 citations in OpenAlex.
- Nfinder: automatic inference of cell neighborhood in 2D and 3D using nuclear markers.BMC bioinformatics · 2023Article
- Bioimage Analysis and Cell Motility.Patterns (New York, N.Y.) · 2021Review
- EPySeg: a coding-free solution for automated segmentation of epithelia using deep learning.Development (Cambridge, England) · 2020Article
- The Role of Tricellulin in Epithelial Jamming and Unjamming via Segmentation of Tricellular Junctions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2020Article
- Three-dimensional microscopy and image analysis methodology for mapping and quantification of nuclear positions in tissues with approximate cylindrical geometry.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- E-cadherin expression pattern during zebrafish embryonic epidermis development.F1000Research · 2018Article
- Using cell deformation and motion to predict forces and collective behavior in morphogenesis.Seminars in cell & developmental biology · 2017Review
- Deciphering tissue morphodynamics using bioimage informatics.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- SEGGA: a toolset for rapid automated analysis of epithelial cell polarity and dynamics.Development (Cambridge, England) · 2017Article
- Robust cell tracking in epithelial tissues through identification of maximum common subgraphs.Journal of the Royal Society, Interface · 2016Article
- Quantitative dynamics of VE-cadherin at endothelial cell junctions at a glance: basic requirements and current concepts.Discoveries (Craiova, Romania) · 2016Review
- Automated Measurement of Cobblestone Morphology for Characterizing Stem Cell Derived Retinal Pigment Epithelial Cell Cultures.Journal of ocular pharmacology and therapeutics : the official journal of the Association for Ocular Pharmacology and Therapeutics · 2016Article
- TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics.eLife · 2016Article
- EpiTools: An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics.Developmental cell · 2016Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Epithelial morphogenesis generates the shape of tissues, organs and embryos and is fundamental for their proper function. It is a dynamic process that occurs at multiple spatial scales from macromolecular dynamics, to cell deformations, mitosis and apoptosis, to coordinated cell rearrangements that lead to global changes of tissue shape. Using time lapse imaging, it is possible to observe these events at a system level. However, to investigate morphogenetic events it is necessary to develop computational tools to extract quantitative information from the time lapse data. Toward this goal, we developed an image-based computational pipeline to preprocess, segment and track epithelial cells in 4D confocal microscopy data. The computational pipeline we developed, for the first time, detects the adherens junctions of epithelial cells in 3D, without the need to first detect cell nuclei. We accentuate and detect cell outlines in a series of steps, symbolically describe the cells and their connectivity, and employ this information to track the cells. We validated the performance of the pipeline for its ability to detect vertices and cell-cell contacts, track cells, and identify mitosis and apoptosis in surface epithelia of Drosophila imaginal discs. We demonstrate the utility of the pipeline to extract key quantitative features of cell behavior with which to elucidate the dynamics and biomechanical control of epithelial tissue morphogenesis. We have made our methods and data available as an open-source multiplatform software tool called TTT (http://github.com/morganrcu/TTT).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.