title: Segmentation and tracking of adherens junctions in 3D for the analysis of epithelial tissue morphogenesis.
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).
authors.affiliation: Department of Developmental, Molecular & Chemical Biology. Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Rodrigo
authors.initials: R
authors.lastname: Cilla
authors.affiliation: Department of Developmental, Molecular & Chemical Biology. Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Vinodh
authors.initials: V
authors.lastname: Mechery
authors.affiliation: Department of Developmental, Molecular & Chemical Biology. Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Beatriz
authors.initials: B
authors.lastname: Hernandez de Madrid
authors.affiliation: Department of Developmental, Molecular & Chemical Biology. Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Steven
authors.initials: S
authors.lastname: Del Signore
authors.affiliation: Department of Biology, Boston College, Boston, Massachusetts, United States of America.
authors.forename: Ivan
authors.initials: I
authors.lastname: Dotu
authors.affiliation: Department of Developmental, Molecular & Chemical Biology. Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America.
authors.forename: Victor
authors.initials: V
authors.lastname: Hatini
mesh_terms: D022005:Adherens Junctions / Q000502:physiology* / Q000648:ultrastructure*; D000818:Animals; D002448:Cell Adhesion / Q000502:physiology; D058948:Cell Tracking / Q000379:methods; D004330:Drosophila; D004847:Epithelial Cells / Q000166:cytology* / Q000502:physiology*; D021621:Imaging, Three-Dimensional / Q000379:methods*; D018613:Microscopy, Confocal / Q000379:methods; D009024:Morphogenesis / Q000502:physiology*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity