title: TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics.
abstract: Segmentation and tracking of cells in long-term time-lapse experiments has emerged as a powerful method to understand how tissue shape changes emerge from the complex choreography of constituent cells. However, methods to store and interrogate the large datasets produced by these experiments are not widely available. Furthermore, recently developed methods for relating tissue shape changes to cell dynamics have not yet been widely applied by biologists because of their technical complexity. We therefore developed a database format that stores cellular connectivity and geometry information of deforming epithelial tissues, and computational tools to interrogate it and perform multi-scale analysis of morphogenesis. We provide tutorials for this computational framework, called TissueMiner, and demonstrate its capabilities by comparing cell and tissue dynamics in vein and inter-vein subregions of the Drosophila pupal wing. These analyses reveal an unexpected role for convergent extension in shaping wing veins.
authors.affiliation: Division of Cell Polarity, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.|Institut Pasteur, Paris, France.
authors.forename: Raphaël
authors.identifier: 0000-0002-2441-9274
authors.initials: R
authors.lastname: Etournay
authors.affiliation: Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.|Department of Physics, Syracuse University, Syracuse, United States.
authors.forename: Matthias
authors.identifier: 0000-0001-9118-1270
authors.initials: M
authors.lastname: Merkel
authors.affiliation: Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
authors.forename: Marko
authors.identifier: 0000-0003-2360-3982
authors.initials: M
authors.lastname: Popović
authors.affiliation: Division of Cell Polarity, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Holger
authors.initials: H
authors.lastname: Brandl
authors.affiliation: Division of Cell Polarity, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Natalie A
authors.initials: NA
authors.lastname: Dye
authors.affiliation: Institut de Biologie du Développement de Marseille, Marseille, France.
authors.forename: Benoît
authors.initials: B
authors.lastname: Aigouy
authors.affiliation: Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.|The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London, United Kingdom.
authors.forename: Guillaume
authors.identifier: 0000-0001-7041-1292
authors.initials: G
authors.lastname: Salbreux
authors.affiliation: Division of Cell Polarity, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
authors.forename: Suzanne
authors.initials: S
authors.lastname: Eaton
authors.affiliation: Institut Pasteur, Paris, France.
authors.forename: Frank
authors.identifier: 0000-0003-4731-9185
authors.initials: F
authors.lastname: Jülicher
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D004330:Drosophila / Q000502:physiology; D004848:Epithelium / Q000502:physiology*; D007091:Image Processing, Computer-Assisted / Q000379:methods; D009024:Morphogenesis; D059008:Time-Lapse Imaging
keywords: D. melanogaster; cell biology; computational biology; epithelial cells; epithelial dynamics; systems biology