title: EpiTools: An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics.
abstract: Epithelia grow and undergo extensive rearrangements to achieve their final size and shape. Imaging the dynamics of tissue growth and morphogenesis is now possible with advances in time-lapse microscopy, but a true understanding of their complexities is limited by automated image analysis tools to extract quantitative data. To overcome such limitations, we have designed a new open-source image analysis toolkit called EpiTools. It provides user-friendly graphical user interfaces for accurately segmenting and tracking the contours of cell membrane signals obtained from 4D confocal imaging. It is designed for a broad audience, especially biologists with no computer-science background. Quantitative data extraction is integrated into a larger bioimaging platform, Icy, to increase the visibility and usability of our tools. We demonstrate the usefulness of EpiTools by analyzing Drosophila wing imaginal disc growth, revealing previously overlooked properties of this dynamic tissue, such as the patterns of cellular rearrangements.
authors.affiliation: Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland.
authors.forename: Davide
authors.initials: D
authors.lastname: Heller
authors.affiliation: Digital Imaging Research Centre, Faculty of Science, Engineering and Computing, Kingston University, Kingston-upon-Thames KT1 2EE, UK.
authors.forename: Andreas
authors.initials: A
authors.lastname: Hoppe
authors.affiliation: Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
authors.forename: Simon
authors.initials: S
authors.lastname: Restrepo
authors.affiliation: Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland; Institute of Applied Simulations, Zürich University of Applied Sciences, Einsiedlerstrasse 31a, 8820 Wädenswil, Switzerland; SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Genopode, 1015 Lausanne, Switzerland.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Gatti
authors.affiliation: Apoptosis and Proliferation Control Laboratory, Lincoln's Inn Fields Laboratory, Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.
authors.forename: Alexander L
authors.initials: AL
authors.lastname: Tournier
authors.affiliation: Apoptosis and Proliferation Control Laboratory, Lincoln's Inn Fields Laboratory, Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Tapon
authors.affiliation: Institute of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.
authors.forename: Konrad
authors.initials: K
authors.lastname: Basler
authors.affiliation: MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK. Electronic address: y.mao@ucl.ac.uk.
authors.forename: Yanlan
authors.initials: Y
authors.lastname: Mao
mesh_terms: D000818:Animals; D048430:Cell Shape / Q000502:physiology*; D058948:Cell Tracking / Q000379:methods; D004330:Drosophila / Q000254:growth & development / Q000378:metabolism; D004848:Epithelium / Q000378:metabolism; D007091:Image Processing, Computer-Assisted / Q000379:methods; D008856:Microscopy, Fluorescence / Q000379:methods; D009024:Morphogenesis / Q000502:physiology*; D014921:Wings, Animal / Q000166:cytology / Q000254:growth & development
keywords: epithelial dynamics; image analysis; network description