EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics

Heller, Davide, Hoppe, Andreas, Restrepo, Simon, Gatti, Lorenzo, Tournier, Alexander L., Tapon, Nicolas, Basler, Konrad and Mao, Yanlan (2016) EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics. Developmental Cell, 36(1), pp. 103-116. ISSN (print) 1534-5807

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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.

Item Type: Article
Additional Information: This work was supported by the Medical Research Council [Fellowship no. MR/L009056/1], Cancer Research UK, Kanton of Zurich and the Swiss National Science Foundation.
Research Area: Computer science and informatics
Faculty, School or Research Centre: Faculty of Science, Engineering and Computing (until 2017) > Digital Imaging Research Centre (DIRC)
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Depositing User: Anna Englund
Date Deposited: 09 Feb 2016 14:37
Last Modified: 11 Apr 2016 15:13
DOI: https://doi.org/10.1016/j.devcel.2015.12.012
URI: http://eprints.kingston.ac.uk/id/eprint/33911

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