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; Mao, Yanlan

doi:10.21256/zhaw-4376

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-4376

Publication type:	Article in scientific journal
Type of review:	Peer review (publication)
Title:	EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics
Authors:	Heller, Davide Hoppe, Andreas Restrepo, Simon Gatti, Lorenzo Tournier, Alexander L. Tapon, Nicolas Basler, Konrad Mao, Yanlan
DOI:	10.21256/zhaw-4376 10.1016/j.devcel.2015.12.012
Published in:	Developmental Cell
Volume(Issue):	36
Issue:	1
Page(s):	103
Pages to:	116
Issue Date:	2016
Publisher / Ed. Institution:	Cell Press
ISSN:	1534-5807 1878-1551
Language:	English
Subjects:	Epithelial dynamics; Image analysis; Network description; Cell Shape; Epithelium; Fluorescence microscopy; Morphogenesis; Cell tracking; Computer-assisted image processing
Subject (DDC):	005: Computer programming, programs and data 571: Physiology and related subjects
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.
URI:	https://digitalcollection.zhaw.ch/handle/11475/16376
Fulltext version:	Published version
License (according to publishing contract):	CC BY 4.0: Attribution 4.0 International
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Computational Life Sciences (ICLS)
Appears in collections:	Publikationen Life Sciences und Facility Management

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Heller, D., Hoppe, A., Restrepo, S., Gatti, L., Tournier, A. L., Tapon, N., Basler, K., & Mao, Y. (2016). EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics. Developmental Cell, 36(1), 103–116. https://doi.org/10.21256/zhaw-4376

Heller, D. et al. (2016) ‘EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics’, Developmental Cell, 36(1), pp. 103–116. Available at: https://doi.org/10.21256/zhaw-4376.

D. Heller et al., “EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics,” Developmental Cell, vol. 36, no. 1, pp. 103–116, 2016, doi: 10.21256/zhaw-4376.

HELLER, Davide, Andreas HOPPE, Simon RESTREPO, Lorenzo GATTI, Alexander L. TOURNIER, Nicolas TAPON, Konrad BASLER und Yanlan MAO, 2016. EpiTools : an open-source image analysis toolkit for quantifying epithelial growth dynamics. Developmental Cell. 2016. Bd. 36, Nr. 1, S. 103–116. DOI 10.21256/zhaw-4376

Heller, Davide, Andreas Hoppe, Simon Restrepo, Lorenzo Gatti, Alexander L. Tournier, Nicolas Tapon, Konrad Basler, and Yanlan Mao. 2016. “EpiTools : An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics.” Developmental Cell 36 (1): 103–16. https://doi.org/10.21256/zhaw-4376.

Heller, Davide, et al. “EpiTools : An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics.” Developmental Cell, vol. 36, no. 1, 2016, pp. 103–16, https://doi.org/10.21256/zhaw-4376.