EpiTools: An Open-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics

Epithelia grow and undergo extensive rearrangements to achieve their final size and shape. To the capture of the dynamic nature of a growing epithelium and to help reveal novel properties of developing epithelial organs live imaging and automated image processing software are needed. To this end we have designed a new open-source image analysis toolkit called EpiTools. It allows automated image analysis tools to extract quantitative such that one can image the dynamics of tissue growth and morphogenesis and take advantages of the advances in time-lapse microscopy. EpiTools 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 demonstrated 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.

The Epitools Pipeline

Selected References

Heller, D., Hoppe, A., Restrepo, S., Gatti, L., Tournier, A.L., Tapon, N., Basler, K., and Mao, Y. (2016). EpiTools: An Ope{Willecke 2011 #100}n-Source Image Analysis Toolkit for Quantifying Epithelial Growth Dynamics. Developmental cell 36, 103-116.

Zartman, J., Restrepo, S., and Basler, K. (2013). A high-throughput template for optimizing Drosophila organ culture with response-surface methods. Development (Cambridge, England) 140, 667-674.