Speaker
Description
Epithelial tissue dynamics is tightly controlled spatio-temporally in numerous developmental processes and this precision is essential for the correct formation and homeostasis of organs. Quantifying epithelia dynamics is an important step in understanding this regulation but usually involves huge movies spanning thousands of cells and several hours. Thus, efficient and user-friendly tools are required to assist biologists to extract quantitative information from such big data. In this context, I will present three important pipelines: DeXtrusion, an open-source pipeline based on recurrent neural networks to automatically detect rare cellular events, LocalZBackProj, a python utility to recover 3D cell positions from the 2D projections, and EpiCure, a napari-based plugin to ease manual correction of segmentation and tracking of epithelia. The main focus of our tools, developed with back-and-forth interactions with the users in our institute, is to provide user-friendly tools to reduce manual annotation time and propose easy and interactive visualization and quantification.
| Authors | Gaëlle Letort*, Alexis Villars, Léo Valon, Nicolas Dray, Arthur Michaut, Tom Cumming, Minh Son Phan, Jerome Gros, Francois Schweisguth, Laure Bally-Cuif, Jean-Yves Tinevez, Romain Levayer |
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| Keywords | epithelia, recurrent neural networks, user-friendly, napari, manual annotation |
