2 research outputs found

    EpiGraph: an open-source platform to quantify epithelial organization

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    Here we present EpiGraph, an image analysis tool that quantifies epithelial organization. Our method combines computational geometry and graph theory to measure the degree of order of any packed tissue. EpiGraph goes beyond the traditional polygon distribution analysis, capturing other organizational traits that improve the characterization of epithelia. EpiGraph can objectively compare the rearrangements of epithelial cells during development and homeostasis to quantify how the global ensemble is affected. Importantly, it has been implemented in the open-access platform Fiji. This makes EpiGraph very user friendly, with no programming skills required.España Ministerio de Economia, Industria y Competitividad BFU2016-74975-PEspaña, Programa Ramón y Cajal (PI13/ 01347

    CartoCell, a high-content pipeline for 3D image analysis, unveils cell morphology patterns in epithelia

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    Decades of research have not yet fully explained the mechanisms of epithelial self-organization and 3D packing. Single-cell analysis of large 3D epithelial libraries is crucial for understanding the assembly and function of whole tissues. Combining 3D epithelial imaging with advanced deep-learning segmentation methods is essential for enabling this high-content analysis. We introduce CartoCell, a deep-learning-based pipeline that uses small datasets to generate accurate labels for hundreds of whole 3D epithelial cysts. Our method detects the realistic morphology of epithelial cells and their contacts in the 3D structure of the tissue. CartoCell enables the quantification of geometric and packing features at the cellular level. Our single-cell cartography approach then maps the distribution of these features on 2D plots and 3D surface maps, revealing cell morphology patterns in epithelial cysts. Additionally, we show that CartoCell can be adapted to other types of epithelial tissues.Ministerio de Ciencia e Innovación PID2019-103900GB-I00, PID2020-120367GB-I00, PID2021-126701OB-I00Junta de Andalucía US-1380953, PY18-631Ministerio de Economía y Competitividad BES-2022-07778
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