EpiGraph: an open-source platform to quantify epithelial organization

Abstract

Summary 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. Availability and implementation EpiGraph is available at https://imagej.net/EpiGraph and the code is accessible (https://github.com/ComplexOrganizationOfLivingMatter/Epigraph) under GPLv3 license. Supplementary information Supplementary data are available at Bioinformatics online.

The complex three-dimensional organization of epithelial tissues

“…3D). Subsequent studies introduced elements of Graph theory (see Box 1, Glossary) to analyze the polygonal distribution of cell contacts and, in some cases, to quantify the epithelial topology under physiological and pathological conditions (Escudero et al, 2011;Kursawe et al, 2016;Sánchez-Gutiérrez et al, 2013;Vicente-Munuera et al, 2020;Yamashita and Michiue, 2014). Other complementary methods combined the polygon distribution analysis with the application of in silico models, such as vertex models (see Box 1, Glossary) or Voronoi tessellations, trying to reproduce and explain the biological behavior by mathematical/computational means (Aland et al, 2015;Bi et al, 2016;Curran et al, 2017;Farhadifar et al, 2007).…”

Seven challenges in the multiscale modeling of multicellular tissues

“…Another common approach is to evolve the system to a dynamic equilibrium that is not sensitive to the choice of initial condition, as in the case of many homeostatic tissues such as the skin (Li et al, 2013) or gut epithelium (van Leeuwen et al, 2009). For developing tissues undergoing morphogenesis, an alternative approach is to derive initial conditions such as cell packing directly based on microscopy images (Iber et al, 2016) or via extracted summary statistics (Vicente-Munuera et al, 2019). Here, one should bear in mind variability in structures and it may be more important to capture essential patterns and conserved properties of tissue organization rather than use a specific example.…”

Seven Challenges in the Multiscale Modelling of Multicellular Tissues

“…Another common approach is to evolve the system to a dynamic equilibrium that is not sensitive to the choice of initial condition, as in the case of many homeostatic tissues such as the skin (Li et al, 2013) or gut epithelium (van Leeuwen et al, 2009). For developing tissues undergoing morphogenesis, an alternative approach is to derive initial conditions such as cell packing directly based on microscopy images (Iber et al, 2016) or via extracted summary statistics (Vicente-Munuera et al, 2019). Here, one should bear in mind variability in structures and it may be more important to capture essential patterns and conserved properties of tissue organization rather than use a specific example.…”