EpiGraph: an open-source platform to quantify epithelial organization

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

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

Mechanisms of epithelial packing in proliferative tissues

Tissue morphogenesis is intimately linked with the complex changes that occur in the shape and organization of individual cells. In curved epithelia, cells possess the capacity to intercalate along their own apico-basal axes adopting a distinct shape named “scutoid”. This conformation facilitates the minimization of energy within the tissue. However, despite to the association of several geometric and biophysical factors with this 3D reorganisation, the dynamic changes underlying scutoid formation remain poorly understood. To better understand this complex phenomenon, we use live-imaging of a spheroidal epithelium, the sea star embryo, coupled with deep learning-based segmentation, to dissect the relative contributions of cell density, tissue compaction, and cell proliferation on epithelial architecture. Taking advantage of this model system we have performed physical compression experiments to identify cell density as the factor promoting scutoid formation at a global level. We also find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids and their formation tends to be more frequent in highly compacted regions. Finally, when comparing wildtype and compressed embryos with computational models, it becomes evident that tissue compaction and cell density is not sufficient to explain the high incidence of scutoids in a developing epithelium. Therefore, we explore the role of dynamic factors as local cell division throughout the tracking of individual cells. The results indicate most cells acquiring the “scutoidal” shape do so shortly after cell division potentially helping in the accommodation of the new cells within the tissue after the local increase of cell density. In conclusion, the induction of apico-basal intercalations in the sea star embryo might be an efficient way to address the increasing pressure on the tissue at both local and global levels. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development

Local and global changes in cell density induce reorganisation of 3D packing in a proliferating epithelium

Tissue morphogenesis is intimately linked to the changes in shape and organisation of individual cells. In curved epithelia, cells can intercalate along their own apicobasal axes, adopting a shape named ‘scutoid’ that allows energy minimization in the tissue. Although several geometric and biophysical factors have been associated with this 3D reorganisation, the dynamic changes underlying scutoid formation in 3D epithelial packing remain poorly understood. Here, we use live imaging of the sea star embryo coupled with deep learning-based segmentation to dissect the relative contributions of cell density, tissue compaction and cell proliferation on epithelial architecture. We find that tissue compaction, which naturally occurs in the embryo, is necessary for the appearance of scutoids. Physical compression experiments identify cell density as the factor promoting scutoid formation at a global level. Finally, the comparison of the developing embryo with computational models indicates that the increase in the proportion of scutoids is directly associated with cell divisions. Our results suggest that apico-basal intercalations appearing immediately after mitosis may help accommodate the new cells within the tissue. We propose that proliferation in a compact epithelium induces 3D cell rearrangements during development