As animals develop, tissue bending contributes to shape the organs into complex three-dimensional structures. However, the architecture and packing of curved epithelia remains largely unknown. Here ...we show by means of mathematical modelling that cells in bent epithelia can undergo intercalations along the apico-basal axis. This phenomenon forces cells to have different neighbours in their basal and apical surfaces. As a consequence, epithelial cells adopt a novel shape that we term "scutoid". The detailed analysis of diverse tissues confirms that generation of apico-basal intercalations between cells is a common feature during morphogenesis. Using biophysical arguments, we propose that scutoids make possible the minimization of the tissue energy and stabilize three-dimensional packing. Hence, we conclude that scutoids are one of nature's solutions to achieve epithelial bending. Our findings pave the way to understand the three-dimensional organization of epithelial organs.
The original version of this Article contained an error in ref. 39, which incorrectly cited 'Fristrom, D. & Fristrom, J. W. in The Development of Drosophila melanogaster (eds. Bate, M. & ...Martinez-Arias, A.) II, (Cold spring harbor laboratory press, 1993)'. The correct reference is 'Condic, M.L, Fristrom, D. & Fristrom, J.W. Apical cell shape changes during Drosophila imaginal leg disc elongation: a novel morphogenetic mechanism. Development 111: 23-33 (1991)'. Furthermore, the last sentence of the fourth paragraph of the introduction incorrectly omitted citation of work by Rupprecht et al. The correct citation is given below. These errors have now been corrected in both the PDF and HTML versions of the Article. Rupprecht, J.F., Ong, K.H., Yin, J., Huang, A., Dinh, H.H., Singh, A.P., Zhang, S., Yu, W. & Saunders, T.E. Geometric constraints alter cell arrangements within curved epithelial tissues. Mol. Biol. Cell 28, 3582-3594 (2017).
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.
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•CartoCell exploits a small training dataset for accurate high-content 3D segmentation•CartoCell enables quantification of morphological features at the cellular level•Using CartoCell, we generate a “cartography” of morphological patterns in 3D•CartoCell applies to diverse epithelial models
A major bottleneck in developing neural networks for cell segmentation is the need for labor-intensive manual curation to develop a training dataset. The present work addresses this limitation by developing an automated image-analysis pipeline that utilizes small datasets to generate accurate labels of cells in complex 3D epithelial contexts. The overall goal is to provide an automatic and feasible method to achieve high-quality epithelial reconstructions and to enable high-content analysis of morphological features, which can improve our understanding of how these tissues self-organize.
Analyzing 3D epithelia at the cell level becomes challenging when dealing with hundreds of samples without a training dataset. Andrés-San Román et al. introduce CartoCell, a deep-learning pipeline that employs a small annotated dataset to achieve high-content cyst segmentation coupled with detailed analysis and cartography of cell features.
Surface curvature both emerges from, and influences the behavior of, living objects at length scales ranging from cell membranes to single cells to tissues and organs. The relevance of surface ...curvature in biology is supported by numerous experimental and theoretical investigations in recent years. In this review, first, a brief introduction to the key ideas of surface curvature in the context of biological systems is given and the challenges that arise when measuring surface curvature are discussed. Giving an overview of the emergence of curvature in biological systems, its significance at different length scales becomes apparent. On the other hand, summarizing current findings also shows that both single cells and entire cell sheets, tissues or organisms respond to curvature by modulating their shape and their migration behavior. Finally, the interplay between the distribution of morphogens or micro‐organisms and the emergence of curvature across length scales is addressed with examples demonstrating these key mechanistic principles of morphogenesis. Overall, this review highlights that curved interfaces are not merely a passive by‐product of the chemical, biological, and mechanical processes but that curvature acts also as a signal that co‐determines these processes.
Curvature as a local descriptor for shape has been revealed to play a fundamental role in the development of biological systems. Advanced 3D characterization methods allow its quantification across time and length scales indicating that cells and tissue growth can cause emergence of curved surfaces but in turn curvature also acts as a trigger for specific biological processes.
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.
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.
Due to the information overload we are faced with nowadays, personalization services are becoming almost essential, in order to find relevant information tailored to each individual or group of ...people with common interests. Therefore, it is very important to be able to build efficient and robust personalization techniques to be part of these services. The evaluation step is a crucial stage in their development and improvement, so much more research is needed to overcome this issue. We have proposed an automatic evaluation methodology for personalized information retrieval systems (ASPIRE), which joins the advantages of both system-centred (repeatable, comparable and generalizable results) and user-centred (considers the user) evaluation approaches, and makes the evaluation process easy and fast. Its reliability and robustness have been assessed by means of a user-oriented evaluation. ASPIRE may be considered as an interesting alternative to the costly and difficult user studies, able to discriminate between either different personalization techniques or different parameter configurations of a given personalization method.
Epithelial cell organization and the mechanical stability of tissues are closely related. In this context, it has been recently shown that packing optimization in bended or folded epithelia is ...achieved by an energy minimization mechanism that leads to a complex cellular shape: the “scutoid”. Here, we focus on the relationship between this shape and the connectivity between cells. We use a combination of computational, experimental, and biophysical approaches to examine how energy drivers affect the three-dimensional (3D) packing of tubular epithelia. We propose an energy-based stochastic model that explains the 3D cellular connectivity. Then, we challenge it by experimentally reducing the cell adhesion. As a result, we observed an increment in the appearance of scutoids that correlated with a decrease in the energy barrier necessary to connect with new cells. We conclude that tubular epithelia satisfy a quantitative biophysical principle that links tissue geometry and energetics with the average cellular connectivity.
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•Cells in tubular epithelia present apico-basal intercalations that minimize the energy•An image analysis pipeline quantifies the 3D connectivity at the cellular level•An energy-based biophysical model predicts the 3D cellular connectivity•The reduction of cell adhesion causes an increase in apico-basal intercalations
The complexity of curved epithelia poses a challenge to quantify their organization and the energy cues that regulate the 3D cellular connectivity. Gómez-Gálvez et al. use a biophysical model, based on computational and experimental data, to uncover a quantitative principle that explains the 3D cellular connectivity in tubular epithelia.
Purpose - The purpose of this paper is to present an overview of the reorganisation of the Andalusian Parliament's digital library to improve the electronic representation and access of its official ...corpus by taking advantage of a document's internal organisation. Video recordings of the parliamentary sessions have also been integrated with their corresponding textual transcriptions.Design methodology approach - After analysing the state of the Andalusian Parliament's digital library and determining the aspects that could be improved both in the repository and access mechanisms, this paper describes each component of the developed integrated information system.Findings - A methodology has been developed to tackle the problem and this could be applied to other similar institutions and organisations. Exploiting the internal structure of the parliament's official documents has also proved to be extremely interesting for users as they are directed towards the most relevant parts of the documents.Originality value - The paper presents an application of an information retrieval system for structured documents to a real framework and the integration of multimedia sources (e.g. text and video) for retrieval purposes.
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