{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T02:56:02Z","timestamp":1787021762643,"version":"build-2736575974"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1012681","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T00:00:00Z","timestamp":1737936000000}}],"reference-count":83,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2025,1,10]],"date-time":"2025-01-10T00:00:00Z","timestamp":1736467200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Plan Cancer","award":["C18006BS"],"award-info":[{"award-number":["C18006BS"]}]},{"name":"Plan cancer","award":["C20048BS"],"award-info":[{"award-number":["C20048BS"]}]},{"DOI":"10.13039\/501100006556","name":"Centre Hospitalier Universitaire de Toulouse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006556","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100015760","name":"Inserm Transfert","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100015760","id-type":"DOI","asserted-by":"publisher"}]},{"name":"R\u00e9gion Occitanie"},{"name":"Universit\u00e9 Paul Sabatier"},{"name":"R\u00e9gion Occitanie"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>Understanding the interplay between biology and mechanics in tissue architecture is challenging, particularly in terms of 3D tissue organization. Addressing this challenge requires a biological model enabling observations at multiple levels from cell to tissue, as well as theoretical and computational approaches enabling the generation of a synthetic model that is relevant to the biological model and allowing for investigation of the mechanical stresses experienced by the tissue. Using a monolayer human colon epithelium organoid as a biological model, freely available tools (Fiji, Cellpose, Napari, Morphonet, or Tyssue library), and the commercially available Abaqus FEM solver, we combined vertex and FEM approaches to generate a comprehensive viscoelastic finite element model of the human colon organoid and demonstrated its flexibility. We imaged human colon organoid development for 120 hours, following the evolution of the organoids from an immature to a mature morphology. According to the extracted architectural\/geometric parameters of human colon organoids at various stages of tissue architecture establishment, we generated organoid active vertex models. However, this approach did not consider the mechanical aspects involved in the organoids\u2019 morphological evolution. Therefore, we applied a finite element method considering mechanical loads mimicking osmotic pressure, external solicitation, or active contraction in the vertex model by using the Abaqus FEM solver. Integration of finite element analysis (FEA) into the vertex model achieved a better fit with the biological model. Therefore, the FEM model provides a basis for depicting cell shape, tissue deformation, and cellular-level strain due to imposed stresses. In conclusion, we demonstrated that a combination of vertex and FEM approaches, combining geometrical and mechanical parameters, improves modeling of alterations in organoid morphology over time and enables better assessment of the mechanical cues involved in establishing the architecture of the human colon epithelium.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1012681","type":"journal-article","created":{"date-parts":[[2025,1,10]],"date-time":"2025-01-10T15:18:35Z","timestamp":1736522315000},"page":"e1012681","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":11,"title":["Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell"],"prefix":"10.1371","volume":"21","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0110-9388","authenticated-orcid":true,"given":"Julien","family":"Laussu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deborah","family":"Michel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"L\u00e9a","family":"Magne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2462-9842","authenticated-orcid":true,"given":"Stephane","family":"Segonds","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven","family":"Marguet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimitri","family":"Hamel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muriel","family":"Quaranta-Nicaise","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Frederick","family":"Barreau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel","family":"Mas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vincent","family":"Velay","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5637-5504","authenticated-orcid":true,"given":"Florian","family":"Bugarin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1057-8151","authenticated-orcid":true,"given":"Audrey","family":"Ferrand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2025,1,10]]},"reference":[{"key":"pcbi.1012681.ref001","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.gde.2021.10.005","article-title":"Digesting the mechanobiology of the intestinal epithelium","volume":"72","author":"C Perez-Gonzalez","year":"2022","journal-title":"Curr Opin Genet Dev"},{"issue":"6444","key":"pcbi.1012681.ref002","doi-asserted-by":"crossref","first-page":"956","DOI":"10.1126\/science.aaw7567","article-title":"Organoids by design","volume":"364","author":"T Takebe","year":"2019","journal-title":"Science"},{"issue":"7341","key":"pcbi.1012681.ref003","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature09941","article-title":"Self-organizing optic-cup morphogenesis in three-dimensional culture","volume":"472","author":"M Eiraku","year":"2011","journal-title":"Nature"},{"issue":"3","key":"pcbi.1012681.ref004","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1038\/ncb3312","article-title":"Organoids as an in vitro model of human development and disease","volume":"18","author":"A Fatehullah","year":"2016","journal-title":"Nat Cell Biol"},{"issue":"21","key":"pcbi.1012681.ref005","doi-asserted-by":"crossref","first-page":"4452","DOI":"10.1242\/dev.096628","article-title":"Artificial three-dimensional niches deconstruct pancreas development in vitro","volume":"140","author":"C Greggio","year":"2013","journal-title":"Development"},{"issue":"7467","key":"pcbi.1012681.ref006","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1038\/nature12517","article-title":"Cerebral organoids model human brain development and microcephaly","volume":"501","author":"MA Lancaster","year":"2013","journal-title":"Nature"},{"issue":"7244","key":"pcbi.1012681.ref007","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/nature07935","article-title":"Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche","volume":"459","author":"T Sato","year":"2009","journal-title":"Nature"},{"issue":"7332","key":"pcbi.1012681.ref008","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1038\/nature09691","article-title":"Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro","volume":"470","author":"JR Spence","year":"2011","journal-title":"Nature"},{"issue":"7574","key":"pcbi.1012681.ref009","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1038\/nature15695","article-title":"Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis","volume":"526","author":"M Takasato","year":"2015","journal-title":"Nature"},{"key":"pcbi.1012681.ref010","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1146\/annurev.physiol.010908.163145","article-title":"Stem cells, self-renewal, and differentiation in the intestinal epithelium","volume":"71","author":"LG van der Flier","year":"2009","journal-title":"Annu Rev Physiol"},{"issue":"1","key":"pcbi.1012681.ref011","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1038\/s41467-019-09010-6","article-title":"Stem cell proliferation is induced by apoptotic bodies from dying cells during epithelial tissue maintenance","volume":"10","author":"CK Brock","year":"2019","journal-title":"Nat Commun"},{"issue":"12","key":"pcbi.1012681.ref012","doi-asserted-by":"crossref","first-page":"1074","DOI":"10.1038\/nphys3471","article-title":"A density-independent rigidity transition in biological tissues","volume":"11","author":"D Bi","year":"2015","journal-title":"Nature Physics"},{"issue":"2","key":"pcbi.1012681.ref013","doi-asserted-by":"crossref","first-page":"021011","DOI":"10.1103\/PhysRevX.6.021011","article-title":"Motility-driven glass and jamming transitions in biological tissues","volume":"6","author":"D Bi","year":"2016","journal-title":"Physical Review X"},{"key":"pcbi.1012681.ref014","first-page":"1371","article-title":"Pegoraro, Yu Long Han, Jessie Huang, David A. Roberts, Haiqian Yang, Jeffrey J. Fredberg, Darrell N. Kotton, Dapeng Bi, Ming Guo. Collective curvature sensing and fluidity in three-dimensional multicellular systems","volume":"18","author":"AD Wenhui Tang","year":"2022","journal-title":"Nature Physics"},{"key":"pcbi.1012681.ref015","first-page":"629","article-title":"Publisher Correction: Geometric constraints during epithelial jamming","volume":"14","author":"L Atia","year":"2018","journal-title":"Nature Physics"},{"key":"pcbi.1012681.ref016","first-page":"7","article-title":"Cellular aspect ratio and cell division mechanics underlie the patterning of cell progeny in diverse mammalian epithelia","author":"KL McKinley","year":"2018","journal-title":"Elife"},{"issue":"7538","key":"pcbi.1012681.ref017","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nature14152","article-title":"Apico-basal forces exerted by apoptotic cells drive epithelium folding","volume":"518","author":"B Monier","year":"2015","journal-title":"Nature"},{"issue":"4","key":"pcbi.1012681.ref018","doi-asserted-by":"crossref","first-page":"624","DOI":"10.1016\/j.cub.2019.12.025","article-title":"Osmotic Gradients in Epithelial Acini Increase Mechanical Tension across E-cadherin, Drive Morphogenesis, and Maintain Homeostasis","volume":"30","author":"V Narayanan","year":"2020","journal-title":"Curr Biol"},{"issue":"11","key":"pcbi.1012681.ref019","doi-asserted-by":"crossref","first-page":"3875","DOI":"10.1016\/j.celrep.2020.02.074","article-title":"Mechanical Stress Regulates Epithelial Tissue Integrity and Stiffness through the FGFR\/Erk2 Signaling Pathway during Embryogenesis","volume":"30","author":"N Kinoshita","year":"2020","journal-title":"Cell Rep"},{"key":"pcbi.1012681.ref020","doi-asserted-by":"crossref","first-page":"012031","DOI":"10.1088\/1757-899X\/1037\/1\/012031","article-title":"Analyze of shape memory wires behavior under external solicitation using finite elements analysis (FEA).","volume":"1037","author":"DC Burlacu L","year":"2021","journal-title":"IOP Conf Ser: Mater Sci Eng"},{"issue":"186","key":"pcbi.1012681.ref021","doi-asserted-by":"crossref","first-page":"20210851","DOI":"10.1098\/rsif.2021.0851","article-title":"Geometrical characterization of active contraction pulses in epithelial cells using the two-dimensional vertex model","volume":"19","author":"F Perez-Verdugo","year":"2022","journal-title":"J R Soc Interface"},{"issue":"6","key":"pcbi.1012681.ref022","doi-asserted-by":"crossref","first-page":"946","DOI":"10.1242\/dev.143693","article-title":"The physics of organoids: a biophysical approach to understanding organogenesis","volume":"144","author":"S Dahl-Jensen","year":"2017","journal-title":"Development"},{"key":"pcbi.1012681.ref023","first-page":"47","article-title":"How computational models can help unlock biological systems","author":"GW Brodland","year":"2015","journal-title":"Semin Cell Dev Biol"},{"issue":"6","key":"pcbi.1012681.ref024","doi-asserted-by":"crossref","first-page":"e1005569","DOI":"10.1371\/journal.pcbi.1005569","article-title":"Active Vertex Model for cell-resolution description of epithelial tissue mechanics","volume":"13","author":"DL Barton","year":"2017","journal-title":"PLoS Comput Biol"},{"issue":"23","key":"pcbi.1012681.ref025","doi-asserted-by":"crossref","first-page":"4214","DOI":"10.1242\/dev.151274","article-title":"Computer modeling in developmental biology: growing today, essential tomorrow","volume":"144","author":"J. Sharpe","year":"2017","journal-title":"Development"},{"issue":"1720","key":"pcbi.1012681.ref026","article-title":"Vertex models: from cell mechanics to tissue morphogenesis","volume":"372","author":"S Alt","year":"2017","journal-title":"Philos Trans R Soc Lond B Biol Sci"},{"issue":"3","key":"pcbi.1012681.ref027","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1007\/s00285-011-0464-y","article-title":"Incorporating chemical signalling factors into cell-based models of growing epithelial tissues","volume":"65","author":"AM Smith","year":"2012","journal-title":"J Math Biol"},{"key":"pcbi.1012681.ref028","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.jcp.2016.03.054","article-title":"Mixed-hybrid and vertex-discontinuous-Galerkin finite element modeling of multiphase compositional flow on 3D unstructured grids","volume":"315","author":"J Moortgat","year":"2016","journal-title":"Journal of Computational Physics"},{"key":"pcbi.1012681.ref029","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.1016\/j.cma.2005.05.049","article-title":"Immersed finite element method and its applications to biological systems","volume":"195","author":"WK Liu","year":"2006","journal-title":"Computer Methods in Applied Mechanics and Engineering"},{"key":"pcbi.1012681.ref030","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.jmbbm.2013.11.022","article-title":"Structural finite element analysis to explain cell mechanics variability.","volume":"38","author":"S Barreto","year":"2014","journal-title":"J Mech Behav Biomed Mater"},{"key":"pcbi.1012681.ref031","first-page":"4","author":"N Slomka","year":"2011","journal-title":"Finite Element Modeling of Cellular Mechanics Experiments"},{"key":"pcbi.1012681.ref032","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1098\/rspa.2002.1060","article-title":"Review Paper: Continuum biomechanics of soft biological tissues","volume":"459","author":"JD Humphrey","year":"2003","journal-title":"Proceedings of the Royal Society of London, Series A: Mathematical, Physical and Engineering Sciences"},{"issue":"7754","key":"pcbi.1012681.ref033","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1038\/s41586-019-1146-y","article-title":"Self-organization and symmetry breaking in intestinal organoid development","volume":"569","author":"D Serra","year":"2019","journal-title":"Nature"},{"key":"pcbi.1012681.ref034","doi-asserted-by":"crossref","first-page":"656795","DOI":"10.3389\/fcell.2021.656795","article-title":"Cytolethal Distending Toxin Promotes Replicative Stress Leading to Genetic Instability Transmitted to Daughter Cells.","volume":"9","author":"W Tremblay","year":"2021","journal-title":"Front Cell Dev Biol"},{"issue":"12","key":"pcbi.1012681.ref035","doi-asserted-by":"crossref","first-page":"1634","DOI":"10.1038\/s41592-022-01663-4","article-title":"Cellpose 2.0: how to train your own model.","volume":"19","author":"M Pachitariu","year":"2022","journal-title":"Nat Methods.PubMed Central PMCID"},{"issue":"1","key":"pcbi.1012681.ref036","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/s41592-020-01018-x","article-title":"Cellpose: a generalist algorithm for cellular segmentation","volume":"18","author":"C Stringer","year":"2021","journal-title":"Nat Methods"},{"key":"pcbi.1012681.ref037","first-page":"10","article-title":"3D cell neighbour dynamics in growing pseudostratified epithelia","author":"HF Gomez","year":"2021","journal-title":"Elife"},{"issue":"1","key":"pcbi.1012681.ref038","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1073\/pnas.1312076111","article-title":"Theory of epithelial sheet morphology in three dimensions","volume":"111","author":"E Hannezo","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"pcbi.1012681.ref039","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1007\/s10237-012-0458-8","article-title":"Modeling cell proliferation for simulating three-dimensional tissue morphogenesis based on a reversible network reconnection framework","volume":"12","author":"S Okuda","year":"2013","journal-title":"Biomech Model Mechanobiol"},{"issue":"24","key":"pcbi.1012681.ref040","doi-asserted-by":"crossref","first-page":"2095","DOI":"10.1016\/j.cub.2007.11.049","article-title":"The influence of cell mechanics, cell-cell interactions, and proliferation on epithelial packing","volume":"17","author":"R Farhadifar","year":"2007","journal-title":"Curr Biol"},{"key":"pcbi.1012681.ref041","doi-asserted-by":"crossref","first-page":"405","DOI":"10.3389\/fbioe.2020.00405","article-title":"Development of a New 3D Hybrid Model for Epithelia Morphogenesis","volume":"8","author":"F Ioannou","year":"2020","journal-title":"Front Bioeng Biotechnol"},{"issue":"7","key":"pcbi.1012681.ref042","doi-asserted-by":"crossref","first-page":"1670","DOI":"10.1016\/j.bpj.2016.03.009","article-title":"Shape Transformations of Epithelial Shells.","volume":"110","author":"M Misra","year":"2016","journal-title":"Biophys J"},{"key":"pcbi.1012681.ref043","doi-asserted-by":"crossref","first-page":"2973","DOI":"10.21105\/joss.02973","article-title":"Tyssue: an epithelium simulation library","volume":"6","author":"S Theis","year":"2021","journal-title":"Journal of Open Source Software"},{"issue":"1","key":"pcbi.1012681.ref044","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1007\/s10237-019-01204-7","article-title":"A quantitative high-resolution computational mechanics cell model for growing and regenerating tissues","volume":"19","author":"P Van Liedekerke","year":"2020","journal-title":"Biomech Model Mechanobiol"},{"issue":"47","key":"pcbi.1012681.ref045","doi-asserted-by":"crossref","first-page":"19298","DOI":"10.1073\/pnas.1205258109","article-title":"Volume conservation principle involved in cell lengthening and nucleus movement during tissue morphogenesis","volume":"109","author":"MA Gelbart","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"1","key":"pcbi.1012681.ref046","doi-asserted-by":"crossref","first-page":"1011","DOI":"10.1038\/s42003-021-02539-7","article-title":"Causal contributors to tissue stiffness and clinical relevance in urology","volume":"4","author":"L Martinez-Vidal","year":"2021","journal-title":"Commun Biol"},{"issue":"5","key":"pcbi.1012681.ref047","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1111\/boc.201600078","article-title":"Are cancer cells really softer than normal cells","volume":"109","author":"C Alibert","year":"2017","journal-title":"Biol Cell"},{"issue":"5","key":"pcbi.1012681.ref048","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1016\/j.devcel.2020.07.019","article-title":"Buckling of an Epithelium Growing under Spherical Confinement","volume":"54","author":"A Trushko","year":"2020","journal-title":"Dev Cell"},{"issue":"3","key":"pcbi.1012681.ref049","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1016\/j.bpj.2014.06.033","article-title":"If cell mechanics can be described by elastic modulus: study of different models and probes used in indentation experiments","volume":"107","author":"N Guz","year":"2014","journal-title":"Biophys J"},{"key":"pcbi.1012681.ref050","first-page":"582","author":"R. von Mises","year":"1913","journal-title":"Mechanik der festen Korper im plastisch- deformablen Zustand Nachrichten von der Gesellschaft der Wissenschaften zu Gottingen Mathematisch-Physikalische"},{"issue":"4","key":"pcbi.1012681.ref051","doi-asserted-by":"crossref","first-page":"998","DOI":"10.1016\/j.bpj.2014.07.013","article-title":"Passive mechanical forces control cell-shape change during Drosophila ventral furrow formation","volume":"107","author":"O Polyakov","year":"2014","journal-title":"Biophys J"},{"issue":"7","key":"pcbi.1012681.ref052","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1038\/s41556-021-00700-2","article-title":"Cell fate coordinates mechano-osmotic forces in intestinal crypt formation","volume":"23","author":"Q Yang","year":"2021","journal-title":"Nat Cell Biol"},{"issue":"20","key":"pcbi.1012681.ref053","doi-asserted-by":"crossref","first-page":"3132","DOI":"10.1016\/j.cub.2017.09.005","article-title":"Viscoelastic Dissipation Stabilizes Cell Shape Changes during Tissue Morphogenesis","volume":"27","author":"R Clement","year":"2017","journal-title":"Curr Biol"},{"issue":"20","key":"pcbi.1012681.ref054","doi-asserted-by":"crossref","first-page":"e102497","DOI":"10.15252\/embj.2019102497","article-title":"Tissue rheology in embryonic organization","volume":"38","author":"NI Petridou","year":"2019","journal-title":"EMBO J"},{"issue":"6","key":"pcbi.1012681.ref055","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/j.devcel.2015.11.018","article-title":"Stable Force Balance between Epithelial Cells Arises from F-Actin Turnover","volume":"35","author":"JN Jodoin","year":"2015","journal-title":"Dev Cell"},{"issue":"6","key":"pcbi.1012681.ref056","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/ncb3525","article-title":"Actin cortex architecture regulates cell surface tension","volume":"19","author":"P Chugh","year":"2017","journal-title":"Nat Cell Biol"},{"issue":"10","key":"pcbi.1012681.ref057","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/j.tcb.2012.07.001","article-title":"Actin cortex mechanics and cellular morphogenesis","volume":"22","author":"G Salbreux","year":"2012","journal-title":"Trends Cell Biol"},{"issue":"4","key":"pcbi.1012681.ref058","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1016\/j.jcf.2019.10.022","article-title":"Forskolin-induced swelling of intestinal organoids correlates with disease severity in adults with cystic fibrosis and homozygous F508del mutations","volume":"19","author":"KM de Winter-de Groot","year":"2020","journal-title":"J Cyst Fibros"},{"issue":"4","key":"pcbi.1012681.ref059","doi-asserted-by":"crossref","first-page":"e1002025","DOI":"10.1371\/journal.pcbi.1002025","article-title":"Cell-sorting at the A\/P boundary in the Drosophila wing primordium: a computational model to consolidate observed non-local effects of Hh signaling","volume":"7","author":"S Schilling","year":"2011","journal-title":"PLoS Comput Biol"},{"issue":"12","key":"pcbi.1012681.ref060","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1038\/ncb1798","article-title":"Nature and anisotropy of cortical forces orienting Drosophila tissue morphogenesis","volume":"10","author":"M Rauzi","year":"2008","journal-title":"Nat Cell Biol"},{"issue":"6514","key":"pcbi.1012681.ref061","article-title":"Apical stress fibers enable a scaling between cell mechanical response and area in epithelial tissue","volume":"370","author":"JM Lopez-Gay","year":"2020","journal-title":"Science"},{"issue":"3","key":"pcbi.1012681.ref062","doi-asserted-by":"crossref","first-page":"e1006273","DOI":"10.1371\/journal.pcbi.1006273","article-title":"Quantitative cell-based model predicts mechanical stress response of growing tumor spheroids over various growth conditions and cell lines","volume":"15","author":"P Van Liedekerke","year":"2019","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"pcbi.1012681.ref063","doi-asserted-by":"crossref","first-page":"e1006577","DOI":"10.1371\/journal.pcbi.1006577","article-title":"Agent-based modeling of morphogenetic systems: Advantages and challenges","volume":"15","author":"CM Glen","year":"2019","journal-title":"PLoS Comput Biol"},{"issue":"7","key":"pcbi.1012681.ref064","doi-asserted-by":"crossref","first-page":"745","DOI":"10.1038\/s41556-021-00699-6","article-title":"Mechanical compartmentalization of the intestinal organoid enables crypt folding and collective cell migration","volume":"23","author":"C Perez-Gonzalez","year":"2021","journal-title":"Nat Cell Biol"},{"issue":"11","key":"pcbi.1012681.ref065","doi-asserted-by":"crossref","first-page":"2291","DOI":"10.1016\/j.bpj.2013.11.4498","article-title":"Vertex models of epithelial morphogenesis","volume":"106","author":"AG Fletcher","year":"2014","journal-title":"Biophys J"},{"issue":"6\u20131","key":"pcbi.1012681.ref066","doi-asserted-by":"crossref","first-page":"064611","DOI":"10.1103\/PhysRevE.105.064611","article-title":"Anomalous elasticity of a cellular tissue vertex model","volume":"105","author":"A Hernandez","year":"2022","journal-title":"Phys Rev E"},{"key":"pcbi.1012681.ref067","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1038\/s42254-020-0184-6","article-title":"Measuring mechanical stress in living tissues","volume":"2","author":"M G\u00f3mez-Gonz\u00e1lez","year":"2020","journal-title":"Nature Review Physics"},{"issue":"11","key":"pcbi.1012681.ref068","doi-asserted-by":"crossref","first-page":"1024","DOI":"10.1016\/j.cub.2013.04.049","article-title":"Fluid shear stress on endothelial cells modulates mechanical tension across VE-cadherin and PECAM-1","volume":"23","author":"DE Conway","year":"2013","journal-title":"Curr Biol"},{"issue":"7","key":"pcbi.1012681.ref069","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1038\/s41592-022-01508-0","article-title":"Automated high-speed 3D imaging of organoid cultures with multi-scale phenotypic quantification","volume":"19","author":"A Beghin","year":"2022","journal-title":"Nat Methods"},{"issue":"7730","key":"pcbi.1012681.ref070","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/s41586-018-0671-4","article-title":"Active superelasticity in three-dimensional epithelia of controlled shape","volume":"563","author":"E Latorre","year":"2018","journal-title":"Nature"},{"issue":"4","key":"pcbi.1012681.ref071","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1038\/s43588-024-00620-9","article-title":"SimuCell3D: three-dimensional simulation of tissue mechanics with cell polarization","volume":"4","author":"S Runser","year":"2024","journal-title":"Nat Comput Sci"},{"key":"pcbi.1012681.ref072","first-page":"9","article-title":"Sonic hedgehog signaling directs patterned cell remodeling during cranial neural tube closure","author":"ER Brooks","year":"2020","journal-title":"Elife"},{"issue":"1","key":"pcbi.1012681.ref073","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/s12915-021-01122-0","article-title":"Single-cell analysis of cell fate bifurcation in the chordate Ciona","volume":"19","author":"KM Winkley","year":"2021","journal-title":"BMC Biol"},{"issue":"1","key":"pcbi.1012681.ref074","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.ydbio.2009.05.540","article-title":"Unfolding a chordate developmental program, one cell at a time: invariant cell lineages, short-range inductions and evolutionary plasticity in ascidians","volume":"332","author":"P. Lemaire","year":"2009","journal-title":"Dev Biol"},{"key":"pcbi.1012681.ref075","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.semcdb.2022.04.015","article-title":"Mapping and exploring the organoid state space using synthetic biology","volume":"141","author":"TH Tan","year":"2023","journal-title":"Semin Cell Dev Biol"},{"issue":"7","key":"pcbi.1012681.ref076","first-page":"676","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"J Schindelin","year":"2012","journal-title":"Nat MethodsPubMed Central PMCID"},{"key":"pcbi.1012681.ref077","author":"N Sofroniew","year":"2022","journal-title":"Pe\u00f1a-Castellanos G napari: a multi-dimensional image viewer for Python"},{"issue":"6500","key":"pcbi.1012681.ref078","doi-asserted-by":"crossref","DOI":"10.1126\/science.aar5663","article-title":"Contact area-dependent cell communication and the morphological invariance of ascidian embryogenesis","volume":"369","author":"L Guignard","year":"2020","journal-title":"Science"},{"issue":"1","key":"pcbi.1012681.ref079","first-page":"2812","article-title":"MorphoNet: an interactive online morphological browser to explore complex multi-scale data","volume":"10","author":"B Leggio","year":"2019","journal-title":"Nat CommunPubMed Central PMCID"},{"key":"pcbi.1012681.ref080","article-title":"Vedo, a python module for scientific analysis and visualization of 3D objects and point clouds","author":"M Musy","journal-title":"Zenodo"},{"issue":"5","key":"pcbi.1012681.ref081","first-page":"190057","article-title":"Volumetric finite-element modelling of biological growth","volume":"9","author":"R Kennaway","year":"2019","journal-title":"PubMed Central PMCID"},{"issue":"1","key":"pcbi.1012681.ref082","first-page":"2960","article-title":"Scutoids are a geometrical solution to three-dimensional packing of epithelia","volume":"9","author":"P Gomez-Galvez","year":"2018","journal-title":"at Commun"},{"key":"pcbi.1012681.ref083","doi-asserted-by":"crossref","first-page":"2848","DOI":"10.1016\/j.ijsolstr.2012.04.027","article-title":"Modeling and simulation of relaxation in viscoelastic open cell materials and structures","volume":"49","author":"HE Pettermann","year":"2012","journal-title":"International Journal of Solids and Structures"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1012681","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T00:00:00Z","timestamp":1737936000000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012681","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,1,27]],"date-time":"2025-01-27T13:57:02Z","timestamp":1737986222000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1012681"}},"subtitle":[],"editor":[{"given":"Nir","family":"Gov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2025,1,10]]},"references-count":83,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2025,1,10]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1012681","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,1,10]]}}}