ArticleNature methods2023
Embryo mechanics cartography: inference of 3D force atlases from fluorescence microscopy.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 62 citations in OpenAlex.
- From pixels to patterns: the AI revolution in stem cell-derived models.Nature methods · 2026Review
- TiFM2.0 - versatile mechanical measurement and actuation in live embryos.Development (Cambridge, England) · 2026Article
- Mechanics of compression-driven morphogenesis.Development (Cambridge, England) · 2026Review
- Multicellular simulations with shape and volume constraints using optimal transport.Science advances · 2026Article
- Advancing mechanobiology from single molecules to complex cellular systems.Nature nanotechnology · 2026Review
- Beyond integration: towards benchmarks for developmental potential in human stem cell-derived embryo models.Human reproduction update · 2026Review
- Whole tissue imaging of cellular boundaries at sub-micron resolutions for deep learning cell segmentation: Applications in the analysis of epithelial bending of ectoderm.Developmental dynamics : an official publication of the American Association of Anatomists · 2026Article
- stVCR: spatiotemporal dynamics of single cells.Nature methods · 2026Article
- Guidance for 3D traction force microscopy today and in the next decade.Nature methods · 2026Review
- Marine Model Organisms for Mechanobiology Studies.Results and problems in cell differentiation · 2026Review
- A large-scale balloon model of confluent cells validates stress inference from geometry.npj biological physics and mechanics · 2026Article
- EmbSAM: cell boundary localization and Segment Anything Model for fast images of developing embryos.Communications biology · 2025Article
- Fifty high-content light sheet fluorescence microscopy datasets of Tribolium castaneum embryogenesis.Scientific data · 2025Article
- Deciphering cell-fate trajectories using spatiotemporal single-cell transcriptomic data.NPJ systems biology and applications · 2025Review
- Active foam dynamics of tissue spheroid fusion.Nature communications · 2025Article
- Mapping single-cell rheology of ascidian embryos in the cleavage stages using AFM.Biophysical journal · 2025Article
- A thermodynamic perspective on mammalian neural crest ingression.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Capturing nematic order on tissue surfaces of arbitrary geometry.Nature communications · 2025Article
- Dynamic forces drive cell and organ morphology changes during embryonic development.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- CellMet: Extracting 3D shape and topology metrics from confluent cells within tissues.PLoS computational biology · 2025Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Tissue morphogenesis results from a tight interplay between gene expression, biochemical signaling and mechanics. Although sequencing methods allow the generation of cell-resolved spatiotemporal maps of gene expression, creating similar maps of cell mechanics in three-dimensional (3D) developing tissues has remained a real challenge. Exploiting the foam-like arrangement of cells, we propose a robust end-to-end computational method called 'foambryo' to infer spatiotemporal atlases of cellular forces from fluorescence microscopy images of cell membranes. Our method generates precise 3D meshes of cells' geometry and successively predicts relative cell surface tensions and pressures. We validate it with 3D foam simulations, study its noise sensitivity and prove its biological relevance in mouse, ascidian and worm embryos. 3D force inference allows us to recover mechanical features identified previously, but also predicts new ones, unveiling potential new insights on the spatiotemporal regulation of cell mechanics in developing embryos. Our code is freely available and paves the way for unraveling the unknown mechanochemical feedbacks that control embryo and tissue morphogenesis.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.