ArticleNature communications2020
Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Cell size reduction distinctly scales spindle elongation and chromosome segregation in C. elegans.Nature communications · 2026Article
- Persistent homology-based segmentation tool for membrane images.Cell reports methods · 2026Article
- EmbSAM: cell boundary localization and Segment Anything Model for fast images of developing embryos.Communications biology · 2025Article
- Assessing the relative contributions of mosaic and regulatory developmental modes from single-cell trajectories.PLoS computational biology · 2025Article
- Cell size reduction scales spindle elongation but not chromosome segregation inResearch square · 2025Article
- Timelapse-based 3D reconstruction of blastocysts reveals 3D morphologies of human blastocysts.NPJ digital medicine · 2025Article
- Temporal Analysis of Embryonic Epidermal Morphogenesis inInternational journal of molecular sciences · 2025Article
- Cell size reduction scales spindle elongation but not chromosome segregation inbioRxiv : the preprint server for biology · 2025Article
- Cell lineage-resolved embryonic morphological map reveals signaling associated with cell fate and size asymmetry.Nature communications · 2025Article
- An effective method for quantification, visualization, and analysis of 3D cell shape during early embryogenesis.Quantitative biology (Beijing, China) · 2025Article
- Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy.Nature communications · 2025Article
- Apico-basal intercalations enable the integrity of curved epithelia.Computational and structural biotechnology journal · 2025Article
- Computational Methods for Image Analysis in Craniofacial Development and Disease.Journal of dental research · 2024Review
- Deep learning-based enhancement of fluorescence labeling for accurate cell lineage tracing during embryogenesis.Bioinformatics (Oxford, England) · 2024Article
- Article
- CShaperApp: Segmenting and analyzing cellular morphologies of the developingQuantitative biology (Beijing, China) · 2024Article
- Advancing insights into microgravity induced muscle changes using Caenorhabditis elegans as a model organism.NPJ microgravity · 2024Review
- Characterizing Cellular Physiological States with Three-Dimensional Shape Descriptors for Cell Membranes.Membranes · 2024Article
- A mathematical framework for understanding the spontaneous emergence of complexity applicable to growing multicellular systems.PLoS computational biology · 2024Article
- Automated Cell Lineage Reconstruction using Label-Free 4D Microscopy.bioRxiv : the preprint server for biology · 2024Article
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8 authors.
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Abstract
The invariant development and transparent body of the nematode Caenorhabditis elegans enables complete delineation of cell lineages throughout development. Despite extensive studies of cell division, cell migration and cell fate differentiation, cell morphology during development has not yet been systematically characterized in any metazoan, including C. elegans. This knowledge gap substantially hampers many studies in both developmental and cell biology. Here we report an automatic pipeline, CShaper, which combines automated segmentation of fluorescently labeled membranes with automated cell lineage tracing. We apply this pipeline to quantify morphological parameters of densely packed cells in 17 developing C. elegans embryos. Consequently, we generate a time-lapse 3D atlas of cell morphology for the C. elegans embryo from the 4- to 350-cell stages, including cell shape, volume, surface area, migration, nucleus position and cell-cell contact with resolved cell identities. We anticipate that CShaper and the morphological atlas will stimulate and enhance further studies in the fields of developmental biology, cell biology and biomechanics.
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