Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation

Jianfeng Cao, Guoye Guan, Vincy Wing Sze Ho, Ming Kin Wong, Lu Yan Chan, Chao Tang*, Zhongying Zhao*, Hong Yan*

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

31 Citations (Scopus)


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.

Original languageEnglish
Article number6254
Number of pages14
JournalNature Communications
Issue number1
Publication statusPublished - Dec 2020

Scopus Subject Areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)


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