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 () and Hong Yan ()
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Jianfeng Cao: City University of Hong Kong
Guoye Guan: Peking University
Vincy Wing Sze Ho: Hong Kong Baptist University
Ming-Kin Wong: Hong Kong Baptist University
Lu-Yan Chan: Hong Kong Baptist University
Chao Tang: Peking University
Zhongying Zhao: Hong Kong Baptist University
Hong Yan: City University of Hong Kong

Nature Communications, 2020, vol. 11, issue 1, 1-14

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19863-x

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