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

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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Author(s)

  • Guoye Guan
  • Vincy Wing Sze Ho
  • Ming-Kin Wong
  • Lu-Yan Chan
  • Chao Tang
  • Zhongying Zhao

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Detail(s)

Original languageEnglish
Article number6254
Journal / PublicationNature Communications
Volume11
Online published7 Dec 2020
Publication statusPublished - 2020

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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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Citation Format(s)

Establishment of a morphological atlas of the Caenorhabditis elegans embryo using deep-learning-based 4D segmentation. / Cao, Jianfeng; Guan, Guoye; Ho, Vincy Wing Sze; Wong, Ming-Kin; Chan, Lu-Yan; Tang, Chao; Zhao, Zhongying; Yan, Hong.

In: Nature Communications, Vol. 11, 6254, 2020.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review