Establishment of a Morphological Atlas of the Caenorhabditis Elegans Embryo Using Deep-learning-based 4D Segmentation

Overview

Journal Nat Commun

Specialty Biology

Date 2020 Dec 8

PMID 33288755

Citations 29

Authors

Jianfeng Cao

Guoye Guan

Vincy Wing Sze Ho

Ming-Kin Wong

Lu-Yan Chan

Chao Tang

Zhongying Zhao

Hong Yan

Affiliations

Soon will be listed here.

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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