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

## TL;DR

Scientists created a detailed 3D map of C. elegans embryos using a new automated system called CShaper to track cell shapes and movements during development.

## Contribution

The novel contribution is the development of CShaper, an automated pipeline for 4D segmentation and lineage tracing, enabling systematic morphological analysis of C. elegans embryos.

## Key findings

- A time-lapse 3D atlas of cell morphology was generated for C. elegans embryos from 4- to 350-cell stages.
- Morphological parameters such as cell shape, volume, surface area, and cell-cell contacts were quantified across 54 developmental stages.
- The automated pipeline CShaper combines membrane segmentation with lineage tracing to enable large-scale morphological analysis.

## 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.

The systematic characterization of C. elegans morphology during development has yet to be performed. Here, the authors produce a 3D atlas of C. elegans morphology from 17 embryos and 54 developmental stages, using an automated pipeline, CShaper (combining segmentation of fluorescently labeled membranes with automated cell lineage tracing).