# An effective method for quantification, visualization, and analysis of 3D cell shape during early embryogenesis

## TL;DR

This paper introduces a new method for analyzing and visualizing 3D cell shapes during early embryonic development, enabling detailed quantification and lineage tracking.

## Contribution

The novel 3DCSQ method integrates spherical grids, harmonics, and PCA to quantify and analyze complex 3D cell shapes with local detail and reconstruction capability.

## Key findings

- 3DCSQ successfully identifies and quantifies reproducible cellular patterns in C. elegans embryos.
- The method enables lineage analysis of cell shape changes during embryogenesis.
- 3DCSQ provides a systematized approach for cell shape description and differentiation monitoring.

## Abstract

Embryogenesis is the most basic process in developmental biology. Effectively and simply quantifying cell shape is challenging for the complex and dynamic 3D embryonic cells. Traditional descriptors such as volume, surface area, and mean curvature often fall short, providing only a global view and lacking in local detail and reconstruction capability. Addressing this, we introduce an effective integrated method, 3D Cell Shape Quantification (3DCSQ), for transforming digitized 3D cell shapes into analytical feature vectors, named eigengrid (proposed grid descriptor like eigen value), eigenharmonic, and eigenspectrum. We uniquely combine spherical grids, spherical harmonics, and principal component analysis for cell shape quantification. We demonstrate 3DCSQ’s effectiveness in recognizing cellular morphological phenotypes and clustering cells. Applied to Caenorhabditis elegans embryos of 29 living embryos from 4‐ to 350‐cell stages, 3DCSQ identifies and quantifies biologically reproducible cellular patterns including distinct skin cell deformations. We also provide automatically cell shape lineaging analysis program. This method not only systematizes cell shape description and evaluation but also monitors cell differentiation through shape changes, presenting an advancement in biological imaging and analysis.