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

Over the past 30 years, biology and computer scientists give great efforts on quantifying 3D cell shape and analyze their interactive behaviors. 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. Recent advancements in imaging technology have enabled the processes of dynamic, time-lapse fluorescence images, facilitating the 3D cell morphology map in developing organisms like Caenorhabditis elegans (C. elegans). Transferring these genetic parts to non-model organisms is challenging due to host-specific gene expression mechanisms, metabolism, and varying DNA vectors. The exploration of how cell shape correlates with cell fate during C. elegans embryogenesis has been hindered by a scarcity of high-quality data on living 3D cell shapes. Thus, an integrated quantification and analysis method is highly desired.

Recently, a collaborative team from the City University of Hong Kong, Peking University, and the Centre for Intelligent Multidimensional Data Analysis Limited at Hong Kong Science Park published an article "An effective method for quantification, visualization and analysis of 3D cell shape during early embryogenesis" in the journal Quantitative Biology. They introduce an effective integrated method, 3D Cell Shape Quantification (3DCSQ), for transforming digitized 3D cell shapes into analytical feature vectors, named eigengrid, eigenharmonic and eigenspecturm. We uniquely combine spherical grids, spherical harmonics, and principal component analysis for cell shape quantification. 3DCSQ's effectiveness in recognizing cellular morphological phenotypes and clustering cells is demonstrated. Applied to C. 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. The team also provides an automatic cell shape lineaging analysis program. Their 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.

Figure 1 illustrates the lineage cell morphology map and shape quantification way, as well as 3DCSQ’s visualization ability. The digitized cellular 3D images 3DCSQ and the visualization of 17 compressed quantitative embryos as well as their lineaging cell shape visualization examples. Cells over time is quantified and visualized on cell lineaging during embryogenesis. 3DCSQ is designed to quantitatively assess, visualize, and analyze cellular morphologies, particularly focusing on the embryogenesis of C. elegans from the 4- to 350-cell stages.