An effective model for quantification of cell 3Dshape in early embryogenesis

Background: The developmental process is featured by fabulous morphogenesis in multicellular organisms. Describing morphological changes quantitatively concretes the way to investigating both intra and inter cell regulations on cell fate. While Caenorhabditis elegans has been used as a model for cell and development studies for a long time, the exploration of how cell shape is precisely controlled keeps obscured by the lack of methods to model morphological features. Currently, in order to characterize the features of cell shape involved in cell migration and differentiation, there is an increasing demand in analyzing cell shape systematically, especially when many works have contributed to cell reconstruction. Results: In this work, Spherical harmonics and Principal component analysis integrated Cell Shape quantification Models (SPCSMs) is proposed to represent cell shapes in a low-dimensional shape space. SPCSMs incorporates a complete pipeline to quantify cell shapes and analyze their morphological phenotypes in three dimensional (3D) reconstructions. Based on the framework, we extract biological patterns in the lineage of C. elegans embryo before 350-cell stage, during which all hypodermis cells deformed like a funnel and can be recognized by this shape pattern. Finally, SPCSMs is compared with two cell shape representation methods, which substantiates the effectiveness and robustness of our method. Conclusion: SPCSMs provides a general method to decribe shapes in low-dimensional shape space with compact parameters. It can quantify the shapes of cells from single-cell resolution images obtained over one-minute intervals, making it possible for the recognition of developmental patterns in cell lineages. SPCSMs is expected to be an effective model for biologists to explore the relationships between the shapes of cells and their fates.