UC San Diego

Tracking nuclei and subcellular structures such as cell membranes is important to understand development in molecular biology. In transparent embryos, such as C. elegans, fluorescently labeled uclei and cell membranes can be imaged in three-dimensional time-lapse (4D) videos. The rapid advances in microscopy technology and the transparency of C. elegans enable automated tracking. In the first part of the dissertation, we present nuclei tracking algorithms that are able to track nuclei both in early and in later development stages in C. elegans embryos. These new methods have made it possible to obtain the first complete cell lineages of C. elegans embryos through morphogenetic stages. We analyze cellular neighborhoods and coordinated cell migrations quantitatively. In the second part, we present algorithms for tracking epithelial cell junctions in C. elegans embryos. Our approaches make it possible to generate the first quantitative description of the dynamics of epithelial shape changes during epidermal enclosure. Our nuclei and cell junction tracking algorithms generate robust tracking results with less human effort than manual curation and allow quantitative analysis of cell dynamics