During normal embryonic development, the cells follow a remarkably coordinated migration and differentiation program, many details of which remain a mystery. In situ automated analyses of the behaviors of human embryonic stem cells (hESCs) in culture would lead to better understanding of analogous interplay between cellular migration and differentiation in developmental models. We are developing automated tools to track hESC migration and cell lineages during differentiation into various cell types and structures. In these culture models, we report on differentiation of hESCs into cells of mesodermal lineage, endothelial blood vessel-like structures and neurons. Here we use semi-automated techniques to investigate formation of these biological units, and show "migration maps" created from time-lapse movies of H2B-GFP-expressing differentiating hESCs. We discuss the goals of fully automated image analysis for tracking cell migration and lineages.