This Feature Application shows the enormous potential of Nanolive technology for observing stem cells in 3D for long periods of time, at unprecedented spatial and temporal resolution (case study 1). We use our technology to capture all the phases of mitosis (case study 2) and the dynamics of stress fiber formation (case study 3), in unparalleled detail. We then showcase our most ground-breaking contribution to this research field, monitoring the sub-cellular morphological changes that occur during stem cell differentiation. We focus on neural differentiation at the single cell (case study 4) and population level (case study 5), before examining the temporal evolution of osteogenic (case study 6) and chrondrogenic differentiation (case study 7) in high resolution.