Formation of the blood vessels involves complex endothelial morphogenesis, including directional cell migration and lumen formation. Understanding the cell biological processes underlying vessel formation in vivo requires the ability to analyse the behaviour of single cells at high spatiotemporal resolution within developing tissues, which has been challenging. Taking advantage of the genetic tools and optical clarity of zebrafish embryos, Brant Weinstein and colleagues (p. 2951) develop a robust method to label both the nuclei and membranes of individual endothelial cells (ECs) and monitor their behaviour using two-photon imaging. Using these tools, they first investigate the cellular basis of the plexin D1 knockdown phenotype. Their data suggest that the defective migration of ECs in plexin D1 morphants can be attributed to differences in the protrusive activity of wild-type versus morphant ECs. In a second set of experiments, the authors show that lumens form both within and between ECs, suggesting that multiple mechanisms contribute to tubulogenesis in this system. In addition to providing insights into the cellular basis of vessel formation, this work presents a set of tools that should be valuable to the community for future analyses.