The structural and functional development of the permanent mammalian kidney or metanephros is a complex process involving the actions of thousands of gene products, complex cell movements and tissue patterning in three dimensions (3D). This review focuses on the recent advances made in imaging technology, processing and analysis combined with mouse genetics and the generation of protein-reporter mice which has enabled us to monitor the development and movement of defined cell populations within the developing kidney in 3D and over time (4D).