Genome editing using the CRISPR–Cas9 system allows the manipulation of specific genes. Mikuni et al. use this approach to insert sequences encoding protein tags into genes of interest in neural progenitors in the embryonic mouse brain, enabling them to map endogenous protein localization in the adult brain with high resolution and specificity. They further show that the system has potential for multiplex labelling, ultrastructual imaging and live imaging of protein dynamics.