Quantum dots (QDs) embedded in nanowires represent one of the most promising technologies for applications in quantum photonics. Self-assembled bottom-up fabrication is attractive to overcome the technological challenges involved in a top-down approach, but it needs post-growth investigations in order to understand the self-organization process. We investigate the QD formation by selfsegregation in AlxGa1-xAs shells as a function of thickness and cross-section morphology. By analysing light emission from several hundreds of emitters, we find that there is a certain thickness threshold for the observation of the QDs. The threshold becomes smaller if a thin AlAs layer is pre-deposited between the GaAs nanowire core and the AlxGa1-xAs shell. Our results evidence the development of the quantum emitters during the shell growth and provide more guidance for their use in quantum photonics. (C) 2015 AIP Publishing LLC.