Autophagy is a system of bulk degradation of macromolecules and organelles that is conserved in eukaryotes from yeast to mammals, and is essential for maintaining cell homeostasis. The crucial event in this process is the formation of an autophagosome that contains the cytoplasmic materials and delivers them to the lysosome for degradation. In yeast, there are 18 autophagy-related (ATG) genes that are essential for autophagosome formation in response to starvation. Autophagy requires the generation of a cup-shaped membrane sac, called the isolation membrane (IM), from the pre-autophagosomal structure (PAS). Progress in understanding the detailed functions of the Atg proteins during IM expansion has been obstructed because it had not been possible to discriminate between the IM and PAS, owing to the resolution limit of light microscopy. Now (p. 2534), Kuninori Suzuki, Yoshinori Ohsumi and colleagues address this problem. Using fluorescent microscopy, the authors visualise expanding IMs as cup-shaped structures in Saccharomyces cerevisiae by enlarging a selective cargo of autophagosomes, and then finely map the localisation of individual Atg proteins. For example, they show that the IM is closely associated with the endoplasmic reticulum (ER) at ER exit sites, and that three Atg proteins localise adjacently to the ER exit sites at the IM. Taken together, these data suggest that Atg proteins have individual roles at spatially distinct sites during IM expansion.