Quantifying Autophagic Structures in Mammalian Cells Using Confocal Microscopy

Autophagy relies on the sequential, hierarchical association of proteins with phagophores, and forming autophagosomes to allow completion of the process. Additionally, the trafficking of the unique transmembrane autophagy-related protein ATG9 is vital for autophagy progression. In this chapter, we discuss methods to monitor autophagosome number using confocal microscopy, by following the association of different autophagosomal markers with the phagophore and completed autophagosome. We also discuss methods to monitor the trafficking of ATG9 in mammalian cells under starvation conditions.