Central to the process of macroautophagy (hereafter autophagy) is the formation of autophagosomes, double-membrane vesicles that sequester cytoplasmic cargo, including proteins, lipids and organelles, for lysosomal degradation and macromolecule recycling. Tight regulation of both autophagic activity and capacity is crucial to secure cellular homeostasis and aberrant autophagy is tightly linked to the development of many human diseases. Hence it is of great importance to accurately measure autophagy progression in health and disease. Members of the human WIPI β-propeller proteins associate with autophagosomal membranes due to specific phosphatidylinositol 3-phosphate (PtdIns3P) binding at the onset of autophagy. The specific autophagosomal localization of both WIPI1 and WIPI2 (refered to as WIPI puncta) has been employed to assess autophagy using fluorescence microscopy methods, such as confocal and live-cell video microscopy and was extended for automated high-throughput image acquisition and analyses procedures. We here provide an overview on the employment of human WIPI members for the assessment of autophagy in higher eukaryotic cells, suitable for systems biology approaches such as mathematical modelling.