Abstract
Autophagy is an intracellular degradation process that mediates the clearance of cytoplasmic components. As well as being an important function for cellular homeostasis, autophagy also promotes the removal of aberrant protein accumulations, such as those seen in conditions like neurodegeneration. The dynamic nature of autophagy requires precise methods to examine the process at multiple stages. The protocols described herein enable the dissection of the complete autophagy process (the "autophagy flux"). These allow for the elucidation of which stages of autophagy may be altered in response to various diseases and treatments.