Abstract
Electron microscopy (EM) is considered the gold standard for studying macroautophagy and mitophagy, essential cellular processes for brain health. Here, we present a protocol using EM to analyze autophagosomes and mitophagosomes in the mouse amygdala. We describe the preparation of brain sections, followed by staining and EM imaging. We then detail the steps to identify and analyze autophagosome-like and mitophagosome-like structures. This protocol can be easily adapted to analyze autophagosomes and mitophagosomes in other mouse brain regions. For complete details on the use and execution of this protocol, please refer to Duan et al. (2021).