A protein-fragment complementation assay (PCA) for detecting and localizing intracellular protein-protein interactions (PPIs) was built by bisection of miniSOG, a fluorescent flavoprotein derived from the light, oxygen, voltage (LOV)-2 domain of Arabidopsis phototropin. When brought together by interacting proteins, the fragments reconstitute a functional reporter that permits tagged protein complexes to be visualized by fluorescence light microscopy (LM), and then by standard as well as “multicolor” electron microscopy (EM) via the photooxidation of 3–3’-diaminobenzidine (DAB) and its derivatives. Boassa et al. describe the use of split-miniSOG for the visualization of protein aggregates associated with neurodegenerative diseases. This study shows the general utility of this reversible system for detection of spatial organization of molecular complexes in mammalian cells at nanometer resolution.