Electron microscopy is instrumental in the development of our understanding of biological systems. Although electron microscopy reveals ultrastructure with nanoscale resolution, it does not provide the same information as optical fluorescence microscopy regarding the location of proteins within a cellular context. Many researchers seek to extend the use of cathodoluminescence (CL) to the biological sciences to form a direct correlation of protein location and function with the ultrastructure. Success using traditional (optical) fluorophores has been limited due to the damage caused by the electron beam. Notwithstanding, researchers use CL successfully to image Alexa 488 to determine the roles of the targeted monocytes in cell growth.

Other researchers are want to develop and deploy multi-colored inorganic, electron-hard CL tags for use in optical and electron microscopes, such as nano-diamonds or -phosphors. For example, early results based on lanthanide-doped ceramic nanoparticles suggest that with the optimization of nanoparticle composition, synthesis protocols, and electron imaging conditions can enable high signal-to-noise localization of biomolecules with a sub-20-nm resolution, limited only by the nanoparticle size.