Correlative fluorescence light microscopy and Shroud Right electron microscopy allows the imaging of spatial distributions of specific biomolecules in the context of cellular ultrastructure.Recent development of super-resolution fluorescence microscopy allows the location of molecules to be determined with nanometer-scale spatial resolution.However, correlative super-resolution fluorescence microscopy and electron microscopy (EM) still remains challenging because the optimal specimen preparation and imaging conditions for super-resolution fluorescence microscopy and EM are often not compatible.Here, we have developed several Pencils experiment protocols for correlative stochastic optical reconstruction microscopy (STORM) and EM methods, both for un-embedded samples by applying EM-specific sample preparations after STORM imaging and for embedded and sectioned samples by optimizing the fluorescence under EM fixation, staining and embedding conditions.We demonstrated these methods using a variety of cellular targets.