Fluorescence light microscopy (LM) and electron microscopy (EM) are two of the most widely used imaging modalities for probing cellular structures. In particular, recent development of super-resolution fluorescence microscopy allows the location of molecules to be determined with nanometer-scale spatial resolution. In the first part of this talk I present my works in developing methods of several correlative super-resolution fluorescence light microscopy (LM) and electron microscopy (EM) assays by combining stochastic optical reconstruction microscopy (STORM). Here, I have developed several 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. I demonstrated these methods using a variety of cellular targets. In the second part of the talk, I present my work in applying super-resolution microscopy to investigate the distributions and interactions of purine biosynthetic enzymes organization complex called purinosomes within the cell. We use single-cell super-resolution and confocal microscopy to characterize purinosome localization and motions in HPRT-deficient LND (Lesch–Nyhan syndrom) fibroblasts and provide insights into how purinosomes meet a cell’s purine demand. Our results highlight how purinosomes are further spatiotemporally organized in cells by their dynamic interplay with mitochondria and microtubules. Lastly, I will present my recent work in single-molecule spectroscopy, namely spectrally resolved stochastic optical reconstruction microscopy (SR-STORM). By recording both the images and emission spectra of thousands of single fluorescent molecules stochastically generated from the ring-opening reaction of a spiropyran, we provide mechanistic insights into its multi-path reaction pathways.