New advances in fluorescence microscopy make possible the localization of thousands of molecules with nanometer resolution inside living cells. This calls for the development of new statistical tools in spatial analysis to characterize molecules' distribution, and the spatial coupling between different molecules in multi-color microscopy. We will present the tools that we have recently developed. These are based on the mathematical analysis of the Ripley’s K function, and allow to test statistically the randomness of molecules’ distribution inside individual cells, and also to measure the coupling between different molecules labeled in different colors. We will show some of the main biological applications of our tools.