I am very pleased to report that Nature Protocols published our protocol dedicated to quantification of spatial correlations of fluorescent markers. Delightfully, editors of the journal presented it as a featured protocol. In the published protocol, we examined interactions of proteins by detecting their overlap using fluorescent markers. The observed overlap was then quantified to serve as a measure of spatial correlation. We reduced the contribution of the background in the images to be analyzed using CoLocalizer Pro and a custom software created by Dr. Yong Wu of UCLA. Colocalization was estimated using protein proximity index (PPI) and a correlation coefficient. PPI provided separate values of colocalization for each channel, while correlation coefficient determined the overall colocalization. We used computer-simulated and real biological images to showcase how the protocol works. The protocol minimizes human bias and can be universally applied to various cell types in which there is the need to understand protein-protein interactions. We encourage cell and molecular biologists studying protein-protein interactions to include our protocol to the arsenal of their research tools.
