I want to know what’s the best plug-in available to do a co-localization analysis of two channels (red and green). I’m using the RG2B_Colocalization plug-in to mark the co-localization in yellow. Basically, I would need something to analyze the presence of yellow fluorescence throughout the stacks, while taking in account the possible background noise.
See the Colocalization guide for details on how to successfully perform quantitative colocalization analysis. Definitely avoid qualitative analysis (i.e., looking for “yellow” visually) because color maps are relative and arbitrary, and you cannot trust your eyes.