Coloc 2 is Fiji's plugin for colocalization analysis. It implements and performs the pixel intensity correlation over space methods of Pearson, Manders, Costes, Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing.

Also included here are the old no longer supported plugins: Colocalization Threshold and Colocalization Test We only use these for comparison with Coloc_2, and don't suggest you actually use them for real work.

For more details, see http://imagej.net/Coloc_2