Coloc 2 is ImageJ2 and 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 depreciated unsupported plugins Colocalization Threshold and Colocalization Test

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