→Pixel intensity spatial correlation analysis: add original article link, pdf on fiji wiki server.
These coefficients measure the significance of true colocalization. The significance test is derived to evaluate the probability that the measured value of r from the two colors is significantly greater than values of r that would be calculated if there was only random overlap. This test is performed by randomly scrambling the blocks of pixels (instead of individual pixels, because each pixel's intensity is correlated with its neighboring pixels) in one image, and then measuring the correlation of this image with the other (unscrambled) image. You can get more details in [[Media:Costes etalColoc.pdf|Costes et al.]]
Other methods include ICCS (image cross correlation spectroscopy) and a derivative of that called PPI (protein proximity index. Maybe someone wants to add PPI to Coloc_2 plugin?
==== Object-based overlap analysis ====