ImageJ - Fiji
Tony Collins (and others?)
no longer actively supported, unlikely to be stable enough for real use. Use Coloc_2
Sets the thresholds for colocalization analysis, and also calculates Manders coefficients, 2D histogram / scatter plot, and other stats.
See the great documentation for this plugin at Colocalization Analysis#Colocalization_Threshold. The method is that implemented in Costes et al. This uses a Pearson’s correlation above and below the thresholds to iteratively find where the correlation between the two images is 0 and sets the thresholds there. It is pretty robust and importantly is reproducible and non subjective.
Use of this plugin should be followed by use of the Colocalization Test plugin, to see of the results are statistically significant and better then random overlap of the signal in the images.
See also the Colocalization Analysis tutorial.