Separate fluorescent labelling with different fluorophores is a typically used protocol to determine the colocalization of the two distinct biological elements in the overlapping microscopic images. Most of the algorithms utilized to analyze colocalization correlate global distributions of fluorescence intensities and do not provide any spatial representation of colocalization within the correlated specimens. 1 To overcome this limitation, an advanced colocalization analysis has been proposed by Jaskolski et al. 2 This inventive algorithm generates a map of correlations between pairs of corresponding pixels in the two investigated images which allows for both quantification and visualization of colocalization. The algorithm was successfully tested on simulated images as well as on biological specimens, becoming an important contribution to colocalization analyses. Unfortunately, the applicability of the method is limited because there is no computational tool that offers the algorithm among available commercial and public domain software. The presented work disseminates Colocalization Colormap–an ImageJ3 plugin that implements the method created by Jaskolski et al. 2 with the aim to extend its applicability for research.