Colocalisation analysis
Quantitative analysis of colocalisation covers the quantitative aspects of spatial correlation of pixels in different channels of an 2D or 3D image. You can calculate the percentage of colocalisation and other values. Notice that the results are highly dependent on the quality of the input data (noise, signal level, bleaching, optical aberrations and channel alignment etc.) and the fraction of events choosen by your input.
Have a look at ImageJ colocalisation packages and many additional informations in:
References
General reference
Handbook of Biological Confocal Microscopy
Springer-Verlag Heidelberg (2006)
Quantification of colocalization
Automatic and quantitative measurement of protein-protein colocalization in live cells
Biophys. J. 86 (6), 3993-4003 (2006)
Median filtering, fluorograms etc.
New methods to evaluate colocalization of fluorophores in immunocytochemical preparations as exemplified by a study on A2A and D2 receptors in Chinese hamster ovary cells
J. Histochem. Cytochem. 53 (8), 941-53 (2005)
Deconvolution
Deconvolution improves colocalization analysis of multiple fluorochromes in 3D confocal data sets more than filtering techniques
J. Microsc. 208 (2), 134-147 (2002)
Colocalization analysis yields superior results after image restoration
Microsc. Res. Tech. 64 (2), 103-112 (2004)