Confocal microscopy permits the analysis of the subcellular distribution of proteins. Colocalization between target proteins and specific markers of differential cell compartments provides an efficient approach to studying protein traffic. In this chapter, we describe an automated method to denoise confocal microscopy images and assess the colocalization of their stainings using ImageJ software. As a step further from conventional single colocalization measurements, in the proposed method, we analyze stacks of three different stainings using two-by-two comparisons. To demonstrate the reliability and usefulness of our proposal, the method was used to compare the traffic of the voltage-gated Kv1.3 potassium channel, which is a well-defined plasma membrane protein, in the presence and absence of KCNE4, a regulatory subunit that strongly retains the channel intracellularly.
Keywords: Colocalization; Confocal microscopy; ImageJ; Potassium channel; Protein traffic; Subcellular distribution.