Intercellular communication via gap junction channels can be quantified by several methods based on diffusion of fluorescent dyes or metabolites. Given the variation in intercellular coupling of cells, even under untreated control conditions, it is of essence to quantify the coupling between numerous cells to obtain reliable estimates of metabolic coupling. Quantification is often based on manual counting of fluorescent cells, which is both time consuming and may include some degree of subjectivity. In this report we introduce a technique based on digital image analysis and the software for the analysis is presented together with a detailed protocol in the on-line supplementary material (http://bmi.ku.dk/matlab_program/). Fluorescent dye was introduced in connexin 43- expressing C6-glioma cells by in situ electroporation and fluorescence intensity was measured in the electroporated cells and in cells receiving dye by intercellular diffusion. The analysis performed is semi-automatic and comparison with traditional cell counting shows that this method reliably determines the effect of uncoupling by several interventions. This new method of analysis yields a rapid and objective quantification process with a high degree of reproducibility.