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Microarray is a powerful tool for simultaneous study of the behaviour of thousands of genes through analysis of produced images. The correct segmentation of each `spot` of the microarray image is a critical step in the analysis of the results of an experiment. A graph-based method is proposed which automatically performs the segmentation. The performance of the algorithm is tested both on real and simulated images. The proposed algorithm successfully detected spots of different sizes and shapes under the presence of variable noise levels. The simulation results proved that the suggested approach has high segmentation accuracy.