The method is for intracellular counting and segmentation of viral particles in an image. An image is provided that has a plurality of items therein. A radius range of viral particles is determined. Round items in the image having a radius within the predetermined radius range are identified. Elliptical items that are formable from the predetermined radius range are determined. The round and elliptical items identified into groups are sorted. The viral particles among the round and elliptical items are identified. For example, the method may be used for intracellular counting and segmentation of siRNA treated human cytomegaloviral particles in TEM images.