In processing images of arrays of differently-dyed particles or microbeads ("beads"), a template cluster map of the array is first generated of a first set of such beads. Each cluster is bounded and designated with an identifier. A project cluster map is then generated of an array of a different set of the differently-dyed beads. Both the template and project cluster maps are transformed into respective image plots, having regions thereof representing the density of the clusters, and the regions of the template image plot are marked for identification. The boundaries and identifiers of the regions in the template image plot are transformed to the project image plot, and the watershed algorithm is applied to the transformed boundaries in the project image plot in order to generate a set of expanded and identified regions. Finally, beads in the project cluster map are identified by correlating them with identified, expanded regions in the project image plot.