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.