A dual band filter set was designed to allow the simultaneous viewing of two fluorochromes (fluorescein isothiocyanate (FITC) and 4',6-diamidino-2-phenylindole (DAPI)) so that Cryptosporidium oocysts and sporozoites can be viewed together. Simultaneous viewing increases accuracy and decreases examination time as compared to current Environmental Protection Agency (EPA) Method 1623 for the detection of Cryptosporidium and Giardia in water by filtration/IMS/FA (Immunomagnetic Separation/Fluorescent Antibodies). Additionally, a microscope equipped with a programmable, motorized stage, CCD camera, and display monitor was used to facilitate well slide evaluation in a quick and precise fashion ensuring complete coverage without overlap and eliminating the optical strain associated with counting hundreds of images through an eyepiece.