Abstract : Ballast water treatment systems must be stringently tested relative to the Coast Guard's proposed ballast water discharge standard for live organisms prior to Coast Guard approval for routine shipboard use. Analysis for live organisms in sparsely populated samples is time limited and labor intensive. Skilled staff must use a microscope to observe, count, and verify the viability of live organisms greater than or equal to 10 microns and less than 50 microns in minimum dimension. This program built upon previous work performed by the Naval Research Laboratory to develop data management, data archive, and data analysis protocols for counting and determining the viability of organisms greater than or equal to 50 urn in minimum dimension. Results documented in this report clearly demonstrate the protocols are appropriate for organisms in the smaller size class, and they provide a high degree of confidence that automated methods can be further developed to process samples during production testing to determine the efficacy of ballast water management systems. The findings in this report are the result of initial research into the potential to automate protist analyses and provide the most current information available at the conclusion of this initial research effort. Additional automation research efforts are ongoing and may affect details reported herein.