Abstract : Ballast water management 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 viability of live organisms less than or equal to 50 micrometer in size. An automated method was sought to significantly reduce staff time and effort, maintain consistency, and provide an archive of analytical results. Commercially available laboratory equipment and computer software were used in conjunction with specially developed pattern recognition software. This report provides a description of the equipment required and the protocol developed. A step-by-step protocol is also provided. The findings in this report are the result of continued research into the potential to automate zooplankton 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.