Microscopy is a daily ritual in most shellfish aquaculture facilities: counting and measuring organisms and investigating quality are critical to success. However, this can take hours each day, and results may vary dramatically between operators. Other techniques have since been developed for counting phytoplankton and are now being utilized by hatcheries to speed up and tighten up their daily microscopy tasks. One such technique, flow imaging microscopy, utilizes high-speed imaging to automatically image, count, and measure organisms as they flow past a camera. In this presentation, we will demonstrate how flow imaging microscopy is used for a variety of organisms (e.g. microalgae, oysters, mussels, clams) at multiple points in their development (e.g. fertilization and larval development) in research-forward shellfish hatcheries. This presentation will cover methodologies used for counting, measuring & classifying organisms of interest using flow imaging microscopy and associated data used for hatchery operations.