Single cell photosynthetic organisms, the phytoplankton, generate roughly 50% of the oxygen produced each year on the planet and are the base of the marine food web on which life in the ocean depends. Flow cytometry is the most accurate method for counting and identifying phytoplankton populations in the ocean. The DeepCyte submersible flow cytometer represents a significant advancement in flow cytometry instrumentation and is characterized by high sensitivity, low power consumption, compact size, and low maintenance. DeepCyte is designed detect the smallest phytoplankton populations (0.5-10 µm) while suspended underwater from an autonomous buoy platform. This size range encompasses the most abundant phytoplankton populations found in both open ocean and coastal environments from the tropics to the poles. In this project, the DeepCyte instrument and buoy platform will be iterated to a final design by repackaging the instrument components into a smaller volume to facilitate easier deployment of the instrument and buoy package. Automated calibration and alignment routines will be developed to improve measurement quality while deployed autonomously. Finally, previously developed automated flow cytometry data analysis and visualization software will be implemented on the instrument to generate a real-time data feed for broadcast to research vessels and to shore. Fully processed data will be available through public repositories and presented on a publicly accessible data po