Photosynthetic efficiency is increasingly recognized as an integration of plant responses to dynamic environments, establishing the need for data sets from both field trials and controlled environments. A robotic field scanner phenotyping platform at the University of Arizona is equipped with a high-throughput chlorophyll fluorescence imaging system capable of collecting data on field trials for genetic studies of a photosynthetic trait (Fv/Fm). A description of the fluorescence imaging system is provided in addition to methods for measurements across experimental field plots and a test to determine the impact of variable plant heights. The overall focus is on aspects of field applications of a chlorophyll fluorescence imaging system that differ from analogous systems in controlled environments.