Field experiments were conducted in 2017 and 2018 in west Tennessee to determine if Canopeo, an image analysis tool available as a smartphone app, could be used to supplement current methods to estimate cotton, Gossypium hirsutum L., seedling health in small-plot research tests. A total of six tests, providing a range of cotton seedling health, were used in this analysis. Cotton seedlings in replicated small-plot tests were visually rated for vigor and thrips (Thysanoptera: Thripidae) injury. A photograph of the center two rows of each plot was taken and analyzed to determine green canopy cover using Canopeo. Additionally, above ground biomass samples were collected in three of the tests. Strong correlations were observed between green canopy cover and biomass, green canopy cover and vigor, and thrips injury ratings and biomass. These data suggest that green canopy cover assessment using Canopeo is a useful and non-destructive way to objectively assess treatment effects on plant health in small-plot cotton research trials.