Using R-based image analysis to quantify rusts on perennial ryegrass

Crown and stem rust are major diseases of perennial ryegrass (Lolium perenne L.). Plant breeders and pathologists often rate rust severity in the field using the modified Cobb scale, but this method is subjective and labor intensive. A novel, open-source system using ImageJ and R was developed to quantify pustule number and area using digital images collected from spaced plants in the field. The computer-processing pipeline included development of training data for prediction of pixel identity using random forest and noise reduction spatial processing. Raters and the computer scored rust severity on plant images of varying complexity including whole-plant (WP), five-leaf (FL), and single-leaf (SL) image series. Computer accuracy was determined using the SL, while the FL series gave insight into the true value of WP severity. Rater ability was assessed using a panel of nine scientists with varying levels of disease rating experience. Results showed rater perceptions of crown rust severit...