A Latent Variable Model for Plant Stress Phenotyping Using Deep Learning

With a growing population and a changing climate, increasing crop yields in a diversity of environmental conditions is becoming increasingly important. Studying genome-by-environment (GxE) effects is a critical path for such improvements, and high-throughput plant phenotyping is necessary for carrying out such experiments at scale. Image-based phenotyping techniques offer a scalable, non-destructive way of quantifying plants' responses to their environment - however, these techniques can be cumbersome and subjective. Each image dataset is unique, and requires either a hand-crafted image processing pipeline or a large annotated training set, which can be expensive and time-consuming. Additionally, researchers must select what feature is to be used to quantify changes due to the treatment, such as biomass, colour, the number of organs, or some other visual indication of the individual's response to its environment. This dissertation explores image-based plant phenotyping, beginning with a discussion of image processing tools.