TriNet: Exploring More Affordable and Generalisable Remote Phenotyping with Explainable Deep Models

In this study, we propose a scalable deep learning approach to automated phenotyping using UAV multispectral imagery, exemplified by yellow rust detection in winter wheat. We adopt a high granularity scoring method (1 to 9 scale) to align with international standards and plant breeders’ needs. Using a lower spatial resolution (60m flight height at 2.5cm GSD), we reduce the data volume by a factor of 3.4, making large-scale phenotyping faster and more cost-effective while obtaining results comparable to those of the state-of-the-art. Our model incorporates explainability components to optimise spectral bands and flight schedules, achieving top-3 accuracies of 0.87 for validation and 0.67 and 0.70 on two separate test sets. We demonstrate that a minimal set of bands (EVI, Red, and GNDVI) can achieve results comparable to more complex setups, highlighting the potential for cost-effective solutions. Additionally, we show that high performance can be maintained with fewer time steps, reducing operational complexity. Our interpretable model components improve performance through regularisation and provide actionable insights for agronomists and plant breeders. This scalable and explainable approach offers an efficient solution for yellow rust phenotyping and can be adapted for other phenotypes and species, with future work focusing on optimising the balance between spatial, spectral, and temporal resolutions.