Monitoring crop development and health using UAV-based hyperspectral imagery and machine learning

  • Yoseline Angel

Student thesis: Doctoral Thesis


Agriculture faces many challenges related to the increasing food demands of a growing global population and the sustainable use of resources in a changing environment. To address them, we need reliable information sources, like exploiting hyperspectral satellite, airborne, and ground-based remote sensing data to observe phenological traits through a crops growth cycle and gather information to precisely diagnose when, why, and where a crop is suffering negative impacts. By combining hyperspectral capabilities with unmanned aerial vehicles (UAVs), there is an increased capacity for providing time-critical monitoring and new insights into patterns of crop development. However, considerable effort is required to effectively utilize UAV-integrated hyperspectral systems in crop-modeling and crop-breeding tasks. Here, a UAV-based hyperspectral solution for mapping crop physiological parameters was explored within a machine learning framework. To do this, a range of complementary measurements were collected from a field-based phenotyping experiment, based on a diversity panel of wild tomato (Solanum pimpinellifolium) that were grown under fresh and saline conditions. From the UAV data, positionally accurate reflectance retrievals were produced using a computationally robust automated georectification and mosaicking methodology. The resulting multitemporal UAV data were then employed to retrieve leaf-chlorophyll (Chl) dynamics via a machine learning framework. Several approaches were evaluated to identify the best-performing regression supervised methods. An investigation of two learning strategies (i.e., sequential and retraining) and the value of using spectral bands and vegetation indices (VIs) as prediction features was also performed. Finally, the utility of UAVbased hyperspectral phenotyping was demonstrated by detecting the effects of salt-stress on the different tomato accessions by estimating the salt-induced senescence index from the retrieved Chl dynamics, facilitating the identification of salt-tolerant candidates for future investigations. This research illustrates the potential of UAV-based hyperspectral imaging for plant phenotyping and precision agriculture. In particular, a) developing systematic imaging calibration and pre-processing workflows; b) exploring machine learning-driven tools for retrieving plant phenological dynamics; c) establishing a plant stress detection approach from hyperspectral-derived metrics; and d) providing new insights into using computer vision, big-data analytics, and modeling strategies to deal effectively with the complexity of the UAV-based hyperspectral data in mapping plant physiological indicators.
Date of AwardJul 2021
Original languageEnglish (US)
Awarding Institution
  • Biological, Environmental Sciences and Engineering
SupervisorMatthew McCabe (Supervisor)


  • Hyperspectral Imagery
  • machine learning
  • UAV
  • precision agriculture
  • phenotyping
  • remote sensing

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