Deriving crop information from remotely sensed data is an important strategy for precision agriculture. Small unmanned aerial systems (UAS) have emerged in recent years as a versatile remote sensing tool that can provide precisely-timed, fine-grained data for informing management responses to intra-field crop variability (e.g., nutrient status and pest damage). UAS sensors with high spectral resolution used to compute informative vegetation indices, however, are practically limited by high cost and data dimensionality. This research extends spectral analysis for remote crop monitoring to investigate the relationship between crop health and 3D canopy structure using low-cost UAS equipped with consumer-grade RGB cameras. We used flue-cured tobacco as a case study due to its known sensitivity to fertility variation and nutrient-specific symptomology. Fertilizer treatments were applied to induce plant health variability in a 0.5 ha field of flue-cured tobacco. Multi-view stereo images from three UAS surveys collected during crop development were processed into orthoimages used to compute a visible band spectral index and photogrammetric point clouds using Structure from Motion (SfM). Plant structural metrics were then computed from detailed high resolution canopy surface models (0.05 m resolution) interpolated from the photogrammetric point clouds. The UAS surveys were complimented by nutrient status measurements obtained from plant tissues. The relationships between foliar nitrogen (N), phosphorus (P), potassium (K), and boron (B) concentrations and the UAS-derived metrics were assessed using multiple linear regression. Symptoms of N and K deficiencies were well captured and differentiated by the structural metrics. The strongest relationship observed was between canopy shape and N foliar concentration (adj. r2 = 0.59, increasing to adj. r2 = 0.81 when combined with the spectral index). B foliar concentration was consistently better predicted by canopy structure with a maximum adj. r2 = 0.41 observed at the latest growth stage surveyed. Overall, combining information about canopy structure and spectral reflectance increased model fit for all measured nutrients compared to spectral alone. These results suggest that an important relationship exists between relative canopy shape and crop health that can be leveraged to improve the usefulness of low cost UAS for precision agriculture.

Invasive nonnative plant pests can cause extensive environmental and economic damage and are very difficult to eradicate once established. Phytosanitary inspections that aim to prevent biological invasions by limiting movement of nonnative plant pests across borders are a critical component of the biosecurity continuum. Inspections can also provide valuable information about when and where plant pests are crossing national boundaries. However, only a limited portion of the massive volume of goods imported daily can be inspected, necessitating a highly targeted, riskbased strategy. Furthermore, since inspections must prioritize detection and efficiency, their outcomes generally cannot be used to make inferences about risk for cargo pathways as a whole. Phytosanitary agencies need better tools for quantifying pests going undetected and designing risk-based inspection strategies appropriate for changing operational conditions. In this research, we present PoPS (Pest or Pathogen Spread) Border, an open-source consignment inspection simulator for measuring inspection outcomes under various cargo contamination scenarios to support recommendations for inspection protocols and estimate pest slippage rates. We used the tool to estimate contamination rates of historical interception data, quantify tradeoffs in effectiveness and workload for inspection strategies, and identify vulnerabilities in sampling protocols as changes in cargo configurations and contamination occur. These use cases demonstrate how this simulation approach permits testing inspection strategies and measuring quantities that would otherwise be impossible in a field-based setting. This work represents the first steps toward a decision support tool for creating dynamic inspection protocols that respond to changes in available resources, workload, and commerce trends.

Non-native pests and diseases pose a risk of economic and environmental damage to managed and natural U.S. forests and agriculture. The U.S. Department of Agriculture (USDA) Animal and Plant Health Inspection Service (APHIS) Plant Protection and Quarantine (PPQ) protects the health of U.S. agriculture and natural resources against invasive pests and diseases through efforts to prevent the entry, establishment, and spread of non-native pests and diseases. Because each pest or disease has its own idiosyncratic characteristics, analyzing risk is highly complex. To help PPQ better respond to pest and disease threats, we developed the Spatial Analytic Framework for Advanced Risk Information Systems (SAFARIS), an integrated system designed to provide a seamless environment for producing predictive models. SAFARIS integrates pest biology information, climate and non-climate data drivers, and predictive models to provide users with readily accessible and easily customizable tools to analyze pest and disease risks. The phenology prediction models, spread forecasting models, and other climate-based analytical tools in SAFARIS help users understand which areas are suitable for establishment, when surveys would be most fruitful, and aid in other analyses that inform decision-making, operational efforts, and rapid response. Here we introduce the components of SAFARIS and provide two use cases demonstrating how pest-specific models developed with SAFARIS tools support PPQ in its mission. Although SAFARIS is designed to address the needs of PPQ, the flexible, web-based framework is publicly available, allowing any user to leverage the available data and tools to model pest and disease risks.