Using UAV-Based Imagery to Determine Volume, Groundcover, and Growth Rate Characteristics of Lentil (Lens culinaris Medik.)

Plant growth rate is an essential phenotypic parameter for crop physiologists and plant breeders to understand in order to quantify potential crop productivity based on specific stages throughout the growing season. While plant growth rate information can be attained though manual collection of biomass, this procedure is rarely performed due to the prohibitively large effort and destruction of plant material that is required. Unmanned Aerial Vehicles (UAVs) offer great potential for rapid collection of imagery which can be utilized for quantification of plant growth rate. In this study, six diverse lines of lentil were grown in three replicates of microplots with six biomass collection time-points throughout the growing season over five site-years. Aerial imagery of each biomass collection time point was collected from a UAV and utilized to produce stitched two-dimensional orthomosaics and three-dimensional point clouds. Analysis of this imagery produced quantification of groundcover and vegetation volume on an individual plot basis. Comparison with manually-measured above-ground biomass suggests strong correlation, indicating great potential for UAVs to be utilized in plant breeding programs for evaluation of groundcover and vegetation volume. Nonlinear logistic models were fit to multiple data collection points throughout the growing season. The growth rate and G50, which is the number of growing degree days (GDD) required to accumulate 50 % of maximum growth, parameters of the model are capable of quantifying growth rate, and have potential utility in plant research and plant breeding programs. Predicted maximum volume was identified as a potential proxy for whole-plot biomass measurement. Six new phenotypes have been described that can be accurately and efficiently collected from field trials with the use of UAV’s or other overhead image-collection systems. These phenotypes are; Area Growth Rate, Area G50, Area Maximum Predicted Growth, Volume Growth Rate, Volume G50, and Volume Maximum Predicted Growth

The Application of an Unmanned Aerial System and Machine Learning Techniques for Red Clover-Grass Mixture Yield Estimation under Variety Performance Trials

A significant trend has developed with the recent growing interest in the estimation of aboveground biomass of vegetation in legume-supported systems in perennial or semi-natural grasslands to meet the demands of sustainable and precise agriculture. Unmanned aerial systems (UAS) are a powerful tool when it comes to supporting farm-scale phenotyping trials. In this study, we explored the variation of the red clover-grass mixture dry matter (DM) yields between temporal periods (one- and two-year cultivated), farming operations [soil tillage methods (STM), cultivation methods (CM), manure application (MA)] using three machine learning (ML) techniques [random forest regression (RFR), support vector regression (SVR), and artificial neural network (ANN)] and six multispectral vegetation indices (VIs) to predict DM yields. The ML evaluation results showed the best performance for ANN in the 11-day before harvest category (R2 = 0.90, NRMSE = 0.12), followed by RFR (R2 = 0.90 NRMSE = 0.15), and SVR (R2 = 0.86, NRMSE = 0.16), which was furthermore supported by the leave-one-out cross-validation pre-analysis. In terms of VI performance, green normalized difference vegetation index (GNDVI), green difference vegetation index (GDVI), as well as modified simple ratio (MSR) performed better as predictors in ANN and RFR. However, the prediction ability of models was being influenced by farming operations. The stratified sampling, based on STM, had a better model performance than CM and MA. It is proposed that drone data collection was suggested to be optimum in this study, closer to the harvest date, but not later than the ageing stage

Remote Sensing for Precision Nitrogen Management

This book focuses on the fundamental and applied research of the non-destructive estimation and diagnosis of crop leaf and plant nitrogen status and in-season nitrogen management strategies based on leaf sensors, proximal canopy sensors, unmanned aerial vehicle remote sensing, manned aerial remote sensing and satellite remote sensing technologies. Statistical and machine learning methods are used to predict plant-nitrogen-related parameters with sensor data or sensor data together with soil, landscape, weather and/or management information. Different sensing technologies or different modelling approaches are compared and evaluated. Strategies are developed to use crop sensing data for in-season nitrogen recommendations to improve nitrogen use efficiency and protect the environment

Uumanned Aerial Vehicle Data Analysis For High-throughput Plant Phenotyping

The continuing population is placing unprecedented demands on worldwide crop yield production and quality. Improving genomic selection for breeding process is one essential aspect for solving this dilemma. Benefitted from the advances in high-throughput genotyping, researchers already gained better understanding of genetic traits. However, given the comparatively lower efficiency in current phenotyping technique, the significance of phenotypic traits has still not fully exploited in genomic selection. Therefore, improving HTPP efficiency has become an urgent task for researchers. As one of the platforms utilized for collecting HTPP data, unmanned aerial vehicle (UAV) allows high quality data to be collected within short time and by less labor. There are currently many options for customized UAV system on market; however, data analysis efficiency is still one limitation for the fully implementation of HTPP. To this end, the focus of this program was data analysis of UAV acquired data. The specific objectives were two-fold, one was to investigate statistical correlations between UAV derived phenotypic traits and manually measured sorghum biomass, nitrogen and chlorophyll content. Another was to conduct variable selection on the phenotypic parameters calculated from UAV derived vegetation index (VI) and plant height maps, aiming to find out the principal parameters that contribute most in explaining winter wheat grain yield. Corresponding, two studies were carried out. Good correlations between UAV-derived VI/plant height and sorghum biomass/nitrogen/chlorophyll in the first study suggested that UAV-based HTPP has great potential in facilitating genetic improvement. For the second study, variable selection results from the single-year data showed that plant height related parameters, especially from later season, contributed more in explaining grain yield. Advisor: Yeyin Sh

Remote Sensing in Agriculture: State-of-the-Art

The Special Issue on “Remote Sensing in Agriculture: State-of-the-Art” gives an exhaustive overview of the ongoing remote sensing technology transfer into the agricultural sector. It consists of 10 high-quality papers focusing on a wide range of remote sensing models and techniques to forecast crop production and yield, to map agricultural landscape and to evaluate plant and soil biophysical features. Satellite, RPAS, and SAR data were involved. This preface describes shortly each contribution published in such Special Issue

Sentinel-2 Data and Unmanned Aerial System Products to Support Crop and Bare Soil Monitoring: Methodology Based on a Statistical Comparison between Remote Sensing Data with Identical Spectral Bands

The growing need for sustainable management approaches of crops and bare soils requires measurements at a multiple scale (space and time) field system level, which have become increasingly accurate. In this context, proximal and satellite remote sensing data cooperation seems good practice for the present and future. The primary purpose of this work is the development of a sound protocol based on a statistical comparison between Copernicus Sentinel-2 MIS satellite data and a multispectral sensor mounted on an Unmanned Aerial Vehicle (UAV), featuring spectral deployment identical to Sentinel-2. The experimental dataset, based on simultaneously acquired proximal and Sentinel-2 data, concerns an agricultural field in Pisa (Tuscany), cultivated with corn. To understand how the two systems, comparable but quite different in terms of spatial resolution and atmosphere impacts, can effectively cooperate to create a value-added product, statistical tests were applied on bands and the derived Vegetation and Soil index. Overall, as expected, due to the mentioned impacts, the outcomes show a heterogeneous behavior with a difference between the coincident bands as well for the derived indices, modulated in the same manner by the phenological status (e.g., during the canopy developments) or by vegetation absence. Instead, similar behavior between two sensors occurred during the maturity phase of crop plants

Development and Evaluation of Unmanned Aerial Vehicles for High Throughput Phenotyping of Field-based Wheat Trials.

Growing demands for increased global yields are driving researchers to develop improved crops, capable of securing higher yields in the face of significant challenges including climate change and competition for resources. However, abilities to measure favourable physical characteristics (phenotypes) of key crops in response to these challenges is limited. For crop breeders and researchers, current abilities to phenotype field-based experiments with sufficient precision, resolution and throughput is restricting any meaningful advances in crop development. This PhD thesis presents work focused on the development and evaluation of Unmanned Aerial Vehicles (UAVs) in combination with remote sensing technologies as a solution for improved phenotyping of field-based crop experiments. Chapter 2 presents first, a review of specific target phenotypic traits within the categories of crop morphology and spectral reflectance, together with critical review of current standard measurement protocols. After reviewing phenotypic traits, focus turns to UAVs and UAV specific technologies suitable for the application of crop phenotyping, including critical evaluation of both the strengths and current limitations associated with UAV methods and technologies, highlighting specific areas for improvement. Chapter 3 presents a published paper successfully developing and evaluating Structure from Motion photogrammetry for accurate (R2 ≥ 0.93, RMSE ≤ 0.077m, and Bias ≤ -0.064m) and temporally consistent 3D reconstructions of wheat plot heights. The superior throughput achieved further facilitated measures of crop growth rate through the season; whilst very high spatial resolutions highlighted both the inter- and intra-plot variability in crop heights, something unachievable with the traditional manual ruler methods. Chapter 4 presents published work developing and evaluating modified Commercial ‘Off the Shelf’ (COTS) cameras for obtaining radiometrically calibrated imagery of canopy spectral reflectance. Specifically, development focussed on improving application of these cameras under variable illumination conditions, via application of camera exposure, vignetting, and irradiance corrections. Validation of UAV derived Normalised Difference Vegetation Index (NDVI) against a ground spectrometer from the COTS cameras (0.94 ≤ R2 ≥ 0.88) indicated successful calibration and correction of the cameras. The higher spatial resolution obtained from the COTS cameras, facilitated the assessment of the impact of background soil reflectance on derived mean Normalised Difference Vegetation Index (NDVI) measures of experimental plots, highlighting the impact of incomplete canopy on derived indices. Chapter 5 utilises the developed methods and cameras from Chapter 4 to assess the impact of nitrogen fertiliser application on the formation and senescence dynamics of canopy traits over multiple growing seasons. Quantification of changes in canopy reflectance, via NDVI, through three select trends in the wheat growth cycle were used to assess any impact of nitrogen on these periods of growth. Results showed consistent impact of zero nitrogen application on crop canopies within all three development phases. Additional results found statistically significant positive correlations between quantified phases and harvest metrics (e.g. final yield), with greatest correlations occurring within the second (Full Canopy) and third (Senescence) phases. Chapter 6 focuses on evaluation of the financial costs and throughput associated with UAVs; with specific focus on comparison to conventional methods in a real-world phenotyping scenario. A ‘cost throughput’ analysis based on real-world experiments at Rothamsted Research, provided quantitative assessment demonstrating both the financial savings (£4.11 per plot savings) and superior throughput obtained (229% faster) from implementing a UAV based phenotyping strategy to long term phenotyping of field-based experiments. Overall the methods and tools developed in this PhD thesis demonstrate UAVs combined with appropriate remote sensing tools can replicate and even surpass the precision, accuracy, cost and throughput of current strategies