Advancements in Multi-temporal Remote Sensing Data Analysis Techniques for Precision Agriculture

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An Evaluation of Unmanned Aerial System Multispectral and Thermal Infrared Data as Information for Agricultural Crop and Irrigation Management

Spatial irrigation management has been steadily advancing over the last several years. A current issue with managing irrigation spatially on sub-field scale is the inability to readily collect the spatial field data necessary to properly manage irrigation. Multispectral and thermal infrared imagery used in informing irrigation management decisions was previously collected by satellite and manned aircraft remote sensing platforms. These remote sensing platforms pose issues concerning economic feasibility, revisit intervals, and weather factors that inhibit the collection of data. Recent developments in unmanned aerial systems, which provide an additional means of collecting multispectral and thermal infrared data, have the potential to provide supplemental data during periods of missing satellite data or to completely replace satellite and manned aircraft remote sensing platforms. As unmanned aerial system remote sensing platforms are a relatively new technology, there are uncertainties regarding how these systems compare to previous and more well-known remote sensing platforms. Some of these uncertainties include how to properly collect, process, and calibrate data acquired by these systems so that the end products are accurate and can by used in scientific applications. This work evaluated two different unmanned aerial systems with integrated multispectral and thermal infrared cameras to determine the best methods of collecting, processing, and calibrating data. Three different multispectral image calibration methods were evaluated and compared against Landsat satellite reflectance products and ground-based reflectance tarps. The thermal infrared image calibration consisted of correcting for emissivity and atmospheric effects, and was compared to in-field infrared thermometers. Relationships for estimating maize leaf area index, crop height, and fraction of vegetation cover were redefined and evaluated based on various vegetation indices derived from the unmanned aerial system calibrated multispectral imagery. This work also addressed some of the challenges and obstacles related to deploying unmanned aerial systems for remote sensing in agricultural applications. Advisors: Wayne E. Woldt and Christopher M.U. Neal

Mapping urban tree species in a tropical environment using airborne multispectral and LiDAR data

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial TechnologiesAccurate and up-to-date urban tree inventory is an essential resource for the development of strategies towards sustainable urban planning, as well as for effective management and preservation of biodiversity. Trees contribute to thermal comfort within urban centers by lessening heat island effect and have a direct impact in the reduction of air pollution. However, mapping individual trees species normally involves time-consuming field work over large areas or image interpretation performed by specialists. The integration of airborne LiDAR data with high-spatial resolution and multispectral aerial image is an alternative and effective approach to differentiate tree species at the individual crown level. This thesis aims to investigate the potential of such remotely sensed data to discriminate 5 common urban tree species using traditional Machine Learning classifiers (Random Forest, Support Vector Machine, and k-Nearest Neighbors) in the tropical environment of Salvador, Brazil. Vegetation indices and texture information were extracted from multispectral imagery, and LiDAR-derived variables for tree crowns, were tested separately and combined to perform tree species classification applying three different classifiers. Random Forest outperformed the other two classifiers, reaching overall accuracy of 82.5% when using combined multispectral and LiDAR data. The results indicate that (1) given the similarity in spectral signature, multispectral data alone is not sufficient to distinguish tropical tree species (only k-NN classifier could detect all species); (2) height values and intensity of crown returns points were the most relevant LiDAR features, combination of both datasets improved accuracy up to 20%; (3) generation of canopy height model derived from LiDAR point cloud is an effective method to delineate individual tree crowns in a semi-automatic approach

Can a combination of UAV-derived vegetation indices with biophysical variables improve yield variability assessment in smallholder farms?

Open Access Journal; Published online: 09 Dec 2020The rapid assessment of maize yields in a smallholder farming system is important for understanding its spatial and temporal variability and for timely agronomic decision-support. We assessed the predictability of maize grain yield using unmanned aerial/air vehicle (UAV)-derived vegetation indices (VI) with (out) biophysical variables on smallholder farms. High-resolution imageries were acquired with UAV-borne multispectral sensor at four and eight weeks after sowing (WAS) on 31 farmer managed fields (FMFs) and 12 nearby nutrient omission trials (NOTs) sown with two genotypes (hybrid and open-pollinated maize) across five locations within the core maize region of Nigeria. Acquired multispectral imageries were post-processed into three VIs, normalized difference VI (NDVI), normalized difference red-edge (NDRE), and green-normalized difference VI (GNDVI) while plant height (Ht) and percent canopy cover (CC) were measured within georeferenced plot locations. Result shows that the nutrient status had a significant effect on the grain yield (and variability) in NOTs, with a maximum grain yield of 9.3 t/ha, compared to 5.4 t/ha in FMFs. Generally, there was no relationship between UAV-derived VIs and grain yield at 4WAS (r 0.1), but significant correlations were observed at 8WAS (r ≤ 0.3; p < 0.001). Ht was positively correlated with grain yield at 4WAS (r = 0.5, R2 = 0.25, p < 0.001) and more strongly at 8WAS (r = 0.7, R2 = 0.55, p < 0.001), while the relationship between CC and yield was only significant at 8WAS. By accounting for within- and between-field variations in NOTs and FMFs (separately), predictability of grain yield from UAV-derived VIs was generally low (R2 ≤ 0.24); however, the inclusion of ground-measured biophysical variable (mainly Ht) improved the explained yield variability (R2 ≥ 0.62, Root Mean Square Error of Prediction, RMSEP ≤ 0.35) in NOTs but not in FMFs. We conclude that yield prediction with UAV-acquired imageries (before harvest) is more reliable under controlled experimental conditions (NOTs), compared to actual farmer managed fields where various confounding agronomic factors can amplify noise-signal ratio

Yield predictions of four hybrids of maize (Zea mays) using multispectral images obtained from RPAS in the coast of Peru

Early assessment of crop development is a key aspect of precision agriculture. Shortening the time of response before a deficit of irrigation, nutrients and damage by diseases is one of the usual concerns in agriculture. Early prediction of crop yields can increase profitability in the farmer's economy. In this study we aimed to predict the yield of four maize commercial hybrids (Dekalb7508, Advanta9313, MH_INIA619 and Exp_05PMLM) using remotely sensed spectral vegetation indices (VI). A total of 10 VI (NDVI, GNDVI, GCI, RVI, NDRE, CIRE, CVI, MCARI, SAVI, and CCCI) were considered for evaluating crop yield and plant cover at 31, 39, 42, 46 and 51 days after sowing (DAS). A multivariate analysis was applied using principal component analysis (PCA), linear regression, and r-Pearson correlation. In the present study, highly significant correlations were found between plant cover with VIs at 46 (GNDVI, GCI, RVI, NDRE, CIRE and CCCI) and 51 DAS (GNDVI, GCI, NDRE, CIRE, CVI, MCARI and CCCI). The PCA indicated a clear discrimination of the dates evaluated with VIs at 31, 39 and 51 DAS. The inclusion of the CIRE and NDRE in the prediction model contributed to estimate the performance, showing greater precision at 51 DAS. The use of RPAS to monitor crops allows optimizing resources and helps in making timely decisions in agriculture in Peru

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

The utility of very-high resolution unmanned aerial vehicles (UAV) imagery in monitoring the spatial and temporal variations in leaf moisture content of smallholder maize farming systems.

Masters Degree. University of KwaZulu-Natal, Pietermaritzburg.Maize moisture stress, resulting from rainfall variability, is a primary challenge in the production of rain-fed maize farming, especially in water-scarce regions such as southern Africa. Quantifying maize moisture variations throughout the growing season can support agricultural decision-making and prompt the rapid and robust detection of smallholder maize moisture stress. Unmanned Aerial Vehicles (UAVs), equipped with light-weight multispectral sensors, provide spatially explicit near real-time information for determining maize moisture content at farm scale. Therefore, this study evaluated the utility of UAV derived multispectral imagery in estimating maize leaf moisture content indicators on smallholder farming systems throughout the maize growing season. The first objective of the study was to conduct a comparative analysis in order to evaluate the performance of five regression techniques (support vector regression, random forest regression, decision trees regression, artificial neural network regression and the partial least squares regression) in predicting maize water content indicators (i.e. equivalent water thickness (EWT), fuel moisture content (FMC) and specific leaf area (SLA)), and determine the most suitable indicator of smallholder maize water content variability based on multispectral UAV data. The results illustrated that both NIR and red-edge derived spectral variables were critical in characterising maize moisture indicators on smallholder farms. Furthermore, the best models for estimating EWT, FMC and SLA were derived from the random forest regression algorithm with a relative root mean square error (rRMSE) of 3.13%, 1% and 3.48 %, respectively. Additionally, EWT and FMC yielded the highest predictive performance of maize leaf moisture and demonstrated the best correlation with remotely sensed data. The study’s second objective was to evaluate the utility of UAVderived multispectral imagery in estimating the temporal variability of smallholder maize moisture content across the maize growing season using the optimal maize moisture indicators. The findings illustrated that the NIR and red-edge wavelengths were influential in characterising maize moisture variability with the best models for estimating maize EWT and FMC resulting in a rRMSE of 2.27 % and 1%, respectively. Furthermore, the early reproductive stage was the most optimal for accurately estimating maize EWT and FMC using UAVproximal remote sensing. The findings of this study demonstrate the prospects of UAV- derived multispectral data for deriving insightful information on maize moisture availability and overall health conditions. This study serves as fundamental step towards the creation of an early maize moisture stress detection and warning systems, and contributes towards climate change adaptation and resilience of smallholder maize farming

UAV and field spectrometer based remote sensing for maize phenotyping, varietal discrimination and yield forecasting.

Doctoral Degree. University of KwaZulu-Natal, Pietermaritzburg.Maize is the major staple food crop in the majority of Sub-Saharan African (SSA) countries. However, production statistics (croplands and yields) are rarely measured, and where they are recorded, accuracy is poor because the statistics are updated through the farm survey method, which is error-prone and is time-consuming, and expensive. There is an urgent need to use affordable, accurate, timely, and readily accessible data collection and spatial analysis tools, including robust data extraction and processing techniques for precise yield forecasting for decision support and early warning systems. Meeting Africa’s rising food demand, which is driven by population growth and low productivity requires doubling the current production of major grain crops like maize by 2050. This requires innovative approaches and mechanisms that support accurate yield forecasting for early warning systems coupled with accelerated crop genetic improvement. Recent advances in remote sensing and geographical information system (GIS) have enabled detailed cropland mapping, spatial analysis of land suitability, crop type, and varietal discrimination, and ultimately grain yield forecasting in the developed world. However, although remote sensing and spatial analysis afforded us unprecedented opportunities for detailed data collection, their application in maize in Africa is still limited. In Africa, the challenge of crop yield forecasting using remote sensing is a daunting task because agriculture is highly fragmented, cropland is spatially heterogeneous, and cropping systems are highly diverse and mosaic. The dearth of data on the application of remote sensing and GIS in crop yield forecasting and land suitability analysis is not only worrying but catastrophic to food security monitoring and early warning systems in a continent burdened with chronic food shortages. Furthermore, accelerated crop genetic improvement to increase yield and achieve better adaptation to climate change is an issue of increasing urgency in order to satisfy the ever-increasing food demand. Recently, crop improvement programs are exploring the use of remotely sensed data that can be used cost-effectively for varietal evaluation and analysis in crop phenotyping, which currently remains a major bottleneck in crop genetic improvement. Yet studies on evaluation of maize varietal response to abiotic and biotic stresses found in the target production environments are limited. Therefore, the aim of this study was to model spatial land suitability for maize production using GIS and explore the potential use of field spectrometer and unmanned aerial vehicles (UAV) based remotely sensed data in maize varietal discrimination, high-throughput phenotyping, and yield prediction. Firstly, an overview of major remote-sensing platforms and their applicability to estimating maize grain yield in the African agricultural context, including research challenges was provided. Secondly, maize land suitability analysis using GIS and analytical hierarchical process (AHP) was performed in Zimbabwe. Finally, the utility of proximal and UAV-based remotely sensed data for maize phenotyping, varietal discrimination, and yield forecasting were explored. The results showed that the use of remote sensing data in estimating maize yield in the African agricultural systems is still limited and obtaining accurate and reliable maize yield estimates using remotely sensed data remains a challenge due to the highly fragmented and spatially heterogeneous nature of the cropping systems. Our results underscored the urgent need to use sensors with high spatial, temporal and spectral resolution, coupled with appropriate classification techniques and accurate ground truth data in estimating maize yield and its spatiotemporal dynamics in heterogeneous African agricultural landscapes for designing appropriate food security interventions. In addition, using modern spatial analysis tools is effective in assessing land suitability for targeting location-specific interventions and can serve as a decision support tool for policymakers and land-use planners regarding maize production and varietal placement. Discriminating maize varieties using remotely sensed data is crucial for crop monitoring, high throughput phenotyping, and yield forecasting. Using proximal sensing, our study showed that maize varietal discrimination is possible at certain phenological growth stages at the field level, which is crucial for yield forecasting and varietal phenotyping in crop improvement. In addition, the use of proximal remote sensing data with appropriate pre-processing algorithms such as auto scaling and generalized least squares weighting significantly improved the discrimination ability of partial least square discriminant analysis, and identify optimal spectral bands for maize varietal discrimination. Using proximal sensing was not only able to discriminate maize varieties but also identified the ideal phenological stage for varietal discrimination. Flowering and onset of senescence appeared to be the most ideal stages for accurate varietal discrimination using our data. In this study, we also demonstrated the potential use of UAV-based remotely sensed data in maize varietal phenotyping in crop improvement. Using multi-temporal UAV-derived multispectral data and Random Forest (RF) algorithm, our study identified not only the optimal bands and indices but also the ideal growth stage for accurate varietal phenotyping under maize streak virus (MSV) infection. The RF classifier selected green normalized difference vegetation index (GNDVI), green Chlorophyll Index (CIgreen), Red-edge Chlorophyll Index (CIred-edge), and the Red band as the most important variables for classification. The results demonstrated that spectral bands and vegetation indices measured at the vegetative stage are the most important for the classification of maize varietal response to MSV. Further analysis to predict MSV disease and grain yield using UAV-derived multispectral imaging data using multiple models showed that Red and NIR bands were frequently selected in most of the models that gave the highest prediction precision for grain yield. Combining the NIR band with Red band improved the explanatory power of the prediction models. This was also true with the selected indices. Thus, not all indices or bands measure the same aspect of biophysical parameters or crop productivity, and combining them increased the joint predictive power, consequently increased complementarity. Overall, the study has demonstrated the potential use of spatial analysis tools in land suitability analysis for maize production and the utility of remotely sensed data in maize varietal discrimination, phenotyping, and yield prediction. These results are useful for targeting location-specific interventions for varietal placement and integrating UAV-based high-throughput phenotyping systems in crop genetic improvement to address continental food security, especially as climate change accelerates

Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

Advances in automation and data science have led agriculturists to seek real-time, high-quality, high-volume crop data to accelerate crop improvement through breeding and to optimize agronomic practices. Breeders have recently gained massive data-collection capability in genome sequencing of plants. Faster phenotypic trait data collection and analysis relative to genetic data leads to faster and better selections in crop improvement. Furthermore, faster and higher-resolution crop data collection leads to greater capability for scientists and growers to improve precision-agriculture practices on increasingly larger farms; e.g., site-specific application of water and nutrients. Unmanned aerial vehicles (UAVs) have recently gained traction as agricultural data collection systems. Using UAVs for agricultural remote sensing is an innovative technology that differs from traditional remote sensing in more ways than strictly higher-resolution images; it provides many new and unique possibilities, as well as new and unique challenges. Herein we report on processes and lessons learned from year 1-the summer 2015 and winter 2016 growing seasons-of a large multidisciplinary project evaluating UAV images across a range of breeding and agronomic research trials on a large research farm. Included are team and project planning, UAV and sensor selection and integration, and data collection and analysis workflow. The study involved many crops and both breeding plots and agronomic fields. The project's goal was to develop methods for UAVs to collect high-quality, high-volume crop data with fast turnaround time to field scientists. The project included five teams: Administration, Flight Operations, Sensors, Data Management, and Field Research. Four case studies involving multiple crops in breeding and agronomic applications add practical descriptive detail. Lessons learned include critical information on sensors, air vehicles, and configuration parameters for both. As the first and most comprehensive project of its kind to date, these lessons are particularly salient to researchers embarking on agricultural research with UAVs