UAV and Machine Learning Based Refinement of a Satellite-Driven Vegetation Index for Precision Agriculture

Precision agriculture is considered to be a fundamental approach in pursuing a low-input, high-efficiency, and sustainable kind of agriculture when performing site-specific management practices. To achieve this objective, a reliable and updated description of the local status of crops is required. Remote sensing, and in particular satellite-based imagery, proved to be a valuable tool in crop mapping, monitoring, and diseases assessment. However, freely available satellite imagery with low or moderate resolutions showed some limits in specific agricultural applications, e.g., where crops are grown by rows. Indeed, in this framework, the satellite's output could be biased by intra-row covering, giving inaccurate information about crop status. This paper presents a novel satellite imagery refinement framework, based on a deep learning technique which exploits information properly derived from high resolution images acquired by unmanned aerial vehicle (UAV) airborne multispectral sensors. To train the convolutional neural network, only a single UAV-driven dataset is required, making the proposed approach simple and cost-effective. A vineyard in Serralunga d'Alba (Northern Italy) was chosen as a case study for validation purposes. Refined satellite-driven normalized difference vegetation index (NDVI) maps, acquired in four different periods during the vine growing season, were shown to better describe crop status with respect to raw datasets by correlation analysis and ANOVA. In addition, using a K-means based classifier, 3-class vineyard vigor maps were profitably derived from the NDVI maps, which are a valuable tool for growers

Crop Phenology Detection Using High Spatio-Temporal Resolution Data Fused from SPOT5 and MODIS Products

Timely and efficient monitoring of crop phenology at a high spatial resolution are crucial for the precise and effective management of agriculture. Recently, satellite-derived vegetation indices (VIs), such as the Normalized Difference Vegetation Index (NDVI), have been widely used for the phenology detection of terrestrial ecosystems. In this paper, a framework is proposed to detect crop phenology using high spatio-temporal resolution data fused from Systeme Probatoire d'Observation de la Tarre5 (SPOT5) and Moderate Resolution Imaging Spectroradiometer (MODIS) images. The framework consists of a data fusion method to produce a synthetic NDVI dataset at SPOT5’s spatial resolution and at MODIS’s temporal resolution and a phenology extraction algorithm based on NDVI time-series analysis. The feasibility of our phenology detection approach was evaluated at the county scale in Shandong Province, China. The results show that (1) the Spatial and Temporal Adaptive Reflectance Fusion Model (STARFM) algorithm can accurately blend SPOT5 and MODIS NDVI, with an R2 of greater than 0.69 and an root mean square error (RMSE) of less than 0.11 between the predicted and referenced data; and that (2) the estimated phenology parameters, such as the start and end of season (SOS and EOS), were closely correlated with the field-observed data with an R2 of the SOS ranging from 0.68 to 0.86 and with an R2 of the EOS ranging from 0.72 to 0.79. Our research provides a reliable approach for crop phenology mapping in areas with high fragmented farmland, which is meaningful for the implementation of precision agriculture

Evaluation of the Uncertainty in Satellite-Based Crop State Variable Retrievals Due to Site and Growth Stage Specific Factors and Their Potential in Coupling with Crop Growth Models

Coupling crop growth models and remote sensing provides the potential to improve our understanding of the genotype x environment x management (G X E X M) variability of crop growth on a global scale. Unfortunately, the uncertainty in the relationship between the satellite measurements and the crop state variables across different sites and growth stages makes it diffcult to perform the coupling. In this study, we evaluate the effects of this uncertainty with MODIS data at the Mead, Nebraska Ameriflux sites (US-Ne1, US-Ne2, and US-Ne3) and accurate, collocated Hybrid-Maize (HM) simulations of leaf area index (LAI) and canopy light use effciency (LUECanopy). The simulations are used to both explore the sensitivity of the satellite-estimated genotype X management (G X M) parameters to the satellite retrieval regression coeffcients and to quantify the amount of uncertainty attributable to site and growth stage specific factors. Additional ground-truth datasets of LAI and LUECanopy are used to validate the analysis. The results show that uncertainty in the LAI/satellite measurement regression coeffcients lead to large uncertainty in the G X Mparameters retrievable from satellites. In addition to traditional leave-one-site-out regression analysis, the regression coeffcient uncertainty is assessed by evaluating the retrieval performance of the temporal change in LAI and LUECanopy. The weekly change in LAI is shown to be retrievable with a correlation coeffcient absolute value (|r|) of 0.70 and root-mean square error (RMSE) value of 0.4, which is significantly better than the performance expected if the uncertainty was caused by random error rather than secondary effects caused by site and growth stage specific factors (an expected |r| value of 0.36 and RMSE value of 1.46 assuming random error). As a result, this study highlights the importance of accounting for site and growth stage specific factors in remote sensing retrievals for future work developing methods coupling remote sensing with crop growth models

Improving Retrievals of Crop Vegetation Parameters from Remote Sensing Data

Agricultural systems are difficult to model because crop growth is driven by the strongly nonlinear interaction of Genotype x Environment x Management (G x E x M) factors. Due to the nonlinearity in the interaction of these factors, the amount of data necessary to develop and utilize models to accurately predict the performance of agricultural systems at an operational scale is large. Satellite remote sensing provides the potential to vastly increase the amount of data available for modelling agricultural systems as a result of its high revisit time and spatial coverage. Unfortunately, there have been significant difficulties in deploying remote sensing for many agricultural modelling applications because of the uncertainty involved in the retrievals. In this dissertation, we show that collecting farmer-provided agro-managment information has the potential to reduce the uncertainty in the retrieval products obtained from remote sensing observations. Specifically, both field-scale and regional-scale analysis are used to show that secondary factor variability is a very significant cause of uncertainty in both crop growth modelling and agricultural remote sensing that needs to be addressed through increased data collection. In order to address this need for increased data availability, a method is developed that allows geolocated crop growth model simulations to be used to train satellite-based crop state variable retrievals, which is then validated at regional scale. The method developed provides a general robust methodology to create a large-scale platform that would allow farmers to share data with government agencies and universities to improve crop state variable retrievals and crop growth modelling and provide farmers, government, industry, and researchers with insights and predictive capability into crop growth at both field and regional scales

Landsat-based operational wheat area estimation model for Punjab, Pakistan

Wheat in Punjab province of Pakistan is grown during the Rabi (winter) season within a heterogeneous smallholder agricultural system subject to a range of pressures including water scarcity, climate change and variability, and management practices. Punjab is the breadbasket of Pakistan, representing over 70% of national wheat production. Timely estimation of cultivated wheat area can serve to inform decision-making in managing harvests with regard to markets and food security. The current wheat area and yield reporting system, operated by the Punjab Crop Reporting Service (CRS) delivers crop forecasts several months after harvest. The delayed production data cannot contribute to in-season decision support systems. There is a need for an alternative cost-effective, efficient and timely approach on producing wheat area estimates, in ensuring food security for the millions of people in Pakistan. Landsat data, medium spatial and temporal resolutions, offer a data source for characterizing wheat in smallholder agriculture landscapes. This dissertation presents methods for operational mapping of wheat cultivate area using within growing season Landsat time-series data. In addition to maps of wheat cover in Punjab, probability-based samples of in-situ reference data were allocated using the map as a stratifier. A two-stage probability based cluster field sample was used to estimate area and assess map accuracies. The before-harvest wheat area estimates from field-based sampling and Landsat map were found to be comparable to official post-harvest data produced by the CRS Punjab. This research concluded that Landsat medium resolution data has sufficient spatial and temporal coverage for successful wall-to-wall mapping of wheat in Punjab’s smallholder agricultural system. Freely available coarse and medium spatial resolution satellite data such as MODIS and Landsat perform well in characterizing industrial cropping systems; commercial high spatial resolution satellite data are often advocated as an alternative for characterizing fine-scale land tenure agricultural systems such as that found in Punjab. Commercial 5 m spatial resolution RapidEye data from the peak of the winter wheat growing season were used as sub-pixel training data in mapping wheat with the growing season free 30 m Landsat time series data from the 2014-15 growing season. The use of RapidEye to calibrate mapping algorithms did not produce significantly higher overall accuracies ( ± standard error) compared to traditional whole pixel training of Landsat-based 30 m data. Continuous wheat mapping yielded an overall accuracy of 88% (SE = ±4%) in comparison to 87% (SE = ±4%) for categorical wheat mapping, leading to the finding that sub-pixel training data are not required for winter wheat mapping in Punjab. Given sufficient expertise in supervised classification model calibration, freely available Landsat data are sufficient for crop mapping in the fine-scale land tenure system of Punjab. For winter wheat mapping in Punjab and other similar landscapes, training data for supervised classification may be collected directly from Landsat images with probability based stratified random sampling as reference data without the need for high-resolution reference imagery. The research concluded by exploring the use of automated models in wheat area mapping and area estimation using growing season Landsat time-series data. The automated classification tree model resulted in wheat / not wheat maps with comparable accuracies compared to results achieved with traditional manual training. In estimating area, automated wheat maps from previous growing seasons can serve as a stratifier in the allocation of current season in-situ reference data, and current growing season maps can serve as an auxiliary variable in model-assisted area estimation procedures. The research demonstrated operational implementation of robust automated mapping in generating timely, accurate, and precise wheat area estimates. Such information is a critical input to policy decisions, and can help to ensure appropriate post-harvest grain management to address situations arising from surpluses or shortages in crop production

Crop growth and yield monitoring in smallholder agricultural systems:a multi-sensor data fusion approach

Smallholder agricultural systems are highly vulnerable to production risks posed by the intensification of extreme weather events such as drought and flooding, soil degradation, pests, lack of access to agricultural inputs, and political instability. Monitoring the spatial and temporal variability of crop growth and yield is crucial for farm management, national-level food security assessments, and famine early warning. However, agricultural monitoring is difficult in fragmented agricultural landscapes because of scarcity and uncertainty of data to capture small crop fields. Traditional pre- and post-harvest crop monitoring and yield estimation based on fieldwork is costly, slow, and can be unrepresentative of heterogeneous agricultural landscapes as found in smallholder systems in sub-Saharan Africa. Devising accurate and timely crop phenology detection and yield estimation methods can improve our understanding of the status of crop production and food security in these regions.Satellite-based Earth observation (EO) data plays a key role in monitoring the spatial and temporal variability of crop growth and yield over large areas. The small field sizes and variability in management practices in fragmented landscapes requires high spatial and high temporal resolution EO data. This thesis develops and demonstrates methods to investigate the spatiotemporal variability of crop phenology detection and yield estimation using Landsat and MODIS data fusion in smallholder agricultural systems in the Lake Tana sub-basin of Ethiopia. The overall aim is to further broaden the application of multi-sensor EO data for crop growth monitoring in smallholder agricultural systems.The thesis addressed two important aspects of crop monitoring applications of EO data: phenology detection and yield estimation. First, the ESTARFM data fusion workflow was modified based on local knowledge of crop calendars and land cover to improve crop phenology monitoring in fragmented agricultural landscapes. The approach minimized data fusion uncertainties in predicting temporal reflectance change of crops during the growing season and the reflectance value of fused data was comparable to the original Landsat image reserved for validation. The main sources of uncertainty in data fusion are the small field size and abrupt crop growth changes between the base andviiprediction dates due to flooding, weeding, fertiliser application, and harvesting. The improved data fusion approach allowed us to determine crop phenology and estimate LAI more accurately than both the standard ESTARFM data fusion method and when using MODIS data without fusion. We also calibrated and validated a dynamic threshold phenology detection method using maize and rice crop sowing and harvest date information. Crop-specific phenology determined from data fusion minimized the mismatch between EO-derived phenometrics and the actual crop calendar. The study concluded that accurate phenology detection and LAI estimation from Landsat–MODIS data fusion demonstrates the feasibility of crop growth monitoring using multi-sensor data fusion in fragmented and persistently cloudy agricultural landscapes.Subsequently, the validated data fusion and phenology detection methods were implemented to understand crop phenology trends from 2000 to 2020. These trends are often less understood in smallholder agricultural systems due to the lack of high spatial resolution data to distinguish crops from the surrounding natural vegetation. Trends based on Landsat–MODIS fusion were compared with those detected using MODIS alone to assess the contribution of data fusion to discern crop phenometric change. Landsat and MODIS fusion discerned crop and environment-specific trends in the magnitude and direction of crop phenology change. The results underlined the importance of high spatial and temporal resolution EO data to capture environment-specific crop phenology change, which has implications in designing adaptation and crop management practices in these regions.The second important aspect of the crop monitoring problem addressed in this thesis is improving crop yield estimation in smallholder agricultural systems. The large input requirements of crop models and lack of spatial information about the heterogeneous crop-growing environment and agronomic management practices are major challenges to the accurate estimation of crop yield. We assimilated leaf area index (LAI) and phenology information from Landsat–MODIS fusion in a crop model (simple algorithm for yield estimation: SAFY) to obtain reasonably reliable crop yield estimates. The SAFY model is sensitive to the spatial and temporal resolution of the calibration input LAI, phenology information, and the effective light use efficiency (ELUE) parameter, which needs accurate field level inputs during modelviiioptimization. Assimilating fused EO-based phenology information minimized model uncertainty and captured the large management and environmental variation in smallholder agricultural systems.In the final research chapter of the thesis, we analysed the contribution of assimilating LAI at different phenological stages. The frequency and timing of LAI observations influences the retrieval accuracy of the assimilating LAI in crop growth simulation models. The use of (optical) EO data to estimate LAI is constrained by limited repeat frequency and cloud cover, which can reduce yield estimation accuracy. We evaluated the relative contribution of EO observations at different crop growth stages for accurate calibration of crop model parameters. We found that LAI between jointing and grain filling has the highest contribution to SAFY yield estimation and that the distribution of LAI during the key development stages was more useful than the frequency of LAI to improve yield estimation. This information on the optimal timing of EO data assimilation is important to develop better in-season crop yield forecasting in smallholder systems

Crop monitoring and yield estimation using polarimetric SAR and optical satellite data in southwestern Ontario

Optical satellite data have been proven as an efficient source to extract crop information and monitor crop growth conditions over large areas. In local- to subfield-scale crop monitoring studies, both high spatial resolution and high temporal resolution of the image data are important. However, the acquisition of optical data is limited by the constant contamination of clouds in cloudy areas. This thesis explores the potential of polarimetric Synthetic Aperture Radar (SAR) satellite data and the spatio-temporal data fusion approach in crop monitoring and yield estimation applications in southwestern Ontario. Firstly, the sensitivity of 16 parameters derived from C-band Radarsat-2 polarimetric SAR data to crop height and fractional vegetation cover (FVC) was investigated. The results show that the SAR backscatters are affected by many factors unrelated to the crop canopy such as the incidence angle and the soil background and the degree of sensitivity varies with the crop types, growing stages, and the polarimetric SAR parameters. Secondly, the Minimum Noise Fraction (MNF) transformation, for the first time, was applied to multitemporal Radarsat-2 polarimetric SAR data in cropland area mapping based on the random forest classifier. An overall classification accuracy of 95.89% was achieved using the MNF transformation of the multi-temporal coherency matrix acquired from July to November. Then, a spatio-temporal data fusion method was developed to generate Normalized Difference Vegetation Index (NDVI) time series with both high spatial and high temporal resolution in heterogeneous regions using Landsat and MODIS imagery. The proposed method outperforms two other widely used methods. Finally, an improved crop phenology detection method was proposed, and the phenology information was then forced into the Simple Algorithm for Yield Estimation (SAFY) model to estimate crop biomass and yield. Compared with the SAFY model without forcing the remotely sensed phenology and a simple light use efficiency (LUE) model, the SAFY incorporating the remotely sensed phenology can improve the accuracy of biomass estimation by about 4% in relative Root Mean Square Error (RRMSE). The studies in this thesis improve the ability to monitor crop growth status and production at subfield scale

Forage germplasm evaluation and grassland characterization through the use of remote sensing and GIS

Las praderas son ecosistemas con una amplia distribución a nivel mundial y se caracterizan por ser una comunidad compleja debido a la existencia de relaciones entre las especies pratenses, y entre ellas y el ambiente. Si bien la pérdida de praderas se ha debido principalmente a la intensificación agrícola y el cambio de uso de suelo, actualmente se encuentran sometidas a las amenazas y cambios ambientales. El cambio climático es uno de los factores ambientales que más influye sobre las praderas y potencialmente puede reformar los patrones de crecimiento de las comunidades de plantas al cambiar su fenología, lo que es causado principalmente por la disminución de las precipitaciones que reducen la productividad de las praderas. A medida que los climas en todo el planeta se vuelven más cálidos y los patrones de precipitación muestran variaciones significativas, comprender la distribución, fisiología y fenología de las praderas resulta fundamental para predecir la función del ecosistema y la resiliencia del mismo al cambio climático. En consideración a la problemática ambiental existente, los importantes cambios tecnológicos que se han generado a nivel de mejoramiento genético del material forrajero y de las herramientas de teledetección; y la complejidad e importancia de la evaluación de praderas de manera tradicional, surge la necesidad de estudiar el germoplasma forrajero y su adaptación a estos nuevos escenarios aplicando las nuevas tecnologías disponibles. En este contexto, esta tesis presenta los hallazgos de tres trabajos cuyos objetivos pretenden dar respuesta a la problemática expuesta. El primer trabajo tuvo como objetivo evaluar la adaptación de praderas de alfalfa (Medicago sativa) con distintos grados de latencia invernal, bajo riego, en las condiciones ambientales actuales de la Región de Ñuble, Chile. Para cuantificar la adaptación, se midió la disponibilidad, producción y composición química del forraje, además de algunos componentes estructurales de las plantas (proporción y tamaño de hojas). Los resultados de este estudio permitieron concluir que no se evidencian diferencias en productividad o calidad del forraje entre los cultivares evaluados, por lo que se puede decir que el cambio de las condiciones ambientales ha permitido que variedades de alfalfa menos tolerantes al frío, como las de latencia 9, se adapten en la Región Ñuble dadas sus nuevas condiciones ambientales, lo cual permitiría elaborar nuevas pautas de recomendaciones de uso de alfalfa según su latencia y zona geográfica. El segundo trabajo llevado a cabo, abordó la evaluación de praderas compuestas por ballica perenne (Lolium perenne L.) y trébol blanco (Trifolium repens L.) con distinto tamaño de hoja dado por su distinta composición genética), para determinar el comportamiento morfológico de tres cultivares de trébol blanco. A través de este estudio se pudo constatar que variedades de trébol blanco de hoja grande, como Kopu II, presentan mayor área foliar y peso de la hoja, que los tréboles de hoja mediana, no encontrando diferencias en la capacidad estolonifera, al menos durante el primer año de crecimiento, lo que siguiere que existen avances en el mejoramiento genético en tréboles blancos de hoja grande, haciéndolos más competitivos al crecer en mezcla con gramíneas, lo que permitiría mejorar la productividad y longevidad de la pradera mixta y facilitar su manejo. En el último trabajo realizado, se evaluó la condición de crecimiento de las praderas, específicamente en su fenología, usando la Teledetección como una herramienta para ello. El objetivo fue hacer un seguimiento de la fenología de las praderas en Bío Bío, Chile, para identificar posibles alteraciones originadas por el cambio climático, utilizando imágenes del Espectrorradiómetro de imágenes de media resolución (MODIS), el índice de vegetación de diferencia normalizada (NDVI) y series de tiempo. Los hallazgos sugieren que las condiciones climáticas en Bío Bío se han vuelto más propicias para el crecimiento de las praderas, durante el período 2001-2020. Los resultados de este estudio destacan la relación entre la fenología de la pradera y su respuesta a las variables climáticas de precipitación acumulada y temperatura, lo que tiene implicaciones para el desarrollo de marcos de políticas para el manejo y protección de las praderas y su relación con el cambio del clima. Si bien es cierto que los cambios ambientales en términos de temperatura y precipitaciones se han evidenciado desde hace un tiempo, es necesario ir validando su efecto en los materiales forrajeros, dado que la respuesta productiva de éstos puede diferir entre zonas de un área geográfica definida. Otro aspecto a considerar en la evaluación de praderas, es el avance generado en términos de mejoramiento genético del germoplasma forrajero, en el que se reconocen mejoras significativas en productividad, calidad como alimento para el ganado y persistencia al formar praderas (adaptación). Por último, en el contexto de cambio climático y considerando las limitantes espaciales y de manejo que tiene la evaluación tradicional de praderas, se plantea que utilizando como insumo imágenes satelitales y bases de datos climáticas de uso público, se pueden generar herramientas de monitoreo de las praderas a través de la de teledetección