Retrieval of biophysical parameters from multi-sensoral remote sensing data, assimilated into the crop growth model CERES-Wheat

This study investigated the possibilities and constraints for an integrated use of a crop growth model (CERES-Wheat) and earth observation techniques. The assimilation of information derived from earth observation sensors into crop growth models enables regional applications and may also help to improve the profound knowledge of the different involved processes and interactions. Both techniques can contribute to improved use of resources, reduced crop production risks, minimised environmental degradation, and increased farm income. Up to now, crop growth modelling and remote sensing techniquices mostly have been used separately for the assessment of agricultural applications. Crop growth models have made valuable contributions to, e.g., yield forecasting or to management decision support systems. Likewise, remote sensing techniques were successfully utilized in classification of agricultural areas or in the quantification of vegetation characteristics at various spatial and temporal scales. Multisensoral remote sensing approaches for the quantification biophysical variables are rarely realized. Normally the fusion of the data sources is based on the use of one sensor for classification purposes and the other one for the extraction of the desired parameters, based on the map classified previously. Pixel-based fusions between multispectral and SAR data is seldom realised for the assessment of quantitative parameters. The integration of crop growth models and remote sensing techniques by assimilating remotely sensed parameters into the models, is also still an issue of research. Especially, the integration of, e.g., multi-sensor biophysical parameter time-series for the improvement of the model performance, might feature a high potential. The starting point of the presented study was the question, if it is possible to derive the values of important crop variables from various remote sensing data? For the retrieval of these quantitative parameters by the use of various multispectral remote sensing sensors, intercalibration issues between the different retrieved vegetation indices had to be taken into account, in order to assure the comparability. Features influencing the vegetation indices are, e.g., the sensor geometry (like viewing- and solar-angle), atmospherical conditions, topography and spatial or radiometric resolution. However, the factors taken into account within this study are the spectral characteristics of the different sensors, like band position, bandwidth and centre wavelengths, which are described by the relative spectral response functions. Due to different RSR functions of the sensor bands, measured spectral differences occur, because the sensors record different components of the reflectance’s spectra from the monitored targets. These are then also introduced into the derived vegetation indices. The chosen cross-calibration method, intercalibrated the assessed Normalized Difference Vegetation Index and the Weighted Difference Vegetation Index between the various sensor pairs by regression, based on simulated multispectral sensors. Differences between the various assessed remote sensing sensors decreased form around 7% to below 1%. The intercalibration also had a positive impact on the later biophysical retrieval performance, producing sounder retrieval results. For the retrieval of the biophysical parameters empirical and semi-empirical models were assessed. The results indicate that the semi-empirical CLAIR model outperforms the empirical approaches. Not only for the Leaf Area Index retrieval, but also in the cases of all other assessed parameters. Concerning the other remote sensing data type used, the SAR data, it was analysed what potential different polarizations and incidence angles have for the extraction of the quantitative parameters. It became obvious that especially high incidence angles, as provided by the satellite Envisat ASAR, produce sounder retrieval results than lower incidence angles, due to a smaller amount of received soil signal. In the context of the assessed polarizations, sound results for the VV polarization could only be achieved for the retrieval of fresh biomass and the plant water content. For the ASAR sensor modelling fresh biomass and LAI using the HV polarization or the dry biomass using the ratio (HH/HV) was appropriate. As roughness aspects also have an influence on the retrieval performance from biophysical parameters using SAR data, the impact of soil surface and vegetation roughness was additionally considered. Best results were achieved, when also considering roughness features, however due to the need of regional modelling it is more appropriate not to consider them. For the calibration and re-tuning of crop growth models information about important phenological events such as heading/flowering is rather important. After this stage reproductive growth begins, whereby the number of kernels per plant is often calculated from plant weight at flowering and kernel weight is calculated from time and temperature available for dry matter distribution. By the use of the SAR VV time-series this important stage could be successfully extracted. Further methods for pixel-based fused biophysical parameter estimations, using SAR and multispectral data were analysed. By this approach the different features, being monitored of the two systems, are combined for sounder parameter retrieval. The assessed method of combining the multi-sensoral information by linear regression did not bring sound results and was outperformed by single sensor use, only taking into account the multispectral information. Only for the parameter fresh biomass, modelling based on the NDIV and the ASAR ratio slightly outperformed the single sensor modelling approaches. The complex combined modelling by the use of the CLAIR and the Water Cloud Model featured no valid results. For the combination, by using the CLAIR model and multiple regression slight improvements, in contrast to the single multispectral sensor use, were achieved. Especially, during late phenological stages, the assessed VV information improved the modelling results, in comparison to only using the CLAIR model. All the findings could finally be successfully applied for regional estimations. Only the roughness features could not be applied, due to the fact, that it is hard to regionally assess this needed model input parameter. Regional parameter on the basis of remote sensing data, is the major advantage of this technique, due to the large spatial overview given. The second main question was, if it is possible to integrate the crop variables gained from multisensoral data into a crop growth model, increasing the final yield estimation accuracy. Thus far, beneficial linkages between both techniques have been often limited to land use classification via remote sensing for choosing the adequate model and quantification of crop growth and development curves using biophysical parameters derived from remote sensing images for model calibration. Only a few studies actually considered the potentials of remote sensing for model re-initialization of growth and development characteristics of a specific crop, as the here studied winter wheat. Overall, the integration of remotely sensed variables into the crop growth model CERES-Wheat led to an improved final yield estimation accuracy in comparison to an automatic input parameter setting. The assessed final yield bias for the automatic input parameter setting summed up to 6.6%. When re-initializing the most sensitive input parameters (sowing date and fertilizer application date) by the use of remotely sensed biophysical variables the biases ranged from 0.56% overestimation to 5.4% understimation, in dependence of the data series used for assimilation. Whereby, it was assessed that the combined dense data series, considering SAR and multispectral information, slightly outperformed the performance of the full multispectral data series. However, when analysing the assimilation of the multispectral data series in further detail, it became clear that the actually information from the phenological stage ripening declines the modelling performance and thus the final yield estimation accuracy. When neglecting the information from this phenological stage the reduced multispectral data series performed as sound as the dense data series containing SAR and multispectral information. Thus, when the appropriate phenological stages are monitored by multispectral data, additional SAR information does not lead to a model improvement. However, when important dates are not monitored by multispectral images, e.g., due to cloud coverage, the additionally considered SAR information was not able to appropriatly fill these important multispectral time gaps. They even had a more negeative influence on the modelling performance. Overall, the best results could be obtained by assimilating a multispectral data series, covering the crop development during the important phenological stages stem elongation and flowering (without ripening stage), into the CERES-Wheat model. Finally, the integration of remote sensing data in the point-based crop growth model allowed it‘s spatial application for prediction of wheat production at a more regional scale. This approach also outperformed another evaluated method of direct multi-sensoral regional yield estimation. This study has demonstrated that biophysical parameters can be retrieved from remote sensing data and led, when assimilated into a crop growth model, to an improved final yield estimation. However, overall the SAR information did not really have a significant positive effect on the multi-sensoral biophysical parameter retrieval and on the later assimilation process. Thus, overall SAR information should only be considered, when multispectral data acquisitions are tremendously hampered by cloud coverage. The assessed assimilation of remote sensing information into a crop growth model had a positive effect on the final yield estimation performance. The analysed method, combining remote sensing and crop growth model techniques, was succsessfully demonstrated and will gain even more importance in the future for, e.g., decision support systems fine-tuning fertilizer regimes and thus contributing to more environmentally sound and sustained agricultural production

Monitoring crops water needs at high spatio-temporal resolution by synergy of optical/thermal and radar observations

L'optimisation de la gestion de l'eau en agriculture est essentielle dans les zones semi-arides afin de préserver les ressources en eau qui sont déjà faibles et erratiques dues à des actions humaines et au changement climatique. Cette thèse vise à utiliser la synergie des observations de télédétection multispectrales (données radar, optiques et thermiques) pour un suivi à haute résolution spatio-temporelle des besoins en eau des cultures. Dans ce contexte, différentes approches utilisant divers capteurs (Landsat-7/8, Sentinel-1 et MODIS) ont été developpées pour apporter une information sur l'humidité du sol (SM) et le stress hydrique des cultures à une échelle spatio-temporelle pertinente pour la gestion de l'irrigation. Ce travail va parfaitement dans le sens des objectifs du projet REC "Root zone soil moisture Estimates at the daily and agricultural parcel scales for Crop irrigation management and water use impact: a multi-sensor remote sensing approach" (http://rec.isardsat.com/) qui visent à estimer l'humidité du sol dans la zone racinaire (RZSM) afin d'optimiser la gestion de l'eau d'irrigation. Des approches innovantes et prometteuses sont mises en place pour estimer l'évapotranspiration (ET), RZSM, la température de surface du sol (LST) et le stress hydrique de la végétation à travers des indices de SM dérivés des observations multispectrales à haute résolution spatio-temporelle. Les méthodologies proposées reposent sur des méthodes basées sur l'imagerie, la modélisation du transfert radiatif et la modélisation du bilan hydrique et d'énergie et sont appliquées dans une région à climat semi-aride (centre du Maroc). Dans le cadre de ma thèse, trois axes ont été explorés. Dans le premier axe, un indice de RZSM dérivé de LST-Landsat est utilisé pour estimer l'ET sur des parcelles de blé et des sols nus. L'estimation par modélisation de ET a été explorée en utilisant l'équation de Penman-monteith modifiée obtenue en introduisant une relation empirique simple entre la résistance de surface (rc) et l'indice de RZSM. Ce dernier est estimé à partir de la température de surface (LST) dérivée de Landsat, combinée avec les températures extrêmes (en conditions humides et sèches) simulée par un modèle de bilan d'énergie de surface piloté par le forçage météorologique et la fraction de couverture végétale dérivée de Landsat. La méthode utilisée est calibrée et validée sur deux parcelles de blé situées dans la même zone près de Marrakech au Maroc. Dans l'axe suivant, une méthode permettant de récupérer la SM de la surface (0-5 cm) à une résolution spatiale et temporelle élevée est développée à partir d'une synergie entre données radar (Sentinel-1) et thermique (Landsat) et en utilisant un modèle de bilan d'énergie du sol. L'approche développée a été validée sur des parcelles agricoles en sol nu et elle donne une estimation précise de la SM avec une différence quadratique moyenne en comparant à la SM in situ, égale à 0,03 m3 m-3. Dans le dernier axe, une nouvelle méthode est développée pour désagréger la MODIS LST de 1 km à 100 m de résolution en intégrant le SM proche de la surface dérivée des données radar Sentinel-1 et l'indice de végétation optique dérivé des observations Landsat. Le nouvel algorithme, qui inclut la rétrodiffusion S-1 en tant qu'entrée dans la désagrégation, produit des résultats plus stables et robustes au cours de l'année sélectionnée. Dont, 3,35 °C était le RMSE le plus bas et 0,75 le coefficient de corrélation le plus élevé évalués en utilisant le nouvel algorithme.Optimizing water management in agriculture is essential over semi-arid areas in order to preserve water resources which are already low and erratic due to human actions and climate change. This thesis aims to use the synergy of multispectral remote sensing observations (radar, optical and thermal data) for high spatio-temporal resolution monitoring of crops water needs. In this context, different approaches using various sensors (Landsat-7/8, Sentinel-1 and MODIS) have been developed to provide information on the crop Soil Moisture (SM) and water stress at a spatio-temporal scale relevant to irrigation management. This work fits well the REC "Root zone soil moisture Estimates at the daily and agricultural parcel scales for Crop irrigation management and water use impact: a multi-sensor remote sensing approach" (http://rec.isardsat.com/) project objectives, which aim to estimate the Root Zone Soil Moisture (RZSM) for optimizing the management of irrigation water. Innovative and promising approaches are set up to estimate evapotranspiration (ET), RZSM, land surface temperature (LST) and vegetation water stress through SM indices derived from multispectral observations with high spatio-temporal resolution. The proposed methodologies rely on image-based methods, radiative transfer modelling and water and energy balance modelling and are applied in a semi-arid climate region (central Morocco). In the frame of my PhD thesis, three axes have been investigated. In the first axis, a Landsat LST-derived RZSM index is used to estimate the ET over wheat parcels and bare soil. The ET modelling estimation is explored using a modified Penman-Monteith equation obtained by introducing a simple empirical relationship between surface resistance (rc) and a RZSM index. The later is estimated from Landsat-derived land surface temperature (LST) combined with the LST endmembers (in wet and dry conditions) simulated by a surface energy balance model driven by meteorological forcing and Landsat-derived fractional vegetation cover. The investigated method is calibrated and validated over two wheat parcels located in the same area near Marrakech City in Morocco. In the next axis, a method to retrieve near surface (0-5 cm) SM at high spatial and temporal resolution is developed from a synergy between radar (Sentinel-1) and thermal (Landsat) data and by using a soil energy balance model. The developed approach is validated over bare soil agricultural fields and gives an accurate estimates of near surface SM with a root mean square difference compared to in situ SM equal to 0.03 m3 m-3. In the final axis a new method is developed to disaggregate the 1 km resolution MODIS LST at 100 m resolution by integrating the near surface SM derived from Sentinel-1 radar data and the optical-vegetation index derived from Landsat observations. The new algorithm including the S-1 backscatter as input to the disaggregation, produces more stable and robust results during the selected year. Where, 3.35 °C and 0.75 were the lowest RMSE and the highest correlation coefficient assessed using the new algorithm

A survey of image-based computational learning techniques for frost detection in plants

Frost damage is one of the major concerns for crop growers as it can impact the growth of the plants and hence, yields. Early detection of frost can help farmers mitigating its impact. In the past, frost detection was a manual or visual process. Image-based techniques are increasingly being used to understand frost development in plants and automatic assessment of damage resulting from frost. This research presents a comprehensive survey of the state-of the-art methods applied to detect and analyse frost stress in plants. We identify three broad computational learning approaches i.e., statistical, traditional machine learning and deep learning, applied to images to detect and analyse frost in plants. We propose a novel taxonomy to classify the existing studies based on several attributes. This taxonomy has been developed to classify the major characteristics of a significant body of published research. In this survey, we profile 80 relevant papers based on the proposed taxonomy. We thoroughly analyse and discuss the techniques used in the various approaches, i.e., data acquisition, data preparation, feature extraction, computational learning, and evaluation. We summarise the current challenges and discuss the opportunities for future research and development in this area including in-field advanced artificial intelligence systems for real-time frost monitoring

Reviewing the potential of Sentinel-2 in assessing the drought

This paper systematically reviews the potential of the Sentinel-2 (A and B) in assessing drought. Research findings, including the IPCC reports, highlighted the increasing trend in drought over the decades and the need for a better understanding and assessment of this phenomenon. Continuous monitoring of the Earth’s surface is an efficient method for predicting and identifying the early warnings of drought, which enables us to prepare and plan the mitigation procedures. Considering the spatial, temporal, and spectral characteristics, the freely available Sentinel-2 data products are a promising option in this area of research, compared to Landsat and MODIS. This paper evaluates the recent developments in this field induced by the launch of Sentinel-2, as well as the comparison with other existing data products. The objective of this paper is to evaluate the potential of Sentinel-2 in assessing drought through vegetation characteristics, soil moisture, evapotranspiration, surface water including wetland, and land use and land cover analysis. Furthermore, this review also addresses and compares various data fusion methods and downscaling methods applied to Sentinel-2 for retrieving the major bio-geophysical variables used in the analysis of drought. Additionally, the limitations of Sentinel-2 in its direct applicability to drought studies are also evaluated

Implementation of Sensors and Artificial Intelligence for Environmental Hazards Assessment in Urban, Agriculture and Forestry Systems

The implementation of artificial intelligence (AI), together with robotics, sensors, sensor networks, Internet of Things (IoT), and machine/deep learning modeling, has reached the forefront of research activities, moving towards the goal of increasing the efficiency in a multitude of applications and purposes related to environmental sciences. The development and deployment of AI tools requires specific considerations, approaches, and methodologies for their effective and accurate applications. This Special Issue focused on the applications of AI to environmental systems related to hazard assessment in urban, agriculture, and forestry areas

Remote Sensing of Plant Biodiversity

This Open Access volume aims to methodologically improve our understanding of biodiversity by linking disciplines that incorporate remote sensing, and uniting data and perspectives in the fields of biology, landscape ecology, and geography. The book provides a framework for how biodiversity can be detected and evaluated—focusing particularly on plants—using proximal and remotely sensed hyperspectral data and other tools such as LiDAR. The volume, whose chapters bring together a large cross-section of the biodiversity community engaged in these methods, attempts to establish a common language across disciplines for understanding and implementing remote sensing of biodiversity across scales. The first part of the book offers a potential basis for remote detection of biodiversity. An overview of the nature of biodiversity is described, along with ways for determining traits of plant biodiversity through spectral analyses across spatial scales and linking spectral data to the tree of life. The second part details what can be detected spectrally and remotely. Specific instrumentation and technologies are described, as well as the technical challenges of detection and data synthesis, collection and processing. The third part discusses spatial resolution and integration across scales and ends with a vision for developing a global biodiversity monitoring system. Topics include spectral and functional variation across habitats and biomes, biodiversity variables for global scale assessment, and the prospects and pitfalls in remote sensing of biodiversity at the global scale

Remote Sensing of Plant Biodiversity

At last, here it is. For some time now, the world has needed a text providing both a new theoretical foundation and practical guidance on how to approach the challenge of biodiversity decline in the Anthropocene. This is a global challenge demanding global approaches to understand its scope and implications. Until recently, we have simply lacked the tools to do so. We are now entering an era in which we can realistically begin to understand and monitor the multidimensional phenomenon of biodiversity at a planetary scale. This era builds upon three centuries of scientific research on biodiversity at site to landscape levels, augmented over the past two decades by airborne research platforms carrying spectrometers, lidars, and radars for larger-scale observations. Emerging international networks of fine-grain in-situ biodiversity observations complemented by space-based sensors offering coarser-grain imagery—but global coverage—of ecosystem composition, function, and structure together provide the information necessary to monitor and track change in biodiversity globally. This book is a road map on how to observe and interpret terrestrial biodiversity across scales through plants—primary producers and the foundation of the trophic pyramid. It honors the fact that biodiversity exists across different dimensions, including both phylogenetic and functional. Then, it relates these aspects of biodiversity to another dimension, the spectral diversity captured by remote sensing instruments operating at scales from leaf to canopy to biome. The biodiversity community has needed a Rosetta Stone to translate between the language of satellite remote sensing and its resulting spectral diversity and the languages of those exploring the phylogenetic diversity and functional trait diversity of life on Earth. By assembling the vital translation, this volume has globalized our ability to track biodiversity state and change. Thus, a global problem meets a key component of the global solution. The editors have cleverly built the book in three parts. Part 1 addresses the theory behind the remote sensing of terrestrial plant biodiversity: why spectral diversity relates to plant functional traits and phylogenetic diversity. Starting with first principles, it connects plant biochemistry, physiology, and macroecology to remotely sensed spectra and explores the processes behind the patterns we observe. Examples from the field demonstrate the rising synthesis of multiple disciplines to create a new cross-spatial and spectral science of biodiversity. Part 2 discusses how to implement this evolving science. It focuses on the plethora of novel in-situ, airborne, and spaceborne Earth observation tools currently and soon to be available while also incorporating the ways of actually making biodiversity measurements with these tools. It includes instructions for organizing and conducting a field campaign. Throughout, there is a focus on the burgeoning field of imaging spectroscopy, which is revolutionizing our ability to characterize life remotely. Part 3 takes on an overarching issue for any effort to globalize biodiversity observations, the issue of scale. It addresses scale from two perspectives. The first is that of combining observations across varying spatial, temporal, and spectral resolutions for better understanding—that is, what scales and how. This is an area of ongoing research driven by a confluence of innovations in observation systems and rising computational capacity. The second is the organizational side of the scaling challenge. It explores existing frameworks for integrating multi-scale observations within global networks. The focus here is on what practical steps can be taken to organize multi-scale data and what is already happening in this regard. These frameworks include essential biodiversity variables and the Group on Earth Observations Biodiversity Observation Network (GEO BON). This book constitutes an end-to-end guide uniting the latest in research and techniques to cover the theory and practice of the remote sensing of plant biodiversity. In putting it together, the editors and their coauthors, all preeminent in their fields, have done a great service for those seeking to understand and conserve life on Earth—just when we need it most. For if the world is ever to construct a coordinated response to the planetwide crisis of biodiversity loss, it must first assemble adequate—and global—measures of what we are losing

Impact of climate and anthropogenic effects on the energy, water, and carbon budgets of monitored agrosystems: multi-site analysis combining modelling and experimentation

Les terres cultivées représentent une unité importante dans le climat mondial, et en réponse à la population, elles sont en expansion. Il est crucial de comprendre et de quantifier les interactions terre-atmosphère via les échanges d'eau, d'énergie et de carbone. Dans ce contexte, cette thèse a consisté à étudier la variabilité du bilan énergétique en fonction de différentes cultures, phénologies et pratiques agricoles via système Eddy-Covariance. En réponse au manque d'eau dans le sud-ouest de la France, deux modèles de surface (ISBA et ISBA-MEB) ont été évalués sur deux cultures (blé et maïs) pour évaluer leur capacité à estimer les flux d'énergie et d'eau. Enfin, en réponse à la contribution des terres cultivées à l'augmentation du dioxyde de carbone atmosphérique, la capacité du modèle ISBA-MEB à simuler correctement les principaux composants du carbone a été testée sur 11 saisons de maïs et de blé.Croplands represent an important unit within the global climate, and in response to population, they are expanding. Hence, understanding and quantifying the land-atmosphere interactions via water, energy and carbon exchanges is crucial. In this context, the first objective of this thesis studied the variability of the energy balance over different crops, phenologies, and farm practices at Lamasquère and Auradé. Secondly, in response to water scarcity and increasing drought in southwestern France, two land surface models (ISBA and ISBA-MEB) of different configurations were evaluated over some wheat and maize years to test their ability to estimate energy and water fluxes using measurements from an eddy covariance system as reference. Finally, in response to the contribution of croplands to increasing atmospheric carbon dioxide, the capability of the ISBA-MEB model to correctly simulate the major carbon components was tested over 11 seasons of maize and wheat

Estimation spatialisée de la biomasse et des besoins en eau des cultures à l'aide de données satellitales à hautes résolutions spatiale et temporelle : application aux agrosystèmes du sud-ouest de la France

Il existe un lien étroit entre les agrosystèmes et les cycles du carbone (processus de séquestration du carbone dans les sols) et de l'eau (systèmes de production par irrigation). Cette thèse contribue à l'analyse et la validation des méthodes de quantification, sur de grandes surfaces, de la biomasse (cycle du carbone) et des besoins en eau (cycle de l'eau) des agrosystèmes. Pour répondre à cet objectif, des données de télédétection sont assimilées dans un modèle de cultures, SAFY (Simple Algorithm For Yield Estimate), au travers d'une variable biophysique clés, le GAI (Green area index). Des méthodes d'estimation in situ (par proxy-détection) et spatialisées (par inversion de modèles de transfert radiatif) du GAI sont, tout d'abord, étudiées et validées. Les séries temporelles de GAI déterminées à partir des données de télédétection sont ensuite utilisées pour étalonner le modèle SAFY, conduisant à des estimations spatialisées de biomasse et des besoins en eau des cultures. Ces estimations sont validées par confrontation à un dispositif expérimental mis en place entre 2006 et 2010 et situé dans le sud-ouest de la France. Les cultures étudiées sont des cultures d'été non irriguées (tournesol) et irriguées (maïs, soja). Les données de télédétection utilisées pour estimer les séries temporelles de GAI sont issues du capteur Formosat-2. Ces données sont particulièrement pertinentes car elles combinent une haute résolution spatiale (8 m) et une haute fréquence temporelle (1 jour), indispensables pour le suivi des surfaces agricoles.There is a close relationship between agrosystems (or agroecosystems) and carbon (soil carbon sequestration process) and water (irrigation management systems) cycles. This PhD thesis contributes to the analysis and the validation of methods for quantification of agrosystems biomass (carbon cycle) and water needs (water cycle) over large land surfaces. To this end, remote sensing data are assimilated within a crop model, SAFY (Simple Algorithm For Yield Estimate), through a key biophysical variable, the GAI (Green area index). GAI in situ (proxy-detection) and spatialized (inversion of radiative transfer models) estimation methods are first assessed. Secondly, remote sensed time series of GAI are used for the calibration of the SAFY crop model in order to deliver spatial estimates of crop biomass and water needs. These estimations are validated, through direct comparison with an experimental system which is located in the southwest of France and run from 2006 to 2010. Studied crops are maize and soybean, which are irrigated, and also sunflower, which is non-irrigated. Remote sensing data used to estimate the time series of GAI are taken from Formosat-2 sensors. Such data are particularly relevant for the crop monitoring because they combine high spatial resolution (8 m) and high temporal frequency (1 day)