Crop Disease Detection Using Remote Sensing Image Analysis

Pest and crop disease threats are often estimated by complex changes in crops and the applied agricultural practices that result mainly from the increasing food demand and climate change at global level. In an attempt to explore high-end and sustainable solutions for both pest and crop disease management, remote sensing technologies have been employed, taking advantages of possible changes deriving from relative alterations in the metabolic activity of infected crops which in turn are highly associated to crop spectral reflectance properties. Recent developments applied to high resolution data acquired with remote sensing tools, offer an additional tool which is the opportunity of mapping the infected field areas in the form of patchy land areas or those areas that are susceptible to diseases. This makes easier the discrimination between healthy and diseased crops, providing an additional tool to crop monitoring. The current book brings together recent research work comprising of innovative applications that involve novel remote sensing approaches and their applications oriented to crop disease detection. The book provides an in-depth view of the developments in remote sensing and explores its potential to assess health status in crops

Remote sensing and machine learning for prediction of wheat growth in precision agriculture applications

This thesis focuses on remote sensing and machine learning for prediction of wheat growth in precision agriculture applications. Agriculture is the primary productive force, which plays an important role in human activities. Wheat, as one of the essential sources of food, is also a widely planted crop. The impact of weather and climate and some other uncertain factors on wheat production is crucial. Therefore, it is necessary to use reliable and statistically reasonable models for crop growth and yield prediction based on vegetation index variables and other factors, so as to obtain reliable prediction for efficient production. Applying certain artificial intelligence algorithms to the precision agriculture can significantly improve the efficiency of traditional agriculture in crop planting and reduce the consumption of human and natural resources. Remote sensing can objectively, accurately and timely provide a large amount of information for ecological environment and crop growth in agriculture applications. By combining the image and spectral data obtained by remote sensing technology with machine learning, information about wheat growth, yield and insect pests can be learned in time. This thesis focuses on its applications in agriculture, particularly using effective prediction models such as the back propagation neural network and some optimisation algorithms for predicting wheat growth, yield and aphid. The work presented in this thesis address the issues of wheat growth prediction, yield assessment and aphid validation by model building and machine learning algorithm optimisation by means of remote sensing data. Specifically, the following objectives are defined: 1. Analyse multiple vegetation indexes based on the TM 1-4 band data of Landsat satellite and use regression algorithms to train the models and predict wheat growth; 2. Analyse and compare multiple vegetation indexes models by means of spectral data and use regression algorithms to predict wheat yield; 3. Combine spectral vegetation indexes and multiple regression algorithms to predict wheat aphid; 4. Use accurate evaluation criteria for validating the efficacy of the various algorithms. In this thesis, the remote sensing data from the satellite has been applied instead of the airborne-based remote sensing data. Based on the TM 1-4 band image data of Landsat satellite, multiple vegetation indexes were used as the input of regression algorithms. After that, four kinds of regression algorithms such as the multiple linear regression (MR) algorithm, back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm were used to train the model and predict the LAI and SPAD. The prediction results of each algorithm were compared with the ground truth information collected by hand held instruments on the ground. The relationship between wheat yield and spectral data has been studied. Based on the BPNN algorithm, four kinds of models such as visible hyperspectral index (VHI) model, hyperspectral vegetation index (HVI) model, difference hyperspectral index (DHI) model and normalized hyperspectral index (NHI) model have been utilized to predict wheat yield. For the optimal NHI model, three regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm, were compared to predict wheat yield, and RMSE and R-square of the three algorithms were compared and analysed. Finally, the relationship between wheat aphid and spectral data has been investigated. Nine vegetation indexes related to aphid have been estimated from spectral data as the input of regression algorithms. Five kinds of regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm, particle swarm optimisation (PSO) optimised BPNN algorithm, ant colony (ACO) optimisation algorithm optimised BPNN algorithm and cuckoo search (CS) optimised BPNN algorithm have been implemented to predict wheat aphid, which was validated with the ground truth information measured by hand-held instruments on the ground. The prediction results of each algorithm have been analysed. The major original contributions of this thesis are as follows: 1. A variety of optimisation algorithms are used to improve the regression analysis of the BPNN algorithm, so that the prediction results of each model for wheat growth, yield and aphid are more accurate. 2. The spectral characteristics of winter wheat canopy have been analysed. The correlation between the absorption band and the associated physical and chemical properties of crops, specially the red edge slope, with the crop yield and wheat aphid damage is established. 3. Adjusted MSE and un-centered R-square, as accurate evaluation criteria for practical applications, are used to compare the prediction results of the models under different dimensions of the observed data. 4. Improve algorithm training by using the cross-validation method to obtain reliable and stable models for the prediction of wheat growth, yield, and aphid. Through repeated cross-validation, a better model can be obtained in the last. Key word：Precision agriculture; BP network, wheat growth assessment; wheat yield prediction, wheat aphid validationThis thesis focuses on remote sensing and machine learning for prediction of wheat growth in precision agriculture applications. Agriculture is the primary productive force, which plays an important role in human activities. Wheat, as one of the essential sources of food, is also a widely planted crop. The impact of weather and climate and some other uncertain factors on wheat production is crucial. Therefore, it is necessary to use reliable and statistically reasonable models for crop growth and yield prediction based on vegetation index variables and other factors, so as to obtain reliable prediction for efficient production. Applying certain artificial intelligence algorithms to the precision agriculture can significantly improve the efficiency of traditional agriculture in crop planting and reduce the consumption of human and natural resources. Remote sensing can objectively, accurately and timely provide a large amount of information for ecological environment and crop growth in agriculture applications. By combining the image and spectral data obtained by remote sensing technology with machine learning, information about wheat growth, yield and insect pests can be learned in time. This thesis focuses on its applications in agriculture, particularly using effective prediction models such as the back propagation neural network and some optimisation algorithms for predicting wheat growth, yield and aphid. The work presented in this thesis address the issues of wheat growth prediction, yield assessment and aphid validation by model building and machine learning algorithm optimisation by means of remote sensing data. Specifically, the following objectives are defined: 1. Analyse multiple vegetation indexes based on the TM 1-4 band data of Landsat satellite and use regression algorithms to train the models and predict wheat growth; 2. Analyse and compare multiple vegetation indexes models by means of spectral data and use regression algorithms to predict wheat yield; 3. Combine spectral vegetation indexes and multiple regression algorithms to predict wheat aphid; 4. Use accurate evaluation criteria for validating the efficacy of the various algorithms. In this thesis, the remote sensing data from the satellite has been applied instead of the airborne-based remote sensing data. Based on the TM 1-4 band image data of Landsat satellite, multiple vegetation indexes were used as the input of regression algorithms. After that, four kinds of regression algorithms such as the multiple linear regression (MR) algorithm, back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm were used to train the model and predict the LAI and SPAD. The prediction results of each algorithm were compared with the ground truth information collected by hand held instruments on the ground. The relationship between wheat yield and spectral data has been studied. Based on the BPNN algorithm, four kinds of models such as visible hyperspectral index (VHI) model, hyperspectral vegetation index (HVI) model, difference hyperspectral index (DHI) model and normalized hyperspectral index (NHI) model have been utilized to predict wheat yield. For the optimal NHI model, three regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm and particle swarm optimisation (PSO) optimised BPNN algorithm, were compared to predict wheat yield, and RMSE and R-square of the three algorithms were compared and analysed. Finally, the relationship between wheat aphid and spectral data has been investigated. Nine vegetation indexes related to aphid have been estimated from spectral data as the input of regression algorithms. Five kinds of regression algorithms such as back propagation network (BPNN) algorithm, genetic algorithm (GA) optimised BPNN algorithm, particle swarm optimisation (PSO) optimised BPNN algorithm, ant colony (ACO) optimisation algorithm optimised BPNN algorithm and cuckoo search (CS) optimised BPNN algorithm have been implemented to predict wheat aphid, which was validated with the ground truth information measured by hand-held instruments on the ground. The prediction results of each algorithm have been analysed. The major original contributions of this thesis are as follows: 1. A variety of optimisation algorithms are used to improve the regression analysis of the BPNN algorithm, so that the prediction results of each model for wheat growth, yield and aphid are more accurate. 2. The spectral characteristics of winter wheat canopy have been analysed. The correlation between the absorption band and the associated physical and chemical properties of crops, specially the red edge slope, with the crop yield and wheat aphid damage is established. 3. Adjusted MSE and un-centered R-square, as accurate evaluation criteria for practical applications, are used to compare the prediction results of the models under different dimensions of the observed data. 4. Improve algorithm training by using the cross-validation method to obtain reliable and stable models for the prediction of wheat growth, yield, and aphid. Through repeated cross-validation, a better model can be obtained in the last. Key word：Precision agriculture; BP network, wheat growth assessment; wheat yield prediction, wheat aphid validatio

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

The potential for using remote sensing to quantify stress in and predict yield of sugarcane (Saccharum spp. hybrid)

Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010

Modelling spatial variability of coffee (Coffea Arabica L.) crop condition with multispectral remote sensing data.

Doctor of Philosophy in Environmental Science. University of KwaZulu-Natal, Pietermaritzburg, 2017.Abstract available in PDF file

Finding spectral features for the early identification of biotic stress in plants

Early detection of biotic stress in plants is vital for precision crop protection, but hard to achieve. Prediction of plant diseases or weeds at an early stage has significant influence on the extent and effectiveness of crop protection measures. The precise measure depends on specific weeds and plant diseases and their economic thresholds. Weeds and plant diseases at an early stage, however, are difficult to identify. Non-invasive optical sensors with high resolution are promising for early detection of biotic stress. The data of these sensors, e.g. hyperspectral or fluorescence signatures, contain relevant information about the occurrence of pathogens. Shape parameters, derived from bispectral images, have enormous potential for an early identification of weeds in crops. The analysis of this high dimensional data for an identification of weeds and pathogens as early as possible is demanding as the sensor signal is affected by many influencing factors. Nevertheless, advanced methods of machine learning facilitate the interpretation of these signals. Whereas traditional statistics estimate the posterior probability of the class by probability distribution, machine learning methods provide algorithms for optimising prediction accuracy by the discriminant function. Machine learning methods with robust training algorithms play a key role in handling non-linear classification problems. This thesis presents an approach which integrates modern sensor techniques and advanced machine learning methods for an early detection and differentiation of plant diseases and weeds. Support vector machines (SVMs) equipped with non-linear kernels prove as effective and robust classifiers. Furthermore, it is shown that even a presymptomatic identification based on the combination of spectral vegetation indices is realised. Using well-established data analysis methods of this scientific field, this has not achieved so far. Identifying disease specific features from the underlying original high dimensional sensor data selection is conducted. The high dimensionality of data affords a careful selection of relevant and non-redundant features depending on classification problem and feature properties. In the case of fluorescence signatures an extraction of new features is necessary. In this context modelling of signal noise by an analytical description of the spectral signature improves the accuracy of classification substantially. In the case of weed discrimination accuracy is improved by exploiting the hierarchy of weed species. This thesis outlines the potential of SVMs, feature construction and feature selection for precision crop protection. A problem-specific extraction and selection of relevant features, in combination with task-oriented classification methods, is essential for robust identification of pathogens and weeds as early as possible.Früherkennung von biotischem Pflanzenstress ist für den Präzisionspflanzenschutz wesentlich, aber schwierig zu erreichen. Die Vorhersage von Pflanzenkrankheiten und Unkräutern in einem frühen Entwicklungsstadium hat signifikanten Einfluss auf das Ausmaß und die Effektivität einer Pflanzenschutzmaßnahme. Aufgrund der Abhängigkeit einer Maßnahme von der Art der Pflanzenkrankheit oder des Unkrauts und ihrer ökonomischer Schadschwelle ist eine präzise Identifizierung der Schadursache essentiell, aber gerade im Frühstadium durch die Ähnlichkeit der Schadbilder problematisch. Nicht-invasive optische Sensoren mit hoher Auflösung sind vielversprechend für eine Früherkennung von biotischem Pflanzenstress. Daten dieser Sensoren, beispielsweise Hyperspektral- oder Fluoreszenzspektren, enthalten relevante Informationen über das Auftreten von Pathogenen; Formparameter, abgeleitet aus bispektralen Bildern, zeigen großes Potential für die Früherkennung von Unkräutern in Kulturpflanzen. Die Analyse dieser hochdimensionalen Sensordaten unter Berücksichtigung vielfältiger Faktoren ist eine anspruchsvolle Herausforderung. Moderne Methoden des maschinellen Lernens bieten hier zielführende Möglichkeiten. Während die traditionelle Statistik die a-posteriori Wahrscheinlichkeit der Klasse basierend auf Wahrscheinlichkeitsverteilungen schätzt, verwenden maschinelle Lernverfahren Algorithmen für eine Optimierung der Vorhersagegenauigkeit auf Basis diskriminierender Funktionen. Grundlage zur Bearbeitung dieser nicht-linearen Klassi kationsprobleme sind robuste maschinelle Lernverfahren. Die vorliegende Dissertationsschrift zeigt, dass die Integration moderner Sensortechnik mit fortgeschrittenen Methoden des maschinellen Lernens eine Erkennung und Differenzierung von Pflanzenkrankheiten und Unkräutern ermöglicht. Einen wesentlichen Beitrag für eine effektive und robuste Klassifikation leisten Support Vektor Maschinen (SVMs) mit nicht-linearen Kernels. Weiterhin wird gezeigt, dass SVMs auf Basis spektraler Vegetationsindizes die Detektion von Pflanzenkrankheiten noch vor Auftreten visuell wahrnehmbarer Symptome ermöglichen. Dies wurde mit bekannten Verfahren noch nicht erreicht. Zur Identifikation krankheitsspezifischer Merkmale aus den zugrunde liegenden originären hochdimensionalen Sensordaten wurden Merkmale konstruiert und selektiert. Die Selektion ist sowohl vom Klassifikationsproblem als auch von den Eigenschaften der Merkmale abhängig. Im Fall von Fluoreszenzspektren war eine Extraktion von neuen Merkmalen notwendig. In diesem Zusammenhang trägt die Modellierung des Signalrauschens durch eine analytische Beschreibung der spektralen Signatur zur deutlichen Verbesserung der Klassifikationsgenauigkeit bei. Im Fall der Differenzierung von unterschiedlichen Unkräutern erhöht die Ausnutzung der Hierarchie der Unkrautarten die Genauigkeit signifikant. Diese Arbeit zeigt das Potential von Support Vektor Maschinen, Merkmalskonstruktion und Selektion für den Präzisionspflanzenschutz. Eine problemspezifische Extraktion und Selektion relevanter Merkmale in Verbindung mit sachbezogenen Klassifikationsmethoden ermöglichen eine robuste Identifikation von Pathogenen und Unkräutern zu einem sehr frühen Zeitpunkt

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

Detección temprana y discriminación de enfermedades fúngicas en plantas usando espectroscopía in situ

After infection, a plant develops symptoms that appear in different parts of plants; however, at moment in which these symptoms are visible, the plant can already be affected negatively. In addition, plants that remain asymptomatic are pathogens reservoirs, since they can remain infected for most of their development cycle, becoming a source of contamination for entire crop. After the symptoms onset, disease is verified using detection techniques, such as ELISA, Polymerase Chain Reaction, Immunofluorescence, Flow Cytometry, Fluorescence in situ and, Gaseous Metabolite Profiles, among others. However, despite the availability of these techniques, a diseases early detection system based on spectrometry techniques can help to reduce losses caused in crops and prevent a greater spread of disease, with more speed, sensitivity, selectivity and without requiring the samples destruction required for analysis. The aim of this study is to evaluate early detection of plants diseases caused by fungal infections using in situ reflectance spectroscopy. To achieve this, reflectance spectra were measured from leaves of S. lycopersicum infected with a fungus pathogenic strains at various times of pathogenesis before the symptoms of the disease were visible. Additionally, physiological analyzes were performed and were related to reflectance spectra of the infected and healthy plants in different infection periods; also, were developed disease prediction models based on Vis/NIR reflectance data before the visual expression of the symptoms using different multivariate statistical tools. In this study it was possible to characterize the spectral variation in leaves of S. lycopersicum L. infected with F. oxysporum during the incubation period. It was also possible to identify the relevant specific wavelengths in the range of 380-1000 nm that can be used as spectral signatures for the detection and discrimination of vascular wilt in S. lycopersicum. We watch that inoculated tomato plants increased their reflectance in the visible range (Vis) and decreased slowly in the near infrared range (NIRs) measured during incubation, showing marked differences with plants subjected to water stress in the VIS/NIR. Additionally, three ranges were found in the spectrum related to infection by F. oxysporum (510nm-520nm, 650nm-670nm and 700-750nm). Linear discriminant models on spectral reflectance data were able to differentiate between tomatos varieties inoculated with F. oxysporum from healthy ones with accuracies higher than 70% 9 days after inoculation (only with three explanatory variables). Additionally, it was possible to characterize and relate the spectral variance in leaves of S. lycopersicum infected with F. oxysporum with the physiological variation and pathogen concentration in tomato plants during the asymptomatic period of vascular wilt. Photosynthetic parameters derived from gaseous exchange analyzes in the tomato leaves correlated related with four bands in the visible range (Vis). Additionally, five specific bands also correlated highly correlated with the increase of F. oxysporum conidia concentration measured at root: 448-523nm, 624-696nm, 740-960nm, 973-976nm and 992-995nm. These wavelengths allowed classifying correctly 100% the plants inoculated with F. oxysporum of plants subjected to hydric stress and controls in the disease asymptomatic period. Finally, it was possible to develop logistic regression models to predict infection by F. oxysporum in plants, obtaining accuracies and areas under the curve greater than 0.9 for one of the tomato varieties evaluated. The results of this study will contribute to a better understanding of the optical properties of the plant during the development of fungal diseases. These methods will be applicable in development of precision crops, specifically in crop protection, differentiation, quantification, and disease early detection of plant; in addition to, the developed models which can be used as a basic input in the design of technological tools that allow the plant disease detection in real timeDoctorad

Hyperspectral Remote Sensing of Crop Canopy Chlorophyll and Nitrogen: The Relative Importance of Growth Stages

Remote sensing plays an important role in monitoring vegetation dynamics, and has been recognized as a reliable tool for monitoring biochemical and biophysical variations of agricultural crops, such as plant biomass, height, chlorophyll (Chl) and nitrogen (N). Nitrogen is one of the most essential elements in agro-ecosystems because of its direct role in determining crop yield and vegetation productivity, as well as its association with global N and carbon cycles. Canopy remote sensing of plant biochemical (e.g., N) and biophysical parameters (e.g., biomass) is often discussed separately. However, crop canopy structural characteristics and plant morphophysiological variations at different growth stages cause a confounding effect on the analysis and interpretation of the canopy spectral data. This study aimed to (1) understand the underlying mechanisms of canopy structural dynamics (mainly plant biomass and green leaf area) that impact the retrieval of canopy Chl and N at different growth stages, and (2) develop new algorithms and narrow band vegetation indices that may improve the estimation of Chl and N using hyperspectral data collected in the field and simulated by radiative transfer models (RTMs). To achieve the objectives, barley and rice experiments were conducted in Germany and China, respectively, from experimental plots to farmer fields; both empirical and physical models were employed but with an emphasis on the empirical methods. Results suggest that canopy hyperspectral data allow for the estimation of canopy Chl and N. However, with the advance of growth stages, plant growth rate is much faster than the rate at which N is accumulated in the plant mass until the stage of full heading (canopy closure), which results in a decrease of N concentration — the N dilution effect. Thus, growth stages have a significant effect on the correlation between the optical and biological traits of the crop canopy compared to the differences in crop cultivars and types. This effect is confirmed by five years of experimental data of barley and rice crops. Accordingly, empirical models based on different vegetation indices can be calibrated, before and after the canopy closure, which allows for the monitoring of canopy Chl and N status through the entire growing season. This study also suggests that multivariate models such as partial least squares (PLS) and support vector machines (SVM) are relatively resistant to the influence of growth stages and can be used to improve the estimation of canopy Chl and N compared to univariate models based on vegetation indices. To devise a simple approach for the estimation of canopy Chl and N status that is relatively insensitive to the confounding effect of canopy structural characteristics, new vegetation indices, the Ratio of Reflectance Difference Indices (RRDIs), were developed based on the multiple scatter correction (MSC) theory. This type of indices conceptually eliminates the linear influence caused by the confounding effect of multiple scattering and soil background as well as their interactions; therefore, RRDI weakens the effect of canopy structural variations on the analysis of canopy spectra when estimating biochemical variations. For example, the RRDI derived from the red edge (RRDIre) wavelengths proved to be a robust indicator of canopy Chl and N in both barley and rice crops with different cultivars and for the simulated data by RTMs. Therefore, the method is useful for improving the estimation of canopy biochemical parameters. This study improves the understanding of remote estimation of canopy Chl and N status by considering the dynamical co-variations between plant biomass and N across different growth stages and suggests the potential to improve the ability of canopy hyperspectral data to monitor the canopy biogeochemical cycles of agro-ecosystems using remote sensing. Additionally, this study indicates that hyperspectral vegetation indices based on water absorption bands are useful for the detection of crop diseases at the canopy level