Evaluation of Oil-Palm Fungal Disease Infestation with Canopy Hyperspectral Reflectance Data

Fungal disease detection in perennial crops is a major issue in estate management and production. However, nowadays such diagnostics are long and difficult when only made from visual symptom observation, and very expensive and damaging when based on root or stem tissue chemical analysis. As an alternative, we propose in this study to evaluate the potential of hyperspectral reflectance data to help detecting the disease efficiently without destruction of tissues. This study focuses on the calibration of a statistical model of discrimination between several stages of Ganoderma attack on oil palm trees, based on field hyperspectral measurements at tree scale. Field protocol and measurements are first described. Then, combinations of pre-processing, partial least square regression and linear discriminant analysis are tested on about hundred samples to prove the efficiency of canopy reflectance in providing information about the plant sanitary status. A robust algorithm is thus derived, allowing classifying oil-palm in a 4-level typology, based on disease severity from healthy to critically sick stages, with a global performance close to 94%. Moreover, this model discriminates sick from healthy trees with a confidence level of almost 98%. Applications and further improvements of this experiment are finally discussed

A review of neural networks in plant disease detection using hyperspectral data

© 2018 China Agricultural University This paper reviews advanced Neural Network (NN) techniques available to process hyperspectral data, with a special emphasis on plant disease detection. Firstly, we provide a review on NN mechanism, types, models, and classifiers that use different algorithms to process hyperspectral data. Then we highlight the current state of imaging and non-imaging hyperspectral data for early disease detection. The hybridization of NN-hyperspectral approach has emerged as a powerful tool for disease detection and diagnosis. Spectral Disease Index (SDI) is the ratio of different spectral bands of pure disease spectra. Subsequently, we introduce NN techniques for rapid development of SDI. We also highlight current challenges and future trends of hyperspectral data

Detection, identification, and quantification of fungal diseases of sugar beet leaves using imaging and non-imaging hyperspectral techniques

Plant diseases influence the optical properties of plants in different ways. Depending on the host pathogen system and disease specific symptoms, different regions of the reflectance spectrum are affected, resulting in specific spectral signatures of diseased plants. The aim of this study was to examine the potential of hyperspectral imaging and non-imaging sensor systems for the detection, differentiation, and quantification of plant diseases. Reflectance spectra of sugar beet leaves infected with the fungal pathogens Cercospora beticola, Erysiphe betae, and Uromyces betae causing Cercospora leaf spot, powdery mildew, and sugar beet rust, respectively, were recorded repeatedly during pathogenesis. Hyperspectral data were analyzed using various methods of data and image analysis and were compared to ground truth data. Several approaches with different sensors on the measuring scales leaf, canopy, and field have been tested and compared. Much attention was paid on the effect of spectral, spatial, and temporal resolution of hyperspectral sensors on disease recording. Another focus of this study was the description of spectral characteristics of disease specific symptoms. Therefore, different data analysis methods have been applied to gain a maximum of information from spectral signatures. Spectral reflectance of sugar beet was affected by each disease in a characteristic way, resulting in disease specific signatures. Reflectance differences, sensitivity, and best correlating spectral bands differed depending on the disease and the developmental stage of the diseases. Compared to non-imaging sensors, the hyperspectral imaging sensor gave extra information related to spatial resolution. The preciseness in detecting pixel-wise spatial and temporal differences was on a high level. Besides characterization of diseased leaves also the assessment of pure disease endmembers as well as of different regions of typical symptoms was realized. Spectral vegetation indices (SVIs) related to physiological parameters were calculated and correlated to the severity of diseases. The SVIs differed in their sensitivity to the different diseases. Combining the information from multiple SVIs in an automatic classification method with Support Vector Machines, high sensitivity and specificity for the detection and differentiation of diseased leaves was reached in an early stage. In addition to the detection and identification, the quantification of diseases was possible with high accuracy by SVIs and Spectral Angle Mapper classification, calculated from hyperspectral images. Knowledge from measurements under controlled condition was carried over to the field scale. Early detection and monitoring of Cercospora leaf spot and powdery mildew was facilitated. The results of this study contribute to a better understanding of plant optical properties during disease development. Methods will further be applicable in precision crop protection, to realize the detection, differentiation, and quantification of plant diseases in early stages.Nachweis, Identifizierung und Quantifizierung pilzlicher Blattkrankheiten der Zuckerrübe mit abbildenden und nicht-abbildenden hyperspektralen Sensoren Pflanzenkrankheiten wirken sich auf die optischen Eigenschaften von Pflanzen in unterschiedlicher Weise aus. Verschiedene Bereiche des Reflektionsspektrums werden in Abhängigkeit von Wirt-Pathogen System und krankheitsspezifischen Symptomen beeinflusst. Hyperspektrale, nicht-invasive Sensoren bieten die Möglichkeit, optische Veränderungen zu einem frühen Zeitpunkt der Krankheitsentwicklung zu detektieren. Ziel dieser Arbeit war es, das Potential hyperspektraler abbildender und nicht abbildender Sensoren für die Erkennung, Identifizierung und Quantifizierung von Pflanzenkrankheiten zu beurteilen. Zuckerrübenblätter wurden mit den pilzlichen Erregern Cercospora beticola, Erysiphe betae bzw. Uromyces betae inokuliert und die Auswirkungen der Entwicklung von Cercospora Blattflecken, Echtem Mehltau bzw. Rübenrost auf die Reflektionseigenschaften erfasst und mit optischen Bonituren verglichen. Auf den Skalenebenen Blatt, Bestand und Feld wurden Messansätze mit unterschiedlichen Sensoren verglichen. Besonders berücksichtigt wurden hierbei Anforderungen an die spektrale, räumliche und zeitliche Auflösung der Sensoren. Ein weiterer Schwerpunkt lag auf der Beschreibung der spektralen Eigenschaften von charakteristischen Symptomen. Verschiedene Auswerteverfahren wurden mit dem Ziel angewendet, einen maximalen Informationsgehalt aus spektralen Signaturen zu gewinnen. Jede Krankheit beeinflusste die spektrale Reflektion von Zuckerrübenblättern auf charakteristische Weise. Differenz der Reflektion, Sensitivität sowie Korrelation der spektralen Bänder zur Befallsstärke variierten in Abhängigkeit von den Krankheiten. Eine höhere Präzision durch die pixelweise Erfassung räumlicher und zeitlicher Unterschiede von befallenem und gesundem Gewebe konnte durch abbildende Sensoren erreicht werden. Spektrale Vegetationsindizes (SVIs), mit Bezug zu pflanzenphysiologischen Parametern wurden aus den Hyperspektraldaten errechnet und mit der Befallsstärke korreliert. Die SVIs unterschieden sich in ihrer Sensitivität gegenüber den drei Krankheiten. Durch den Einsatz von maschinellem Lernen wurde die kombinierte Information der errechneten Vegetationsindizes für eine automatische Klassifizierung genutzt. Eine hohe Sensitivität sowie eine hohe Spezifität bezüglich der Erkennung und Differenzierung von Krankheiten wurden erreicht. Eine Quantifizierung der Krankheiten war neben der Detektion und Identifizierung mittels SVIs bzw. Klassifizierung mit Spektral Angle Mapper an hyperspektralen Bilddaten möglich. Die Ergebnisse dieser Arbeit tragen zu einem besseren Verständnis der optischen Eigenschaften von Pflanzen unter Pathogeneinfluss bei. Die untersuchten Methoden bieten die Möglichkeit in Anwendungen des Präzisionspflanzenschutzes implementiert zu werden, um eine frühzeitige Erkennung, Differenzierung und Quantifizierung von Pflanzenkrankheiten zu ermöglichen

Terahertz sensing analysis for early detection of ganoderma boninense disease using near infrared (NIR) spectrometer

Ganoderma boninense (G. boninense) infection reduces the productivity of oil palms and causes a significant impact on the economic viability of oil palm plantations. Early detection is critical for the effective management of this disease since there is no effective treatment that can stop the spread of this disease. The proposed system uses integrated hand-held near-infrared spectroscopy (NIRS) for early detection of G. boninense on asymptomatic oil palm seedlings and classification of spectral data using machine learning (ML) techniques. The non-destructive method using NIRS with ML and predictive analytics has the potential to be a highly sensitive and reliable method for the early detection of G. boninense. Spectral data are collected from 6 samples of inoculated and non-inoculated oil palm samples at nursery stages using an integrated NIRS sensor. Chemometrics is performed by implementing principal component analysis (PCA), derivatives and partial least square (PLS) regression to extract the vital information of the spectra. The significant wavelengths are at 1310 nm and 1450 nm which are attributable to ergosterol and water content, respectively. Furthermore, the SG derivatives spectra peaks corresponded to specific functional groups that could be utilized for the detection of G. boninense. These functional groups encompass the third overtone of N-H stretching, the second overtone of C-H stretching, and a combination band involving both C-H stretching and O-H stretching. High-performance liquid chromatography (HPLC) analysis is performed to identify the ergosterol content in oil palm sample. Ergosterol can be used as a biomarker for the detection of G. boninense since it can only be found in the fungal-infested plant. In classification, four different ML algorithms: K-Nearest Neighbour (kNN), Naïve Bayes (NB), Support Vector Machine (SVM) and Decision Tree (DT) are tested to classify healthy and infected oil palm samples. DT algorithm on leaves spectra achieves a satisfactory overall performance compared to the other classifiers with high accuracy up to 93.1% and an F1-score of 92.6%. Therefore, a DT-based predictive analytic on leaves NIR spectral reference data is developed for real-time detection of G. boninense infection. A portable smart G. boninense detection system prototype is developed by implementing the Internet of Things (IoT) into the system which enables the integration of sensors and server to perform prediction of healthy or infected oil palm seedlings. This working prototype showed that this proposed approach is reliable and practical for the early detection of G. boninense in oil palm seedlings

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

Spectral unmixing approach in hyperspectral remote sensing: a tool for oil palm mapping

Las plantaciones de palma de aceite típicamente abarcan grandes áreas, por esto, la teledetección remota se ha convertido en una herramienta útil para el monitoreo avanzado de este cultivo. Este trabajo revisa y evalúa dos enfoques para analizar las plantaciones de palma de aceite a partir de datos de teledetección remota hiperespectral: desmezclado espectral lineal y variabilidad espectral. Además, se propone un marco computacional basado en el desmezclado espectral para la estimación de las fracciones de abundancias de cultivos de palma de aceite. Este enfoque también considera la variabilidad espectral de las firmas en las imágenes hiperespectrales. El marco computacional propuesto modifica el modelo de mezcla lineal mediante la introducción de un vector de pesos, de manera que se puedan identificar las bandas espectrales que menos contribuyen a la estimación de fracciones de abundancias erróneas. Este enfoque aprovecha la detección de los árboles de palma de aceite, ya que permite diferenciarlos de otros materiales en términos de fracciones de abundancia. Los resultados experimentales obtenidos a partir de datos de teledetección remota hiperespectral en el rango de 410-990 nm, muestran mejoras de un 8.18 % en la métrica de Precisión del Usuario (Uacc) en la identificación de palmas de aceite por el marco propuesto con respecto a los métodos tradicionales de desmezclado espectral; el método propuesto logró un 95 % de Uacc. Esto confirma las capacidades del marco computacional formulado y facilita la gestión y el monitoreo de grandes áreas de plantaciones de palma de aceite.Oil palm plantations typically span large areas; therefore, remote sensing has become a useful tool for advanced oil palm monitoring. This work reviews and evaluates two approaches to analyze oil palm plantations based on hyperspectral remote sensing data: linear spectral unmixing and spectral variability. Moreover, a computational framework based on spectral unmixing for the estimation of fractional abundances of oil palm plantations is proposed in this study. Such approach also considers the spectral variability of hyperspectral image signatures. More specifically, the proposed computational framework modifies the linear mixing model by introducing a weighting vector, so that the spectral bands that contribute the least to the estimation of erroneous fractional abundances can be identified. This approach improves palm detection as it allows to differentiate them from other materials in terms of fractional abundances. Experimental results obtained from hyperspectral remote sensing data in the range 410-990 nm show improvements of 8.18 % in User Accuracy (Uacc) in the identification of oil palms by the proposed framework with respect to traditional unmixing methods. Thus, the proposed method achieved a 95% Uacc. This confirms the capabilities of the proposed computational framework and facilitates the management and monitoring of large areas of oil palm plantations

Machine vision detection of pests, diseases, and weeds: A review

Most of mankind’s living and workspace have been or going to be blended with smart technologies like the Internet of Things. The industrial domain has embraced automation technology, but agriculture automation is still in its infancy since the espousal has high investment costs and little commercialization of innovative technologies due to reliability issues. Machine vision is a potential technique for surveillance of crop health which can pinpoint the geolocation of crop stress in the field. Early statistics on crop health can hasten prevention strategies such as pesticide, fungicide applications to reduce the pollution impact on water, soil, and air ecosystems. This paper condenses the proposed machine vision relate research literature in agriculture to date to explore various pests, diseases, and weeds detection mechanisms

A review of remote sensing applications for oil palm studies

Oil palm becomes an increasingly important source of vegetable oil for its production exceeds soybean, sunflower, and rapeseed. The growth of the oil palm industry causes degradation to the environment, especially when the expansion of plantations goes uncontrolled. Remote sensing is a useful tool to monitor the development of oil palm plantations. In order to promote the use of remote sensing in the oil palm industry to support their drive for sustainability, this paper provides an understanding toward the use of remote sensing and its applications to oil palm plantation monitoring. In addition, the existing knowledge gaps are identified and recommendations for further research are given