Image Analysis and Machine Learning in Agricultural Research

Agricultural research has been a focus for academia and industry to improve human well-being. Given the challenges in water scarcity, global warming, and increased prices of fertilizer, and fossil fuel, improving the efficiency of agricultural research has become even more critical. Data collection by humans presents several challenges including: 1) the subjectiveness and reproducibility when doing the visual evaluation, 2) safety when dealing with high toxicity chemicals or severe weather events, 3) mistakes cannot be avoided, and 4) low efficiency and speed. Image analysis and machine learning are more versatile and advantageous in evaluating different plant characteristics, and this could help with agricultural data collection. In the first chapter, information related to different types of imaging (e.g., RGB, multi/hyperspectral, and thermal imaging) was explored in detail for its advantages in different agriculture applications. The process of image analysis demonstrated how target features were extracted for analysis including shape, edge, texture, and color. After acquiring features information, machine learning can be used to automatically detect or predict features of interest such as disease severity. In the second chapter, case studies of different agricultural applications were demonstrated including: 1) leaf damage symptoms, 2) stress evaluation, 3) plant growth evaluation, 4) stand/insect counting, and 5) evaluation for produce quality. Case studies showed that the use of image analysis is often more advantageous than visual rating. Advantages of image analysis include increased objectivity, speed, and more reproducibly reliable results. In the third chapter, machine learning was explored using romaine lettuce images from RD4AG to automatically grade for bolting and compactness (two of the important parameters for lettuce quality). Although the accuracy is at 68.4 and 66.6% respectively, a much larger data base and many improvements are needed to increase the model accuracy and reliability. With the advancement in cameras, computers with high computing power, and the development of different algorithms, image analysis and machine learning have the potential to replace part of the labor and improve the current data collection procedure in agricultural research. Advisor: Gary L. Hei

The Infectious Disease Ontology in the Age of COVID-19

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research

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

Apple scab detection using CNN and Transfer Learning

Received: January 11th, 2021 ; Accepted: April 10th, 2021 ; Published: April 22nd, 2021 ; Correspondence: [email protected] goal of smart and precise horticulture is to increase yield and product quality by simultaneous reduction of pesticide application, thereby promoting the improvement of food security. The scope of this research is apple scab detection in the early stage of development using mobile phones and artificial intelligence based on convolutional neural network (CNN) applications. The research considers data acquisition and CNN training. Two datasets were collected - with images of scab infected fruits and leaves of an apple tree. However, data acquisition is a time-consuming process and scab appearance has a probability factor. Therefore, transfer learning is an appropriate training methodology. The goal of this research was to select the most suitable dataset for transfer learning for the apple scab detection domain and to evaluate the transfer learning impact comparing it with learning from scratch. The statistical analysis confirmed the positive effect of transfer learning on CNN performance with significance level 0.05

A Review on Advances in Automated Plant Disease Detection

Plant diseases cause major yield and economic losses. To detect plant disease at early stages, selecting appropriate techniques is imperative as it affects the cost, diagnosis time, and accuracy. This research gives a comprehensive review of various plant disease detection methods based on the images used and processing algorithms applied. It systematically analyzes various traditional machine learning and deep learning algorithms used for processing visible and spectral range images, and comparatively evaluates the work done in literature in terms of datasets used, various image processing techniques employed, models utilized, and efficiency achieved. The study discusses the benefits and restrictions of each method along with the challenges to be addressed for rapid and accurate plant disease detection. Results show that for plant disease detection, deep learning outperforms traditional machine learning algorithms while visible range images are more widely used compared to spectral images

Techniques of deep learning and image processing in plant leaf disease detection: a review

Computer vision techniques are an emerging trend today. Digital image processing is gaining popularity because of the significant upsurge in the usage of digital images over the internet. Digital image processing is a practice that can help in designing sophisticated high-end machines, which can hold the ophthalmic functionality of the human eye. In agriculture, leaf examination is important for disease identification and fair warning for any deficiency within the plant. Many prominent plant species are facing extinction because of a lack of knowledge. A proper realization of computer vision techniques aid in extracting a significant amount of information from leaf image. This necessitates the requirement of an automatic leaf disease detection method to diagnose disease occurrences and severity, for timely crop management, by spraying pesticides. This study focuses on techniques of digital image processing and machine learning rendered in plant leaf disease detection, which has great potential in precision agriculture. To support this study, techniques exercised by various researchers in recent years are tabulated

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