2,184 research outputs found

    An Image Processing Based Approach for Detection of Nitrogen Status in Winter Wheat Under Mild Drought Stress

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    Abstract. Nitrogen is one of the most important agricultural inputs affecting crop growth, yield and quality in rain-fed cereal production. In this study an image processing based approach was used for detection of nitrogen status in winter wheat. Four N fertilization rates (0, 60, 120 and 240 kg N ha -1 , in total) and two water regimes (irrigated and non-irrigated) were applied to winter wheat. Digital images of the plant canopy were acquired using a Canon camera during the growing season 2012. Different indices were extracted by processing of the images. According to the statistical analyses, all the indices were affected by both N and water supplies. However, Rm, RMB, NRMB, Hue and INT were less sensitive to water supply. Among the indices, crop coverage (CC) showed better results for detection of nitrogen status of the plant. We conclude that digital cameras can be used to assess nitrogen status of winter wheat

    Developing affordable high-throughput plant phenotyping methods for breeding of cereals and tuber crops

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    High-throughput plant phenotyping (HTPP) is a fast, accurate, and non-destructive process for evaluating plants' health and environmental adaptability. HTPP accelerates the identification of agronomic traits of interest, eliminates subjectivism (which is innate to humans), and facilitates the development of adapted genotypes. Current HTPP methods often rely on imaging sensors and computer vision both in the field and under controlled (indoor) conditions. However, their use is limited by the costs and complexity of the necessary instrumentation, data analysis tools, and software. This issue could be overcome by developing more cost-efficient and user-friendly methods that let breeders, farmers, and stakeholders access the benefits of HTPP. To assist such efforts, this thesis presents an ensemble of dedicated affordable phenotyping methods using RGB imaging for a range of key applications under controlled conditions.  The affordable Phenocave imaging system for use in controlled conditions was developed to facilitate studies on the effects of abiotic stresses by gathering data on important plant characteristics related to growth, yield, and adaptation to growing conditions and cultivation systems. Phenocave supports imaging sensors including visible (RGB), spectroscopic (multispectral and hyperspectral), and thermal imaging. Additionally, a pipeline for RGB image analysis was implemented as a plugin for the free and easy-to-use software ImageJ. This plugin has since proven to be an accurate alternative to conventional measurements that produces highly reproducible results. A subsequent study was conducted to evaluate the effects of heat and drought stress on plant growth and grain nutrient composition in wheat, an important staple cereal in Sweden. The effects of stress on plant growth were evaluated using image analysis, while stress-induced changes in the abundance of key plant compounds were evaluated by analyzing the nutrient composition of grains via chromatography. This led to the discovery of genotypes whose harvest quality remains stable under heat and drought stress. The next objective was to evaluate biotic stress; for this case, the effect of the fungal disease Fusarium head blight (FHB) that affects grain development in wheat was investigated. For this purpose, seed phenotyping parameters were used to determine the components and settings of a statistical model, which predicts the occurrence of FHB. The results reveal that grain morphology evaluations, such as length and width, were found to be significantly affected by the disease. Another study was carried out to estimate the disease severity of the common scab (CS) in potatoes, a widely popular food source. CS occurs on the tubers and reduces their visual appeal, significantly affecting their market value. Tubers were analyzed by a deep learning-based method to estimate disease lesion areas caused by CS. Results showed a high correlation between the predictions and expert visual scorings of the disease and proved to be a potential tool for the selection of genotypes that fulfill the market standards and resistance to CS. Both case studies highlight the role of imaging in plant health monitoring and its integration into the larger picture of plant health management.  The methods presented in this work are a starting point for bridging the gap between costs and accessibility to imaging technology. These are affordable and user-friendly resources for generating pivotal knowledge on plant development and genotype selection. In the future, image acquisition of all the methods can be integrated into the Phenocave system, potentially allowing for a more automated and efficient plant health monitoring process, leading to the identification of tolerant genotypes to biotic and abiotic stresses

    Remote Sensing as a Precision Farming Tool in the Nile Valley, Egypt

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    Detecting stress in plants resulting from different stressors including nitrogen deficiency, salinity, moisture, contamination and diseases, is crucial in crop production. In the Nile Valley, crop production is hindered perhaps more fundamentally by issues of water supply and salinity. Predicting stress in crops by conventional methods is tedious, laborious and costly and is perhaps unreliable in providing a spatial context of stress patterns. Accurate and quick monitoring techniques for crop status to detect stress in crops at early growth stages are needed to maximize crop productivity. In this context, remotely sensed data may provide a useful tool in precision farming. This research aims to evaluate the role of in situ hyperspectral and high spatial resolution satellite remote sensing data to detect stress in wheat and maize crops and assess whether moisture induced stress can be distinguished from salinity induced stress spectrally. A series of five greenhouse based experiments on wheat and maize were undertaken subjecting both crops to a range of salinity and moisture stress levels. Spectroradiometry measurements were collected at different growth stages of each crop to assess the relationship between crop biophysical and biochemical properties and reflectance measurements from plant canopies. Additionally, high spatial resolution satellite images including two QuickBird, one ASTER and two SPOT HRV were acquired in south-west Alexandria, Egypt to assess the potential of high spectral and spatial resolution satellite imagery to detect stress in wheat and maize at local and regional scales. Two field work visits were conducted in Egypt to collect ground reference data and coupled with Hyperion imagery acquisition, during winter and summer seasons of 2007 in March (8-30: wheat) and July (12-17: maize). Despite efforts, Hyperion imagery was not acquired due to factors out with the control of this research. Strong significant correlations between crop properties and different vegetation indices derived from both ground based and satellite platforms were observed. RDVI showed a sensitive index to different wheat properties (r > 0.90 with different biophysical properties). In maize, GNDVIbr and Cgreen had strong significant correlations with maize biophysical properties (r > 0.80). PCA showed the possibility to distinguish between moisture and salinity induced stress at the grain filling stages. The results further showed that a combined approach of high (2-5 m) and moderate (15-20) spatial resolution satellite imagery can provide a better mechanistic interpretation of the distribution and sources of stress, despite the typical small size of fields (20-50 m scale). QuickBird imagery successfully detects stress within field and local scales, whereas SPOT HRV imagery is useful in detecting stress at a regional scale, and therefore, can be a robust tool in identifying issues of crop management at a regional scale. Due to the limited spectral capabilities of high spatial resolution images, distinguishing different sources of stress is not directly possible, and therefore, hyperspectral satellite imagery (e.g. Hyperion or HyspIRI) is required to distinguish between moisture and salinity induced stress. It is evident from the results that remotely sensed data acquired by both in situ hyperspectral and high spatial resolution satellite remote sensing can be used as a useful tool in precision farming in the Nile Valley, Egypt. A combined approach of using reliable high spatial and spectral satellite remote sensing data could provide better insight about stress at local and regional scales. Using this technique as a precision farming and management tool will lead to improved crop productivity by limiting stress and consequently provide a valuable tool in combating issues of food supply at a time of rapid population growth

    Proximal hyperspectral imaging detects diurnal and drought-induced changes in maize physiology

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    Hyperspectral imaging is a promising tool for non-destructive phenotyping of plant physiological traits, which has been transferred from remote to proximal sensing applications, and from manual laboratory setups to automated plant phenotyping platforms. Due to the higher resolution in proximal sensing, illumination variation and plant geometry result in increased non-biological variation in plant spectra that may mask subtle biological differences. Here, a better understanding of spectral measurements for proximal sensing and their application to study drought, developmental and diurnal responses was acquired in a drought case study of maize grown in a greenhouse phenotyping platform with a hyperspectral imaging setup. The use of brightness classification to reduce the illumination-induced non-biological variation is demonstrated, and allowed the detection of diurnal, developmental and early drought-induced changes in maize reflectance and physiology. Diurnal changes in transpiration rate and vapor pressure deficit were significantly correlated with red and red-edge reflectance. Drought-induced changes in effective quantum yield and water potential were accurately predicted using partial least squares regression and the newly developed Water Potential Index 2, respectively. The prediction accuracy of hyperspectral indices and partial least squares regression were similar, as long as a strong relationship between the physiological trait and reflectance was present. This demonstrates that current hyperspectral processing approaches can be used in automated plant phenotyping platforms to monitor physiological traits with a high temporal resolution

    Biostimulants in horticulture: evaluation of their mode of action on crops using a platform for high-throughput automated phenotyping

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    In the last decades, with the constant increase in world population, the fast reduction of fertile arable land and the deteriorating environmental conditions, optimization of agriculture has become a priority. The main focus is on increasing the final yield and protecting the crops from unfavourable growing conditions in a sustainable way. A possible solution to this problem is represented by biostimulants, bioactive substances of diverse origins. A very large number of new biostimulants enter the market every year. However, a thorough knowledge of the mode of action of the substances in different crops and in different environmental conditions is still lacking. Traditional testing methods are time-consuming, expensive and, in most cases, destructive. Therefore, in the last years high-throughput automated phenotyping platforms started to be considered an interesting alternative to traditional characterization assays, drawing the attention of biostimulant producers. Different cameras and sensors can be implemented into high-throughput phenotyping platforms, allowing to screen the effects of different substances on a large number of morpho-physiological plant traits in a fast, efficient, cost-effective and non-destructive manner. In our work, we developed a precise methodology to test the effects of a large set of protein hydrolysates on multiple plant species (wheat, Arabidopsis, lettuce and tomato) subjected to abiotic stresses (drought and salinity) at all phenological phases, from seed up to the crop maturity. A large number of morpho-physiological traits of the plants were analysed throughout their life cycle, before and after the application of the PHs substances. The original set of PHs has been subjected to an initial in vitro screening on Arabidopsis plantlets; the substances were applied as seed priming in three different concentrations. The best-performing PHs in control and salt stress conditions have then been used for trials in planta, where they were applied as foliar spray. With the use of a Plant Biostimulant Characterization Index (PBC), we were able to categorize the substances into functional classes according to their mode of action, classifying them as Growth Promoters and /or Stress Alleviators. Leaves of the plants treated with the best- and worst-performing substances were collected and subjected to untargeted metabolomic analysis to elucidate the biochemical pathways activated by the PHs applications. It was clear that the effects of the biostimulants on plants can vary depending on the mode and time of application, the growing conditions, the dose and the plant species they are applied to; therefore, before putting a new biostimulant on the market, it is essential to select the target crop species that could benefit from the treatment. High-throughput automated phenotyping platforms can be an extremely useful tool to speed up the testing process and precisely investigate the effects of the same substance on multiple morpho-physiological traits

    An Evaluation of Unmanned Aircraft Systems\u27 Ability to Assess Stripe Rust in Large Wheat Breeding Nursies

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    Stripe Rust (Puccinia striiformis f. sp. tritici) is a foliar disease that significantly impacts global wheat production, and resistant cultivars provide the most efficient method of control. High-throughput phenotyping using unmanned aircraft systems (UAS) offers a potentially more efficient method for field-based phenotyping compared to visual assessment. Here we tested the ability of remote sensing to predict stripe rust severity in a diverse population of 594 soft red winter wheat lines, planted in single-rows, and evaluated them by visually rating stripe rust intensity and remotely using the dark green color index (DGCI), normalized difference vegetation index (NDVI) and blue NDVI. Significant relationships (p In a second study, the effect of plot size (single-row, two-row and four-row) on relationship between visual and remote sensing data (DGCI and NDVI) was explored. We evaluated a panel of 13 genotypes preselected to range from 0 to 100% severity, planted in three plot sizes across two measurement days. Significant (

    Image Analysis and Machine Learning in Agricultural Research

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    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

    Crop Disease Detection Using Remote Sensing Image Analysis

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    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

    Plant Biology Europe 2018 Conference:Abstract Book

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