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With growing concerns about global food supply and environmental impacts of modern agriculture, we are seeing an increased demand for more horticultural research. While research into plant genetics has seen an increased throughput from recent technological advancements, plant phenotypic research throughput has lagged behind. Improvements in open-source image processing software and image capture hardware have created an opportunity for the development of more competitively-priced, faster data-acquisition tools. These tools could be used to collect measurements of plants' phenotype on a much larger scale without sacrificing data quality. This paper demonstrates the feasibility of creating such a tool. The resulting design utilized stereo vision and image processes in the OpenCV project to measure a representative collection of observable plant traits like leaflet length or plant height. After the stereo camera was assembled and calibrated, visual and stereo images of potato plant canopies and tubers(potatoes) were collected. By processing the visual data, the meaningful regions of the image (the canopy, the leaflets, and the tubers) were identified. The same regions in the stereo images were used to determine plant physical geometry, from which the desired plant measurements were extracted. Using this approach, the tool had an average accuracy of 0.15 inches with respect to distance measurements. Additionally, the tool detected vegetation, tubers, and leaves with average Dice indices of 0.98, 0.84, and 0.75 respectively. To compare the tool's utility to that of traditional implements, a study was conducted on a population of 27 potato plants belonging to 9 separate genotypes. Both newly developed and traditional measurement techniques were used to collect measurements of a variety of the plants' characteristics. A multiple linear regression of the plant characteristics on the plants' genetic data showed that the measurements collected by hand were generally better correlated with genetic characteristics than those collected using the developed tool; the average adjusted coefficient of determination for hand-measurements was 0.77, while that of the tool-measurements was 0.66. Though the aggregation of this platform's results is unsatisfactory, this work has demonstrated that such an alternative to traditional data-collection tools is certainly attainable. / Master of Science

A system for vessel characterization aimed at detecting deep vein thrombosis (DVT) in the lower limbs has been developed and evaluated using ultrasound image processing, location and force sensors measurements, blood flow information and a protocol based on the current clinical standard, compression ultrasound. The goal is to provide an objective and repeatable system to measure DVT in a rapid and standardized manner, as this has been suggested in the literature as an approach to improve overall detection of the disease. The system uses a spatial Kalman filter-based algorithm with an elliptical model in the measurement equation to detect vessel contours in transverse ultrasound images and estimate ellipse parameters, and temporal constant velocity Kalman filters for tracking vessel location in real-time. The vessel characterization also comprises building a 3-D vessel model and performing compression and blood flow assessments to calculate measures that indicate the possibility of DVT in a vessel. A user interface designed for assessing a vessel for DVT was also developed. The system and components were implemented and tested in simulations, laboratory settings, and clinical settings. Contour detection results are good, with mean and rms errors ranging from 1.47-3.64 and 3.69-9.67 pixels, respectively, in simulated and patient images, and parameter estimation errors of 5%. Experiments showed errors of 3-5 pixels for the tracking approaches. The measures for DVT were evaluated, independently and integrated in the system. The complete system was evaluated, with sensitivity of 67-100% and specificity of 50-89.5%. System learnability and memorability were evaluated in a separate user study, with good results. Contributions include a segmentation approach using a full parameter ellipse model in an extended Kalman filter, incorporating multiple measurements, an alternate sampling method for faster parameter convergence and application-specific initialization, and a tracking approach that includes a sub-sampled sum of absolutes similarity calculation and a method to detect vessel bifurcations using flow data. Further contributions include an integrated system for DVT detection that can combine ultrasound B-mode, colour flow and elastography images for vessel characterization, a system interface design focusing on usability that was evaluated with medical professionals, and system evaluations through multiple patient studies.

A system for vessel characterization aimed at detecting deep vein thrombosis (DVT) in the lower limbs has been developed and evaluated using ultrasound image processing, location and force sensors measurements, blood flow information and a protocol based on the current clinical standard, compression ultrasound. The goal is to provide an objective and repeatable system to measure DVT in a rapid and standardized manner, as this has been suggested in the literature as an approach to improve overall detection of the disease. The system uses a spatial Kalman filter-based algorithm with an elliptical model in the measurement equation to detect vessel contours in transverse ultrasound images and estimate ellipse parameters, and temporal constant velocity Kalman filters for tracking vessel location in real-time. The vessel characterization also comprises building a 3-D vessel model and performing compression and blood flow assessments to calculate measures that indicate the possibility of DVT in a vessel. A user interface designed for assessing a vessel for DVT was also developed. The system and components were implemented and tested in simulations, laboratory settings, and clinical settings. Contour detection results are good, with mean and rms errors ranging from 1.47-3.64 and 3.69-9.67 pixels, respectively, in simulated and patient images, and parameter estimation errors of 5%. Experiments showed errors of 3-5 pixels for the tracking approaches. The measures for DVT were evaluated, independently and integrated in the system. The complete system was evaluated, with sensitivity of 67-100% and specificity of 50-89.5%. System learnability and memorability were evaluated in a separate user study, with good results. Contributions include a segmentation approach using a full parameter ellipse model in an extended Kalman filter, incorporating multiple measurements, an alternate sampling method for faster parameter convergence and application-specific initialization, and a tracking approach that includes a sub-sampled sum of absolutes similarity calculation and a method to detect vessel bifurcations using flow data. Further contributions include an integrated system for DVT detection that can combine ultrasound B-mode, colour flow and elastography images for vessel characterization, a system interface design focusing on usability that was evaluated with medical professionals, and system evaluations through multiple patient studies.

A system for vessel characterization aimed at detecting deep vein thrombosis (DVT) in the lower limbs has been developed and evaluated using ultrasound image processing, location and force sensors measurements, blood flow information and a protocol based on the current clinical standard, compression ultrasound. The goal is to provide an objective and repeatable system to measure DVT in a rapid and standardized manner, as this has been suggested in the literature as an approach to improve overall detection of the disease. The system uses a spatial Kalman filter-based algorithm with an elliptical model in the measurement equation to detect vessel contours in transverse ultrasound images and estimate ellipse parameters, and temporal constant velocity Kalman filters for tracking vessel location in real-time. The vessel characterization also comprises building a 3-D vessel model and performing compression and blood flow assessments to calculate measures that indicate the possibility of DVT in a vessel. A user interface designed for assessing a vessel for DVT was also developed. The system and components were implemented and tested in simulations, laboratory settings, and clinical settings. Contour detection results are good, with mean and rms errors ranging from 1.47-3.64 and 3.69-9.67 pixels, respectively, in simulated and patient images, and parameter estimation errors of 5%. Experiments showed errors of 3-5 pixels for the tracking approaches. The measures for DVT were evaluated, independently and integrated in the system. The complete system was evaluated, with sensitivity of 67-100% and specificity of 50-89.5%. System learnability and memorability were evaluated in a separate user study, with good results. Contributions include a segmentation approach using a full parameter ellipse model in an extended Kalman filter, incorporating multiple measurements, an alternate sampling method for faster parameter convergence and application-specific initialization, and a tracking approach that includes a sub-sampled sum of absolutes similarity calculation and a method to detect vessel bifurcations using flow data. Further contributions include an integrated system for DVT detection that can combine ultrasound B-mode, colour flow and elastography images for vessel characterization, a system interface design focusing on usability that was evaluated with medical professionals, and system evaluations through multiple patient studies. / Applied Science, Faculty of / Electrical and Computer Engineering, Department of / Graduate

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2017-04-24T14:27:21Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE__DIOGO_CAVALCANTI_COSTA.pdf: 8696014 bytes, checksum: 6ecb7de16968f61db789940caeae149e (MD5) / Made available in DSpace on 2017-04-24T14:27:21Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) TESE__DIOGO_CAVALCANTI_COSTA.pdf: 8696014 bytes, checksum: 6ecb7de16968f61db789940caeae149e (MD5) Previous issue date: 2015-03-02 / CNPQ / Desde os anos 1960, foram criadas inúmeras técnicas para segmentação de imagens, contudo poucas se aproximam do nível de desempenho humano, sendo essas computacionalmente custosas e inadequadas para aplicação em tempo real. Portanto, nesta tese é apresentada uma técnica de segmentação de baixo custo computacional, baseada em descontinuidades e em multirresolução, voltada à detecção de contornos de objetos em imagens naturais – fotografias do mundo real. A estrutura da técnica proposta é dividida em cinco etapas. Na primeira, atributos de cor e foco são realçados na imagem de entrada. O mapeamento de cor realça as diferenças de cor entre os canais RGB e propicia a detecção de bordas entre os canais de cor por operadores de gradiente. Dois modelos de cor de diferença cromática, RhGhBh e LgC, são propostos para esse fim. Também é proposta a transformada de decomposição de cor que segmenta a escala de cor RGB em canais independentes, isolando as cores aditivas e subtrativas, e os tons de cinza. Assim, é possível mensurar a variação local de cada cor para criar um mapeamento das regiões em foco. Na segunda etapa, uma filtragem morfológica para supressão de texturas suaviza as mudanças abruptas de cor no interior das mesmas, possibilitando a identificação de seus contornos e diminuindo a falsa identificação de bordas internas. Na terceira etapa, oito máscaras orientadas, batizadas de máscaras de detecção de contornos, são usadas para calcular o gradiente local, realçando os contornos dos objetos em detrimento de suas bordas internas. Na quarta etapa, um afinamento em tons de cinza é realizado por meio de um empilhamento topológico das bordas erodidas e suavizadas, no qual os pixels de bordas maximamente centralizados são isolados e afinados morfologicamente. Por fim, na quinta etapa, a intensidade das bordas é corrigida função do gradiente local e da densidade local das bordas, realçando os contornos dos objetos. Comparações com técnicas de segmentação recentes e clássicas são conduzidas com auxílio do Berkeley Segmentation Dataset and Benchmark. Os resultados obtidos posicionam a técnica proposta em quinto lugar no Benchmark, com tempo de processamento inferior a 0,5% do tempo das técnicas melhor classificadas, sendo adequada para uso em tempo real. / Since the 1960’s, numerous image segmentation techniques were developed, however only a few approach human level segmentation, being computationally costly and inadequate to real time applications. Therefore, this Thesis presents a low computational cost multi-resolution and edge-based image segmentation technique for objects’ contour detection in natural images – real world scenes photographs. The proposed technique’s framework is divided into five steps. First, color and focus features are mapped from the input image. The color mapping enhances the color differences between RGB channels, allowing the inter-channel colors edge detection by gradient operators. Two chromatic difference color models are proposed, RhGhBh and LgC. The color decomposition transform is also proposed, which is able to segment the RGB color scale in independent channels, isolating the additive and subtractive colors, and the shades of gray. The transform allows the measurement of the local variation within each color, thus, producing the image´s focus map. In the second step, a morphological texture suppression filtering smoothes abrupt color changes inside textures, allowing textures’ outer edges detection and decreasing the false identification of texture inner edges as objects’ contours. In the third step, eight oriented masks, called contour detection masks, are used to calculate the local gradient, enhancing the objects’ contours over their inner edges. In the fourth step, a grayscale thinning is performed through a topological stacking of eroded and smoothed edges, where the maximally centered edge pixels are isolated and morphologically thinned. Finally, in the fifth step, the edges’ intensities are corrected to reflect the local gradient and the local edges’ density, allowing better identification of objects’ contours. Comparisons with recent and classic segmentation techniques are conducted by the Berkeley Segmentation Dataset and Benchmark. The results rank the proposed segmentation in fith position in the Benchmark, with a processing time below 0.5% of the better ranked techniques, being suitable for real-time applications.

La qualité d’une prise de vue est un point incontournable dans la résolution des problèmes d’imagerie. Un capteur non adapté, un éclairage non contrôlé, ou des conditions variables de la scène observée peuvent être à l’origine de problèmes très difficiles à surmonter. Nous présentons différentes méthodes de traitement d’image permettant de prendre en compte au mieux ces conditions de prise de vue instables. Les approches que nous proposons sont définies dans le cadre du modèle LIP (Logarithmic Image Processing). Dans une première partie, nous nous intéressons à des notions de contraste : le contraste LIP additif et un nouveau contraste LIP multiplicatif, ainsi qu’à leurs métriques associées. De nouveaux outils de traitement basés sur ces notions sont ensuite définis : seuillage, détecteur de contours, reconnaissance de modèle. L’utilisation de ces notions de contraste confère à ces algorithmes la capacité des contrastes LIP à s’adapter à différents types d’images mal conditionnées. Nous proposons ensuite de nouvelles techniques de correction de dynamique d’images en exploitant les opérations LIP. Différentes corrections globales et locales sont présentées ainsi que leurs applications directes : correction de dérive d’éclairement pour du contrôle industriel ou amélioration d’image pour de la visualisation. Nous obtenons notamment une méthode de correction locale dont les résultats se rapprochent de ceux de certaines techniques de tone mapping. En comparaison, notre technique s’avère simple, rapide (temps réel à 30 images par seconde) et réaliste car basée sur une interprétation physique de la problématique / The quality of image acquisitions is crucial in the resolution of imaging problems. Troubles during acquisiton can lead to unstability for image processing algorithms. We propose different methods (thresholding techniques, contour detection, pattern matching) based on new metrics and contrasts in the LIP context. The LIP (Logarithmic Image Processing) model is recognized as an efficient framework to process images acquired in transmitted light and to take into account the human visual system. LIP operations are also useful to simulate varitations of image parameters in situation of reflected light. Finally, we propose new methods of global and local dynamic enhancement in the LIP framework like a real time and realistic local dynamic correction that brings results close to those obtained by certain tone mapping methods

Context : Air being the free source is used in different ways commercially. In earlier days windmills generate power, water, and electricity. The excessive establishment of windmills for commercial purposes affected avifauna. Most of the birds lost their lives due to collisions with windmills. Turbines used to generate power near airports are also one of the causes for the extinction of birdlife. According to a survey in 2011 in Canada a total of 23,300 bird deaths were caused by wind turbines and also it is estimated that the number of deaths would increase to 2,33,000 in the following 10-15 years. Objectives : The main objective of this thesis is to find a suitable software solution to detect the birds on a series of grayscale images in real-time and in minimum full HD resolution with at least a 15 FPS rate. User-Driven Design Methodology is used for developing, tools are Python and Open-CV. Methods : In this research, a system is designed to detect the bird in an HD Video. Possible methods that can be considered are convolutional neural networks (CNN), vision based detection with background subtraction, contour detection and confusion matrix classification. These methods detect birds in raw images and with help of a classifier make it possible to see the bird in desired pixels with full resolution. We will investigate a bird classification method consisting of two steps, background subtraction, and then object classification. Background subtraction is a fundamental method to extract moving objects from a fixed background. For classification, we will use the YOLO v3 model version for object classification. Results : The project is expected to result in a system design and prototype for the bird identification on a grayscale video stream in at least full HD resolution in a minimum of 15 FPS. The bird should be distinguished from other moving objects like wind turbine blades, trees, or clouds. The proposed solution should identify up to 5 birds simultaneously. Conclusion : After completing each step and arriving at the classification, the methods we have tried, such as Haar Cascades and mobile-net SSD, were not providing us with the desired results. So we opted to use YOLO v3, which had the best accuracy in classifying different objects. By using the YOLO v3 classifier, we have detected the bird with 95% accuracy, blades with 90% accuracy, clouds with 80% accuracy, trees with 70% accuracy. Moreover, we conclude that there is a need for further empirical validation of the models in full-scale industry trials.

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