Characterization of vineyard's canopy through fuzzy clustering and svm over color images

In this work we propose an image acquisition and processing methodology (framework) developed for performance in-field grapes and leaves detection and quantification, based on a six step methodology: 1) image segmentation through Fuzzy C-Means with Gustafson Kessel (FCM-GK) clustering; 2) obtaining of FCM-GK outputs (centroids) for acting as seeding for K-Means clustering; 3) Identification of the clusters generated by K-Means using a Support Vector Machine (SVM) classifier. 4) Performance of morphological operations over the grapes and leaves clusters in order to fill holes and to eliminate small pixels clusters; 5)Creation of a mosaic image by Scale-Invariant Feature Transform (SIFT) in order to avoid overlapping between images; 6) Calculation of the areas of leaves and grapes and finding of the centroids in the grape bunches. Image data are collected using a colour camera fixed to a mobile platform. This platform was developed to give a stabilized surface to guarantee that the images were acquired parallel to de vineyard rows. In this way, the platform avoids the distortion of the images that lead to poor estimation of the areas. Our preliminary results are promissory, although they still have shown that it is necessary to implement a camera stabilization system to avoid undesired camera movements, and also a parallel processing procedure in order to speed up the mosaicking process.

Grapevine Yield and Leaf Area Estimation Using Supervised Classification Methodology on RGB Images Taken under Field Conditions

The aim of this research was to implement a methodology through the generation of a supervised classifier based on the Mahalanobis distance to characterize the grapevine canopy and assess leaf area and yield using RGB images. The method automatically processes sets of images, and calculates the areas (number of pixels) corresponding to seven different classes (Grapes, Wood, Background, and four classes of Leaf, of increasing leaf age). Each one is initialized by the user, who selects a set of representative pixels for every class in order to induce the clustering around them. The proposed methodology was evaluated with 70 grapevine (V. vinifera L. cv. Tempranillo) images, acquired in a commercial vineyard located in La Rioja (Spain), after several defoliation and de-fruiting events on 10 vines, with a conventional RGB camera and no artificial illumination. The segmentation results showed a performance of 92% for leaves and 98% for clusters, and allowed to assess the grapevine’s leaf area and yield with R2 values of 0.81 (p < 0.001) and 0.73 (p = 0.002), respectively. This methodology, which operates with a simple image acquisition setup and guarantees the right number and kind of pixel classes, has shown to be suitable and robust enough to provide valuable information for vineyard management.

Methodology for reconstructing early zebrafish development from in vivo multiphoton microscopy

Investigating cell dynamics during early zebrafish embryogenesis requires specific image acquisition and analysis strategies. Multiharmonic microscopy, i.e., second- and third-harmonic generations, allows imaging cell divisions and cell membranes in unstained zebrafish embryos from 1- to 1000-cell stage. This paper presents the design and implementation of a dedicated image processing pipeline (tracking and segmentation) for the reconstruction of cell dynamics during these developmental stages. This methodology allows the reconstruction of the cell lineage tree including division timings, spatial coordinates, and cell shape until the 1000-cell stage with minute temporal accuracy and micrometer spatial resolution. Data analysis of the digital embryos provides an extensive quantitative description of early zebrafish embryogenesis.

Modelización e integración de sistemas de adquisición de datos inteligentes en sistemas de instrumentación para dispositivos de fusión

La obtención de energía a partir de la fusión nuclear por confinamiento magnético del plasma, es uno de los principales objetivos dentro de la comunidad científica dedicada a la energía nuclear. Desde la construcción del primer dispositivo de fusión, hasta la actualidad, se han llevado a cabo multitud de experimentos, que hoy en día, gran parte de ellos dan soporte al proyecto International Thermonuclear Experimental Reactor (ITER). El principal problema al que se enfrenta ITER, se basa en la monitorización y el control del plasma. Gracias a las nuevas tecnologías, los sistemas de instrumentación y control permiten acercarse más a la solución del problema, pero a su vez, es más complicado estandarizar los sistemas de adquisición de datos que se usan, no solo en ITER, sino en otros proyectos de igual complejidad. Desarrollar nuevas implementaciones hardware y software bajo los requisitos de los diagnósticos definidos por los científicos, supone una gran inversión de tiempo, retrasando la ejecución de nuevos experimentos. Por ello, la solución que plantea esta tesis, consiste en la definición de una metodología de diseño que permite implementar sistemas de adquisición de datos inteligentes y su fácil integración en entornos de fusión para la implementación de diagnósticos. Esta metodología requiere del uso de los dispositivos Reconfigurable Input/Output (RIO) y Flexible RIO (FlexRIO), que son sistemas embebidos basados en tecnología Field-Programmable Gate Array (FPGA). Para completar la metodología de diseño, estos dispositivos van a ser soportados por un software basado en EPICS Device Support utilizando la tecnología EPICS software asynDriver. Esta metodología se ha evaluado implementando prototipos para los controladores rápidos de planta de ITER, tanto para casos prácticos de ámbito general como adquisición de datos e imágenes, como para casos concretos como el diagnóstico del fission chamber, implementando pre-procesado en tiempo real. Además de casos prácticos, esta metodología se ha utilizado para implementar casos reales, como el Ion Source Hydrogen Positive (ISHP), desarrollada por el European Spallation Source (ESS Bilbao) y la Universidad del País Vasco. Finalmente, atendiendo a las necesidades que los experimentos en los entornos de fusión requieren, se ha diseñado un mecanismo mediante el cual los sistemas de adquisición de datos, que pueden ser implementados mediante la metodología de diseño propuesta, pueden integrar un reloj hardware capaz de sincronizarse con el protocolo IEEE1588-V2, permitiendo a estos, obtener los TimeStamps de las muestras adquiridas con una exactitud y precisión de decenas de nanosegundos y realizar streaming de datos con TimeStamps. ABSTRACT Fusion energy reaching by means of nuclear fusion plasma confinement is one of the main goals inside nuclear energy scientific community. Since the first fusion device was built, many experiments have been carried out and now, most of them give support to the International Thermonuclear Experimental Reactor (ITER) project. The main difficulty that ITER has to overcome is the plasma monitoring and control. Due to new technologies, the instrumentation and control systems allow an approaching to the solution, but in turn, the standardization of the used data acquisition systems, not only in ITER but also in other similar projects, is more complex. To develop new hardware and software implementations under scientific diagnostics requirements, entail time costs, delaying new experiments execution. Thus, this thesis presents a solution that consists in a design methodology definition, that permits the implementation of intelligent data acquisition systems and their easy integration into fusion environments for diagnostic purposes. This methodology requires the use of Reconfigurable Input/Output (RIO) and Flexible RIO (FlexRIO) devices, based on Field-Programmable Gate Array (FPGA) embedded technology. In order to complete the design methodology, these devices are going to be supported by an EPICS Device Support software, using asynDriver technology. This methodology has been evaluated implementing ITER PXIe fast controllers prototypes, as well as data and image acquisition, so as for concrete solutions like the fission chamber diagnostic use case, using real time preprocessing. Besides of these prototypes solutions, this methodology has been applied for the implementation of real experiments like the Ion Source Hydrogen Positive (ISHP), developed by the European Spallation Source and the Basque country University. Finally, a hardware mechanism has been designed to integrate a hardware clock into RIO/FlexRIO devices, to get synchronization with the IEEE1588-V2 precision time protocol. This implementation permits to data acquisition systems implemented under the defined methodology, to timestamp all data acquired with nanoseconds accuracy, permitting high throughput timestamped data streaming.

What is the optimal stitching orientation from an aerial survey perspective?

Mosaicing is a technique that allows obtaining a large high resolution image by stitching several images together. These base images are usually acquired from an elevated point of view. Until recently, low-altitude image acquisition has been performed typically by using using airplanes, as well as other manned platforms. However, mini unmanned aerial vehicles (MUAV) endowed with a camera have lately made this task more available for small for cicil applications, for example for small farmers in order to obtain accurate agronomic information about their crop fields. The stitching orientation, or the image acquisition orientation usually coincides with the aircraft heading assuming a downwards orientation of the camera. In this paper, the efect of the image orientation in the eficiency of the aerial coverage path planning is studied. Moreover, an algorithm to compute an optimal stitching orientation angle is proposed and results are numerically compared with classical approaches.

Contribuciones en sistemas de adquisición de datos inteligentes para entornos de fusión por confinamiento magnético

Los sistemas de adquisición de datos utilizados en los diagnósticos de los dispositivos de fusión termonuclear se enfrentan a importantes retos planteados en los dispositivos de pulso largo. Incluso en los dispositivos de pulso corto, en los que se analizan los datos después de la descarga, existen aún una gran cantidad de datos sin analizar, lo cual supone que queda una gran cantidad de conocimiento por descubrir dentro de las bases de datos existentes. En la última década, la comunidad de fusión ha realizado un gran esfuerzo para mejorar los métodos de análisis off‐line para mejorar este problema, pero no se ha conseguido resolver completamente, debido a que algunos de estos métodos han de resolverse en tiempo real. Este paradigma lleva a establecer que los dispositivos de pulso largo deberán incluir dispositivos de adquisición de datos con capacidades de procesamiento local, capaces de ejecutar avanzados algoritmos de análisis. Los trabajos de investigación realizados en esta tesis tienen como objetivo determinar si es posible incrementar la capacidad local de procesamiento en tiempo real de dichos sistemas mediante el uso de GPUs. Para ello durante el trascurso del periodo de experimentación realizado se han evaluado distintas propuestas a través de casos de uso reales elaborados para algunos de los dispositivos de fusión más representativos como ITER, JET y TCV. Las conclusiones y experiencias obtenidas en dicha fase han permitido proponer un modelo y una metodología de desarrollo para incluir esta tecnología en los sistemas de adquisición para diagnósticos de distinta naturaleza. El modelo define no sólo la arquitectura hardware óptima para realizar dicha integración, sino también la incorporación de este nuevo recurso de procesamiento en los Sistemas de Control de Supervisión y Adquisición de Datos (SCADA) utilizados en la comunidad de fusión (EPICS), proporcionando una solución completa. La propuesta se complementa con la definición de una metodología que resuelve las debilidades detectadas, y permite trazar un camino de integración de la solución en los estándares hardware y software existentes. La evaluación final se ha realizado mediante el desarrollo de un caso de uso representativo de los diagnósticos que necesitan adquisición y procesado de imágenes en el contexto del dispositivo internacional ITER, y ha sido testeada con éxito en sus instalaciones. La solución propuesta en este trabajo ha sido incluida por la ITER IO en su catálogo de soluciones estándar para el desarrollo de sus futuros diagnósticos. Por otra parte, como resultado y fruto de la investigación de esta tesis, cabe destacar el acuerdo llevado a cabo con la empresa National Instruments en términos de transferencia tecnológica, lo que va a permitir la actualización de los sistemas de adquisición utilizados en los dispositivos de fusión. ABSTRACT Data acquisition systems used in the diagnostics of thermonuclear fusion devices face important challenges due to the change in the data acquisition paradigm needed for long pulse operation. Even in shot pulse devices, where data is mainly analyzed after the discharge has finished , there is still a large amount of data that has not been analyzed, therefore producing a lot of buried knowledge that still lies undiscovered in the data bases holding the vast amount of data that has been generated. There has been a strong effort in the fusion community in the last decade to improve the offline analysis methods to overcome this problem, but it has proved to be insufficient unless some of these mechanisms can be run in real time. In long pulse devices this new paradigm, where data acquisition devices include local processing capabilities to be able to run advanced data analysis algorithms, will be a must. The research works done in this thesis aim to determining whether it is possible to increase local capacity for real‐time processing of such systems by using GPUs. For that, during the experimentation period, various proposals have been evaluated through use cases developed for several of the most representative fusion devices, ITER, JET and TCV. Conclusions and experiences obtained have allowed to propose a model, and a development methodology, to include this technology in systems for diagnostics of different nature. The model defines not only the optimal hardware architecture for achieving this integration, but also the incorporation of this new processing resource in one of the Systems of Supervision Control and Data Acquisition (SCADA) systems more relevant at the moment in the fusion community (EPICS), providing a complete solution. The final evaluation has been performed through a use case developed for a generic diagnostic requiring image acquisition and processing for the international ITER device, and has been successfully tested in their premises. The solution proposed in this thesis has been included by the ITER IO in his catalog of standard solutions for the development of their future diagnostics. This has been possible thanks to the technologic transfer agreement signed with xi National Instruments which has permitted us to modify and update one of their core software products targeted for the acquisition systems used in these devices.

Análise comparativa das alterações periapicais diagnosticadas pela técnica radiográfica do paralelismo e pelo mapeamento tomográfico cintilográfico (com e sem blindador de raios gama)

O diagnóstico precoce de focos de infecção dentários é de fundamental importância para prevenir a ocorrência de maiores injúrias locais ou sistêmicas. Dentre os diversos métodos utilizados para complementar os achados radiológicos das alterações dentoalveolares surge uma alternativa: a cintilografia tomográfica (SPECT/CT), que permite a fusão de achados morfológicos com alterações metabólicas. Com o objetivo de estabelecer o diagnóstico precoce e acurado de processos infecciosos dentários, foram estudadas 320 áreas dentárias em mandíbula e maxila em (10 pacientes de ambos os sexos selecionados por meio de exames clínicos e radiológicos convencionais, seguidos de cintilografia tomográfica com e sem aparato blindador de raios gama. Os exames cintilográficos foram realizados no Serviço de Medicina Nuclear do Hospital Israelita Albert Einstein (HIAE). Para isso, foi administrado para cada paciente o radiofármaco tecnécio 99- metilenodifosfonato (99mTc-MDP) via endovenosa com a dose de 37mBq/3Kg de peso corporal do paciente. Após o período de acúmulo de três horas, foi realizado o protocolo de aquisição de imagens. Todas as imagens foram analisadas por um médico nuclear e um endodontista, com experiência em cintilografia tomográfica. O resultado obtido por meio do exame radiográfico intrabucal pela técnica periapical digital mostraram 6 imagens positivas, em um total de 1,87% da amostra; exame do mapeamento cintilográfico dos ossos da face com a utilização do blindador de raios gâma revelou 9 imagens positivas, correspondendo a 2,81% do total de áreas estudadas, havendo diferença estatisticamente significante ao nível de 95% pelo teste qui-quadrado. Pode-se concluir que o SPECT/CT permitiu identificar as alterações periapicais em maior número quando comparadas ao exame radiográfico periapical e ao mapeamento cintilográfico dos ossos da face com a utilização do blindador de raios gama; o exame de SPCET/CT além de mostrar imagens mais detalhadas, permitiu também localizar com exatidão as áreas alteradas.

Vibration frequency measurement using a local multithreshold technique

In this paper, we demonstrate the use of a video camera for measuring the frequency of small-amplitude vibration movements. The method is based on image acquisition and multilevel thresholding and it only requires a video camera with high enough acquisition rate, not being necessary the use of targets or auxiliary laser beams. Our proposal is accurate and robust. We demonstrate the technique with a pocket camera recording low-resolution videos with AVI-JPEG compression and measuring different objects that vibrate in parallel or perpendicular direction to the optical sensor. Despite the low resolution and the noise, we are able to measure the main vibration modes of a tuning fork, a loudspeaker and a bridge. Results are successfully compared with design parameters and measurements with alternative devices.

Fourier-domain optical coherence tomography: optimization of signal-to-noise ratio in full space

Optical coherence tomography (OCT) is an emerging coherence-domain technique capable of in vivo imaging of sub-surface structures at millimeter-scale depth. Its steady progress over the last decade has been galvanized by a breakthrough detection concept, termed spectral-domain OCT, which has resulted in a dramatic improvement of the OCT signal-to-noise ratio of 150 times demonstrated for weakly scattering objects at video-frame-rates. As we have realized, however, an important OCT sub-system remains sub-optimal: the sample arm traditionally operates serially, i.e. in flying-spot mode. To realize the full-field image acquisition, a Fourier holography system illuminated with a swept-source is employed instead of a Michelson interferometer commonly used in OCT. The proposed technique, termed Fourier-domain OCT, offers a new leap in signal-to-noise ratio improvement, as compared to flying-spot OCT systems, and represents the main thrust of this paper. Fourier-domain OCT is described, and its basic theoretical aspects, including the reconstruction algorithm, are discussed. (C) 2004 Elsevier B.V. All rights reserved.

Signal-to-noise ratio study of full-field Fourier-domain optical coherence tomography

We report a new approach in optical coherence tomography (OCT) called full-field Fourier-domain OCT (3F-OCT). A three-dimensional image of a sample is obtained by digital reconstruction of a three-dimensional data cube, acquired with a Fourier holography recording system, illuminated with a swept source. We present a theoretical and experimental study of the signal-to-noise ratio of the 3F-OCT approach versus serial image acquisition (flying-spot OCT) approach. (c) 2005 Optical Society of America.

2D strain - a new approach to strain and strain rate: the solution to the angle-dependence of tissue Doppler?

Purpose: Tissue Doppler strain rate imaging (SRI) have been validated and applied in various clinical settings, but the clinical use of this modality is still limited due to time-consuming postprocessing, unfavorable signal to noise ratio and major angle dependency of image acquisition. 2D Strain (2DS) measures strain parameters through automated tissue tracking (Lagrangian strain) rather than tissue velocity regression. We sought to compare the accuracy of this technique with SRI and evaluate whether it overcomes the above limitations. Methods: We assessed 26 patients (13 female, age 60±5yrs) at low risk of CAD and with normal DSE at both baseline and peak stress. End systolic strain (ESS), peak systolic strain rate (SR), and timing parameters were measured by two independent observers using SRI and 2D Strain. Myocardial segments were excluded from the analyses if the insonation angle exceeded 30 degrees or if the segments were not visualized; 417 segments were evaluated. Results: Normal ranges for TVI and CEB approaches were comparable for SR (-0.99 ± 0.39 vs -0.88 ± 0.36, p=NS), ESS (-15.1 ± 6.5 vs -14.9 ± 6.3, p=NS), time to end of systole (174 ± 47 vs 174 ± 53, p=NS) and time to peak SR (TTP; 340 ± 34 vs 375 ± 57). The best correlations between the techniques were for time to end systole (rest r=0.6, p

Mechatronic system for performing blood pre-transfusion tests

The blood types determination is essential to perform safe blood transfusions. In emergency situations isadministrated the “universal donor” blood type. However, sometimes, this blood type can cause incom-patibilities in the transfusion receptor. A mechatronic prototype was developed to solve this problem.The prototype was built to meet specific goals, incorporating all the necessary components. The obtainedsolution is close to the final system that will be produced later, at industrial scale, as a medical device.The prototype is a portable and low cost device, and can be used in remote locations. A computer appli-cation, previously developed is used to operate with the developed mechatronic prototype, and obtainautomatically test results. It allows image acquisition, processing and analysis, based on Computer Visionalgorithms, Machine Learning algorithms and deterministic algorithms. The Machine Learning algorithmsenable the classification of occurrence, or alack of agglutination in the mixture (blood/reagents), and amore reliable and a safer methodology as test data are stored in a database. The work developed allowsthe administration of a compatible blood type in emergency situations, avoiding the discontinuity of the“universal donor” blood type stocks, and reducing the occurrence of human errors in the transfusion practice.

Three-dimensional calibration targets for optical coherence tomography

The recent expansion of clinical applications for optical coherence tomography (OCT) is driving the development of approaches for consistent image acquisition. There is a simultaneous need for time-stable, easy-to-use imaging targets for calibration and standardization of OCT devices. We present calibration targets consisting of three-dimensional structures etched into nanoparticle-embedded resin. Spherical iron oxide nanoparticles with a predominant particle diameter of 400 nm were homogeneously dispersed in a two part polyurethane resin and allowed to harden overnight. These samples were then etched using a precision micromachining femtosecond laser with a center wavelength of 1026 nm, 100kHz repetition rate and 450 fs pulse duration. A series of lines in depth were etched, varying the percentage of inscription energy and speed of the translation stage moving the target with respect to the laser. Samples were imaged with a dual wavelength spectral-domain OCT system and point-spread function of nanoparticles within the target was measured.

Three-dimensional calibration targets for optical coherence tomography

The recent expansion of clinical applications for optical coherence tomography (OCT) is driving the development of approaches for consistent image acquisition. There is a simultaneous need for time-stable, easy-to-use imaging targets for calibration and standardization of OCT devices. We present calibration targets consisting of three-dimensional structures etched into nanoparticle-embedded resin. Spherical iron oxide nanoparticles with a predominant particle diameter of 400 nm were homogeneously dispersed in a two part polyurethane resin and allowed to harden overnight. These samples were then etched using a precision micromachining femtosecond laser with a center wavelength of 1026 nm, 100kHz repetition rate and 450 fs pulse duration. A series of lines in depth were etched, varying the percentage of inscription energy and speed of the translation stage moving the target with respect to the laser. Samples were imaged with a dual wavelength spectral-domain OCT system and point-spread function of nanoparticles within the target was measured.

Design of an automated book reader as an assistive technology tool for blind persons

This dissertation introduces a novel automated book reader as an assistive technology tool for persons with blindness. The literature shows extensive work in the area of optical character recognition, but the current methodologies available for the automated reading of books or bound volumes remain inadequate and are severely constrained during document scanning or image acquisition processes. The goal of the book reader design is to automate and simplify the task of reading a book while providing a user-friendly environment with a realistic but affordable system design. This design responds to the main concerns of (a) providing a method of image acquisition that maintains the integrity of the source (b) overcoming optical character recognition errors created by inherent imaging issues such as curvature effects and barrel distortion, and (c) determining a suitable method for accurate recognition of characters that yields an interface with the ability to read from any open book with a high reading accuracy nearing 98%. This research endeavor focuses in its initial aim on the development of an assistive technology tool to help persons with blindness in the reading of books and other bound volumes. But its secondary and broader aim is to also find in this design the perfect platform for the digitization process of bound documentation in line with the mission of the Open Content Alliance (OCA), a nonprofit Alliance at making reading materials available in digital form. The theoretical perspective of this research relates to the mathematical developments that are made in order to resolve both the inherent distortions due to the properties of the camera lens and the anticipated distortions of the changing page curvature as one leafs through the book. This is evidenced by the significant increase of the recognition rate of characters and a high accuracy read-out through text to speech processing. This reasonably priced interface with its high performance results and its compatibility to any computer or laptop through universal serial bus connectors extends greatly the prospects for universal accessibility to documentation.