Estrutura a partir do Movimento em Sistemas Autónomos

Mestrado em Engenharia Electrotécnica e de Computadores - Ramo de Sistemas Autónomos

System-on-chip field-programmable gate array design for onboard real-time hyperspectral unmixing

Hyperspectral instruments have been incorporated in satellite missions, providing large amounts of data of high spectral resolution of the Earth surface. This data can be used in remote sensing applications that often require a real-time or near-real-time response. To avoid delays between hyperspectral image acquisition and its interpretation, the last usually done on a ground station, onboard systems have emerged to process data, reducing the volume of information to transfer from the satellite to the ground station. For this purpose, compact reconfigurable hardware modules, such as field-programmable gate arrays (FPGAs), are widely used. This paper proposes an FPGA-based architecture for hyperspectral unmixing. This method based on the vertex component analysis (VCA) and it works without a dimensionality reduction preprocessing step. The architecture has been designed for a low-cost Xilinx Zynq board with a Zynq-7020 system-on-chip FPGA-based on the Artix-7 FPGA programmable logic and tested using real hyperspectral data. Experimental results indicate that the proposed implementation can achieve real-time processing, while maintaining the methods accuracy, which indicate the potential of the proposed platform to implement high-performance, low-cost embedded systems, opening perspectives for onboard hyperspectral image processing.

Imagiologia Espetral - Análise Forense de Notas e Escrita Manual

A análise forense de documentos é uma das áreas das Ciências Forenses, responsável pela verificação da autenticidade dos documentos. Os documentos podem ser de diferentes tipos, sendo a moeda ou escrita manual as evidências forenses que mais frequentemente motivam a análise. A associação de novas tecnologias a este processo de análise permite uma melhor avaliação dessas evidências, tornando o processo mais célere. Esta tese baseia-se na análise forense de dois tipos de documentos - notas de euro e formulários preenchidos por escrita manual. Neste trabalho pretendeu-se desenvolver técnicas de processamento e análise de imagens de evidências dos tipos referidos com vista a extração de medidas que permitam aferir da autenticidade dos mesmos. A aquisição das imagens das notas foi realizada por imagiologia espetral, tendo-se definidas quatro modalidades de aquisição: luz visível transmitida, luz visível refletida, ultravioleta A e ultravioleta C. Para cada uma destas modalidades de aquisição, foram também definidos 2 protocolos: frente e verso. A aquisição das imagens dos documentos escritos manualmente efetuou-se através da digitalização dos mesmos com recurso a um digitalizador automático de um aparelho multifunções. Para as imagens das notas desenvolveram-se vários algoritmos de processamento e análise de imagem, específicos para este tipo de evidências. Esses algoritmos permitem a segmentação da região de interesse da imagem, a segmentação das sub-regiões que contém as marcas de segurança a avaliar bem como da extração de algumas características. Relativamente as imagens dos documentos escritos manualmente, foram também desenvolvidos algoritmos de segmentação que permitem obter todas as sub-regiões de interesse dos formulários, de forma a serem analisados os vários elementos. Neste tipo de evidências, desenvolveu-se ainda um algoritmo de análise para os elementos correspondentes à escrita de uma sequência numérica o qual permite a obtenção das imagens correspondentes aos caracteres individuais. O trabalho desenvolvido e os resultados obtidos permitiram a definição de protocolos de aquisição de imagens destes tipos de evidências. Os algoritmos automáticos de segmentação e análise desenvolvidos ao longo deste trabalho podem ser auxiliares preciosos no processo de análise da autenticidade dos documentos, o qual, ate então, é feito manualmente. Apresentam-se ainda os resultados dos estudos feitos às diversas evidências, nomeadamente as performances dos diversos algoritmos analisados, bem como algumas das adversidades encontradas durante o processo. Apresenta-se também uma discussão da metodologia adotada e dos resultados, bem como de propostas de continuação deste trabalho, nomeadamente, a extração de características e a implementação de classificadores capazes aferir da autenticidade dos documentos.

Novel optical PVC probes for on-site detection/determination of fluoroquinolones in a solid/liquid interface: Application to the determination of Norfloxacin in aquaculture water

A novel optical disposable probe for screening fluoroquinolones in fish farming waters is presented, having Norfloxacin (NFX) as target compound. The colorimetric reaction takes place in the solid/liquid interface consisting of a plasticized PVC layer carrying the colorimetric reagent and the sample solution. NFX solutions dropped on top of this solid-sensory surface provided a colour change from light yellow to dark orange. Several metals were tested as colorimetric reagents and Fe(III) was selected. The main parameters affecting the obtained colour were assessed and optimised in both liquid and solid phases. The corresponding studies were conducted by visible spectrophotometry and digital image acquisition. The three coordinates of the HSL model system of the collected image (Hue, Saturation and Lightness) were obtained by simple image management (enabled in any computer). The analytical response of the optimised solid-state optical probe against concentration was tested for several mathematical transformations of the colour coordinates. Linear behaviour was observed for logarithm NFX concentration against Hue+Lightness. Under this condition, the sensor exhibited a limit of detection below 50 μM (corresponding to about 16 mg/mL). Visual inspection also enabled semi-quantitative information. The selectivity was ensured against drugs from other chemical groups than fluoroquinolones. Finally, similar procedure was used to prepare an array of sensors for NFX, consisting on different metal species. Cu(II), Mn(II) and aluminon were selected for this purpose. The sensor array was used to detect NFX in aquaculture water, without any prior sample manipulation.

Disposable solid state probe for optical screening of chlorpromazine

We are presenting a simple, low-cost and rapid solid-state optical probe for screening chlorpromazine (CPZ) in aquacultures. The method exploits the colourimetric reaction between CPZ and Fe(III) ion that occurs at a solid/liquid interface, the solid layer consisting of ferric iron entrapped in a layer of plasticized PVC. If solutions containing CPZ are dropped onto such a layer, a colour change occurs from light yellow to dark pink or even light blue, depending on the concentration of CPZ. Visual inspection enables the concentration of CPZ to be estimated. The resulting colouration was also monitored by digital image collection for a more accurate quantification. The three coordinates of the hue, saturation and lightness system were obtained by standard image processing along with mathematical data treatment. The parameters affecting colour were assessed and optimized. Studies were conducted by visible spectrophotometry and digital image acquisition, respectively. The response of the optimized probe towards the concentration of CPZ was tested for several mathematical transformations of the colour coordinates, and a linear relation was found for the sum of hue and luminosity. The limit of detection is 50 μM (corresponding to about 16 μg per mL). The probe enables quick screening for CPZ in real water samples with prior sample treatment.

Protecção radiológica do doente em tomografia computorizada

RESUMO - A preocupação com os conhecimentos, atitudes, crenças e práticas, no que concerne à utilização de radiações ionizantes para fins de diagnóstico, e a sensibilização de todos os agentes envolvidos, médicos, técnicos, físicos, utentes e responsáveis pela Saúde Publica, relativamente aos níveis de radiação emitida nos exames de Tomografia Computorizada (TC), assume particular importância no domínio da Saúde Pública, na medida em que é necessário influenciar o desenvolvimento de práticas que promovam, auditem e garantam a prestação do controlo da qualidade radiológica e dosimétrica nos serviços de Radiologia a nível Nacional. Para tal, e no âmbito da publicação de estudos já realizados ao nível da União Europeia, ―Orientações Europeias dos Critérios de Qualidade para a Tomografia Computorizada (1999) ‖, é proposto estabelecer orientações na realização de estudos que permitam, numa primeira fase, estabelecer a comparação com os resultados obtidos pelos mecanismos de Controlo da Qualidade (CQ), analisar e proceder aos ajustes (se necessário) e, numa segunda fase, implementar uma moldura sistemática de avaliação periódica dos níveis de dose de radiação por exame TC e que permita a monitorização dos dados. Nesse sentido, propõe-se a realização de um Estudo Nacional que envolva a rede hospitalar pública, privada e universitária, partindo da metodologia utilizada em estudos prévios noutros países da Europa, como seja, selecção do equipamento de TC existente na Instituição Hospitalar, onde serão reunidas informações através do preenchimento de questionários relativos ao equipamento a utilizar. Serão recolhidos dados relativos ao utente, ao equipamento e parâmetros de aquisição de imagem, que permitam identificar os níveis de referência de diagnóstico (NRD) em TC, na realidade Portuguesa. Foi efectuado um estudo piloto numa instituição EPE e os valores obtidos não são significativos, nem podem assumir valor preditivo dado o reduzido tamanho da amostra. Apesar disso, sugerem a existência de parâmetros que podem ser alterados e com isso podem fazer variar a dose de radiação utilizada. ENSP/UNL Maria de Fátima Vaz de Carvalho 5 Espera-se obter com este estudo, como foi referido, a base do estabelecimento dos NRD em TC em Portugal. ----------------- ABSTRACT - The purpose of this study, in an empirical point of view, emerges from concern with the knowledge, attitudes, beliefs and practices regarding the use of ionizing radiation for diagnostic purposes and awareness of all actors involved, medical physical, technical, and responsible public health for the development of practices that promote, audited and ensure the provision of radiological quality control and dosing in radiology service at national level. In view of the complexity and characteristics involved in relation to ionizing radiation, all assume their part in protecting the physical integrity of each user and a global perspective, to ensure the safeguarding of public health, while global and globalizing factor. To this end, and in the context of the publication of studies already carried out at European Union level, "European guidelines for quality criteria for computed tomography", it is proposed to establish guidelines in conducting studies to initially establish the comparison with the results obtained by QC and make adjustments if necessary, and subsequently implement a systematic periodic assessment frame that allows monitoring of data. Accordingly, it is proposed to conduct a national study involving the public network, private and University hospitals, that extends from the methodology used in previous studies in other countries of Europe, as is, selection of equipment of existing CT in Hospital Institution, where information will be gathered by filling out questionnaires concerning the equipment to be used. Data will be collected for the wearer, equipment and parameters of image acquisition, identifying diagnostic reference levels (NRD) in CT in Portuguese fact. A pilot study was carried out in an institution EPE and the values obtained are not significant, nor can they take predictive value given the small sample size. Despite this, suggest the existence of parameters that can be changed and this can vary the dose of radiation used It is hoped to get with this study, as mentioned, the basis of the establishment of NRD in CT in Portugal.

Aquisição e Processamento de Imagens de Microscopia em Balística Forense

As novas tecnologias aplicadas ao processamento de imagem e reconhecimento de padrões têm sido alvo de um grande progresso nas últimas décadas. A sua aplicação é transversal a diversas áreas da ciência, nomeadamente a área da balística forense. O estudo de evidências (invólucros e projeteis) encontradas numa cena de crime, recorrendo a técnicas de processamento e análise de imagem, é pertinente pelo facto de, aquando do disparo, as armas de fogo imprimirem marcas únicas nos invólucros e projéteis deflagrados, permitindo relacionar evidências deflagradas pela mesma arma. A comparação manual de evidências encontradas numa cena de crime com evidências presentes numa base de dados, em termos de parâmetros visuais, constitui uma abordagem demorada. No âmbito deste trabalho pretendeu-se desenvolver técnicas automáticas de processamento e análise de imagens de evidências, obtidas através do microscópio ótico de comparação, tendo por base algoritmos computacionais. Estes foram desenvolvidos com recurso a pacotes de bibliotecas e a ferramentas open-source. Para a aquisição das imagens de evidências balísticas foram definidas quatro modalidades de aquisição: modalidade Planar, Multifocus, Microscan e Multiscan. As imagens obtidas foram aplicados algoritmos de processamento especialmente desenvolvidos para o efeito. A aplicação dos algoritmos de processamento permite a segmentação de imagem, a extração de características e o alinhamento de imagem. Este último tem como finalidade correlacionar as evidências e obter um valor quantitativo (métrica), indicando o quão similar essas evidências são. Com base no trabalho desenvolvido e nos resultados obtidos, foram definidos protocolos de aquisição de imagens de microscopia, que possibilitam a aquisição de imagens das regiões passiveis de serem estudadas, assim como algoritmos que permitem automatizar o posterior processo de alinhamento de imagens de evidências, constituindo uma vantagem em relação ao processo de comparação manual.

Geospatial assessment of pest-induced forest damage through the use of UAV-bases NIR imaging and Gi-technology

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Multi-temporal analysis of radiometric changes in satellite images of forest edges to infer selective-logging areas in the Amazon forest

Radiometric changes observed in multi-temporal optical satellite images have an important role in efforts to characterize selective-logging areas. The aim of this study was to analyze the multi-temporal behavior of spectral-mixture responses in satellite images in simulated selective-logging areas in the Amazon forest, considering red/near-infrared spectral relationships. Forest edges were used to infer the selective-logging infrastructure using differently oriented edges in the transition between forest and deforested areas in satellite images. TM/Landsat-5 images acquired at three dates with different solar-illumination geometries were used in this analysis. The method assumed that the radiometric responses between forest with selective-logging effects and forest edges in contact with recent clear-cuts are related. The spatial frequency attributes of red/near infrared bands for edge areas were analyzed. Analysis of dispersion diagrams showed two groups of pixels that represent selective-logging areas. The attributes for size and radiometric distance representing these two groups were related to solar-elevation angle. The results suggest that detection of timber exploitation areas is limited because of the complexity of the selective-logging radiometric response. Thus, the accuracy of detecting selective logging can be influenced by the solar-elevation angle at the time of image acquisition. We conclude that images with lower solar-elevation angles are less reliable for delineation of selecting logging.

Development of procedures for the design, optimization and manufacturing of customized orthopaedic and trauma implants: Geometrical/anatomical modelling from 3D medical imaging

Tese de Doutoramento (Programa Doutoral em Engenharia Biomédica)

Development of a semi-automatic self learning pattern recognition system for the control of electronic boards

This project was funded under the Applied Research Grants Scheme administered by Enterprise Ireland. The project was a partnership between Galway - Mayo Institute of Technology and an industrial company, Tyco/Mallinckrodt Galway. The project aimed to develop a semi - automatic, self - learning pattern recognition system capable of detecting defects on the printed circuits boards such as component vacancy, component misalignment, component orientation, component error, and component weld. The research was conducted in three directions: image acquisition, image filtering/recognition and software development. Image acquisition studied the process of forming and digitizing images and some fundamental aspects regarding the human visual perception. The importance of choosing the right camera and illumination system for a certain type of problem has been highlighted. Probably the most important step towards image recognition is image filtering, The filters are used to correct and enhance images in order to prepare them for recognition. Convolution, histogram equalisation, filters based on Boolean mathematics, noise reduction, edge detection, geometrical filters, cross-correlation filters and image compression are some examples of the filters that have been studied and successfully implemented in the software application. The software application developed during the research is customized in order to meet the requirements of the industrial partner. The application is able to analyze pictures, perform the filtering, build libraries, process images and generate log files. It incorporates most of the filters studied and together with the illumination system and the camera it provides a fully integrated framework able to analyze defects on printed circuit boards.

Non-assisted versus neuro-navigated and XperCT-guided external ventricular catheter placement: a comparative cadaver study.

BACKGROUND AND PURPOSE: Accurate placement of an external ventricular drain (EVD) for the treatment of hydrocephalus is of paramount importance for its functionality and in order to minimize morbidity and complications. The aim of this study was to compare two different drain insertion assistance tools with the traditional free-hand anatomical landmark method, and to measure efficacy, safety and precision. METHODS: Ten cadaver heads were prepared by opening large bone windows centered on Kocher's points on both sides. Nineteen physicians, divided in two groups (trainees and board certified neurosurgeons) performed EVD insertions. The target for the ventricular drain tip was the ipsilateral foramen of Monro. Each participant inserted the external ventricular catheter in three different ways: 1) free-hand by anatomical landmarks, 2) neuronavigation-assisted (NN), and 3) XperCT-guided (XCT). The number of ventricular hits and dangerous trajectories; time to proceed; radiation exposure of patients and physicians; distance of the catheter tip to target and size of deviations projected in the orthogonal plans were measured and compared. RESULTS: Insertion using XCT increased the probability of ventricular puncture from 69.2 to 90.2 % (p = 0.02). Non-assisted placements were significantly less precise (catheter tip to target distance 14.3 ± 7.4 mm versus 9.6 ± 7.2 mm, p = 0.0003). The insertion time to proceed increased from 3.04 ± 2.06 min. to 7.3 ± 3.6 min. (p < 0.001). The X-ray exposure for XCT was 32.23 mSv, but could be reduced to 13.9 mSv if patients were initially imaged in the hybrid-operating suite. No supplementary radiation exposure is needed for NN if patients are imaged according to a navigation protocol initially. CONCLUSION: This ex vivo study demonstrates a significantly improved accuracy and safety using either NN or XCT-assisted methods. Therefore, efforts should be undertaken to implement these new technologies into daily clinical practice. However, the accuracy versus urgency of an EVD placement has to be balanced, as the image-guided insertion technique will implicate a longer preparation time due to a specific image acquisition and trajectory planning.

Testing low-altitude infrared digital photography from a mini-UAV to retrieve information for biological conservation

Satellite remote sensing imagery is used for forestry, conservation and environmental applications, but insufficient spatial resolution, and, in particular, unavailability of images at the precise timing required for a given application, often prevent achieving a fully operational stage. Airborne remote sensing has the advantage of custom-tuned sensors, resolution and timing, but its price prevents using it as a routine technique for the mentioned fields. Some Unmanned Aerial Vehicles might provide a “third way” solution as low-cost techniques for acquiring remotely sensed information, under close control of the end-user, albeit at the expense of lower quality instrumentation and instability. This report evaluates a light remote sensing system based on a remotely-controlled mini-UAV (ATMOS-3) equipped with a color infra-red camera (VEGCAM-1) designed and operated by CATUAV. We conducted a testing mission over a Mediterranean landscape dominated by an evergreen woodland of Aleppo pine (Pinus halepensis) and (Holm) oak (Quercus ilex) in the Montseny National Park (Catalonia, NE Spain). We took advantage of state-of-the-art ortho-rectified digital aerial imagery (acquired by the Institut Cartogràfic de Catalunya over the area during the previous year) and used it as quality reference. In particular, we paid attention to: 1) Operationality of flight and image acquisition according to a previously defined plan; 2) Radiometric and geometric quality of the images; and 3) Operational use of the images in the context of applications. We conclude that the system has achieved an operational stage regarding flight activities, although with meteorological limits set by wind speed and turbulence. Appropriate landing areas can be sometimes limiting also, but the system is able to land on small and relatively rough terrains such as patches of grassland or short matorral, and we have operated the UAV as far as 7 km from the control unit. Radiometric quality is sufficient for interactive analysis, but probably insufficient for automated processing. A forthcoming camera is supposed to greatly improve radiometric quality and consistency. Conventional GPS positioning through time synchronization provides coarse orientation of the images, with no roll information.

Underwater Gigamosaicing

El procés de fusió de dues o més imatges de la mateixa escena en una d'única i més gran és conegut com a Image Mosaicing. Un cop finalitzat el procés de construcció d'un mosaic, els límits entre les imatges són habitualment visibles, degut a imprecisions en els registres fotomètric i geomètric. L'Image Blending és l'etapa del procediment de mosaicing a la que aquests artefactes són minimitzats o suprimits. Existeixen diverses metodologies a la literatura que tracten aquests problemes, però la majoria es troben orientades a la creació de panorames terrestres, imatges artístiques d'alta resolució o altres aplicacions a les quals el posicionament de la càmera o l'adquisició de les imatges no són etapes rellevants. El treball amb imatges subaquàtiques presenta desafiaments importants, degut a la presència d'scattering (reflexions de partícules en suspensió) i atenuació de la llum i a condicions físiques extremes a milers de metres de profunditat, amb control limitat dels sistemes d'adquisició i la utilització de tecnologia d'alt cost. Imatges amb il·luminació artificial similar, sense llum global com la oferta pel sol, han de ser unides sense mostrar una unió perceptible. Les imatges adquirides a gran profunditat presenten una qualitat altament depenent de la profunditat, i la seva degradació amb aquest factor és molt rellevant. El principal objectiu del treball és presentar dels principals problemes de la imatge subaquàtica, seleccionar les estratègies més adequades i tractar tota la seqüència adquisició-procesament-visualització del procés. Els resultats obtinguts demostren que la solució desenvolupada, basada en una Estratègia de Selecció de Límit Òptim, Fusió en el Domini del Gradient a les regions comunes i Emfatització Adaptativa d'Imatges amb baix nivell de detall permet obtenir uns resultats amb una alta qualitat. També s'ha proposat una estratègia, amb possibilitat d'implementació paral·lela, que permet processar mosaics de kilòmetres d'extensió amb resolució de centímetres per píxel.

Optimisation de la cryo microscopie électronique pour les études des minicercles d'ADN

RESUME : Bien que les propriétés physiques de la structure de l'ADN aient été intensivement étudiées pendant plus de 50 ans il y a encore beaucoup de questions importantes qui attendent des réponses. Par exemple, qu'arrive-t-il à la structure de la double hélice d'ADN nue (sans protéines liées) lorsqu'elle est fortement courbée, de la même manière que dans les nucléosomes? Cet ADN nu est-il facilement plié (il reste dans le régime élastique) ou réduit-il la contrainte de flexion en formant des sites hyperflexibles «kinks» (il sort du régime élastique en cassant l'empilement des paires de bases à certains endroits) ? La microscopie électronique peut fournir une réponse à cette question par visualisation directe des minicercles d'ADN de la longueur d'un tour de nucléosome (environ 90 paires de bases). Pour que la réponse soit scientifiquement valide, on doit observer les molécules d'ADN lorsqu'elles sont en suspension dans la solution d'intérêt et sans que des colorations, produits chimiques ou fixatifs n'aient été ajoutés, étant donné que ceux-ci peuvent changer les propriétés de l'ADN. La technique de la cryo-microscopie électronique (cryo-EM) développée par le groupe de Jacques Dubochet au début des années 80, permet la visualisation directe des molécules d'ADN suspendues dans des couche minces vitrifiées de solutions aqueuses. Toutefois, le faible contraste qui caractérise la cryo-EM combinée avec la très petite taille des minicercles d'ADN rendent nécessaire l'optimisation de plusieurs étapes, aussi bien dans la préparation des échantillons que dans le processus d'acquisition d'images afin d'obtenir deux clichés stéréo qui permettent la reconstruction 3-D des minicercles d'ADN. Dans la première partie de ma thèse, je décris l'optimisation de certains paramètres pour la cryoEM et des processus d'acquisition d'image utilisant comme objets de test des plasmides et d'autres molécules d'ADN. Dans la deuxième partie, je .décris comment j'ai construit les minicercles d'ADN de 94 bp et comment j'ai introduit des modifications structurelles comme des coupures ou des lacunes. Dans la troisième partie, je décris l'analyse des reconstructions des rninicercles d'ADN. Cette analyse, appuyée par des tests biochimiques, indique fortement que des molécules d'ADN sont capables de former de petites molécules circulaires de 94 bp sans dépasser les limites d'élasticité, indiquant que les minicercles adoptent une forme circulaire régulière où la flexion est redistribuée le long la molécule. ABSTRACT : Although physical properties of DNA structure have been intensively studied for over 50 years there are still many important questions that need to be answered. For example, what happens to protein-free double-stranded DNA when it is strongly bent, as in DNA forming nucleosomes? Is such protein-free DNA smoothly bent (i.e. it remains within elastic limits of DNA rigidity) or does it release its bending stress by forming sharp kinks (i.e. it exits the elastic regime and breaks the stacking between neighbouring base-pairs in localized regions)? Electron microscopy can provide an answer to this question by directly visualizing DNA minicircles that have the size of nucleosome gyres (ca 90 bp). For the answer to be scientifically valid, one needs to observe DNA molecules while they are still suspended in the solution of interest and no staining chemicals or fixatives have been added since these can change the properties of the DNA. CryoEM techniques developed by Jacques Dubochet's group beginning in the 1980's permit direct visualization of DNA molecules suspended in cryo-vitrified layers of aqueous solutions. However, a relatively weak contrast of cryo-EM preparations combined with the very small size of the DNA minicircles made it necessary to optimize many of the steps and parameters of the cryo-EM specimen preparation and image acquisition processes in order to obtain stereo-pairs of images that permit the 3-D reconstruction of the observed DNA minicircles. In the first part of my thesis I describe the optimization of the cryo-EM preparation and the image acquisition processes using plasmid size DNA molecules as a test object. In the second part, I describe how I formed the 94 by DNA minicircles and how I introduced structural modifications like nicks or gaps. In the third part, I describe the cryo-EM analysis of the constructed DNA minicircles. That analysis, supported by biochemical tests, strongly indicates that DNA minicircles as small as 94 by remain within the elastic limits of DNA structure, i.e. the minicircles adopt a regular circular shape where bending is redistributed along the molecules.