Groundtruth system for underwater benchmarking

Oceans - San Diego, 2013

Structured Light System Calibration for Perception in Underwater Tanks

The process of visually exploring underwater environments is still a complex problem. Underwater vision systems require complementary means of sensor information to help overcome water disturbances. This work proposes the development of calibration methods for a structured light based system consisting on a camera and a laser with a line beam. Two different calibration procedures that require only two images from different viewpoints were developed and tested in dry and underwater environments. Results obtained show, an accurate calibration for the camera/projector pair with errors close to 1 mm even in the presence of a small stereos baseline.

Aquisição por Visão Artificial e Medição Automática de Micro Dureza Vickers

O ensaio de dureza, e mais concretamente o ensaio de micro dureza Vickers, é no universo dos ensaios mecânicos um dos mais utilizados quer seja na indústria, no ensino ou na investigação e desenvolvimento de produto no âmbito das ciências dos materiais. Na grande maioria dos casos, a utilização deste ensaio tem como principal aplicação a caracterização ou controlo da qualidade de fabrico de materiais metálicos. Sendo um ensaio de relativa simplicidade de execução, rapidez e com resultados comparáveis e relacionáveis a outras grandezas físicas das propriedades dos materiais. Contudo, e tratando-se de um método de ensaio cuja intervenção humana é importante, na medição da indentação gerada por penetração mecânica através de um sistema ótico, não deixa de exibir algumas debilidades que daí advêm, como sendo o treino dos técnicos e respetivas acuidades visuais, fenómenos de fadiga visual que afetam os resultados ao longo de um turno de trabalho; ora estes fenómenos afetam a repetibilidade e reprodutibilidade dos resultados obtidos no ensaio. O CINFU possui um micro durómetro Vickers, cuja realização dos ensaios depende de um técnico treinado para a execução do mesmo, apresentando todas as debilidades já mencionadas e que o tornou elegível para o estudo e aplicação de uma solução alternativa. Assim, esta dissertação apresenta o desenvolvimento de uma solução alternativa ao método ótico convencional na medição de micro dureza Vickers. Utilizando programação em LabVIEW da National Instruments, juntamente com as ferramentas de visão computacional (NI Vision), o programa começa por solicitar ao técnico a seleção da câmara para aquisição da imagem digital acoplada ao micro durómetro, seleção do método de ensaio (Força de ensaio); posteriormente o programa efetua o tratamento da imagem (aplicação de filtros para eliminação do ruído de fundo da imagem original), segue-se, por indicação do operador, a zona de interesse (ROI) e por sua vez são identificadas automaticamente os vértices da calote e respetivas distâncias das diagonais geradas concluindo, após aceitação das mesmas, com o respetivo cálculo de micro dureza resultante. Para validação dos resultados foram utilizados blocos-padrão de dureza certificada (CRM), cujos resultados foram satisfatórios, tendo-se obtido um elevado nível de exatidão nas medições efetuadas. Por fim, desenvolveu-se uma folha de cálculo em Excel com a determinação da incerteza associada às medições de micro dureza Vickers. Foram então comparados os resultados nas duas metodologias possíveis, pelo método ótico convencional e pela utilização das ferramentas de visão computacional, tendo-se obtido bons resultados com a solução proposta.

Distributed processing of large remote sensing images using MapReduce - A case of Edge Detection

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

Clinical Outcome and Morphologic Determinants of Mural Thrombus in Abdominal Aortic Endografts

OBJECTIVE:Endograft mural thrombus has been associated with stent graft or limb thrombosis after endovascular aneurysm repair (EVAR). This study aimed to identify clinical and morphologic determinants of endograft mural thrombus accumulation and its influence on thromboembolic events after EVAR. METHODS: A prospectively maintained database of patients treated by EVAR at a tertiary institution from 2000 to 2012 was analyzed. Patients treated for degenerative infrarenal abdominal aortic aneurysms and with available imaging for thrombus analysis were considered. All measurements were performed on three-dimensional center-lumen line computed tomography angiography (CTA) reconstructions. Patients with thrombus accumulation within the endograft's main body with a thickness >2 mm and an extension >25% of the main body's circumference were included in the study group and compared with a control group that included all remaining patients. Clinical and morphologic variables were assessed for association with significant thrombus accumulation within the endograft's main body by multivariate regression analysis. Estimates for freedom from thromboembolic events were obtained by Kaplan-Meier plots. RESULTS: Sixty-eight patients (16.4%) presented with endograft mural thrombus. Median follow-up time was 3.54 years (interquartile range, 1.99-5.47 years). In-graft mural thrombus was identified on 30-day CTA in 22 patients (32.4% of the study group), on 6-month CTA in 8 patients (11.8%), and on 1-year CTA in 17 patients (25%). Intraprosthetic thrombus progressively accumulated during the study period in 40 patients of the study group (55.8%). Overall, 17 patients (4.1%) presented with endograft or limb occlusions, 3 (4.4%) in the thrombus group and 14 (4.1%) in the control group (P = .89). Thirty-one patients (7.5%) received an aortouni-iliac (AUI) endograft. Two endograft occlusions were identified among AUI devices (6.5%; overall, 0.5%). None of these patients showed thrombotic deposits in the main body, nor were any outflow abnormalities identified on the immediately preceding CTA. Estimated freedom from thromboembolic events at 5 years was 95% in both groups (P = .97). Endograft thrombus accumulation was associated with >25% proximal aneurysm neck thrombus coverage at baseline (odds ratio [OR], 1.9; 95% confidence interval [CI], 1.1-3.3), neck length ≤ 15 mm (OR, 2.4; 95% CI, 1.3-4.2), proximal neck diameter ≥ 30 mm (OR, 2.4; 95% CI, 1.3-4.6), AUI (OR, 2.2; 95% CI, 1.8-5.5), or polyester-covered stent grafts (OR, 4.0; 95% CI, 2.2-7.3) and with main component "barrel-like" configuration (OR, 6.9; 95% CI, 1.7-28.3). CONCLUSIONS: Mural thrombus formation within the main body of the endograft is related to different endograft configurations, main body geometry, and device fabric but appears to have no association with the occurrence of thromboembolic events over time.

Microscopy image segmentation by active contour models

In this thesis a semi-automated cell analysis system is described through image processing. To achieve this, an image processing algorithm was studied in order to segment cells in a semi-automatic way. The main goal of this analysis is to increase the performance of cell image segmentation process, without affecting the results in a significant way. Even though, a totally manual system has the ability of producing the best results, it has the disadvantage of taking too long and being repetitive, when a large number of images need to be processed. An active contour algorithm was tested in a sequence of images taken by a microscope. This algorithm, more commonly known as snakes, allowed the user to define an initial region in which the cell was incorporated. Then, the algorithm would run several times, making the initial region contours to converge to the cell boundaries. With the final contour, it was possible to extract region properties and produce statistical data. This data allowed to say that this algorithm produces similar results to a purely manual system but at a faster rate. On the other hand, it is slower than a purely automatic way but it allows the user to adjust the contour, making it more versatile and tolerant to image variations.

Automatic eye blink detection using consumer web cameras

This research aims to advance blinking detection in the context of work activity. Rather than patients having to attend a clinic, blinking videos can be acquired in a work environment, and further automatically analyzed. Therefore, this paper presents a methodology to perform the automatic detection of eye blink using consumer videos acquired with low-cost web cameras. This methodology includes the detection of the face and eyes of the recorded person, and then it analyzes the low-level features of the eye region to create a quantitative vector. Finally, this vector is classified into one of the two categories considered —open and closed eyes— by using machine learning algorithms. The effectiveness of the proposed methodology was demonstrated since it provides unbiased results with classification errors under 5%

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)

Enalapril alters the formation of the collagen matrix in spontaneously hypertensive rats

OBJECTIVE: To assess the effect of the inhibition of the angiotensin-converting enzyme on the collagen matrix (CM) of the heart of newborn spontaneously hypertensive rats (SHR) during embryonic development. METHODS: The study comprised the 2 following groups of SHR (n=5 each): treated group - rats conceived from SHR females treated with enalapril maleate (15 mg. kg-1.day-1) during gestation; and nontreated group - offspring of nontreated females. The newborns were euthanized within the first 24 hours after birth and their hearts were removed and processed for histological study. Three fields per animal were considered for computer-assisted digital analysis and determination of the volume densities (Vv) of the nuclei and CM. The images were segmented with the aid of Image Pro Plus® 4.5.029 software (Media Cybernetics). RESULTS: No difference was observed between the treated and nontreated groups in regard to body mass, cardiac mass, and the relation between cardiac and body mass. A significant reduction in the Vv[matrix] and a concomitant increase in the Vv[nuclei] were observed in the treated group as compared with those in the nontreated group. CONCLUSION: The treatment with enalapril of hypertensive rats during pregnancy alters the collagen content and structure of the myocardium of newborns.

Predicting trabecular bone microdamage initiation and accumulation using a non-linear perfect damage model

Studies evaluating the mechanical behavior of the trabecular microstructure play an important role in our understanding of pathologies such as osteoporosis, and in increasing our understanding of bone fracture and bone adaptation. Understanding of such behavior in bone is important for predicting and providing early treatment of fractures. The objective of this study is to present a numerical model for studying the initiation and accumulation of trabecular bone microdamage in both the pre- and post-yield regions. A sub-region of human vertebral trabecular bone was analyzed using a uniformly loaded anatomically accurate microstructural three-dimensional finite element model. The evolution of trabecular bone microdamage was governed using a non-linear, modulus reduction, perfect damage approach derived from a generalized plasticity stress-strain law. The model introduced in this paper establishes a history of microdamage evolution in both the pre- and post-yield regions

Benchmarking therapeutic drug monitoring software: A review of available computer tools

Therapeutic drug monitoring (TDM) aims to optimize treatments by individualizing dosage regimens based on the measurement of blood concentrations. Dosage individualization to maintain concentrations within a target range requires pharmacokinetic and clinical capabilities. Bayesian calculations currently represent the gold standard TDM approach but require computation assistance. In recent decades computer programs have been developed to assist clinicians in this assignment. The aim of this survey was to assess and compare computer tools designed to support TDM clinical activities. The literature and the Internet were searched to identify software. All programs were tested on personal computers. Each program was scored against a standardized grid covering pharmacokinetic relevance, user friendliness, computing aspects, interfacing and storage. A weighting factor was applied to each criterion of the grid to account for its relative importance. To assess the robustness of the software, six representative clinical vignettes were processed through each of them. Altogether, 12 software tools were identified, tested and ranked, representing a comprehensive review of the available software. Numbers of drugs handled by the software vary widely (from two to 180), and eight programs offer users the possibility of adding new drug models based on population pharmacokinetic analyses. Bayesian computation to predict dosage adaptation from blood concentration (a posteriori adjustment) is performed by ten tools, while nine are also able to propose a priori dosage regimens, based only on individual patient covariates such as age, sex and bodyweight. Among those applying Bayesian calculation, MM-USC*PACK© uses the non-parametric approach. The top two programs emerging from this benchmark were MwPharm© and TCIWorks. Most other programs evaluated had good potential while being less sophisticated or less user friendly. Programs vary in complexity and might not fit all healthcare settings. Each software tool must therefore be regarded with respect to the individual needs of hospitals or clinicians. Programs should be easy and fast for routine activities, including for non-experienced users. Computer-assisted TDM is gaining growing interest and should further improve, especially in terms of information system interfacing, user friendliness, data storage capability and report generation.

Coronary magnetic resonance angiography for assessment of the stent lumen: a phantom study.

PURPOSE: To evaluate the feasibility of visualizing the stent lumen using coronary magnetic resonance angiography in vitro. MATERIAL AND METHODS: Nineteen different coronary stents were implanted in plastic tubes with an inner diameter of 3 mm. The tubes were positioned in a plastic container filled with gel and included in a closed flow circuit (constant flow 18 cm/sec). The magnetic resonance images were obtained with a dual inversion fast spin-echo sequence. For intraluminal stent imaging, subtraction images were calculated from scans with and without flow. Subsequently, intraluminal signal properties were objectively assessed and compared. RESULTS: As a function of the stent type, various degrees of in-stent signal attenuation were observed. Tantalum stents demonstrated minimal intraluminal signal attenuation. For nitinol stents, the stent lumen could be identified, but the intraluminal signal was markedly reduced. Steel stents resulted in the most pronounced intraluminal signal voids. CONCLUSIONS: With the present technique, radiofrequency penetration into the stents is strongly influenced by the stent material. Thesefindings may have important implicationsforfuture stent design and stent imaging strategies.

Motion analysis in terms of wireless video capsule endoscopy

El treball presentat suposa una visió general de l'"Endoscopia amb Càpsula de Vídeo Wireless" i la inspecció de sequències de contraccions intestinals amb les últimes tecnologies de visió per computador. Després de la observació preliminar dels fonaments mèdics requerits, la aplicació de visió per computador es presenta en aquestos termes. En essència, aquest treball proveïx una exhaustiva selecció, descripció i avaluació de cert conjunt de mètodes de processament d'imatges respecte a l'anàlisi de moviment, en el entorn de seqüències d'imatges preses amb una càpsula endoscòpica. Finalment, es presenta una aplicació de software per configurar i emprar de forma ràpida i fàcil un entorn experimental.

Fusion of Multi-Atlas Segmentations with Spatial Distribution Modeling

In recent years, multi-atlas fusion methods have gainedsignificant attention in medical image segmentation. Inthis paper, we propose a general Markov Random Field(MRF) based framework that can perform edge-preservingsmoothing of the labels at the time of fusing the labelsitself. More specifically, we formulate the label fusionproblem with MRF-based neighborhood priors, as an energyminimization problem containing a unary data term and apairwise smoothness term. We present how the existingfusion methods like majority voting, global weightedvoting and local weighted voting methods can be reframedto profit from the proposed framework, for generatingmore accurate segmentations as well as more contiguoussegmentations by getting rid of holes and islands. Theproposed framework is evaluated for segmenting lymphnodes in 3D head and neck CT images. A comparison ofvarious fusion algorithms is also presented.

EEG-based functional brain networks: does the network size matter?

Functional connectivity in human brain can be represented as a network using electroencephalography (EEG) signals. These networks--whose nodes can vary from tens to hundreds--are characterized by neurobiologically meaningful graph theory metrics. This study investigates the degree to which various graph metrics depend upon the network size. To this end, EEGs from 32 normal subjects were recorded and functional networks of three different sizes were extracted. A state-space based method was used to calculate cross-correlation matrices between different brain regions. These correlation matrices were used to construct binary adjacency connectomes, which were assessed with regards to a number of graph metrics such as clustering coefficient, modularity, efficiency, economic efficiency, and assortativity. We showed that the estimates of these metrics significantly differ depending on the network size. Larger networks had higher efficiency, higher assortativity and lower modularity compared to those with smaller size and the same density. These findings indicate that the network size should be considered in any comparison of networks across studies.