Ajuste radiométrico de imagens aéreas digitais

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Segmentação de imagens e reconstrução de modelos aplicada a estruturas ósseas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Estimação de densidades e aplicação em segmentação de imagens

The aim of this work is to study some of the density estimation tec- niques and to apply to the segmentation of medical images. Medical images are used to help the diagnostic of tumor diseases as well as to plan and deliver treatment. A computer image is an array of values representing colors in some scale. The smallest element of the image to which it is possible to assign a value is called pixel. Segmen- tation is the process of dividing the image in portions through the classi¯cation of each pixel. The simplest way of classi¯cation is by thresholding, given the number of portions and the threshold values. Another method is constructing a histogram of the pixel values and assign a portion to each pike. The threshold is the mean between two pikes. As the histogram does not form a smooth curve it is di±cult to discern between true pikes and random variation. Density estimation methods allow the estimation of a smooth curve. Image data can be considered as mixture of different densities. In this project parametric and nonparametric methods for density estimation will be addressed and some of them are applied to CT image data

Programa computacional ODR-ATA para densitometria óssea baseado na densitometria radiografica

Pós-graduação em Ciência Animal - FMVA

Analysis of mesiodistal angulations of preadjusted brackets

Manufacturers offer various prescriptions of preadjusted brackets for use in the "straight-wire" orthodontic technique. However, the need to incorporate bends in the rectangular wires during orthodontic finishing has led to concerns regarding the type of prescription chosen and the credibility of information provided by the manufacturer. The aim of this study was to compare the slot angulations of Roth prescription preadjusted metallic brackets for the maxillary left central incisor and maxillary left canine. For each tooth type, 10 brackets of three commercial brands (GAC, Forestadent and Morelli) were selected. Two individual metal matrices for brackets and tooth positioning were made for each group of teeth. Captured images were obtained by standardized ortho-radial photography with a digital camera. Images were exported and analyzed with the Image J software package. One-way ANOVA and Tukey statistical analyses were performed at the 5% significance level. For brackets of the maxillary left central incisor, differences in mean angulation were observed between the Morelli and GAC groups (p < 0.01) and between the Forestadent and GAC groups (p < 0.01). For brackets of the maxillary left canine, differences in mean angulation were found between the Morelli and GAC groups (p < 0.01) and between the Morelli and Forestadent groups (p < 0.05). In conclusion, despite their same prescription name, the different brands exhibited significantly different angulation measurements.

Utilização de material alternativo para a obtenção e caracterização de biomodelos, por meio da técnica de impressão 3DPRINTER

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

An in vitro comparison of subjective image quality of panoramic views acquired via 2D or 3D imaging

Objectives: The objective of this study is to compare subjective image quality and diagnostic validity of cone-beam CT (CBCT) panoramic reformatting with digital panoramic radiographs. Materials and methods: Four dry human skulls and two formalin-fixed human heads were scanned using nine different CBCTs, one multi-slice CT (MSCT) and one standard digital panoramic device. Panoramic views were generated from CBCTs in four slice thicknesses. Seven observers scored image quality and visibility of 14 anatomical structures. Four observers repeated the observation after 4 weeks. Results: Digital panoramic radiographs showed significantly better visualization of anatomical structures except for the condyle. Statistical analysis of image quality showed that the 3D imaging modalities (CBCTs and MSCT) were 7.3 times more likely to receive poor scores than the 2D modality. Yet, image quality from NewTom VGi® and 3D Accuitomo 170® was almost equivalent to that of digital panoramic radiographs with respective odds ratio estimates of 1.2 and 1.6 at 95% Wald confidence limits. A substantial overall agreement amongst observers was found. Intra-observer agreement was moderate to substantial. Conclusions: While 2D-panoramic images are significantly better for subjective diagnosis, 2/3 of the 3D-reformatted panoramic images are moderate or good for diagnostic purposes. Clinical relevance: Panoramic reformattings from particular CBCTs are comparable to digital panoramic images concerning the overall image quality and visualization of anatomical structures. This clinically implies that a 3D-derived panoramic view can be generated for diagnosis with a recommended 20-mm slice thickness, if CBCT data is a priori available for other purposes.

Development of musculoskeletal models for the design and the pre-clinical validation of hip resurfacing prosthesis

Background. The surgical treatment of dysfunctional hips is a severe condition for the patient and a costly therapy for the public health. Hip resurfacing techniques seem to hold the promise of various advantages over traditional THR, with particular attention to young and active patients. Although the lesson provided in the past by many branches of engineering is that success in designing competitive products can be achieved only by predicting the possible scenario of failure, to date the understanding of the implant quality is poorly pre-clinically addressed. Thus revision is the only delayed and reliable end point for assessment. The aim of the present work was to model the musculoskeletal system so as to develop a protocol for predicting failure of hip resurfacing prosthesis. Methods. Preliminary studies validated the technique for the generation of subject specific finite element (FE) models of long bones from Computed Thomography data. The proposed protocol consisted in the numerical analysis of the prosthesis biomechanics by deterministic and statistic studies so as to assess the risk of biomechanical failure on the different operative conditions the implant might face in a population of interest during various activities of daily living. Physiological conditions were defined including the variability of the anatomy, bone densitometry, surgery uncertainties and published boundary conditions at the hip. The protocol was tested by analysing a successful design on the market and a new prototype of a resurfacing prosthesis. Results. The intrinsic accuracy of models on bone stress predictions (RMSE < 10%) was aligned to the current state of the art in this field. The accuracy of prediction on the bone-prosthesis contact mechanics was also excellent (< 0.001 mm). The sensitivity of models prediction to uncertainties on modelling parameter was found below 8.4%. The analysis of the successful design resulted in a very good agreement with published retrospective studies. The geometry optimisation of the new prototype lead to a final design with a low risk of failure. The statistical analysis confirmed the minimal risk of the optimised design over the entire population of interest. The performances of the optimised design showed a significant improvement with respect to the first prototype (+35%). Limitations. On the authors opinion the major limitation of this study is on boundary conditions. The muscular forces and the hip joint reaction were derived from the few data available in the literature, which can be considered significant but hardly representative of the entire variability of boundary conditions the implant might face over the patients population. This moved the focus of the research on modelling the musculoskeletal system; the ongoing activity is to develop subject-specific musculoskeletal models of the lower limb from medical images. Conclusions. The developed protocol was able to accurately predict known clinical outcomes when applied to a well-established device and, to support the design optimisation phase providing important information on critical characteristics of the patients when applied to a new prosthesis. The presented approach does have a relevant generality that would allow the extension of the protocol to a large set of orthopaedic scenarios with minor changes. Hence, a failure mode analysis criterion can be considered a suitable tool in developing new orthopaedic devices.

Uso di 3d slicer in ambito di ricerca clinica: Una revisione critica delle esperienze di riferimento

Negli ultimi 20 anni il progresso tecnologico ha segnato un profondo cambiamento in svariati ambiti tra i quali quello della Sanità in cui hanno preso vita apparecchiature diagnostiche, cosiddette “digitali native”, come la Tomografia Computerizzata (TC), la Tomografia ad Emissione di Positroni (PET), la Risonanza Magnetica Nucleare (RMN), l’Ecografia. A differenza delle diagnostiche tradizionali, come ad esempio la Radiologia convenzionale, che forniscono come risultato di un esame un’immagine bidimensionale ricavata dalla semplice proiezione di una struttura anatomica indagata, questi nuovi sistemi sono in grado di generare scansioni tomografiche. Disporre di immagini digitali contenenti dati tridimensionali rappresenta un enorme passo in avanti per l’indagine diagnostica, ma per poterne estrapolare e sfruttare i preziosi contenuti informativi occorrono i giusti strumenti che, data la natura delle acquisizioni, vanno ricercati nel mondo dell’Informatica. A tal proposito il seguente elaborato si propone di presentare un software package per la visualizzazione, l’analisi e l’elaborazione di medical images chiamato 3D Slicer che rappresenta un potente strumento di cui potersi avvalere in differenti contesti medici. Nel primo capitolo verrà proposta un’introduzione al programma; Seguirà il secondo capitolo con una trattazione più tecnica in cui verranno approfondite alcune funzionalità basilari del software e altre più specifiche; Infine nel terzo capitolo verrà preso in esame un intervento di endoprotesica vascolare e come grazie al supporto di innovativi sistemi di navigazione chirurgica sia possibile avvalersi di 3D Slicer anche in ambiente intraoperatorio

Pathology hinting as the combination of automatic segmentation with a statistical shape model

With improvements in acquisition speed and quality, the amount of medical image data to be screened by clinicians is starting to become challenging in the daily clinical practice. To quickly visualize and find abnormalities in medical images, we propose a new method combining segmentation algorithms with statistical shape models. A statistical shape model built from a healthy population will have a close fit in healthy regions. The model will however not fit to morphological abnormalities often present in the areas of pathologies. Using the residual fitting error of the statistical shape model, pathologies can be visualized very quickly. This idea is applied to finding drusen in the retinal pigment epithelium (RPE) of optical coherence tomography (OCT) volumes. A segmentation technique able to accurately segment drusen in patients with age-related macular degeneration (AMD) is applied. The segmentation is then analyzed with a statistical shape model to visualize potentially pathological areas. An extensive evaluation is performed to validate the segmentation algorithm, as well as the quality and sensitivity of the hinting system. Most of the drusen with a height of 85.5 microm were detected, and all drusen at least 93.6 microm high were detected.

Correlation between the area of increased autofluorescence surrounding geographic atrophy and disease progression in patients with AMD

PURPOSE: To test the hypothesis that the extension of areas with increased fundus autofluorescence (FAF) outside atrophic patches correlates with the rate of spread of geographic atrophy (GA) over time in eyes with age-related macular degeneration (AMD). METHODS: The database of the multicenter longitudinal natural history Fundus Autofluorescence in AMD (FAM) Study was reviewed for patients with GA recruited through the end of August 2003, with follow-up examinations within at least 1 year. Only eyes with sufficient image quality and with diffuse patterns of increased FAF surrounding atrophy were chosen. In standardized digital FAF images (excitation, 488 nm; emission, >500 nm), total size and spread of GA was measured. The convex hull (CH) of increased FAF as the minimum polygon encompassing the entire area of increased FAF surrounding the central atrophic patches was quantified at baseline. Statistical analysis was performed with the Spearman's rank correlation coefficient (rho). RESULTS: Thirty-nine eyes of 32 patients were included (median age, 75.0 years; interquartile range [IQR], 67.8-78.9); median follow-up, 1.87 years; IQR, 1.43-3.37). At baseline, the median total size of atrophy was 7.04 mm2 (IQR, 4.20-9.88). The median size of the CH was 21.47 mm2 (IQR, 15.19-28.26). The median rate of GA progression was 1.72 mm2 per year (IQR, 1.10-2.83). The area of increased FAF around the atrophy (difference between the CH and the total GA size at baseline) showed a positive correlation with GA enlargement over time (rho=0.60; P=0.0002). CONCLUSIONS: FAF characteristics that are not identified by fundus photography or fluorescein angiography may serve as a prognostic determinant in advanced atrophic AMD. As the FAF signal originates from lipofuscin (LF) in postmitotic RPE cells and since increased FAF indicates excessive LF accumulation, these findings would underscore the pathophysiological role of RPE-LF in AMD pathogenesis.

A method for incorporating residual stresses into patient-specific finite element simulations of arteries with an example on AAAs

Through progress in medical imaging, image analysis and finite element (FE) meshing tools it is now possible to extract patient-specific geometries from medical images of abdominal aortic aneurysms(AAAs), and thus to study clinically-relevant problems via FE simulations. Such simulations allow additional insight into human physiology in both healthy and diseased states. Medical imaging is most often performed in vivo, and hence the reconstructed model geometry in the problem of interest will represent the in vivo state, e.g., the AAA at physiological blood pressure. However, classical continuum mechanics and FE methods assume that constitutive models and the corresponding simulations begin from an unloaded, stress-free reference condition.

Metodología del análisis de imágenes digitales para el estudio del contenido de humedad en vertisoles

Desde finales del siglo pasado, el procesamiento y análisis de imágenes digitales, se ha convertido en una poderosa herramienta para la investigación de las propiedades del suelo a múltiples resoluciones, sin embargo todavía no existen los mejores resultados en cuanto a estos trabajos. El principal problema para investigar el drenaje vertical a partir de la distribución de humedad en un perfil de vertisol es la búsqueda de métodos factibles que usen este procedimiento. El objetivo general es implementar una metodología para el procesamiento y análisis de imágenes digitales, que permita caracterizar la distribución del contenido de humedad de un perfil de vertisol. Para el estudio, doce calicatas fueron excavadas en un Mazic Pellic Vertisol, seis de ellas en mayo 13/2011 y el resto en mayo 19/2011 después de moderados eventos de lluvia. Las imágenes RGB de los perfiles fueron tomadas con una cámara Kodak™; con tamaños seleccionados de 1600 x 945 píxeles cada una fue procesada para homogeneizar el brillo y se aplicaron filtros suavizadores de diferentes tamaños de ventana, hasta obtener el óptimo. Cada imagen se dividió en sus matrices componentes, seleccionando los umbrales de cada una para ser aplicado y obtener el patrón digital binario. Este último fue analizado a través de la estimación de dos exponentes fractales: dimensión de conteo de cajas (DBC) y dimensión fractal de interfase húmedo seco (Di). Además, fueron determinados tres coeficientes prefractales a la máxima resolución: número total de cajas interceptados en el plano del patrón (A), la lagunaridad fractal (λ1) y la entropía de Shannon (S1). Para todas las imágenes obtenidas, basado en la entropía, los análisis de clúster y de histogramas, el filtro espacial de 9x9 resultó ser el de tamaño de ventana óptimo. Los umbrales fueron seleccionados a partir del carácter bimodal de los histogramas. Los patrones binarios obtenidos mostraron áreas húmedas (blancas) y secas (negras) que permitieron su análisis. Todos los parámetros obtenidos mostraron diferencias significativas entre ambos conjuntos de patrones espaciales. Mientras los exponentes fractales aportan información sobre las características de llenado del patrón de humedad, los coeficientes prefractales representan propiedades del suelo investigado. La lagunaridad fractal fue el mejor discriminador entre los patrones de humedad aparente del suelo. ABSTRACT From last century, digital image processing and analysis was converted in a powerful tool to investigate soil properties at multiple resolutions, however, the best final procedure in these works not yet exist. The main problem to study vertical drainage from the moisture distribution, on a vertisol profile, is searching for suitable methods using these procedures. Our aim was to design a digital image processing methodology and its analysis to characterize the moisture content distribution of a vertisol profile. In this research, twelve soil pits were excavated on a bare Mazic Pellic Vertisol, six of them in May 13/2011 and the rest in May 19/2011 after a moderate rainfall event. Digital RGB images were taken from each vertisol pit using a Kodak™ camera selecting a size of 1600x945 pixels. Each soil image was processed to homogenized brightness and then a spatial filter with several window sizes was applied to select the optimum one. The RGB image obtained were divided in each matrix color selecting the best thresholds for each one, maximum and minimum, to be applied and get a digital binary pattern. This one was analyzed by estimating two fractal scaling exponents: box counting dimension (DBC

Optimización de una energía mediante cortes de grafos. Segmentación de imágenes

La segmentación de imágenes puede plantearse como un problema de minimización de una energía discreta. Nos enfrentamos así a una doble cuestión: definir una energía cuyo mínimo proporcione la segmentación buscada y, una vez definida la energía, encontrar un mínimo absoluto de la misma. La primera parte de esta tesis aborda el segundo problema, y la segunda parte, en un contexto más aplicado, el primero. Las técnicas de minimización basadas en cortes de grafos permiten obtener el mínimo de una energía discreta en tiempo polinomial mediante algoritmos de tipo min-cut/max-flow. Sin embargo, estas técnicas solo pueden aplicarse a energías que son representabas por grafos. Un importante reto es estudiar qué energías son representabas así como encontrar un grafo que las represente, lo que equivale a encontrar una función gadget con variables adicionales. En la primera parte de este trabajo se estudian propiedades de las funciones gadgets que permiten acotar superiormente el número de variables adicionales. Además se caracterizan las energías con cuatro variables que son representabas, definiendo gadgets con dos variables adicionales. En la segunda parte, más práctica, se aborda el problema de segmentación de imágenes médicas, base en muchas ocasiones para la diagnosis y el seguimiento de terapias. La segmentación multi-atlas es una potente técnica de segmentación automática de imágenes médicas, con tres aspectos importantes a destacar: el tipo de registro entre los atlas y la imagen objetivo, la selección de atlas y el método de fusión de etiquetas. Este último punto puede formularse como un problema de minimización de una energía. A este respecto introducimos dos nuevas energías representables. La primera, de orden dos, se utiliza en la segmentación en hígado y fondo de imágenes abdominales obtenidas mediante tomografía axial computarizada. La segunda, de orden superior, se utiliza en la segmentación en hipocampos y fondo de imágenes cerebrales obtenidas mediante resonancia magnética. ABSTRACT The image segmentation can be described as the problem of minimizing a discrete energy. We face two problems: first, to define an energy whose minimum provides the desired segmentation and, second, once the energy is defined we must find its global minimum. The first part of this thesis addresses the second problem, and the second part, in a more applied context, the first problem. Minimization techniques based on graph cuts find the minimum of a discrete energy in polynomial time via min-cut/max-flow algorithms. Nevertheless, these techniques can only be applied to graph-representable energies. An important challenge is to study which energies are graph-representable and to construct graphs which represent these energies. This is the same as finding a gadget function with additional variables. In the first part there are studied the properties of gadget functions which allow the number of additional variables to be bounded from above. Moreover, the graph-representable energies with four variables are characterised and gadgets with two additional variables are defined for these. The second part addresses the application of these ideas to medical image segmentation. This is often the first step in computer-assisted diagnosis and monitoring therapy. Multiatlas segmentation is a powerful automatic segmentation technique for medical images, with three important aspects that are highlighted here: the registration between the atlas and the target image, the atlas selection, and the label fusion method. We formulate the label fusion method as a minimization problem and we introduce two new graph-representable energies. The first is a second order energy and it is used for the segmentation of the liver in computed tomography (CT) images. The second energy is a higher order energy and it is used for the segmentation of the hippocampus in magnetic resonance images (MRI).

High-quality conforming hexahedral meshes of patient-specific abdominal aortic aneurysms including their intraluminal thrombi

In order to perform finite element (FE) analyses of patient-specific abdominal aortic aneurysms, geometries derived from medical images must be meshed with suitable elements. We propose a semi-automatic method for generating conforming hexahedral meshes directly from contours segmented from medical images. Magnetic resonance images are generated using a protocol developed to give the abdominal aorta high contrast against the surrounding soft tissue. These data allow us to distinguish between the different structures of interest. We build novel quadrilateral meshes for each surface of the sectioned geometry and generate conforming hexahedral meshes by combining the quadrilateral meshes. The three-layered morphology of both the arterial wall and thrombus is incorporated using parameters determined from experiments. We demonstrate the quality of our patient-specific meshes using the element Scaled Jacobian. The method efficiently generates high-quality elements suitable for FE analysis, even in the bifurcation region of the aorta into the iliac arteries. For example, hexahedral meshes of up to 125,000 elements are generated in less than 130 s, with 94.8 % of elements well suited for FE analysis. We provide novel input for simulations by independently meshing both the arterial wall and intraluminal thrombus of the aneurysm, and their respective layered morphologies.