A non-invasive image based system for early diagnosis of prostate cancer.

Prostate cancer is the second most fatal cancer experienced by American males. The average American male has a 16.15% chance of developing prostate cancer, which is 8.38% higher than lung cancer, the second most likely cancer. The current in-vitro techniques that are based on analyzing a patients blood and urine have several limitations concerning their accuracy. In addition, the prostate Specific Antigen (PSA) blood-based test, has a high chance of false positive diagnosis, ranging from 28%-58%. Yet, biopsy remains the gold standard for the assessment of prostate cancer, but only as the last resort because of its invasive nature, high cost, and potential morbidity rates. The major limitation of the relatively small needle biopsy samples is the higher possibility of producing false positive diagnosis. Moreover, the visual inspection system (e.g., Gleason grading system) is not quantitative technique and different observers may classify a sample differently, leading to discrepancies in the diagnosis. As reported in the literature that the early detection of prostate cancer is a crucial step for decreasing prostate cancer related deaths. Thus, there is an urgent need for developing objective, non-invasive image based technology for early detection of prostate cancer. The objective of this dissertation is to develop a computer vision methodology, later translated into a clinically usable software tool, which can improve sensitivity and specificity of early prostate cancer diagnosis based on the well-known hypothesis that malignant tumors are will connected with the blood vessels than the benign tumors. Therefore, using either Diffusion Weighted Magnetic Resonance imaging (DW-MRI) or Dynamic Contrast Enhanced Magnetic Resonance Imaging (DCE-MRI), we will be able to interrelate the amount of blood in the detected prostate tumors by estimating either the Apparent Diffusion Coefficient (ADC) in the prostate with the malignancy of the prostate tumor or perfusion parameters. We intend to validate this hypothesis by demonstrating that automatic segmentation of the prostate from either DW-MRI or DCE-MRI after handling its local motion, provides discriminatory features for early prostate cancer diagnosis. The proposed CAD system consists of three majors components, the first two of which constitute new research contributions to a challenging computer vision problem. The three main components are: (1) A novel Shape-based segmentation approach to segment the prostate from either low contrast DW-MRI or DCE-MRI data; (2) A novel iso-contours-based non-rigid registration approach to ensure that we have voxel-on-voxel matches of all data which may be more difficult due to gross patient motion, transmitted respiratory effects, and intrinsic and transmitted pulsatile effects; and (3) Probabilistic models for the estimated diffusion and perfusion features for both malignant and benign tumors. Our results showed a 98% classification accuracy using Leave-One-Subject-Out (LOSO) approach based on the estimated ADC for 30 patients (12 patients diagnosed as malignant; 18 diagnosed as benign). These results show the promise of the proposed image-based diagnostic technique as a supplement to current technologies for diagnosing prostate cancer

Fast and robust hybrid framework for infant brain classification from structural MRI : a case study for early diagnosis of autism.

The ultimate goal of this work is to develop a computer-aided diagnosis (CAD) system for early autism diagnosis from infant structural magnetic resonance imaging (MRI). The vital step to achieve this goal is to get accurate segmentation of the different brain structures: whitematter, graymatter, and cerebrospinal fluid, which will be the main focus of this thesis. The proposed brain classification approach consists of two major steps. First, the brain is extracted based on the integration of a stochastic model that serves to learn the visual appearance of the brain texture, and a geometric model that preserves the brain geometry during the extraction process. Secondly, the brain tissues are segmented based on shape priors, built using a subset of co-aligned training images, that is adapted during the segmentation process using first- and second-order visual appearance features of infant MRIs. The accuracy of the presented segmentation approach has been tested on 300 infant subjects and evaluated blindly on 15 adult subjects. The experimental results have been evaluated by the MICCAI MR Brain Image Segmentation (MRBrainS13) challenge organizers using three metrics: Dice coefficient, 95-percentile Hausdorff distance, and absolute volume difference. The proposed method has been ranked the first in terms of performance and speed

Multiple cue integration for robust tracking in dynamic environments: application to video relighting

L'anàlisi de moviment i seguiment d'objectes ha estat un dels pricipals focus d'atenció en la comunitat de visió per computador durant les dues darreres dècades. L'interès per aquesta àrea de recerca resideix en el seu ample ventall d'aplicabilitat, que s'extén des de tasques de navegació de vehicles autònoms i robots, fins a aplications en la indústria de l'entreteniment i realitat virtual.Tot i que s'han aconseguit resultats espectaculars en problemes específics, el seguiment d'objectes continua essent un problema obert, ja que els mètodes disponibles són propensos a ser sensibles a diversos factors i condicions no estacionàries de l'entorn, com ara moviments impredictibles de l'objecte a seguir, canvis suaus o abruptes de la il·luminació, proximitat d'objectes similars o fons confusos. Enfront aquests factors de confusió la integració de múltiples característiques ha demostrat que permet millorar la robustesa dels algoritmes de seguiment. En els darrers anys, degut a la creixent capacitat de càlcul dels ordinadors, hi ha hagut un significatiu increment en el disseny de complexes sistemes de seguiment que consideren simultàniament múltiples característiques de l'objecte. No obstant, la majoria d'aquests algoritmes estan basats enheurístiques i regles ad-hoc formulades per aplications específiques, fent-ne impossible l'extrapolació a noves condicions de l'entorn.En aquesta tesi proposem un marc probabilístic general per integrar el nombre de característiques de l'objecte que siguin necessàries, permetent que interactuin mútuament per tal d'estimar-ne el seu estat amb precisió, i per tant, estimar amb precisió la posició de l'objecte que s'està seguint. Aquest marc, s'utilitza posteriorment per dissenyar un algoritme de seguiment, que es valida en diverses seqüències de vídeo que contenen canvis abruptes de posició i il·luminació, camuflament de l'objecte i deformacions no rígides. Entre les característiques que s'han utilitzat per representar l'objecte, cal destacar la paramatrització robusta del color en un espai de color dependent de l'objecte, que permet distingir-lo del fons més clarament que altres espais de color típicament ulitzats al llarg de la literatura.En la darrera part de la tesi dissenyem una tècnica per re-il·luminar tant escenes estàtiques com en moviment, de les que s'en desconeix la geometria. La re-il·luminació es realitza amb un mètode 'basat en imatges', on la generació de les images de l'escena sota noves condicions d'il·luminació s'aconsegueix a partir de combinacions lineals d'un conjunt d'imatges de referència pre-capturades, i que han estat generades il·luminant l'escena amb patrons de llum coneguts. Com que la posició i intensitat de les fonts d'il.luminació que formen aquests patrons de llum es pot controlar, és natural preguntar-nos: quina és la manera més òptima d'il·luminar una escena per tal de reduir el nombre d'imatges de referència? Demostrem que la millor manera d'il·luminar l'escena (és a dir, la que minimitza el nombre d'imatges de referència) no és utilitzant una seqüència de fonts d'il·luminació puntuals, com es fa generalment, sinó a través d'una seqüència de patrons de llum d'una base d'il·luminació depenent de l'objecte. És important destacar que quan es re-il·luminen seqüències de vídeo, les imatges successives s'han d'alinear respecte a un sistema de coordenades comú. Com que cada imatge ha estat generada per un patró de llum diferent il·uminant l'escena, es produiran canvis d'il·luminació bruscos entre imatges de referència consecutives. Sota aquestes circumstàncies, el mètode de seguiment proposat en aquesta tesi juga un paper fonamental. Finalment, presentem diversos resultats on re-il·luminem seqüències de vídeo reals d'objectes i cares d'actors en moviment. En cada cas, tot i que s'adquireix un únic vídeo, som capaços de re-il·luminar una i altra vegada, controlant la direcció de la llum, la seva intensitat, i el color.Motion analysis and object tracking has been one of the principal focus of attention over the past two decades within the computer vision community. The interest of this research area lies in its wide range of applicability, extending from autonomous vehicle and robot navigation tasks, to entertainment and virtual reality applications.Even though impressive results have been obtained in specific problems, object tracking is still an open problem, since available methods are prone to be sensitive to several artifacts and non-stationary environment conditions, such as unpredictable target movements, gradual or abrupt changes of illumination, proximity of similar objects or cluttered backgrounds. Multiple cue integration has been proved to enhance the robustness of the tracking algorithms in front of such disturbances. In recent years, due to the increasing power of the computers, there has been a significant interest in building complex tracking systems which simultaneously consider multiple cues. However, most of these algorithms are based on heuristics and ad-hoc rules formulated for specific applications, making impossible to extrapolate them to new environment conditions.In this dissertation we propose a general probabilistic framework to integrate as many object features as necessary, permitting them to mutually interact in order to obtain a precise estimation of its state, and thus, a precise estimate of the target position. This framework is utilized to design a tracking algorithm, which is validated on several video sequences involving abrupt position and illumination changes, target camouflaging and non-rigid deformations. Among the utilized features to represent the target, it is important to point out the use of a robust parameterization of the target color in an object dependent colorspace which allows to distinguish the object from the background more clearly than other colorspaces commonly used in the literature.In the last part of the dissertation, we design an approach for relighting static and moving scenes with unknown geometry. The relighting is performed through an -image-based' methodology, where the rendering under new lighting conditions is achieved by linear combinations of a set of pre-acquired reference images of the scene illuminated by known light patterns. Since the placement and brightness of the light sources composing such light patterns can be controlled, it is natural to ask: what is the optimal way to illuminate the scene to reduce the number of reference images that are needed? We show that the best way to light the scene (i.e., the way that minimizes the number of reference images) is not using a sequence of single, compact light sources as is most commonly done, but rather to use a sequence of lighting patterns as given by an object-dependent lighting basis. It is important to note that when relighting video sequences, consecutive images need to be aligned with respect to a common coordinate frame. However, since each frame is generated by a different light pattern illuminating the scene, abrupt illumination changes between consecutive reference images are produced. Under these circumstances, the tracking framework designed in this dissertation plays a central role. Finally, we present several relighting results on real video sequences of moving objects, moving faces, and scenes containing both. In each case, although a single video clip was captured, we are able to relight again and again, controlling the lighting direction, extent, and color.Postprint (published version

Analytical methods fort he study of color in digital images

La descripció qualitativa dels colors que composen una imatge digital és una tasca molt senzilla pel sistema visual humà. Per un ordinador aquesta tasca involucra una gran quantitat de qüestions i de dades que la converteixen en una operació de gran complexitat. En aquesta tesi desenvolupam un mètode automàtic per a la construcció d’una paleta de colors d’una imatge digital, intentant respondre a les diferents qüestions que se’ns plantegen quan treballam amb colors a dins el món computacional. El desenvolupament d’aquest mètode suposa l’obtenció d’un algorisme automàtic de segmentació d’histogrames, el qual és construït en detall a la tesi i diferents aplicacions del mateix son donades. Finalment, també s’explica el funcionament de CProcess, un ‘software’ amigable desenvolupat per a la fàcil comprensió del color

Motion Segmentation Aided Super Resolution Image Reconstruction

This dissertation addresses Super Resolution (SR) Image Reconstruction focusing on motion segmentation. The main thrust is Information Complexity guided Gaussian Mixture Models (GMMs) for Statistical Background Modeling. In the process of developing our framework we also focus on two other topics; motion trajectories estimation toward global and local scene change detections and image reconstruction to have high resolution (HR) representations of the moving regions. Such a framework is used for dynamic scene understanding and recognition of individuals and threats with the help of the image sequences recorded with either stationary or non-stationary camera systems. We introduce a new technique called Information Complexity guided Statistical Background Modeling. Thus, we successfully employ GMMs, which are optimal with respect to information complexity criteria. Moving objects are segmented out through background subtraction which utilizes the computed background model. This technique produces superior results to competing background modeling strategies. The state-of-the-art SR Image Reconstruction studies combine the information from a set of unremarkably different low resolution (LR) images of static scene to construct an HR representation. The crucial challenge not handled in these studies is accumulating the corresponding information from highly displaced moving objects. In this aspect, a framework of SR Image Reconstruction of the moving objects with such high level of displacements is developed. Our assumption is that LR images are different from each other due to local motion of the objects and the global motion of the scene imposed by non-stationary imaging system. Contrary to traditional SR approaches, we employed several steps. These steps are; the suppression of the global motion, motion segmentation accompanied by background subtraction to extract moving objects, suppression of the local motion of the segmented out regions, and super-resolving accumulated information coming from moving objects rather than the whole scene. This results in a reliable offline SR Image Reconstruction tool which handles several types of dynamic scene changes, compensates the impacts of camera systems, and provides data redundancy through removing the background. The framework proved to be superior to the state-of-the-art algorithms which put no significant effort toward dynamic scene representation of non-stationary camera systems

Pattern recognition and machine learning for magnetic resonance images with kernel methods

The aim of this thesis is to apply a particular category of machine learning and pattern recognition algorithms, namely the kernel methods, to both functional and anatomical magnetic resonance images (MRI). This work specifically focused on supervised learning methods. Both methodological and practical aspects are described in this thesis. Kernel methods have the computational advantage for high dimensional data, therefore they are idea for imaging data. The procedures can be broadly divided into two components: the construction of the kernels and the actual kernel algorithms themselves. Pre-processed functional or anatomical images can be computed into a linear kernel or a non-linear kernel. We introduce both kernel regression and kernel classification algorithms in two main categories: probabilistic methods and non-probabilistic methods. For practical applications, kernel classification methods were applied to decode the cognitive or sensory states of the subject from the fMRI signal and were also applied to discriminate patients with neurological diseases from normal people using anatomical MRI. Kernel regression methods were used to predict the regressors in the design of fMRI experiments, and clinical ratings from the anatomical scans

Studies on Colour Image Segmentation Method Based on Finite Left Truncated Bivariate Gaussian Mixture Model with K-Means

Colour Image segmentation is one of the prime requisites for computer vision and analysis. Much work has been reported in literature regarding colour image segmentation under HSI colour space and Gaussian mixture model (GMM). Since the Hue and Saturation values of the pixel in the image are non-negative. And may not be meso-kurtic, it is needed left truncate the Gaussian variate and is used to represent these two features of the colour image. The effect of truncation can not be ignored in developing the model based colour image segmentation. Hence in this paper a left truncated bivariate Gaussian mixture model is utilized to segment the colour image. The correlation between Hue and Saturation plays a predominant role in segmenting the colour images which is observed through experimental results. The expectation maximization (EM) algorithm is used for estimating model parameters. The number of image segments can be initialization of the model parameters are done with K-means algorithm. The performance of the proposed algorithm is studied by calculating the segmentation performance techniques like probabilistic rand index (PRI), global consistency error (GCE) and variation of information (VOI). The utility of the estimated joint probability density function of feature vector of the image is demonstrated through image retrievals. The image quality measures obtained for six images taken from Berkeley image dataset reveals that the proposed algorithm outperforms the existing algorithms in image segmentation and retrievals

Analysis of contrast-enhanced medical images.

Early detection of human organ diseases is of great importance for the accurate diagnosis and institution of appropriate therapies. This can potentially prevent progression to end-stage disease by detecting precursors that evaluate organ functionality. In addition, it also assists the clinicians for therapy evaluation, tracking diseases progression, and surgery operations. Advances in functional and contrast-enhanced (CE) medical images enabled accurate noninvasive evaluation of organ functionality due to their ability to provide superior anatomical and functional information about the tissue-of-interest. The main objective of this dissertation is to develop a computer-aided diagnostic (CAD) system for analyzing complex data from CE magnetic resonance imaging (MRI). The developed CAD system has been tested in three case studies: (i) early detection of acute renal transplant rejection, (ii) evaluation of myocardial perfusion in patients with ischemic heart disease after heart attack; and (iii), early detection of prostate cancer. However, developing a noninvasive CAD system for the analysis of CE medical images is subject to multiple challenges, including, but are not limited to, image noise and inhomogeneity, nonlinear signal intensity changes of the images over the time course of data acquisition, appearances and shape changes (deformations) of the organ-of-interest during data acquisition, determination of the best features (indexes) that describe the perfusion of a contrast agent (CA) into the tissue. To address these challenges, this dissertation focuses on building new mathematical models and learning techniques that facilitate accurate analysis of CAs perfusion in living organs and include: (i) accurate mathematical models for the segmentation of the object-of-interest, which integrate object shape and appearance features in terms of pixel/voxel-wise image intensities and their spatial interactions; (ii) motion correction techniques that combine both global and local models, which exploit geometric features, rather than image intensities to avoid problems associated with nonlinear intensity variations of the CE images; (iii) fusion of multiple features using the genetic algorithm. The proposed techniques have been integrated into CAD systems that have been tested in, but not limited to, three clinical studies. First, a noninvasive CAD system is proposed for the early and accurate diagnosis of acute renal transplant rejection using dynamic contrast-enhanced MRI (DCE-MRI). Acute rejection–the immunological response of the human immune system to a foreign kidney–is the most sever cause of renal dysfunction among other diagnostic possibilities, including acute tubular necrosis and immune drug toxicity. In the U.S., approximately 17,736 renal transplants are performed annually, and given the limited number of donors, transplanted kidney salvage is an important medical concern. Thus far, biopsy remains the gold standard for the assessment of renal transplant dysfunction, but only as the last resort because of its invasive nature, high cost, and potential morbidity rates. The diagnostic results of the proposed CAD system, based on the analysis of 50 independent in-vivo cases were 96% with a 95% confidence interval. These results clearly demonstrate the promise of the proposed image-based diagnostic CAD system as a supplement to the current technologies, such as nuclear imaging and ultrasonography, to determine the type of kidney dysfunction. Second, a comprehensive CAD system is developed for the characterization of myocardial perfusion and clinical status in heart failure and novel myoregeneration therapy using cardiac first-pass MRI (FP-MRI). Heart failure is considered the most important cause of morbidity and mortality in cardiovascular disease, which affects approximately 6 million U.S. patients annually. Ischemic heart disease is considered the most common underlying cause of heart failure. Therefore, the detection of the heart failure in its earliest forms is essential to prevent its relentless progression to premature death. While current medical studies focus on detecting pathological tissue and assessing contractile function of the diseased heart, this dissertation address the key issue of the effects of the myoregeneration therapy on the associated blood nutrient supply. Quantitative and qualitative assessment in a cohort of 24 perfusion data sets demonstrated the ability of the proposed framework to reveal regional perfusion improvements with therapy, and transmural perfusion differences across the myocardial wall; thus, it can aid in follow-up on treatment for patients undergoing the myoregeneration therapy. Finally, an image-based CAD system for early detection of prostate cancer using DCE-MRI is introduced. Prostate cancer is the most frequently diagnosed malignancy among men and remains the second leading cause of cancer-related death in the USA with more than 238,000 new cases and a mortality rate of about 30,000 in 2013. Therefore, early diagnosis of prostate cancer can improve the effectiveness of treatment and increase the patient’s chance of survival. Currently, needle biopsy is the gold standard for the diagnosis of prostate cancer. However, it is an invasive procedure with high costs and potential morbidity rates. Additionally, it has a higher possibility of producing false positive diagnosis due to relatively small needle biopsy samples. Application of the proposed CAD yield promising results in a cohort of 30 patients that would, in the near future, represent a supplement of the current technologies to determine prostate cancer type. The developed techniques have been compared to the state-of-the-art methods and demonstrated higher accuracy as shown in this dissertation. The proposed models (higher-order spatial interaction models, shape models, motion correction models, and perfusion analysis models) can be used in many of today’s CAD applications for early detection of a variety of diseases and medical conditions, and are expected to notably amplify the accuracy of CAD decisions based on the automated analysis of CE images

Image based approach for early assessment of heart failure.

In diagnosing heart diseases, the estimation of cardiac performance indices requires accurate segmentation of the left ventricle (LV) wall from cine cardiac magnetic resonance (CMR) images. MR imaging is noninvasive and generates clear images; however, it is impractical to manually process the huge number of images generated to calculate the performance indices. In this dissertation, we introduce a novel, fast, robust, bi-directional coupled parametric deformable models that are capable of segmenting the LV wall borders using first- and second-order visual appearance features. These features are embedded in a new stochastic external force that preserves the topology of the LV wall to track the evolution of the parametric deformable models control points. We tested the proposed segmentation approach on 15 data sets in 6 infarction patients using the Dice similarity coefficient (DSC) and the average distance (AD) between the ground truth and automated segmentation contours. Our approach achieves a mean DSC value of 0.926±0.022 and mean AD value of 2.16±0.60 mm compared to two other level set methods that achieve mean DSC values of 0.904±0.033 and 0.885±0.02; and mean AD values of 2.86±1.35 mm and 5.72±4.70 mm, respectively. Also, a novel framework for assessing both 3D functional strain and wall thickening from 4D cine cardiac magnetic resonance imaging (CCMR) is introduced. The introduced approach is primarily based on using geometrical features to track the LV wall during the cardiac cycle. The 4D tracking approach consists of the following two main steps: (i) Initially, the surface points on the LV wall are tracked by solving a 3D Laplace equation between two subsequent LV surfaces; and (ii) Secondly, the locations of the tracked LV surface points are iteratively adjusted through an energy minimization cost function using a generalized Gauss-Markov random field (GGMRF) image model in order to remove inconsistencies and preserve the anatomy of the heart wall during the tracking process. Then the circumferential strains are straight forward calculated from the location of the tracked LV surface points. In addition, myocardial wall thickening is estimated by co-allocation of the corresponding points, or matches between the endocardium and epicardium surfaces of the LV wall using the solution of the 3D laplace equation. Experimental results on in vivo data confirm the accuracy and robustness of our method. Moreover, the comparison results demonstrate that our approach outperforms 2D wall thickening estimation approaches