A Log-Euclidean and Total Variation based Variational Framework for Computational Sonography

We propose a spatial compounding technique and variational framework to improve 3D ultrasound image quality by compositing multiple ultrasound volumes acquired from different probe orientations. In the composite volume, instead of intensity values, we estimate a tensor at every voxel. The resultant tensor image encapsulates the directional information of the underlying imaging data and can be used to generate ultrasound volumes from arbitrary, potentially unseen, probe positions. Extending the work of Hennersperger et al., we introduce a log-Euclidean framework to ensure that the tensors are positive-definite, eventually ensuring non-negative images. Additionally, we regularise the underpinning ill-posed variational problem while preserving edge information by relying on a total variation penalisation of the tensor field in the log domain. We present results on in vivo human data to show the efficacy of the approach.Comment: SPIE Medical Imaging 201

A comparative evaluation for liver segmentation from spir images and a novel level set method using signed pressure force function

Thesis (Doctoral)--Izmir Institute of Technology, Electronics and Communication Engineering, Izmir, 2013Includes bibliographical references (leaves: 118-135)Text in English; Abstract: Turkish and Englishxv, 145 leavesDeveloping a robust method for liver segmentation from magnetic resonance images is a challenging task due to similar intensity values between adjacent organs, geometrically complex liver structure and injection of contrast media, which causes all tissues to have different gray level values. Several artifacts of pulsation and motion, and partial volume effects also increase difficulties for automatic liver segmentation from magnetic resonance images. In this thesis, we present an overview about liver segmentation methods in magnetic resonance images and show comparative results of seven different liver segmentation approaches chosen from deterministic (K-means based), probabilistic (Gaussian model based), supervised neural network (multilayer perceptron based) and deformable model based (level set) segmentation methods. The results of qualitative and quantitative analysis using sensitivity, specificity and accuracy metrics show that the multilayer perceptron based approach and a level set based approach which uses a distance regularization term and signed pressure force function are reasonable methods for liver segmentation from spectral pre-saturation inversion recovery images. However, the multilayer perceptron based segmentation method requires a higher computational cost. The distance regularization term based automatic level set method is very sensitive to chosen variance of Gaussian function. Our proposed level set based method that uses a novel signed pressure force function, which can control the direction and velocity of the evolving active contour, is faster and solves several problems of other applied methods such as sensitivity to initial contour or variance parameter of the Gaussian kernel in edge stopping functions without using any regularization term

Inverse problems in medical ultrasound images - applications to image deconvolution, segmentation and super-resolution

In the field of medical image analysis, ultrasound is a core imaging modality employed due to its real time and easy-to-use nature, its non-ionizing and low cost characteristics. Ultrasound imaging is used in numerous clinical applications, such as fetus monitoring, diagnosis of cardiac diseases, flow estimation, etc. Classical applications in ultrasound imaging involve tissue characterization, tissue motion estimation or image quality enhancement (contrast, resolution, signal to noise ratio). However, one of the major problems with ultrasound images, is the presence of noise, having the form of a granular pattern, called speckle. The speckle noise in ultrasound images leads to the relative poor image qualities compared with other medical image modalities, which limits the applications of medical ultrasound imaging. In order to better understand and analyze ultrasound images, several device-based techniques have been developed during last 20 years. The object of this PhD thesis is to propose new image processing methods allowing us to improve ultrasound image quality using postprocessing techniques. First, we propose a Bayesian method for joint deconvolution and segmentation of ultrasound images based on their tight relationship. The problem is formulated as an inverse problem that is solved within a Bayesian framework. Due to the intractability of the posterior distribution associated with the proposed Bayesian model, we investigate a Markov chain Monte Carlo (MCMC) technique which generates samples distributed according to the posterior and use these samples to build estimators of the ultrasound image. In a second step, we propose a fast single image super-resolution framework using a new analytical solution to the l2-l2 problems (i.e., $\ell_2$-norm regularized quadratic problems), which is applicable for both medical ultrasound images and piecewise/ natural images. In a third step, blind deconvolution of ultrasound images is studied by considering the following two strategies: i) A Gaussian prior for the PSF is proposed in a Bayesian framework. ii) An alternating optimization method is explored for blind deconvolution of ultrasound

Image segmentation and reconstruction of 3D surfaces from carotid ultrasound images

Tese de doutoramento. Engenharia Electrotécnica e de Computadores. Faculdade de Engenharia. Universidade do Porto. 200

Nephroblastoma in MRI Data

The main objective of this work is the mathematical analysis of nephroblastoma in MRI sequences. At the beginning we provide two different datasets for segmentation and classification. Based on the first dataset, we analyze the current clinical practice regarding therapy planning on the basis of annotations of a single radiologist. We can show with our benchmark that this approach is not optimal and that there may be significant differences between human annotators and even radiologists. In addition, we demonstrate that the approximation of the tumor shape currently used is too coarse granular and thus prone to errors. We address this problem and develop a method for interactive segmentation that allows an intuitive and accurate annotation of the tumor. While the first part of this thesis is mainly concerned with the segmentation of Wilms’ tumors, the second part deals with the reliability of diagnosis and the planning of the course of therapy. The second data set we compiled allows us to develop a method that dramatically improves the differential diagnosis between nephroblastoma and its precursor lesion nephroblastomatosis. Finally, we can show that even the standard MRI modality for Wilms’ tumors is sufficient to estimate the developmental tendencies of nephroblastoma under chemotherapy

Computer-Assisted Algorithms for Ultrasound Imaging Systems

Ultrasound imaging works on the principle of transmitting ultrasound waves into the body and reconstructs the images of internal organs based on the strength of the echoes. Ultrasound imaging is considered to be safer, economical and can image the organs in real-time, which makes it widely used diagnostic imaging modality in health-care. Ultrasound imaging covers the broad spectrum of medical diagnostics; these include diagnosis of kidney, liver, pancreas, fetal monitoring, etc. Currently, the diagnosis through ultrasound scanning is clinic-centered, and the patients who are in need of ultrasound scanning has to visit the hospitals for getting the diagnosis. The services of an ultrasound system are constrained to hospitals and did not translate to its potential in remote health-care and point-of-care diagnostics due to its high form factor, shortage of sonographers, low signal to noise ratio, high diagnostic subjectivity, etc. In this thesis, we address these issues with an objective of making ultrasound imaging more reliable to use in point-of-care and remote health-care applications. To achieve the goal, we propose (i) computer-assisted algorithms to improve diagnostic accuracy and assist semi-skilled persons in scanning, (ii) speckle suppression algorithms to improve the diagnostic quality of ultrasound image, (iii) a reliable telesonography framework to address the shortage of sonographers, and (iv) a programmable portable ultrasound scanner to operate in point-of-care and remote health-care applications

Foetal echocardiographic segmentation

Congenital heart disease affects just under one percentage of all live births [1]. Those defects that manifest themselves as changes to the cardiac chamber volumes are the motivation for the research presented in this thesis. Blood volume measurements in vivo require delineation of the cardiac chambers and manual tracing of foetal cardiac chambers is very time consuming and operator dependent. This thesis presents a multi region based level set snake deformable model applied in both 2D and 3D which can automatically adapt to some extent towards ultrasound noise such as attenuation, speckle and partial occlusion artefacts. The algorithm presented is named Mumford Shah Sarti Collision Detection (MSSCD). The level set methods presented in this thesis have an optional shape prior term for constraining the segmentation by a template registered to the image in the presence of shadowing and heavy noise. When applied to real data in the absence of the template the MSSCD algorithm is initialised from seed primitives placed at the centre of each cardiac chamber. The voxel statistics inside the chamber is determined before evolution. The MSSCD stops at open boundaries between two chambers as the two approaching level set fronts meet. This has significance when determining volumes for all cardiac compartments since cardiac indices assume that each chamber is treated in isolation. Comparison of the segmentation results from the implemented snakes including a previous level set method in the foetal cardiac literature show that in both 2D and 3D on both real and synthetic data, the MSSCD formulation is better suited to these types of data. All the algorithms tested in this thesis are within 2mm error to manually traced segmentation of the foetal cardiac datasets. This corresponds to less than 10% of the length of a foetal heart. In addition to comparison with manual tracings all the amorphous deformable model segmentations in this thesis are validated using a physical phantom. The volume estimation of the phantom by the MSSCD segmentation is to within 13% of the physically determined volume

Multi-Modal Similarity Learning for 3D Deformable Registration of Medical Images

Alors que la perspective de la fusion d images médicales capturées par des systèmes d imageries de type différent est largement contemplée, la mise en pratique est toujours victime d un obstacle théorique : la définition d une mesure de similarité entre les images. Des efforts dans le domaine ont rencontrés un certain succès pour certains types d images, cependant la définition d un critère de similarité entre les images quelle que soit leur origine et un des plus gros défis en recalage d images déformables. Dans cette thèse, nous avons décidé de développer une approche générique pour la comparaison de deux types de modalités donnés. Les récentes avancées en apprentissage statistique (Machine Learning) nous ont permis de développer des solutions innovantes pour la résolution de ce problème complexe. Pour appréhender le problème de la comparaison de données incommensurables, nous avons choisi de le regarder comme un problème de plongement de données : chacun des jeux de données est plongé dans un espace commun dans lequel les comparaisons sont possibles. A ces fins, nous avons exploré la projection d un espace de données image sur l espace de données lié à la seconde image et aussi la projection des deux espaces de données dans un troisième espace commun dans lequel les calculs sont conduits. Ceci a été entrepris grâce à l étude des correspondances entre les images dans une base de données images pré-alignées. Dans la poursuite de ces buts, de nouvelles méthodes ont été développées que ce soit pour la régression d images ou pour l apprentissage de métrique multimodale. Les similarités apprises résultantes sont alors incorporées dans une méthode plus globale de recalage basée sur l optimisation discrète qui diminue le besoin d un critère différentiable pour la recherche de solution. Enfin nous explorons une méthode qui permet d éviter le besoin d une base de données pré-alignées en demandant seulement des données annotées (segmentations) par un spécialiste. De nombreuses expériences sont conduites sur deux bases de données complexes (Images d IRM pré-alignées et Images TEP/Scanner) dans le but de justifier les directions prises par nos approches.Even though the prospect of fusing images issued by different medical imagery systems is highly contemplated, the practical instantiation of it is subject to a theoretical hurdle: the definition of a similarity between images. Efforts in this field have proved successful for select pairs of images; however defining a suitable similarity between images regardless of their origin is one of the biggest challenges in deformable registration. In this thesis, we chose to develop generic approaches that allow the comparison of any two given modality. The recent advances in Machine Learning permitted us to provide innovative solutions to this very challenging problem. To tackle the problem of comparing incommensurable data we chose to view it as a data embedding problem where one embeds all the data in a common space in which comparison is possible. To this end, we explored the projection of one image space onto the image space of the other as well as the projection of both image spaces onto a common image space in which the comparison calculations are conducted. This was done by the study of the correspondences between image features in a pre-aligned dataset. In the pursuit of these goals, new methods for image regression as well as multi-modal metric learning methods were developed. The resulting learned similarities are then incorporated into a discrete optimization framework that mitigates the need for a differentiable criterion. Lastly we investigate on a new method that discards the constraint of a database of images that are pre-aligned, only requiring data annotated (segmented) by a physician. Experiments are conducted on two challenging medical images data-sets (Pre-Aligned MRI images and PET/CT images) to justify the benefits of our approach.CHATENAY MALABRY-Ecole centrale (920192301) / SudocSudocFranceF

Combining Shape and Learning for Medical Image Analysis

Automatic methods with the ability to make accurate, fast and robust assessments of medical images are highly requested in medical research and clinical care. Excellent automatic algorithms are characterized by speed, allowing for scalability, and an accuracy comparable to an expert radiologist. They should produce morphologically and physiologically plausible results while generalizing well to unseen and rare anatomies. Still, there are few, if any, applications where today\u27s automatic methods succeed to meet these requirements.\ua0The focus of this thesis is two tasks essential for enabling automatic medical image assessment, medical image segmentation and medical image registration. Medical image registration, i.e. aligning two separate medical images, is used as an important sub-routine in many image analysis tools as well as in image fusion, disease progress tracking and population statistics. Medical image segmentation, i.e. delineating anatomically or physiologically meaningful boundaries, is used for both diagnostic and visualization purposes in a wide range of applications, e.g. in computer-aided diagnosis and surgery.The thesis comprises five papers addressing medical image registration and/or segmentation for a diverse set of applications and modalities, i.e. pericardium segmentation in cardiac CTA, brain region parcellation in MRI, multi-organ segmentation in CT, heart ventricle segmentation in cardiac ultrasound and tau PET registration. The five papers propose competitive registration and segmentation methods enabled by machine learning techniques, e.g. random decision forests and convolutional neural networks, as well as by shape modelling, e.g. multi-atlas segmentation and conditional random fields