Segmentation and quantitative evaluation of brain MRI data with a multi-phase three-dimensional implicit deformable model

Segmentation of three-dimensional anatomical brain images into tissue classes has applications in both clinical and research settings. This paper presents the implementation and quantitative evaluation of a four-phase three-dimensional active contour implemented with a level set framework for automated segmentation of brain MRIs. The segmentation algorithm performs an optimal partitioning of three-dimensional data based on homogeneity measures that naturally evolves to the extraction of different tissue types in the brain. Random seed initialization was used to speed up numerical computation and avoid the need for a priori information. This random initialization ensures robustness of the method to variation of user expertise, biased a priori information and errors in input information that could be influenced by variations in image quality. Experimentation on three MRI brain data sets showed that an optimal partitioning successfully labeled regions that accurately identified white matter, gray matter and cerebrospinal fluid in the ventricles. Quantitative evaluation of the segmentation was performed with comparison to manually labeled data and computed false positive and false negative assignments of voxels for the three organs. We report high accuracy for the two comparison cases. These results demonstrate the efficiency and flexibility of this segmentation framework to perform the challenging task of automatically extracting brain tissue volume contours

Multi-scale active shape description in medical imaging

Shape description in medical imaging has become an increasingly important research field in recent years. Fast and high-resolution image acquisition methods like Magnetic Resonance (MR) imaging produce very detailed cross-sectional images of the human body - shape description is then a post-processing operation which abstracts quantitative descriptions of anatomically relevant object shapes. This task is usually performed by clinicians and other experts by first segmenting the shapes of interest, and then making volumetric and other quantitative measurements. High demand on expert time and inter- and intra-observer variability impose a clinical need of automating this process. Furthermore, recent studies in clinical neurology on the correspondence between disease status and degree of shape deformations necessitate the use of more sophisticated, higher-level shape description techniques. In this work a new hierarchical tool for shape description has been developed, combining two recently developed and powerful techniques in image processing: differential invariants in scale-space, and active contour models. This tool enables quantitative and qualitative shape studies at multiple levels of image detail, exploring the extra image scale degree of freedom. Using scale-space continuity, the global object shape can be detected at a coarse level of image detail, and finer shape characteristics can be found at higher levels of detail or scales. New methods for active shape evolution and focusing have been developed for the extraction of shapes at a large set of scales using an active contour model whose energy function is regularized with respect to scale and geometric differential image invariants. The resulting set of shapes is formulated as a multiscale shape stack which is analysed and described for each scale level with a large set of shape descriptors to obtain and analyse shape changes across scales. This shape stack leads naturally to several questions in regard to variable sampling and appropriate levels of detail to investigate an image. The relationship between active contour sampling precision and scale-space is addressed. After a thorough review of modem shape description, multi-scale image processing and active contour model techniques, the novel framework for multi-scale active shape description is presented and tested on synthetic images and medical images. An interesting result is the recovery of the fractal dimension of a known fractal boundary using this framework. Medical applications addressed are grey-matter deformations occurring for patients with epilepsy, spinal cord atrophy for patients with Multiple Sclerosis, and cortical impairment for neonates. Extensions to non-linear scale-spaces, comparisons to binary curve and curvature evolution schemes as well as other hierarchical shape descriptors are discussed

Image processing for plastic surgery planning

This thesis presents some image processing tools for plastic surgery planning. In particular, it presents a novel method that combines local and global context in a probabilistic relaxation framework to identify cephalometric landmarks used in Maxillofacial plastic surgery. It also uses a method that utilises global and local symmetry to identify abnormalities in CT frontal images of the human body. The proposed methodologies are evaluated with the help of several clinical data supplied by collaborating plastic surgeons

The deep structure of Gaussian scale space images

In order to be able to deal with the discrete nature of images in a continuous way, one can use results of the mathematical field of 'distribution theory'. Under almost trivial assumptions, like 'we know nothing', one ends up with convolving the image with a Gaussian filter. In this manner scale is introduced by means of the filter's width. The ensemble of the image and its convolved versions at al scales is called a 'Gaussian scale space image'. The filter's main property is that the scale derivative equals the Laplacean of the spatial variables: it is the Greens function of the so-called Heat, or Diffusion, Equation. The investigation of the image all scales simultaneously is called 'deep structure'. In this thesis I focus on the behaviour of the elementary topological items 'spatial critical points' and 'iso-intensity manifolds'. The spatial critical points are traced over scale. Generically they are annihilated and sometimes created pair wise, involving extrema and saddles. The locations of these so-called 'catastrophe events' are calculated with sub-pixel precision. Regarded in the scale space image, these spatial critical points form one-dimensional manifolds, the so-called critical curves. A second type of critical points is formed by the scale space saddles. They are the only possible critical points in the scale space image. At these points the iso-intensity manifolds exhibit special behaviour: they consist of two touching parts, of which one intersects an extremum that is part of the critical curve containing the scale space saddle. This part of the manifold uniquely assigns an area in scale space to this extremum. The remaining part uniquely assigns it to 'other structure'. Since this can be repeated, automatically an algorithm is obtained that reveals the 'hidden' structure present in the scale space image. This topological structure can be hierarchically presented as a binary tree, enabling one to (de-)select parts of it, sweeping out parts, simplify, etc. This structure can easily be projected to the initial image resulting in an uncommitted 'pre-segmentation': a segmentation of the image based on the topological properties without any user-defined parameters or whatsoever. Investigation of non-generic catastrophes shows that symmetries can easily be dealt with. Furthermore, the appearance of creations is shown to be nothing but (instable) protuberances at critical curves. There is also biological inspiration for using a Gaussian scale space, since the visual system seems to use Gaussian-like filters: we are able of seeing and interpreting multi-scale

Multiresolution Segmentation of Natural Images: From linear to Non-Linear Scale-Space Representations

In this paper, we introduce a framework that merges classical ideas borrowed from scale-space and multi-resolution segmentation with non-linear partial differential equations. A non-linear scale-space stack is constructed by means of an appropriate diffusion equation. This stack is analyzed and a tree of coherent segments is constructed based on relationships between different scale layers. Pruning this tree proves to be a very efficient tool for unsupervised segmentation of different classes of images (e.g. natural, medical ...). This technique is light on the computational point of view and can be extended to non-scalar data in a straightforward manner

Medical Image Analysis: Progress over two decades and the challenges ahead

International audienceThe analysis of medical images has been woven into the fabric of the pattern analysis and machine intelligence (PAMI) community since the earliest days of these Transactions. Initially, the efforts in this area were seen as applying pattern analysis and computer vision techniques to another interesting dataset. However, over the last two to three decades, the unique nature of the problems presented within this area of study have led to the development of a new discipline in its own right. Examples of these include: the types of image information that are acquired, the fully three-dimensional image data, the nonrigid nature of object motion and deformation, and the statistical variation of both the underlying normal and abnormal ground truth. In this paper, we look at progress in the field over the last 20 years and suggest some of the challenges that remain for the years to come

Three--dimensional medical imaging: Algorithms and computer systems

This paper presents an introduction to the field of three-dimensional medical imaging It presents medical imaging terms and concepts, summarizes the basic operations performed in three-dimensional medical imaging, and describes sample algorithms for accomplishing these operations. The paper contains a synopsis of the architectures and algorithms used in eight machines to render three-dimensional medical images, with particular emphasis paid to their distinctive contributions. It compares the performance of the machines along several dimensions, including image resolution, elapsed time to form an image, imaging algorithms used in the machine, and the degree of parallelism used in the architecture. The paper concludes with general trends for future developments in this field and references on three-dimensional medical imaging

3D Quantification and Description of the Developing Zebrafish Cranial Vasculature

Background: Zebrafish are an excellent model to study cardiovascular development and disease. Transgenic reporter lines and state-of-the-art microscopy allow 3D visualization of the vasculature in vivo. Previous studies relied on subjective visual interpretation of vascular topology without objective quantification. Thus, there is the need to develop analysis approaches that model and quantify the zebrafish vasculature to understand the effect of development, genetic manipulation or drug treatment. Aim: To establish an image analysis pipeline to extract quantitative 3D parameters describing the shape and topology of the zebrafish vasculature, and examine how these are impacted during development, disease, and by chemicals. Methods: Experiments were performed in zebrafish embryos, conforming with UK Home Office regulations. Image acquisition of transgenic zebrafish was performed using a Z.1 Zeiss light-sheet fluorescence microscope. Pre-processing, enhancement, registration, segmentation, and quantification methods were developed and optimised using open-source software, Fiji (Fiji 1.51p; National Institutes of Health, Bethesda, USA). Results: Motion correction was successfully applied using Scale Invariant Feature Transform (SIFT), and vascular enhancement based on vessel tubularity (Sato filter) exceeded general filter outcomes. Following evaluation and optimisation of a variety of segmentation methods, intensity-based segmentation (Otsu thresholding) was found to deliver the most reliable segmentation, allowing 3D vascular volume measurement. Following successful segmentation of the cerebral vasculature, a workflow to quantify left-right intra-sample symmetry was developed, finding no difference from 2-to-5dpf. Next, the first vascular inter-sample registration using a manual landmark-based approach was developed and it was found that conjugate direction search allowed automatic inter-sample registration. This enabled extraction of age-specific regions of similarity and variability between different individual embryos from 2-to-5dpf. A workflow was developed to quantify vascular network length, branching points, diameter, and complexity, showing reductions in zebrafish without blood flow. Also, I discovered and characterised a previously undescribed endothelial cell membrane behaviour termed kugeln. Conclusion: A workflow that successfully extracts the zebrafish vasculature and enables detailed quantification of a wide variety of vascular parameters was developed

Segmentação pulmonar em estudos de tomografia axial computorizada

Doutoramento em Engenharia ElectrónicaA Tomografia Axial Computorizada (TAC) é um dos meios complementares de diagnóstico médico mais eficiente no estudo das regiões pulmonares. Os métodos de segmentação pulmonar em imagens produzidas por esta modalidade são necessários sempre que se pretenda determinar áreas ou volumes, ou obter informação densitómetria; podem ainda ser integrados no pré-processamento de uma aplicação que envolva a visualização dos pulmões. No âmbito deste trabalho foram desenvolvidos três métodos de segmentação pulmonar, baseados na análise da distribuição dos níveis de cinzento da imagem de TAC da região torácica e na utilização de técnicas morfológicas, bem como no conceito de contornos activos. O método que produziu melhores resultados demonstrou ser capaz de localizar a zona de separação dos pulmões quando estes se encontram visualmente sobrepostos. Foi ainda desenvolvido um método com uma abordagem tridimensional, que processa em simultâneo a informação relativa a todas as secções do exame, e apresenta como principais vantagens a facilidade de identificação da traqueia e brônquios, bem como de múltiplas zonas de contacto entre pulmões. O desempenho como detector de contornos pulmonares, do melhor dos três primeiros métodos de segmentação desenvolvidos, e na ausência de ground truth, foi comparado com o desempenho de seis radiologistas. Também o método de segmentação tridimensional foi avaliado. Além da segmentação dos pulmões, também a segmentação de estruturas pulmonares se torna necessária quando se pretende quantificar áreas e volumes ou ainda proceder a medições densitómetrias dessas estruturas; o que pode ser utilizado no diagnóstico e seguimento de várias patologias como o enfisema bolhoso, que se caracteriza pela presença de bolhas de ar nos pulmões. Sendo assim, foram desenvolvidos três métodos de segmentação para detectar estas bolhas: o primeiro método processa os dados secção a secção e avalia a coerência longitudinal, o segundo utiliza um threshold global e operações morfológicas em 3D e o terceiro utiliza uma versão modificada do modelo deformável level-set tridimensional. Na segmentação de bolhas de ar pulmonares, que apresentam níveis de cinzento muito baixos, o ruído torna-se um problema relevante, sobretudo se as imagens corresponderem a exames de TAC de alta resolução. Assim, para atenuar o ruído das imagens, foi utilizado um conjunto de filtros e estudada a sua influência nos resultados produzidos pelos métodos de segmentação desenvolvidos. Este estudo foi realizado sobre imagens sintetizadas e imagens reais contendo bolhas naturais e artificiais a que se adicionou ruído. Finalmente, e no sentido de ilustrar a utilidade dos métodos propostos, descreve-se um exemplo de uma aplicação que permite discriminar e quantificar as zonas enfisematosas dos pulmões, bem como visualizá-las secção a secção e tridimensionalmente.X-ray Computed Tomography (CT) is one of the most efficient medical diagnosis tools and has currently a widespread usage in the study of the pulmonary region. Lung segmentation methods are necessary to compute areas or volumes or to perform densitometry; they can also be used as a pre-processing task in pulmonary visualization. In this work, three segmentation methods based on the gray level distribution analysis of CT thoracic images, morphologic techniques and active contours were developed. The method that produced best results proved to be able to locate lung boundaries even when lungs are visually superimposed on the images. Another pulmonary segmentation method using a tridimensional approach was developed; this method processes simultaneously information concerning all sections of the CT exam and has the main advantages of an easy identification of trachea and bronchi, as well as detection of multiple contact zones between lungs. Due to the lack of a ground truth, the performance of the best of the first three segmentation methods was compared with the performance of six radiologists. The tridimensional method was also evaluated. Not only the lung segmentation, but also the segmentation of pulmonary structures is needed for diagnosis and follow-up of a variety of diseases, as it is the case of the bulbous emphysema, characterized by the presence of air bubbles inside the lungs. Thus, three segmentation methods were developed to detect these bubbles, the first method processes the exam section by section and analysis longitudinal coherence, the second method uses a 3D approach with a global threshold and morphologic operations, and the third method uses a modified version of the 3D level-set deformable model. Since air bubbles have very low gray levels, noise becomes a relevant problem in their segmentation, especially in high resolution CT exams. Therefore, to reduce noise, several filters were used and their influence on the results produced by the segmentation methods was analyzed. This study was performed using synthesized and real images with natural and artificial air bubbles, to which noise was added. Finally, and to illustrate the usefulness of the proposed methods, an application was developed that allows discriminating and quantifying pulmonary emphysematous regions, as well as visualizing those regions section by section and tridimensionally.FSEPRODEP IIIFundação Calouste GulbenkianFundação Luso-Americana para o Desenvolviment