Multi-Object Geodesic Active Contours (MOGAC): A Parallel Sparse-Field Algorithm for Image Segmentation

An important task for computer vision systems is to segment adjacent structures in images without producing gaps or overlaps. Multi-object Level Set Methods (MLSM) perform this task with the benefit of sub-pixel accuracy. However, current implementations of MLSM are not as computationally or memory efficient as their region growing and graph cut counterparts which lack sub-pixel accuracy. To address this performance gap, we present a novel parallel implementation of MLSM that leverages the sparse properties of the segmentation algorithm to minimize its memory footprint for multiple objects. The new method, Multi-Object Geodesic Active Contours (MOGAC), can represent N objects with just two functions: a label image and unsigned distance field. The time complexity of the algorithm is shown to be O((M^d)/P) for M^d pixels and P processing units in dimension d={2,3}, independent of the number of objects. Results are presented for 2D and 3D image segmentation problems

Skull Stripping of Neonatal Brain MRI: Using Prior Shape Information with Graph Cuts

ISSN:0897-1889ISSN:1618-727

Topology on digital label images

International audienceIn digital imaging, after several decades devoted to the study of topological properties of binary images, there is an increasing need of new methods enabling to take into (topological) consideration n-ary images (also called label images). Indeed, while binary images enable to handle one object of interest, label images authorise to simultaneously deal with a plurality of objects, which is a frequent requirement in several application fields. In this context, one of the main purposes is to propose topology-preserving transformation procedures for such label images, thus extending the ones (e.g., growing, reduction, skeletonisation) existing for binary images. In this article, we propose, for a wide range of digital images, a new approach that permits to locally modify a label image, while preserving not only the topology of each label set, but also the topology of any arrangement of the labels understood as the topology of any union of label sets. This approach enables in particular to unify and extend some previous attempts devoted to the same purpose

Automatic Mesh-Based Segmentation of Multiple Organs in MR Images

La segmentation de structures anatomiques multiples dans des images de résonance magnétique (RM) est souvent requise dans des applications de génie biomédical telles que la simulation numérique, la chirurgie guidée par l’image, la planification de traitements, etc. De plus, il y a un besoin croissant pour une segmentation automatique d’organes multiples et de structures complexes à partir de cette modalité d’imagerie. Il existe plusieurs techniques de segmentation multi-objets qui ont été appliquées avec succès sur des images de tomographie axiale à rayons-X (CT). Cependant, dans le cas des images RM cette tâche est plus difficile en raison de l’inhomogénéité des intensités dans ces images et de la variabilité dans l’apparence des structures anatomiques. Par conséquent, l’état de l’art sur la segmentation multi-objets sur des images RM est beaucoup plus faible que celui sur les images CT. Parmi les travaux qui portent sur la segmentation d’images RM, les approches basées sur la segmentation de régions sont sensibles au bruit et la non uniformité de l’intensité dans les images. Les approches basées sur les contours ont de la difficulté à regrouper les informations sur les contours de sorte à produire un contour fermé cohérent. Les techniques basées sur les atlas peuvent avoir des problèmes en présence de structures complexes avec une grande variabilité anatomique. Les modèles déformables représentent une des méthodes les plus populaire pour la détection automatique de différents organes dans les images RM. Cependant, ces modèles souffrent encore d’une limitation importante qui est leur sensibilité à la position initiale et la forme du modèle. Une initialisation inappropriée peut conduire à un échec dans l’extraction des frontières des objets. D’un autre côté, le but ultime d’une segmentation automatique multi-objets dans les images RM est de produire un modèle qui peut aider à extraire les caractéristiques structurelles d’organes distincts dans les images. Les méthodes d’initialisation automatique actuelles qui utilisent différents descripteurs ne réussissent pas complètement l’extraction d’objets multiples dans les images RM. Nous avons besoin d’exploiter une information plus riche qui se trouve dans les contours des organes. Dans ce contexte les maillages adaptatifs anisotropiques semblent être une solution potentielle au problème soulevé. Les maillages adaptatifs anisotropiques construits à partir des images RM contiennent de l’information à un plus haut niveau d’abstraction représentant les éléments, d’une orientation et d’une forme donnée, qui constituent les différents organes dans l’image. Les méthodes existantes pour la construction de maillages adaptatifs sont basées sur les intensités dans l’image et possèdent une limitation pratique qui est l’alignement inadéquat des éléments du maillage en présence de contours inclinés dans l’image. Par conséquent, nous avons aussi besoin d’améliorer le processus d’adaptation de maillage pour produire une meilleure représentation de l’image basée sur un maillage.----------ABSTRACT: Segmentation of multiple anatomical structures in MR images is often required for biomedical engineering applications such as clinical simulation, image-guided surgery, treatment planning, etc. Moreover, there is a growing need for automatic segmentation of multiple organs and complex structures from this medical imaging modality. Many successful multi-object segmentation attempts were introduced for CT images. However in the case of MR images it is a more challenging task due to intensity inhomogeneity and variability of anatomy appearance. Therefore, state-of-the-art in multi-object MR segmentation is very inferior to that of CT images. In literature dealing with MR image segmentation, the region-based approaches are sensitive to noise and non-uniformity in the input image. The edge-based approaches are challenging to group the edge information into a coherent closed contour. The atlas-based techniques can be problematic for complicated structures with anatomical variability. Deformable models are among the most popular methods for automatic detection of different organs in MR images. However they still have an important limitation which is that they are sensitive to initial position and shape of the model. An unsuitable initialization may provide failure to capture the true boundaries of the objects. On the other hand, a useful aim for an automatic multi-object MR segmentation is to provide a model which promotes understanding of the structural features of the distinct objects within the MR images. The current automatic initialization methods which have used different descriptors are not completely successful in extracting multiple objects from MR images and we need to find richer information that is available from edges. In this regard, anisotropic adaptive meshes seem to be a potential solution to the aforesaid limitation. Anisotropic adaptive meshes constructed from MR images contain higher level, abstract information about the anatomical structures of the organs within the image retained as the elements shape and orientation. Existing methods for constructing adaptive meshes based on image features have a practical limitation where manifest itself in inadequate mesh elements alignment to inclined edges in the image. Therefore, we also have to enhance mesh adaptation process to provide a better mesh-based representation. In this Ph.D. project, considering the highlighted limitations we are going to present a novel method for automatic segmentation of multiple organs in MR images by incorporating mesh adaptation techniques. In our progress, first, we improve an anisotropic adaptation process for the meshes that are constructed from MR images where the mesh elements align adequately to the image content and improve mesh anisotropy along edges in all directions. Then the resulting adaptive meshes are used for initialization of multiple active models which leads to extract initial object boundaries close to the true boundaries of multiple objects simultaneously. Finally, the Vector Field Convolution method is utilized to guide curve evolution towards the object boundaries to obtain the final segmentation results and present a better performance in terms of speed and accuracy

Toward Controllable and Robust Surface Reconstruction from Spatial Curves

Reconstructing surface from a set of spatial curves is a fundamental problem in computer graphics and computational geometry. It often arises in many applications across various disciplines, such as industrial prototyping, artistic design and biomedical imaging. While the problem has been widely studied for years, challenges remain for handling different type of curve inputs while satisfying various constraints. We study studied three related computational tasks in this thesis. First, we propose an algorithm for reconstructing multi-labeled material interfaces from cross-sectional curves that allows for explicit topology control. Second, we addressed the consistency restoration, a critical but overlooked problem in applying algorithms of surface reconstruction to real-world cross-sections data. Lastly, we propose the Variational Implicit Point Set Surface which allows us to robustly handle noisy, sparse and non-uniform inputs, such as samples from spatial curves

Deformable Image Registration in the Analysis of Multiple Sclerosis

In medical image analysis, image registration is the task of finding corresponding features in two or more images, and using them to solve for the transformation that best aligns the images. Knowing the alignment allows information, such as landmarks and functional metrics, to be easily transferred between images, and allows them to be analyzed together. This dissertation focuses on the development of deformable image registration techniques for the analysis of multiple sclerosis (MS), a neurodegenerative disease that damages the myelin sheath of nervous tissue. MS is known to affect the entire central nervous system (CNS), and can result in the loss of sensorimotor control, cognition, and vision. Hence, the four primary contributions of this dissertation are on the development and application of deformable image registration in the three areas of the CNS that are most currently studied for MS -- the spinal cord, the retina, and the brain. First, for spinal cord magnetic resonance imaging (MRI), an approach is presented that uses deformable registration to provide atlas priors for automatic topology-preserving segmentation of the spinal cord and cerebrospinal fluid. The method shows high accuracy and robustness when compared to manual raters, and allows spinal cord atrophy to be analyzed on large datasets without manual segmentations. Second, for spinal cord diffusion tensor imaging, a pipeline is presented that uses deformable registration to correct for susceptibility distortions in the images. The pipeline allows for accurate computation of spinal cord diffusion metrics, which are shown to be significantly correlated with clinical measures of sensorimotor function and disability levels. Third, for optical coherence tomography (OCT) of the retina, a deformable registration technique is presented that constrains the transformation to follow the OCT acquisition geometry. 3D voxel-based analysis using the algorithm found significant differences between healthy and MS cohorts in regions of the retina that is consistent with previous findings using 2D analysis. Lastly, for brain MRI, a multi-channel registration framework is presented that can use distance transforms and image synthesis to improve registration accuracy. Together, these techniques have enabled several types of analysis that were previously unavailable for the study of MS