Computational Methods for Segmentation of Multi-Modal Multi-Dimensional Cardiac Images

Segmentation of the heart structures helps compute the cardiac contractile function quantified via the systolic and diastolic volumes, ejection fraction, and myocardial mass, representing a reliable diagnostic value. Similarly, quantification of the myocardial mechanics throughout the cardiac cycle, analysis of the activation patterns in the heart via electrocardiography (ECG) signals, serve as good cardiac diagnosis indicators. Furthermore, high quality anatomical models of the heart can be used in planning and guidance of minimally invasive interventions under the assistance of image guidance. The most crucial step for the above mentioned applications is to segment the ventricles and myocardium from the acquired cardiac image data. Although the manual delineation of the heart structures is deemed as the gold-standard approach, it requires significant time and effort, and is highly susceptible to inter- and intra-observer variability. These limitations suggest a need for fast, robust, and accurate semi- or fully-automatic segmentation algorithms. However, the complex motion and anatomy of the heart, indistinct borders due to blood flow, the presence of trabeculations, intensity inhomogeneity, and various other imaging artifacts, makes the segmentation task challenging. In this work, we present and evaluate segmentation algorithms for multi-modal, multi-dimensional cardiac image datasets. Firstly, we segment the left ventricle (LV) blood-pool from a tri-plane 2D+time trans-esophageal (TEE) ultrasound acquisition using local phase based filtering and graph-cut technique, propagate the segmentation throughout the cardiac cycle using non-rigid registration-based motion extraction, and reconstruct the 3D LV geometry. Secondly, we segment the LV blood-pool and myocardium from an open-source 4D cardiac cine Magnetic Resonance Imaging (MRI) dataset by incorporating average atlas based shape constraint into the graph-cut framework and iterative segmentation refinement. The developed fast and robust framework is further extended to perform right ventricle (RV) blood-pool segmentation from a different open-source 4D cardiac cine MRI dataset. Next, we employ convolutional neural network based multi-task learning framework to segment the myocardium and regress its area, simultaneously, and show that segmentation based computation of the myocardial area is significantly better than that regressed directly from the network, while also being more interpretable. Finally, we impose a weak shape constraint via multi-task learning framework in a fully convolutional network and show improved segmentation performance for LV, RV and myocardium across healthy and pathological cases, as well as, in the challenging apical and basal slices in two open-source 4D cardiac cine MRI datasets. We demonstrate the accuracy and robustness of the proposed segmentation methods by comparing the obtained results against the provided gold-standard manual segmentations, as well as with other competing segmentation methods

Biomechanical study of intervertebral disc degeneration

Degeneration and age affect the biomechanics of the intervertebral disc, by reducing its stiffness, flexibility and shock absorption capacities against daily movement and spinal load. The biomechanical characterization of intervertebral discs is achieved by conducting mechanical testing to vertebra-disc-vertebra segments and applying axial, shear, bend and torsion loads, statically or dynamically, with load magnitudes corresponding to the physiological range. However, traditional testing does not give a view of the load and deformation states of the disc components: nucleus pulposus, annulus fibrosus and endplate. Thus, the internal state of stress and strains of the disc can only be predicted by numerical methods, one of which is the finite element method. The objective of this thesis was, to study the biomechanics of degenerated intervertebral discs to load conditions in compression, bending and torsion, by using mechanical testing and a finite element model of disc degeneration, based on magnetic resonance imaging (MRI). Therefore, lumbar discs obtained from cadavers corresponding to spinal levels L2-L3 and L4-L5 with mild to severe degeneration were used. Intervertebral osteochondrosis and spondylosis deformans were identified, being the disc space collapse, the most striking feature. Next, all discs were tested to static and dynamic load conditions, the results gained corresponded to the disc stiffness (in compression, bending and torsion), stress relaxation and dynamic response. Of these, the stiffness response was used to validate the disc model. The testing results suggest that discs with advanced degeneration over discs with mild degeneration are, less rigid in compression, less stiffer under bending and torsion, showed less radial bulge, and reduce their viscoelastic and damping properties. This study shows that degeneration has an impact on the disc biomechanical properties which can jeopardize normal functionality. Development of one finite element model of disc degeneration started by choosing a MRI of a L2-L3 disc. Segmentation of vertebra bone and disc materials followed, and were based on pixel brightness and radiology fundamentals, then a finite element mesh was created to account for the disc irregular shape. The disc materials were modeled as hyperelastic and the bone materials were modeled as orthotropic and isotropic. Adjustment of material properties was based on integrity of the annulus fibrosus, giving a stiffness value matching that of a mild degeneration disc. Then, validation of the model was performed, and included a study of the distributions of stress and strain under loads of compression, bending and torsion. The results from all load simulations show that the disc undergoes large deformations. In contrast, the vertebrae are subjected to higher stress but with negligible deformations. In compression, the model predicted formation of symmetrical disc bulge which agree with the testing behavior. The nucleus pulposus showed to be the principal load carrier with negative principal stresses and strains. In bending and torsion, the annulus fibrosus showed to be the principal load carrier with large symmetrical principal strains and stresses for the former loading and large shearing for the latter. The study showed the importance of soft tissue deformation, mostly noticed in advanced degeneration. In contrast, the higher stresses in the vertebra over those of the intervertebral disc showed the relevance of bone predisposition to fracture. Such kind of studies, should contribute to the understanding of the biomechanics of the intervertebral disc.La degeneración y edad afectan la biomecánica del disco intervertebral, reduciendo la capacidad de rigidez, flexibilidad y atenuación de impactos, contra el movimiento y carga del raquis. La caracterización biomecánica del disco se realiza con ensayos mecánicos a segmentos de vértebra-disco-vértebra y aplicando cargas axiales, cortantes, flexión y torsión, estáticas ó dinámicas, con magnitudes de carga según el intervalo fisiológico. Sin embargo, las pruebas tradicionales no dan una visión de los estados de carga y deformación de los componentes del disco: núcleo pulposo, anillo fibroso y placa terminal. Por lo tanto, el estado interno de esfuerzos y deformaciones del disco, solo puede ser predicho con métodos numéricos, uno de los cuales es el método de elemento finito. El objetivo de esta tesis fue, estudiar la biomecánica de discos intervertebrales degenerados a las condiciones de carga en compresión, flexión y torsión, mediante el uso de ensayos mecánicos y de un modelo de elementos finitos de la degeneración de disco, basado en imágenes con resonancia magnética (MRI). Por lo tanto, se usaron discos lumbares L2-L3 y L4-L5 obtenidos de cadáveres, con degeneración leve a severa. Se identificó osteocondrosis intervertebral y espondilosis deformante, siendo el colapso del espacio intervertebral el aspecto más relevante. Luego, todos los discos fueron ensayados a condiciones de carga estática y dinámica, y los resultados correspondieron a la rigidez del disco (a compresión, flexión y torsión), a la relajación de tensiones y a la respuesta dinámica. De éstos, la rigidez fue usada para validar el modelo de disco. Los resultados de los ensayos sugieren que los discos con degeneración avanzada sobre aquellos con degeneración leve son, menos rigidos a compresión, menos rigidos a flexión y torsión, presentan menor protuberancia radial, y reducen sus propiedades viscoelásticas y de amortiguamiento. El estudio muestra que la degeneración impacta las propiedades biomecánicas del disco, poniendo en riesgo la funcionalidad normal. El desarollo de un modelo de elementos finitos de la degeneración de disco inició eligiendo una secuencia de resonancia magnética de un disco L2-L3. La segmentación de los materiales del disco y de las vértebras se realizó basado en intensidad de brillo del pixel y en fundamentos de radiología, y se creó una malla de elementos finitos correspondiente a la forma irregular del disco. Los materiales del disco se modelaron como hiperelásticos y los tejidos óseos se modelaron como materiales ortotrópicos e isotrópicos. El ajuste de propiedades de los materiales fue basado en la integridad del anillo fibroso, y dio una rigidez correspondiente a la de un disco con degeneración leve. Luego, se realizó la validación del modelo, e incluyó un estudio de las distribuciones de esfuerzo y deformación a las condiciones de carga en compresión, flexión y torsión. Los resultados de todas las simulaciones de carga mostraron que el disco es sometido a grandes deformaciones. En contraste, las vértebras fueron sometidas a mayores esfuerzos pero con deformaciones insignificantes. En compresión, el modelo predijo la formación de una protuberancia radial simétrica, en concordancia con la experimentación. El núcleo pulposo mostró ser el portador principal de carga, con tensiones y deformaciones principales negativas. En flexión y torsión, el anillo fibroso mostró ser el portador principal de carga, con grandes deformaciones y tensiones principales simétricas para la primera carga, y con grandes tensiones cortantes para la segunda carga. El estudio mostró la importancia de las deformaciones de los tejidos blandos, principalmente notados en la degeneración avanzada. Por el contrario, las tensiones mayores en los cuerpos vertebrales sobre aquellas del disco intervertebral mostraron la relevancia de la predisposición a las fracturas óseas. Este tipo de estudio debe contribuir a la comprensión de la biomecánica del disco intervertebral

Cultivate Quantitative Magnetic Resonance Imaging Methods to Measure Markers of Health and Translate to Large Scale Cohort Studies

Magnetic Resonance Imaging (MRI) is an indispensable tool in healthcare and research, with a growing demand for its services. The appeal of MRI stems from its non-ionizing radiation nature, ability to generate high-resolution images of internal organs and structures without invasive procedures, and capacity to provide quantitative assessments of tissue properties such as ectopic fat, body composition, and organ volume. All without long term side effects. Nine published papers are submitted which show the cultivation of quantitative measures of ectopic fat within the liver and pancreas using MRI, and the process of validating whole-body composition and organ volume measurements. All these techniques have been translated into large-scale studies to improve health measurements in large population cohorts. Translating this work into large-scale studies, including the use of artificial intelligence, is included. Additionally, an evaluation accompanies these published studies, appraising the evolution of these quantitative MRI techniques from the conception to their application in large cohort studies. Finally, this appraisal provides a summary of future work on crowdsourcing of ground truth training data to facilitate its use in wider applications of artificial intelligence.In conclusion, this body of work presents a portfolio of evidence to fulfil the requirements of a PhD by published works at the University of Salford

Advanced Applications of Rapid Prototyping Technology in Modern Engineering

Rapid prototyping (RP) technology has been widely known and appreciated due to its flexible and customized manufacturing capabilities. The widely studied RP techniques include stereolithography apparatus (SLA), selective laser sintering (SLS), three-dimensional printing (3DP), fused deposition modeling (FDM), 3D plotting, solid ground curing (SGC), multiphase jet solidification (MJS), laminated object manufacturing (LOM). Different techniques are associated with different materials and/or processing principles and thus are devoted to specific applications. RP technology has no longer been only for prototype building rather has been extended for real industrial manufacturing solutions. Today, the RP technology has contributed to almost all engineering areas that include mechanical, materials, industrial, aerospace, electrical and most recently biomedical engineering. This book aims to present the advanced development of RP technologies in various engineering areas as the solutions to the real world engineering problems

Image Registration Workshop Proceedings

Automatic image registration has often been considered as a preliminary step for higher-level processing, such as object recognition or data fusion. But with the unprecedented amounts of data which are being and will continue to be generated by newly developed sensors, the very topic of automatic image registration has become and important research topic. This workshop presents a collection of very high quality work which has been grouped in four main areas: (1) theoretical aspects of image registration; (2) applications to satellite imagery; (3) applications to medical imagery; and (4) image registration for computer vision research

Morphology-based interslice interpolation on manual segmentations of joint bones and muscles in MRI

This paper presents a validation study on the application of a novel interslice interpolation technique for musculoskeletal structure segmentation of articulated joints and muscles on human magnetic resonance imaging data. The interpolation technique is based on morphological shape-based interpolation combined with intensity based voxel classification. Shape-based interpolation in the absence of the original intensity image has been investigated intensively. However, in some applications of medical image analysis, the intensity image of the slice to be interpolated is available. For example, when manual segmentation is conducted on selected slices, the segmentation on those unselected slices can be obtained by interpolation. We proposed a two- step interpolation method to utilize both the shape information in the manual segmentation and local intensity information in the image. The method was tested on segmentations of knee, hip and shoulder joint bones and hamstring muscles. The results were compared with two existing interpolation methods. Based on the calculated Dice similarity coefficient and normalized error rate, the proposed method outperformed the other two methods