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

On Motion Parameterizations in Image Sequences from Fixed Viewpoints

This dissertation addresses the problem of parameterizing object motion within a set of images taken with a stationary camera. We develop data-driven methods across all image scales: characterizing motion observed at the scale of individual pixels, along extended structures such as roads, and whole image deformations such as lungs deforming over time. The primary contributions include: a) fundamental studies of the relationship between spatio-temporal image derivatives accumulated at a pixel, and the object motions at that pixel,: b) data driven approaches to parameterize breath motion and reconstruct lung CT data volumes, and: c) defining and offering initial results for a new class of Partially Unsupervised Manifold Learning: PUML) problems, which often arise in medical imagery. Specifically, we create energy functions for measuring how consistent a given velocity vector is with observed spatio-temporal image derivatives. These energy functions are used to fit parametric snake models to roads using velocity constraints. We create an automatic data-driven technique for finding the breath phase of lung CT scans which is able to replace external belt measurements currently in use clinically. This approach is extended to automatically create a full deformation model of a CT lung volume during breathing or heart MRI during breathing and heartbeat. Additionally, motivated by real use cases, we address a scenario in which a dataset is collected along with meta-data which describes some, but not all, aspects of the dataset. We create an embedding which displays the remaining variability in a dataset after accounting for variability related to the meta-data

Basic Science to Clinical Research: Segmentation of Ultrasound and Modelling in Clinical Informatics

The world of basic science is a world of minutia; it boils down to improving even a fraction of a percent over the baseline standard. It is a domain of peer reviewed fractions of seconds and the world of squeezing every last ounce of efficiency from a processor, a storage medium, or an algorithm. The field of health data is based on extracting knowledge from segments of data that may improve some clinical process or practice guideline to improve the time and quality of care. Clinical informatics and knowledge translation provide this information in order to reveal insights to the world of improving patient treatments, regimens, and overall outcomes. In my world of minutia, or basic science, the movement of blood served an integral role. The novel detection of sound reverberations map out the landscape for my research. I have applied my algorithms to the various anatomical structures of the heart and artery system. This serves as a basis for segmentation, active contouring, and shape priors. The algorithms presented, leverage novel applications in segmentation by using anatomical features of the heart for shape priors and the integration of optical flow models to improve tracking. The presented techniques show improvements over traditional methods in the estimation of left ventricular size and function, along with plaque estimation in the carotid artery. In my clinical world of data understanding, I have endeavoured to decipher trends in Alzheimer’s disease, Sepsis of hospital patients, and the burden of Melanoma using mathematical modelling methods. The use of decision trees, Markov models, and various clustering techniques provide insights into data sets that are otherwise hidden. Finally, I demonstrate how efficient data capture from providers can achieve rapid results and actionable information on patient medical records. This culminated in generating studies on the burden of illness and their associated costs. A selection of published works from my research in the world of basic sciences to clinical informatics has been included in this thesis to detail my transition. This is my journey from one contented realm to a turbulent one

Amoeboid Shape Dynamics on Flat and Topographically Modified Surfaces

I present an analysis of the shape dynamics of the amoeba Dictyostelium discoideum, a model system for the study of cellular migration. To better understand cellular migration in complicated 3-D environments, cell migration was studied on simple 3-D surfaces, such as cliffs and ridges. D. discoideum interact with surfaces without forming mature focal adhesion complexes. The cellular response to the surface topography was characterized by measuring and looking for patterns in cell shape. Dynamic cell shape is a measure of the interaction between the internal biochemical state of a cell and its external environment. For D. discoideum migrating on flat surfaces, waves of high boundary curvature were observed to travel from the cell front to the cell back. Curvature waves are also easily seen in cells that do not adhere to a surface, such as cells that are electrostatically repelled from the coverslip or cells that are extended over the edge of micro-fabricated cliffs. At the leading edge of adhered cells, these curvature waves are associated with protrusive activity, suggesting that protrusive motion can be thought of as a wave-like process. The wave-like character of protrusions provides a plausible mechanism for the ability of cells to swim in viscous fluids and to navigate complex 3-D topography. Patterning of focal adhesion complexes has previously been implicated in contact guidance (polarization or migration parallel to linear topographical structures). However, significant contact guidance is observed in D. discoideum, which lack focal adhesion complexes. Analyzing the migration of cells on nanogratings of ridges spaced various distances apart, ridges spaced about 1.5 micrometers apart were found to guide cells best. Contact guidance was modeled as an interaction between wave-like processes internal to the cell and the periodicity of the nanograting. The observed wavelength and speed of the oscillations that best couple to the surface are consistent with those of protrusive dynamics. Dynamic sensing via actin or protrusive dynamics might then play a role in contact guidance

Model and Appearance Based Analysis of Neuronal Morphology from Different Microscopy Imaging Modalities

The neuronal morphology analysis is key for understanding how a brain works. This process requires the neuron imaging system with single-cell resolution; however, there is no feasible system for the human brain. Fortunately, the knowledge can be inferred from the model organism, Drosophila melanogaster, to the human system. This dissertation explores the morphology analysis of Drosophila larvae at single-cell resolution in static images and image sequences, as well as multiple microscopy imaging modalities. Our contributions are on both computational methods for morphology quantification and analysis of the influence of the anatomical aspect. We develop novel model-and-appearance-based methods for morphology quantification and illustrate their significance in three neuroscience studies. Modeling of the structure and dynamics of neuronal circuits creates understanding about how connectivity patterns are formed within a motor circuit and determining whether the connectivity map of neurons can be deduced by estimations of neuronal morphology. To address this problem, we study both boundary-based and centerline-based approaches for neuron reconstruction in static volumes. Neuronal mechanisms are related to the morphology dynamics; so the patterns of neuronal morphology changes are analyzed along with other aspects. In this case, the relationship between neuronal activity and morphology dynamics is explored to analyze locomotion procedures. Our tracking method models the morphology dynamics in the calcium image sequence designed for detecting neuronal activity. It follows the local-to-global design to handle calcium imaging issues and neuronal movement characteristics. Lastly, modeling the link between structural and functional development depicts the correlation between neuron growth and protein interactions. This requires the morphology analysis of different imaging modalities. It can be solved using the part-wise volume segmentation with artificial templates, the standardized representation of neurons. Our method follows the global-to-local approach to solve both part-wise segmentation and registration across modalities. Our methods address common issues in automated morphology analysis from extracting morphological features to tracking neurons, as well as mapping neurons across imaging modalities. The quantitative analysis delivered by our techniques enables a number of new applications and visualizations for advancing the investigation of phenomena in the nervous system

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

Faster than the blink of an eye

Arboreal snakes such as the amazon tree boa (Corallus hortulanus) are able to cantilever large sections of their body for very long periods of time with seemingly minimal muscular effort. From this cantilevered position they exert quick strikes as well as compensate for any movement of the object from which they cantilever. The mechanisms of muscle coordination required for the dynamic switch between resting and strike have been hypothesized for terrestrial puff adders (Bitis arietans) to result from the vast and unique musculo-tendon arrangement of the snake's epaxial muscles put under pre-strike tension, i.e. a spring-like mechanism where the snake is able to store a large amount of energy in tendons which can then be later quickly released. Furthermore, while muscle activity during gap crossing or extension activities has been described for an arboreal species, it is not clear how the stationary snake's muscles compensate for perturbations of the anchoring object, e.g. as happens in the wild with a branch swaying in the breeze. Using a self-built high-speed 3D tracking system along with a novel method for collecting chronic multi-electrode bipolar electromyography (EMG) information, my data is not only unsupportive of the elastic energy-storing strike hypothesis but provides insights to the muscle coordination required for stabilization in a moving, as well as stationary, environment