Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Generalized Delaunay triangulations : graph-theoretic properties and algorithms

This thesis studies different generalizations of Delaunay triangulations, both from a combinatorial and algorithmic point of view. The Delaunay triangulation of a point set S, denoted DT(S), has vertex set S. An edge uv is in DT(S) if it satisfies the empty circle property: there exists a circle with u and v on its boundary that does not enclose points of S. Due to different optimization criteria, many generalizations of the DT(S) have been proposed. Several properties are known for DT(S), yet, few are known for its generalizations. The main question we explore is: to what extent can properties of DT(S) be extended for generalized Delaunay graphs? First, we explore the connectivity of the flip graph of higher order Delaunay triangulations of a point set S in the plane. The order-k flip graph might be disconnected for k = 3, yet, we give upper and lower bounds on the flip distance from one order-k triangulation to another in certain settings. Later, we show that there exists a length-decreasing sequence of plane spanning trees of S that converges to the minimum spanning tree of S with respect to an arbitrary convex distance function. Each pair of consecutive trees in the sequence is contained in a constrained convex shape Delaunay graph. In addition, we give a linear upper bound and specific bounds when the convex shape is a square. With focus still on convex distance functions, we study Hamiltonicity in k-order convex shape Delaunay graphs. Depending on the convex shape, we provide several upper bounds for the minimum k for which the k-order convex shape Delaunay graph is always Hamiltonian. In addition, we provide lower bounds when the convex shape is in a set of certain regular polygons. Finally, we revisit an affine invariant triangulation, which is a special type of convex shape Delaunay triangulation. We show that many properties of the standard Delaunay triangulations carry over to these triangulations. Also, motivated by this affine invariant triangulation, we study different triangulation methods for producing other affine invariant geometric objects.Esta tesis estudia diferentes generalizaciones de la triangulación de Delaunay, tanto desde un punto de vista combinatorio como algorítmico. La triangulación de Delaunay de un conjunto de puntos S, denotada DT(S), tiene como conjunto de vértices a S. Una arista uv está en DT(S) si satisface la propiedad del círculo vacío: existe un círculo con u y v en su frontera que no contiene ningún punto de S en su interior. Debido a distintos criterios de optimización, se han propuesto varias generalizaciones de la DT (S). Hoy en día, se conocen bastantes propiedades de la DT(S), sin embargo, poco se sabe sobre sus generalizaciones. La pregunta principal que exploramos es: ¿Hasta qué punto las propiedades de la DT(S) se pueden extender para generalizaciones de gráficas de Delaunay? Primero, exploramos la conectividad de la gráfica de flips de las triangulaciones de Delaunay de orden alto de un conjunto de puntos S en el plano. La gráfica de flips de triangulaciones de orden k = 3 podría ser disconexa, sin embargo, nosotros damos una cota superior e inferior para la distancia en flips de una triangulación de orden k a alguna otra cuando S cumple con ciertas características. Luego, probamos que existe una secuencia de árboles generadores sin cruces tal que la suma total de la longitud de las aristas con respecto a una distancia convexa arbitraria es decreciente y converge al árbol generador mínimo con respecto a la distancia correspondiente. Cada par de árboles consecutivos en la secuencia se encuentran en una triangulación de Delaunay con restricciones. Adicionalmente, damos una cota superior lineal para la longitud de la secuencia y cotas específicas cuando el conjunto convexo es un cuadrado. Aún concentrados en distancias convexas, estudiamos hamiltonicidad en las gráficas de Delaunay de distancia convexa de k-orden. Dependiendo en la distancia convexa, exhibimos diversas cotas superiores para el mínimo valor de k que satisface que la gráfica de Delaunay de distancia convexa de orden-k es hamiltoniana. También damos cotas inferiores para k cuando el conjunto convexo pertenece a un conjunto de ciertos polígonos regulares. Finalmente, re-visitamos una triangulación afín invariante, la cual es un caso especial de triangulación de Delaunay de distancia convexa. Probamos que muchas propiedades de la triangulación de Delaunay estándar se preservan en estas triangulaciones. Además, motivados por esta triangulación afín invariante, estudiamos diferentes algoritmos que producen otros objetos geométricos afín invariantes

Rigidity and Fluidity in Living and Nonliving Matter

Many of the standard equilibrium statistical mechanics techniques do not readily apply to non-equilibrium phase transitions such as the fluid-to-disordered solid transition found in repulsive particulate systems. Examples of repulsive particulate systems are sand grains and colloids. The first part of this thesis contributes to methods beyond equilibrium statistical mechanics to ultimately understand the nature of the fluid-to-disordered solid transition, or jamming, from a microscopic basis. In Chapter 2 we revisit the concept of minimal rigidity as applied to frictionless, repulsive soft sphere packings in two dimensions with the introduction of the jamming graph. Minimal rigidity is a purely combinatorial property encoded via Laman\u27s theorem in two dimensions. It constrains the global, average coordination number of the graph, for instance. Minimal rigidity, however, does not address the geometry of local mechanical stability. The jamming graph contains both properties of global mechanical stability at the onset of jamming and local mechanical stability. We demonstrate how jamming graphs can be constructed using local rules via the Henneberg construction such that these graphs are of the constraint percolation type, where percolation is the study of connected structures in disordered networks. We then probe how jamming graphs destabilize, or become fluid-like, by deleting an edge/contact in the graph and computing the resulting rigid cluster distribution. We also uncover a new potentially diverging lengthscale associated with the random deletion of contacts. In Chapter 3 we study several constraint percolation models, such as k-core percolation and counter-balance percolation, on hyperbolic lattices to better understand the role of loops in such models. The constraints in these percolation models incorporate aspects of local mechanical rigidity found in jammed systems. The expectation is that since these models are indeed easier to analyze than the more complicated problem of jamming, we will gain insight into which constraints affect the nature of the jamming transition and which do not. We find that k = 3-core percolation on the hyperbolic lattice remains a continuous phase transition despite the fact that the loop structure of hyperbolic lattices is different from Euclidean lattices. We also contribute towards numerical techniques for analyzing percolation on hyperbolic lattices. In Chapters 4 and 5 we turn to living matter, which is also nonequilibrium in a very local way in that each constituent has its own internal energy supply. In Chapter 4 we study the fluidity of a cell moving through a confluent tissue, i.e. a group of cells with no gaps between them, via T1 transitions. A T1 transition allows for an edge swap so that a cell can come into contact with new neighbors. Cell migration is then generated by a sequence of such swaps. In a simple four cell system we compute the energy barriers associated with this transition. We then find that the energy barriers in a larger system are rather similar to the four cell case. The many cell case, however, more easily allows for the collection of statistics of these energy barriers given the disordered packings of cell observed in experiments. We find that the energy barriers are exponentially distributed. Such a finding implies that glassy dynamics is possible in a confluent tissue. Finally, in chapter 5 we turn to single cell migration in the extracellular matrix, another native environment of a cell. Experiments suggest that the migration of some cells in the three-dimensional ext ra cellular matrix bears strong resemblance to one-dimensional cell migration. Motivated by this observation, we construct and study a minimal one-dimensional model cell made of two beads and an active spring moving along a rigid track. The active spring models the stress fibers with their myosin-driven contractility and alpha-actinin-driven extendability, while the friction coefficients of the two beads describe the catch/slip bond behavior of the integrins in focal adhesions. Net motion arises from an interplay between active contractility (and passive extendability) of the stress fibers and an asymmetry between the front and back of the cell due to catch bond behavior of integrins at the front of the cell and slip bond behavior of integrins at the back. We obtain reasonable cell speeds with independently estimated parameters. Our model highlights the role of alpha-actinin in three-dimensional cell motility and does not require Arp2/3 actin filament nucleation for net motion

Hashing for Similarity Search: A Survey

Similarity search (nearest neighbor search) is a problem of pursuing the data items whose distances to a query item are the smallest from a large database. Various methods have been developed to address this problem, and recently a lot of efforts have been devoted to approximate search. In this paper, we present a survey on one of the main solutions, hashing, which has been widely studied since the pioneering work locality sensitive hashing. We divide the hashing algorithms two main categories: locality sensitive hashing, which designs hash functions without exploring the data distribution and learning to hash, which learns hash functions according the data distribution, and review them from various aspects, including hash function design and distance measure and search scheme in the hash coding space