A Markov Random Field Based Approach to 3D Mosaicing and Registration Applied to Ultrasound Simulation

A novel Markov Random Field (MRF) based method for the mosaicing of 3D ultrasound volumes is presented in this dissertation. The motivation for this work is the production of training volumes for an affordable ultrasound simulator, which offers a low-cost/portable training solution for new users of diagnostic ultrasound, by providing the scanning experience essential for developing the necessary psycho-motor skills. It also has the potential for introducing ultrasound instruction into medical education curriculums. The interest in ultrasound training stems in part from the widespread adoption of point-of-care scanners, i.e. low cost portable ultrasound scanning systems in the medical community. This work develops a novel approach for producing 3D composite image volumes and validates the approach using clinically acquired fetal images from the obstetrics department at the University of Massachusetts Medical School (UMMS). Results using the Visible Human Female dataset as well as an abdominal trauma phantom are also presented. The process is broken down into five distinct steps, which include individual 3D volume acquisition, rigid registration, calculation of a mosaicing function, group-wise non-rigid registration, and finally blending. Each of these steps, common in medical image processing, has been investigated in the context of ultrasound mosaicing and has resulted in improved algorithms. Rigid and non-rigid registration methods are analyzed in a probabilistic framework and their sensitivity to ultrasound shadowing artifacts is studied. The group-wise non-rigid registration problem is initially formulated as a maximum likelihood estimation, where the joint probability density function is comprised of the partially overlapping ultrasound image volumes. This expression is simplified using a block-matching methodology and the resulting discrete registration energy is shown to be equivalent to a Markov Random Field. Graph based methods common in computer vision are then used for optimization, resulting in a set of transformations that bring the overlapping volumes into alignment. This optimization is parallelized using a fusion approach, where the registration problem is divided into 8 independent sub-problems whose solutions are fused together at the end of each iteration. This method provided a speedup factor of 3.91 over the single threaded approach with no noticeable reduction in accuracy during our simulations. Furthermore, the registration problem is simplified by introducing a mosaicing function, which partitions the composite volume into regions filled with data from unique partially overlapping source volumes. This mosaicing functions attempts to minimize intensity and gradient differences between adjacent sources in the composite volume. Experimental results to demonstrate the performance of the group-wise registration algorithm are also presented. This algorithm is initially tested on deformed abdominal image volumes generated using a finite element model of the Visible Human Female to show the accuracy of its calculated displacement fields. In addition, the algorithm is evaluated using real ultrasound data from an abdominal phantom. Finally, composite obstetrics image volumes are constructed using clinical scans of pregnant subjects, where fetal movement makes registration/mosaicing especially difficult. Our solution to blending, which is the final step of the mosaicing process, is also discussed. The trainee will have a better experience if the volume boundaries are visually seamless, and this usually requires some blending prior to stitching. Also, regions of the volume where no data was collected during scanning should have an ultrasound-like appearance before being displayed in the simulator. This ensures the trainee\u27s visual experience isn\u27t degraded by unrealistic images. A discrete Poisson approach has been adapted to accomplish these tasks. Following this, we will describe how a 4D fetal heart image volume can be constructed from swept 2D ultrasound. A 4D probe, such as the Philips X6-1 xMATRIX Array, would make this task simpler as it can acquire 3D ultrasound volumes of the fetal heart in real-time; However, probes such as these aren\u27t widespread yet. Once the theory has been introduced, we will describe the clinical component of this dissertation. For the purpose of acquiring actual clinical ultrasound data, from which training datasets were produced, 11 pregnant subjects were scanned by experienced sonographers at the UMMS following an approved IRB protocol. First, we will discuss the software/hardware configuration that was used to conduct these scans, which included some custom mechanical design. With the data collected using this arrangement we generated seamless 3D fetal mosaics, that is, the training datasets, loaded them into our ultrasound training simulator, and then subsequently had them evaluated by the sonographers at the UMMS for accuracy. These mosaics were constructed from the raw scan data using the techniques previously introduced. Specific training objectives were established based on the input from our collaborators in the obstetrics sonography group. Important fetal measurements are reviewed, which form the basis for training in obstetrics ultrasound. Finally clinical images demonstrating the sonographer making fetal measurements in practice, which were acquired directly by the Philips iU22 ultrasound machine from one of our 11 subjects, are compared with screenshots of corresponding images produced by our simulator

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

Study of time-lapse processing for dynamic hydrologic conditions

The usefulness of dynamic display techniques in exploiting the repetitive nature of ERTS imagery was investigated. A specially designed Electronic Satellite Image Analysis Console (ESIAC) was developed and employed to process data for seven ERTS principal investigators studying dynamic hydrological conditions for diverse applications. These applications include measurement of snowfield extent and sediment plumes from estuary discharge, Playa Lake inventory, and monitoring of phreatophyte and other vegetation changes. The ESIAC provides facilities for storing registered image sequences in a magnetic video disc memory for subsequent recall, enhancement, and animated display in monochrome or color. The most unique feature of the system is the capability to time lapse the imagery and analytic displays of the imagery. Data products included quantitative measurements of distances and areas, binary thematic maps based on monospectral or multispectral decisions, radiance profiles, and movie loops. Applications of animation for uses other than creating time-lapse sequences are identified. Input to the ESIAC can be either digital or via photographic transparencies

Vascular patterning of subcutaneous mouse fibrosarcomas expressing individual VEGF isoforms can be differentiated using angiographic optical coherence tomography

Subcutaneously implanted experimental tumors in mice are commonly used in cancer research. Despite their superficial location, they remain a challenge to image noninvasively at sufficient spatial resolution for microvascular studies. Here we evaluate the capabilities of optical coherence tomography (OCT) angiography for imaging such tumors directly through the murine skin in-vivo. Datasets were collected from mouse tumors derived from fibrosarcoma cells genetically engineered to express only single splice variant isoforms of vascular endothelial growth factor A (VEGF); either VEGF120 or VEGF188 (fs120 and fs188 tumors respectively). Measured vessel diameter was found to be significantly (p<0.001) higher for fs120 tumors (60.7±4.9μm) compared to fs188 tumors (45.0±4.0μm). The fs120 tumors also displayed significantly higher vessel tortuosity, fractal dimension and density. The ability to differentiate between tumor types with OCT suggests that the visible abnormal vasculature is representative of the tumor microcirculation, providing a robust, non-invasive method for observing the longitudinal dynamics of the subcutaneous tumor microcirculation

CUPOLETS: Chaotic unstable periodic orbits theory and applications

Recent theoretical work suggests that periodic orbits of chaotic systems are a rich source of qualitative information about the dynamical system. The presence of unstable periodic orbits located densely on the attractor is a typical characteristic of chaotic systems. This abundance of unstable periodic orbits can be utilized in a wide variety of theoretical and practical applications [19]. In particular, chaotic communication techniques and methods of controlling chaos depend on this property of chaotic attractors [12, 13]. In the first part of this thesis, a control scheme for stabilizing the unstable periodic orbits of chaotic systems is presented and the properties of these orbits are investigated. The technique allows for creation of thousands of periodic orbits. These approximated chaotic unstable periodic orbits are called cupolets (C&barbelow;haotic U&barbelow;nstable P&barbelow;eriodic O&barbelow;rbit- lets). We show that these orbits can be passed through a phase transformation to a compact cupolet state that possesses a wavelet-like structure and can be used to construct adaptive bases. The cupolet transformation can be regarded as an alternative to Fourier and wavelet transformations. In fact, this new framework provides a continuum between Fourier and wavelet transformations and can be used in variety of applications such as data and music compression, as well as image and video processing. The key point in this method is that all of these different dynamical behaviors are easily accessible via small controls. This technique is implemented in order to produce cupolets which are essentially approximate periodic orbits of the chaotic system. The orbits are produced with small perturbations which in turn suggests that these orbits might not be very far away from true periodic orbits. The controls can be considered as external numerical errors that happen at some points along the computer generated orbits. This raises the question of shadowability of these orbits. It is very interesting to know if there exists a true orbit of the system with a slightly different initial condition that stays close to the computer generated orbit. This true orbit, if it exists, is called a shadow and the computer generated orbit is then said to be shadowable by a true orbit. We will present two general purpose shadowing theorems for periodic and nonperiodic orbits of ordinary differential equations. The theorems provide a way to establish the existence of true periodic and non-periodic orbits near the approximated ones. Both theorems are suitable for computations and the shadowing distances, i.e., the distance between the true orbits and approximated orbits are given by quantities computable form the vector field of the differential equation

Three-Dimensional Microstructure Characterization of Surface-Crystallized Glass Ceramics

Die dreidimensionale Mikrostruktur, welche bei der Oberflächenkristallisation von Glaskeramiken entsteht, wird mittels einer neuartigen Methode zur Präparation von abgesenkten Probenoberflächen untersucht. Diese Initialkantensektionierungsmethode, welche auf der Erzeugung von Scharten in der Probenoberfläche und anschließender Glanzwinkelionenstrahlerosion basiert, erlaubt das rapide Freilegen von großflächigen Schichten in wohldefinierten Tiefen unterhalb der ursprünglichen Probenoberfläche. In dieser Dissertation werden mehrere Variationen der Technik durch Kombination von Laserablation, Ionenbreit- sowie Ionenfeinstrahlerosion untersucht und miteinander verglichen. Die in Bezug auf Schnittgeometrie und Probengüte relevanten, experimentellen Parameter werden bestimmt und bewertet. Ein Modell zur Beschreibung der zeitlichen Evolution der Probengeometrie während des Erosionsvorgangs wird auf Grundlage von Simulationen und analytischen Näherungen aufgestellt und mit experimentellen Ergebnissen verglichen. Schließlich wird die Initialkantensektionierungsmethode mit Elektronenrückstreubeugung kombiniert um Wachstumseffekte bei der Oberflächenkristallisation von Diopsid- und Ba2TiSi2O8-Fresnoitglaskeramiken zu untersuchen.:1 Introduction 1.1 Motivation 1.2 Aims and Objectives 2 Literature Review 2.1 Sample Preparation for Electron Backscatter Diffraction Studies 2.2 Serial Sectioning Methods 2.3 Microstructure Characterization of Glass Ceramics using EBSD 2.4 Interim Conclusion 3 Theory 3.1 Erosion of a Surface Under Ion Bombardment 3.1.1 Sputtering 3.1.2 Kinetic Theory of Surface Evolution 3.1.3 Numerical Simulation of Surface Erosion 3.1.4 Erosion of a Surface With Initial Notches 3.2 Electron Backscatter Diffraction 3.2.1 Measurement Principle 3.2.2 Representation of Orientations and Texture 4 Methods and Materials 4.1 Sample Preparation and Processing 4.2 Surface Metrology 4.3 Microstructure Analysis 4.4 Materials 5 Erosion of Surfaces With Initial Notches 5.1 Evaluation of Surface Processing Methods 5.1.1 Notch Creation 5.1.2 Terrace Formation by Glancing-Angle Ion Beam Erosion 5.2 Surface Properties in the Terrace Region 5.2.1 Terrace Roughness 5.2.2 Ion Beam Induced Amorphization 5.3 Evolution of Surface Geometry 5.3.1 Linear Model 5.3.2 Simulations 5.3.3 Experimental Results 5.4 Discussion 5.4.1 Sample Processing 5.4.2 Sample Quality 5.4.3 Kinetic Model of Surface Evolution 6 Depth-Resolved Microstructure Characterization Using Initial Notches 6.1 Diopside 6.2 Ba2TiSi2O8 fresnoite (BTS) 6.3 Discussion 6.3.1 Methodological Aspects of Initial Notch Sectioning 6.3.2 Microstructure Analysis on Surface-Crystallized Glass Ceramics 7 Summary and OutlookThree-dimensional microstructures resulting from surface crystallization of glass ceramics are studied using a novel sample sectioning method. Based on the creation of notches on the sample surface and subsequent glancing-angle ion beam erosion, initial notch sectioning enables the rapid excavation of large subsurface layers at well-defined depths. In this thesis, several variations of this technique using different combinations of laser ablation, broad and focused ion beam erosion are realized and compared to each other. Relevant parameters controlling the section geometry and quality are determined. A model of the surface evolution kinetics is developed using simulations and analytical estimates, which is compared to experimental results. Finally, initial notch sectioning in combination with electron backscatter diffraction is applied to elucidate growth phenomena in the surface crystallization of diopside and Ba2TiSi2O8 fresnoite glass ceramics.:1 Introduction 1.1 Motivation 1.2 Aims and Objectives 2 Literature Review 2.1 Sample Preparation for Electron Backscatter Diffraction Studies 2.2 Serial Sectioning Methods 2.3 Microstructure Characterization of Glass Ceramics using EBSD 2.4 Interim Conclusion 3 Theory 3.1 Erosion of a Surface Under Ion Bombardment 3.1.1 Sputtering 3.1.2 Kinetic Theory of Surface Evolution 3.1.3 Numerical Simulation of Surface Erosion 3.1.4 Erosion of a Surface With Initial Notches 3.2 Electron Backscatter Diffraction 3.2.1 Measurement Principle 3.2.2 Representation of Orientations and Texture 4 Methods and Materials 4.1 Sample Preparation and Processing 4.2 Surface Metrology 4.3 Microstructure Analysis 4.4 Materials 5 Erosion of Surfaces With Initial Notches 5.1 Evaluation of Surface Processing Methods 5.1.1 Notch Creation 5.1.2 Terrace Formation by Glancing-Angle Ion Beam Erosion 5.2 Surface Properties in the Terrace Region 5.2.1 Terrace Roughness 5.2.2 Ion Beam Induced Amorphization 5.3 Evolution of Surface Geometry 5.3.1 Linear Model 5.3.2 Simulations 5.3.3 Experimental Results 5.4 Discussion 5.4.1 Sample Processing 5.4.2 Sample Quality 5.4.3 Kinetic Model of Surface Evolution 6 Depth-Resolved Microstructure Characterization Using Initial Notches 6.1 Diopside 6.2 Ba2TiSi2O8 fresnoite (BTS) 6.3 Discussion 6.3.1 Methodological Aspects of Initial Notch Sectioning 6.3.2 Microstructure Analysis on Surface-Crystallized Glass Ceramics 7 Summary and Outloo

Angiography and Monitoring of Hemodynamic Signals in the Brain via Optical Coherence Tomography

The brain is a complex network of interconnected neurons with each cell functioning as a nonlinear processing unit. Neural responses to stimulus can be described by activity in neurons. While blood flow changes have been associated with neural activity and are critical to brain function, this neurovascular coupling is not well understood. This work presents a technique for neurovascular interrogation, combining optogenetics and optical coherence tomography. Optogenetics is a recently developed neuromodulation technique to control activity in the brain using light with precise spatial neuronal control and high temporal resolution. Using this method, cells act as light-gated ion channels and respond to photo stimulation by increasing or decreasing activity. Spectral-domain optical coherence tomography (SD-OCT) is a noninvasive imaging modality that has the ability to image millimeter range depth and with micrometer resolution. SD-OCT has been shown to image rodent cortical microvasculature in-vivo and detect hemodynamic changes in blood vessels. Our proposed system combines optogenetics and SD-OCT to image cortical patches of the brain with the capability of simultaneously stimulating the brain. The combination allows investigation of the hemodynamic changes in response to neural stimulation. Our results detected changes in blood vessel diameter and velocity before, during and after optogenetic stimulation and is presented

Graph-Based methodology for Multi-Scale generation of energy analysis models from IFC

Process digitalisation and automation is unstoppable in all industries, including construction. However, its widespread adoption, even for non-experts, demands easy-to-use tools that reduce technical requirements. BIM to BEM (Building Energy Models) workflows are a clear example, where ad-hoc prepared models are needed. This paper describes a methodology, based on graph techniques, to automate it by highly reducing the input BIM requirements found in similar approaches, being applicable to almost any IFC. This is especially relevant in retrofitting, where reality capture tools (e.g., 3D laser scanning, object recognition in drawings) are prone to create geometry clashes and other inconsistencies, posing higher challenges for automation. Another innovation presented is its multi-scale nature, efficiently addressing the surroundings impact in the energy model. The application to selected test cases has been successful and further tests are ongoing, considering a higher variety of BIM models in relation to tools and techniques used and model sizes.The authors would like to express the gratitude to the European Commission by funding the research projects BIM4REN, EPCRECAST and ENSNARE (Grant Agreement No. 820773, 893118 and 958445, respectively), under the Horizon 2020 programme, where the presented work was conducted. This manuscript reflects only the authors’ views, and the Commission is not responsible for any use that may be made of the information it contains