Regularized Multigrid Optimization for Material Reconstruction from Single Medical X-ray Images

This thesis presents a novel technique for the estimation of 3D structural and material composition of anatomies imaged with X-rays. These estimates are produced from a single image with associated X-ray detector data. This method is made possible with access to software for X-ray simulation and segmentation, both developed by and provided to us by IBEX Innovations. This work combines existing concepts from optimization and multi-grid methods to present a novel concept for using domain knowledge to sufficiently constrain an otherwise unsolvable problem to produce valuable output. Specifically, it is shown that by transforming knowledge about the shape and composition of anatomies into regularizing functions, we can produce models of their internal structure that are accurate enough to simulate X-ray scatter, and thereby remove noise from the final images in a physics-guided way. By introducing weighted penalties for results that do not conform to expectations from domain knowledge, which are informed by IBEX’s neural network for X-ray segmentation, we can estimate the shape and material composition of a 3D object from a single image which - in theory - does not contain enough information to produce such a model. This work makes use of an X-ray simulation tool and associated data created by IBEX innovations and provided to us. We have created an optimization algorithm that iteratively processes this data with the IBEX simulation tool, then updates the estimated material composition of the imaged anatomy by imposing regularizing functions that penalize models that do not conform to our expectations about real anatomies. This is implemented on multi-grid, showing improved reconstruction quality and speed by producing coarse models first, followed by a custom algorithm for optimally selecting coarsening and refining of the model to produce the most accurate model. By using IBEX’s simulation algorithm, we show that we can constrain an otherwise ill-posed problem. These novel tools allow us to solve the problem of estimating 3D material composition from a single image, by considering simple features of organic shapes such as continuity and smoothness. We demonstrate that with access to sufficiently powerful simulation tools, even simple assumptions about our target facilitate intuitive material estimations. The algorithm presented in this thesis has certain limitations. We are only able to produce models of anatomies at low resolutions, constructed of just two distinct materials, without fully capturing the 3D structure of the anatomy. Nonetheless, we demonstrate that it is possible to capture enough structural information to produce an accurate scatter estimate, which would not be possible without the research we present here. These limitations are imposed to simplify our solutions such that they can be found using conventional hardware, and to constrain our problem into the scope of feasibility. Furthermore, the choice to limit our models to 2.5D and just two materials reflects the models used by IBEX Innovations and their X-ray simulation method, which we require for our optimization. To our understanding, no other published work in this field has applied an approach like ours to X-ray image reconstruction. Inferring from a single image not just depth information, but also an abstraction of information about the internal structure, in a way that is physically motivated. We hope that this concept could be applied to other problems in future, where systems are well understood but hindered by limited data availability or high capture costs

Rhodopseudomonas palustris : a model of bacterial differentiation

Differentiation in the budding photosynthetic bacterium Rhodopseudomonas palustris was studied both in its own right and in the context of other comparable bacteria; particularly R. acidophila and Rhodomicrobium vannielii. Together, these three Rhodospirillaceae present a gradient of morphogenetic complexity ideally suited to differentiation studies. Semi-defined conditions were determined which gave consistent morphology and fast growth rates. Heterogeneous cultures of R. palustris were then synchronised by selecting swarmer cells by sucrose gradient sedimentation. Morphology and ultrastructure of the cell division cycle exhibited by R. palustria were examined in some detail and compared with R. acidophila. Both organisms exhibited differentiation at the sub-cellular level and by dividing to give two dissimilar cells. The distribution of cell types, stepwise doublings, particle volume distributions, optical density changes, cell motility, protein and DNA synthesis and probably also RNA synthesis were all examined during synchronous growth of R. palustris. Penicillin treatment showed that cell growth was by polar, unidirectional synthesis of wall material, Nalidixic acid, which inhibits DNA replication, modified the cell development by inhibiting cell division and giving rise to abnormal cell elongation. Studies with nalidixic acid also confirmed that there was periodic DNA synthesis during the normal cell cycle. Observations on the location of cell division in elongated cells after removal of the nalidixic acid, considered alongside the polar unidirectional mode of cell growth, allowed a model correlating chromosome replication and cell envelope growth to be proposed. Some preliminary investigations were made of mutants of R. palustris. Temperature-sensitive mutants were obtained, but these did not appear to be blocked at any particular stage of development. A phage specific for one strain of H. palustris was investigated and appeared to be temperature-sensitive in some step of its growth cycle. This might permit its use for transduction. Both temperature-sensitive mutants and a method of genetic transfer were considered invaluable for further studies of the control of R. palustris differentiation

Program representation size in an intermediate language with intersection and union types

The CIL compiler for core Standard ML compiles whole programs using a novel typed intermediate language (TIL) with intersection and union types and flow labels on both terms and types. The CIL term representation duplicates portions of the program where intersection types are introduced and union types are eliminated. This duplication makes it easier to represent type information and to introduce customized data representations. However, duplication incurs compile-time space costs that are potentially much greater than are incurred in TILs employing type-level abstraction or quantification. In this paper, we present empirical data on the compile-time space costs of using CIL as an intermediate language. The data shows that these costs can be made tractable by using sufficiently fine-grained flow analyses together with standard hash-consing techniques. The data also suggests that non-duplicating formulations of intersection (and union) types would not achieve significantly better space complexity.National Science Foundation (CCR-9417382, CISE/CCR ESS 9806747); Sun grant (EDUD-7826-990410-US); Faculty Fellowship of the Carroll School of Management, Boston College; U.K. Engineering and Physical Sciences Research Council (GR/L 36963, GR/L 15685

Investigations into novel electrochemical technology for boar taint detection and vitamin analysis

This thesis presents the evaluation of the novel electrochemical sensor and biosensor technology developed for the direct analysis of boar taint compounds in adipose tissue (European Patent 2966441). Gas chromatographic methods and extraction procedures were adapted for the evaluation of the novel sensor technology. The methodologies for the non-destructive sensor technology were evaluated by analysing stored porcine adipose tissue, the samples were subsequently analysed by the destructive gas-chromatographic methodologies for comparison. The results from two analytical methods correlated well for both compounds of interest in a laboratory environment. Consequently, the sensor and biosensor were integrated into a dual system and evaluated in the laboratory. The dual electrochemical system was optimised for simultaneous measurement. The prototype was taken to an abattoir, the subcutaneous adipose tissue of carcasses were analysed online then the section was removed and stored before analysis via the laboratory based extraction and gas-chromatographic analysis procedures. The quantitative data correlation indicates that this technology is viable for its proposed industrial application.Other endogenous compounds in boar tissue were also identified prior to sample analysis during a literature review. The reported electrochemical behaviour and concentration ranges of these compounds were used to identify compounds which could result in the novel technology displaying false positive or false negative responses. During this preliminary investigation the identified compounds did not respond at the novel technology in a similar manner to the analytes of interest under physiological conditions. However, under basic electrolyte conditions an anodic response for 3 B-vitamin compounds was observed. As a secondary study to the boar taint analysis a simple voltammetric assay was developed to exploit this behaviour and applied to the analysis of a food product and pharmaceutical supplement

A novel electroanalytical approach to the measurement of B vitamins in food supplements based on screen-printed carbon sensors

© 2017 Elsevier B.V. This paper describes the development of a novel electrochemical assay for the measurement of water-soluble vitamins in food and pharmaceutical products. The optimum conditions for the determination of vitamin B1 (thiamine), B2 (riboflavin) and B6 (pyridoxine) in phosphate buffer were established using cyclic voltammetry in conjunction with screen printed carbon electrodes (SPCEs). The optimum current response for all three vitamins was achieved in 0.1 M phosphate buffer pH 11 using an initial potential of −1.0 V. Using square wave voltammetry, the linear ranges for thiamine, riboflavin, and pyridoxine were found to be: 15–110 µg/ml, 0.1–20 µg/ml, and 2–80 µg/ml respectively. The application of the method to a commercial food product yielded a recovery of 95.78% for riboflavin, with a coefficient of variation (CV) of 3.38% (n = 5). The method was also applied to a multi-vitamin supplement for the simultaneous determination of thiamine, riboflavin and pyridoxine. In both cases only simple dilution with buffer followed by centrifugation was required prior to analysis. The resulting square wave voltammetric signals were completely resolved with Ep values of −0.7 V, +0.2 V, and +0.6 V respectively. The recoveries determined for the vitamin B complex in a commercial supplement product were found to be 110%, 114%, and 112% respectively (CV = 7.14%, 6.28%. 5.66% respectively, n = 5)

Recent TEM studies of precipitate growth mechanisms

In this review recent results of transmission electron microscopy studies of precipitation in a number of model binary alloy systems are presented. Emphasis is placed on identifying (i) the nature of the structural change occurring during the transformations, and (ii) the crystal lattice defects and deformation modes required to accommodate the growing precipitate in the parent phase. Precipitation reactions are classified in terms of their transformation strains, and simple predictive models for the precipitate morphology are developed for each case. Brief discussions are also given on the nature of a general plate precipitate interface and the effect of crystal symmetry on morphological distributions.Des exemples récents d'étude par microscopie électronique en transmission sont analysés dans cette revue. L'accent est mis sur l'identification (i) de la nature des modifications de structure intervenant lors des transformations, (ii) des défauts cristallins et des modes de déformation nécessaires à la croissance du précipité dans la phase mère. Un classement des réactions de précipitation est effectué selon les mécanismes de déformation mis en jeu. Des modèles simples permettant de prévoir la morphologie des précipités sont précisés dans chaque cas. Des éléments de discussion concernant la nature de l'interface entre la matrice et un précipité quelconque en plaquette sont également fournis. Les effets de la symétrie cristalline sur les distributions de forme sont brièvement abordés