Transmission electron tomography: quality assessment and enhancement for three-dimensional imaging of nanostructures

Nanotechnology has revolutionised humanity's capability in building microscopic systems by manipulating materials on a molecular and atomic scale. Nan-osystems are becoming increasingly smaller and more complex from the chemical perspective which increases the demand for microscopic characterisation techniques. Among others, transmission electron microscopy (TEM) is an indispensable tool that is increasingly used to study the structures of nanosystems down to the molecular and atomic scale. However, despite the effectivity of this tool, it can only provide 2-dimensional projection (shadow) images of the 3D structure, leaving the 3-dimensional information hidden which can lead to incomplete or erroneous characterization. One very promising inspection method is Electron Tomography (ET), which is rapidly becoming an important tool to explore the 3D nano-world. ET provides (sub-)nanometer resolution in all three dimensions of the sample under investigation. However, the fidelity of the ET tomogram that is achieved by current ET reconstruction procedures remains a major challenge. This thesis addresses the assessment and advancement of electron tomographic methods to enable high-fidelity three-dimensional investigations. A quality assessment investigation was conducted to provide a quality quantitative analysis of the main established ET reconstruction algorithms and to study the influence of the experimental conditions on the quality of the reconstructed ET tomogram. Regular shaped nanoparticles were used as a ground-truth for this study. It is concluded that the fidelity of the post-reconstruction quantitative analysis and segmentation is limited, mainly by the fidelity of the reconstructed ET tomogram. This motivates the development of an improved tomographic reconstruction process. In this thesis, a novel ET method was proposed, named dictionary learning electron tomography (DLET). DLET is based on the recent mathematical theorem of compressed sensing (CS) which employs the sparsity of ET tomograms to enable accurate reconstruction from undersampled (S)TEM tilt series. DLET learns the sparsifying transform (dictionary) in an adaptive way and reconstructs the tomogram simultaneously from highly undersampled tilt series. In this method, the sparsity is applied on overlapping image patches favouring local structures. Furthermore, the dictionary is adapted to the specific tomogram instance, thereby favouring better sparsity and consequently higher quality reconstructions. The reconstruction algorithm is based on an alternating procedure that learns the sparsifying dictionary and employs it to remove artifacts and noise in one step, and then restores the tomogram data in the other step. Simulation and real ET experiments of several morphologies are performed with a variety of setups. Reconstruction results validate its efficiency in both noiseless and noisy cases and show that it yields an improved reconstruction quality with fast convergence. The proposed method enables the recovery of high-fidelity information without the need to worry about what sparsifying transform to select or whether the images used strictly follow the pre-conditions of a certain transform (e.g. strictly piecewise constant for Total Variation minimisation). This can also avoid artifacts that can be introduced by specific sparsifying transforms (e.g. the staircase artifacts the may result when using Total Variation minimisation). Moreover, this thesis shows how reliable elementally sensitive tomography using EELS is possible with the aid of both appropriate use of Dual electron energy loss spectroscopy (DualEELS) and the DLET compressed sensing algorithm to make the best use of the limited data volume and signal to noise inherent in core-loss electron energy loss spectroscopy (EELS) from nanoparticles of an industrially important material. Taken together, the results presented in this thesis demonstrates how high-fidelity ET reconstructions can be achieved using a compressed sensing approach.

PREVALENCE OF IRON DEFICIENCY ANAEMIA AND DIETARY IRON INTAKE AMONG INFANTS AGED SIX TO NINE MONTHS IN KEIYO SOUTH SUB COUNTY, KENYA

The increased prevalence of iron deficiency among infants can be attributed to the consumption of an iron deficient diet or a diet that interferes with iron absorption at the critical time of infancy, among other factors. The gradual shift from breast milk to other foods and liquids is a transition period which greatly contributes to iron deficiency anaemia (IDA). The purpose of this research was to assess iron deficiency anaemia among infants aged six to nine months in Keiyo South Sub County. The specific objectives of this study were: to establish the prevalence of infants with iron deficiency anaemia and dietary iron intake among infants aged 6 to 9 months. The cross sectional study design was adopted in this survey. This study was conducted in three health facilities in Keiyo South Sub County. The infants were selected by use of a two stage cluster sampling procedure. Systematic random sampling was then used to select a total of 244 mothers and their infants. Eighty two (82) infants were selected from Kamwosor sub-district hospital and eighty one (81) from both Nyaru and Chepkorio health facilities. Interview schedules, 24-hour dietary recall and food frequency questionnaires were used for collection of dietary iron intake. Biochemical tests were carried out by use of the Hemo-control photochrometer at the health facilities. Infants whose hemoglobin levels were less than 11g/dl were considered anaemic. Further, peripheral blood smears were conducted to ascertain the type of nutritional anaemia. Data was analyzed using the Statistical Package for Social Sciences (SPSS) computer software version 17, 2009. Dietary iron intake was analyzed using the NutriSurvey 2007 computer software. Results indicated that the mean hemoglobin values were 11.3± 0.84 g/dl. Twenty one percent (21.7%) of the infants had anaemia and further 100% of peripheral blood smears indicated iron deficiency anaemia. Dietary iron intake was a predictor of iron deficiency anaemia in this study (t=-3.138; p=0.01). Iron deficiency anaemia was evident among infants in Keiyo South Sub County. The Ministry of Health should formulate and implement policies on screening for anaemia and ensure intensive nutrition education on iron rich diets during child welfare clinics.

Leadership competencies in the requirements phase of IS/IT development projects

Doutoramento em Gestão

Adaptive Software Fault Prediction Approach Using Object-Oriented Metrics

As users continually request additional functionality, software systems will continue to grow in their complexity, as well as in their susceptibility to failures. Particularly for sensitive systems requiring higher levels of reliability, faulty system modules may increase development and maintenance cost. Hence, identifying them early would support the development of reliable systems through improved scheduling and quality control. Research effort to predict software modules likely to contain faults, as a consequence, has been substantial. Although a wide range of fault prediction models have been proposed, we remain far from having reliable tools that can be widely applied to real industrial systems. For projects with known fault histories, numerous research studies show that statistical models can provide reasonable estimates at predicting faulty modules using software metrics. However, as context-specific metrics differ from project to project, the task of predicting across projects is difficult to achieve. Prediction models obtained from one project experience are ineffective in their ability to predict fault-prone modules when applied to other projects. Hence, taking full benefit of the existing work in software development community has been substantially limited. As a step towards solving this problem, in this dissertation we propose a fault prediction approach that exploits existing prediction models, adapting them to improve their ability to predict faulty system modules across different software projects.

Experiences with an Object-Oriented, Multi-Stage Language

Metaphor is a multi-stage programming language extension to an imperative, object-oriented language in the style of C# or Java. This paper discusses some issues we faced when applying multi-stage language design concepts to an imperative base language and run-time environment. The issues range from dealing with pervasive references and open code to garbage collection and implementing cross-stage persistence.

Improving the Flexibility of Active Grids through Web Services

Active Grids are a form of grid infrastructure where the grid network is active and programmable. These grids directly support applications with value added services such as data migration, compression, adaptation and monitoring. Services such as these are particularly important for eResearch applications which by their very nature are performance critical and data intensive. We propose an architecture for improving the flexibility of Active Grids through web services. These enable Active Grid services to be easily and flexibly configured, monitored and deployed from practically any platform or application. The architecture is called WeSPNI ('Web Services based on Programmable Networks Infrastructure'). We present the architecture together with some early experimental results on using web services to monitor data movement in an active grid.

Testing a framework for the quality of process models: A case study

Process modeling can be regarded as the currently most popular form of conceptual modeling. Research evidence illustrates how process modeling is applied across the different information system life cycle phases for a range of different applications, such as configuration of Enterprise Systems, workflow management, or software development. However, a detailed discussion of critical factors of the quality of process models is still missing. This paper proposes a framework consisting of six quality factors, which is derived from a comprehensive literature review. It then presents in a case study, a utility provider, who had designed various business process models for the selection of an Enterprise System. The paper summarizes potential means of conducting a successful process modeling initiative and evaluates the described modeling approach within the Guidelines of Modeling (GoM) framework. An outlook shows the potential lessons learnt, and concludes with insights to the next phases of this study.

Program Annotations: Feedback for Students Learning to Program

This paper presents a novel program annotation mechanism which enables students to obtain feedback from tutors on their programs in a far simpler and more efficient way than is possible with, for example, email. A common scenario with beginning students is to email tutors with copies of their malfunctioning programs. Unfortunately the emailed program often bears little resemblance to the program the student has been trying to make work; often it is incomplete, a different version and corrupted. We propose an annotation mechanism enabling students to simply and easily annotate their programs with comments asking for help. Similarly our mechanism enables tutors to view students’ programs and to reply to their comments in a simple and structured fashion. This means students can get frequent and timely feedback on their programs; tutors can provide such feedback efficiently, and hence students’ learning is greatly improved.

Work at hand : an exploration of gesture in the context of work and everyday life to inform the design of gestural input devices

This research explores gestures used in the context of activities in the workplace and in everyday life in order to understand requirements and devise concepts for the design of gestural information applicances. A collaborative method of video interaction analysis devised to suit design explorations, the Video Card Game, was used to capture and analyse how gesture is used in the context of six different domains: the dentist's office; PDA and mobile phone use; the experimental biologist's laboratory; a city ferry service; a video cassette player repair shop; and a factory flowmeter assembly station. Findings are presented in the form of gestural themes, derived from the tradition of qualitative analysis but bearing some similarity to Alexandrian patterns. Implications for the design of gestural devices are discussed.

Springboards into design : exploring multiple representations of interaction in a dental surgery

This paper demonstrates that in order to understand and design for interactions in complex work environments, a variety of representational artefacts must be developed and employed. A study was undertaken to explore the design of better interaction technologies to support patient record keeping in a dental surgery. The domain chosen is a challenging real context that exhibits problems that could potentially be solved by ubiquitous computing and multi-modal interaction technologies. Both transient and durable representations were used to develop design understandings. We describe the representations, the kinds of insights developed from the representations and the way that the multiple representations interact and carry forward in the design process.