Open-source virtual bronchoscopy for image guided navigation

This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance.

Thomas Davis's education policies: theory and practice

This thesis explores the education policies of Thomas Davis. On the eve of the Great Famine Ireland was economically impoverished and politically dependent. The Irish people had a subservient mentality, were mainly uneducated and were unaware of their potential. He believed that education would develop a self-reliant, self-sufficient people; it would create a new generation of leaders and citizens necessary to transform Ireland into a prosperous, independent nation. This thesis explores his education philosophy which was political in orientation; he called for reform of university education so that it would educate leaders who were knowledgeable, patriotic and responsible. He formulated a curriculum which consisted of knowledge that would have direct use and application in public life; his curriculum included moral philosophy, oratory, philological studies and history. His contribution to the debate on the Queens Colleges bill, 1845, is explored including his public disagreement with Daniel O’Connell on the principle of multi-denominational education. This work also examines his policies on learning methodologies and teaching methods. It provides details of his thoughts on learning by experience, by observation, book learning and learning in the home. It focuses on the deficiencies evident in the system of teaching and learning that operated in Trinity College Dublin and it provides an analysis of his preferred method of instruction: Lyceum teaching. This thesis also explores his national curriculum in history and Irish culture which was designed to forge a sense of national identity, to win support for repeal and to develop the principle of nationality. He formulated a national curriculum to counteract the absence of national knowledge in the state schools, to provide the people with a positive self-image and ultimately to empower them to reclaim Ireland and to develop it. Davis knew the power of education and he used it as an instrument of political and social change.

The examination of the traditional femininity and women’s lives in ancient China

This thesis explores the evolution of the concept of traditional Chinese femininity in relation to women’s lives in ancient China (221 BCE – A.D.1840). It proposes that the traditional Chinese femininity had been trying to seek a balance between the permanent principles and contingency plans for the stability and development of the society, which caused women’s humiliation and freedom. In reality, politicians and thinkers in ancient China had been transforming the concept of femininity itself to make it more adaptable to the social conditions of that time. This may be discussed in terms of three aspects. Firstly, the traditional concept of Chinese human relationships, including the ethical order, always emphasised the influence of individual behaviour on others and the overall stability and linked development of family, society and nation. Thus, both men and women, must be placed within this interrelated, interacting and cooperating relationship. Secondly, the association of family and country created an overlap of family and public affairs, which, objectively, facilitated the movement of women from the inner to the public arena. Thirdly, the notions of political and ethical morality and of men’s virtues and women’s virtues were integrated because of the union of family and nation. Therefore, typically virtuous women could be a source of encouragement for men and, furthermore, men formulated their virtues in the public space by formulating women’s virtues in the private space. The shaping of the gender image and concept of women in ancient China reflected the country’s changing cultural and gender norms. Chinese femininity and lifestyles, like Chinese history, were a continuous presence in the society but were also constantly changing. Through this study, it could be noted that Chinese women were not hidden and that their subjectivity and the concepts motivating them were not merely devised by a male-dominated society and culture.

Beyond simple imaging with energetic beams – nanopatterning, correlative microscopy and statistical analysis of inclusions

Electron microscopy (EM) has advanced in an exponential way since the first transmission electron microscope (TEM) was built in the 1930’s. The urge to ‘see’ things is an essential part of human nature (talk of ‘seeing is believing’) and apart from scanning tunnel microscopes which give information about the surface, EM is the only imaging technology capable of really visualising atomic structures in depth down to single atoms. With the development of nanotechnology the demand to image and analyse small things has become even greater and electron microscopes have found their way from highly delicate and sophisticated research grade instruments to key-turn and even bench-top instruments for everyday use in every materials research lab on the planet. The semiconductor industry is as dependent on the use of EM as life sciences and pharmaceutical industry. With this generalisation of use for imaging, the need to deploy advanced uses of EM has become more and more apparent. The combination of several coinciding beams (electron, ion and even light) to create DualBeam or TripleBeam instruments for instance enhances the usefulness from pure imaging to manipulating on the nanoscale. And when it comes to the analytic power of EM with the many ways the highly energetic electrons and ions interact with the matter in the specimen there is a plethora of niches which evolved during the last two decades, specialising in every kind of analysis that can be thought of and combined with EM. In the course of this study the emphasis was placed on the application of these advanced analytical EM techniques in the context of multiscale and multimodal microscopy – multiscale meaning across length scales from micrometres or larger to nanometres, multimodal meaning numerous techniques applied to the same sample volume in a correlative manner. In order to demonstrate the breadth and potential of the multiscale and multimodal concept an integration of it was attempted in two areas: I) Biocompatible materials using polycrystalline stainless steel and II) Semiconductors using thin multiferroic films. I) The motivation to use stainless steel (316L medical grade) comes from the potential modulation of endothelial cell growth which can have a big impact on the improvement of cardio-vascular stents – which are mainly made of 316L – through nano-texturing of the stent surface by focused ion beam (FIB) lithography. Patterning with FIB has never been reported before in connection with stents and cell growth and in order to gain a better understanding of the beam-substrate interaction during patterning a correlative microscopy approach was used to illuminate the patterning process from many possible angles. Electron backscattering diffraction (EBSD) was used to analyse the crystallographic structure, FIB was used for the patterning and simultaneously visualising the crystal structure as part of the monitoring process, scanning electron microscopy (SEM) and atomic force microscopy (AFM) were employed to analyse the topography and the final step being 3D visualisation through serial FIB/SEM sectioning. II) The motivation for the use of thin multiferroic films stems from the ever-growing demand for increased data storage at lesser and lesser energy consumption. The Aurivillius phase material used in this study has a high potential in this area. Yet it is necessary to show clearly that the film is really multiferroic and no second phase inclusions are present even at very low concentrations – ~0.1vol% could already be problematic. Thus, in this study a technique was developed to analyse ultra-low density inclusions in thin multiferroic films down to concentrations of 0.01%. The goal achieved was a complete structural and compositional analysis of the films which required identification of second phase inclusions (through elemental analysis EDX(Energy Dispersive X-ray)), localise them (employing 72 hour EDX mapping in the SEM), isolate them for the TEM (using FIB) and give an upper confidence limit of 99.5% to the influence of the inclusions on the magnetic behaviour of the main phase (statistical analysis).