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Our ability to analyze the microstructure of biological tissue in three dimensions (3D) has proven invaluable in modeling its functionality, and therefore providing a better understanding of the basic mechanisms of life. Volumetric imaging of tissue at the cellular level, using serial imaging of consecutive tissue sections, provides such ability to acquire microstructure in 3D. Three-dimensional light microscopy in biology can be broadly classified as using either optical sectioning or physical sectioning. Due to the inherent limitations on the depth resolution in optical sectioning, and the recent introduction of novel techniques, physical sectioning has become the sought-out method to obtain high-resolution volumetric tissue structure data. To meet this demand with increased processing speed in 3D biological imaging, this thesis provides an engineering study and formulation of the tissue sectioning process. The knife-edge scanning microscopy (KESM), a novel physical sectioning and imaging instrument developed in the Brain Networks Laboratory at Texas A&M University, has been used for the purpose of this study. However, the modes of characterizing chatter and its measurement are equally applicable to all current variants of 3D biological microscopy using physical sectioning. We focus on chatter in the physical sectioning process, principally characterizing it by its geometric and optical attributes. Some important nonlinear dynamical models of chatter in the sectioning process, drawn from the metal machining literature, are introduced and compared with observed measurements of chatter in the tissue cutting process. To understand the effects of the embedding polymer on tissue sectioning, we discuss methods to characterize the polymer material and present polymer measurements. Image processing techniques are introduced as a method to abate chatter artifacts in the volumetric data that has already been obtained. Ultra-precise machining techniques, using (1) free-form nanomachining and (2) an oscillating knife, are introduced as potential ways to acquire chatter-free higher-resolution volumetric data in less time. Finally, conclusions of our study and future work conclude the thesis. In this thesis, we conclude that to achieve ultrathin sectioning and high-resolution imaging, embedded plastic should be soft. To overcome the machining defects of soft plastics, we suggested free-form nanomachining and sectioning with an oscillating knife.

Our ability to analyze the microstructure of biological tissue in three dimensions (3D) has proven invaluable in modeling its functionality, and therefore providing a better understanding of the basic mechanisms of life. Volumetric imaging of tissue at the cellular level, using serial imaging of consecutive tissue sections, provides such ability to acquire microstructure in 3D. Three-dimensional light microscopy in biology can be broadly classified as using either optical sectioning or physical sectioning. Due to the inherent limitations on the depth resolution in optical sectioning, and the recent introduction of novel techniques, physical sectioning has become the sought-out method to obtain high-resolution volumetric tissue structure data. To meet this demand with increased processing speed in 3D biological imaging, this thesis provides an engineering study and formulation of the tissue sectioning process. The knife-edge scanning microscopy (KESM), a novel physical sectioning and imaging instrument developed in the Brain Networks Laboratory at Texas A&M University, has been used for the purpose of this study. However, the modes of characterizing chatter and its measurement are equally applicable to all current variants of 3D biological microscopy using physical sectioning. We focus on chatter in the physical sectioning process, principally characterizing it by its geometric and optical attributes. Some important nonlinear dynamical models of chatter in the sectioning process, drawn from the metal machining literature, are introduced and compared with observed measurements of chatter in the tissue cutting process. To understand the effects of the embedding polymer on tissue sectioning, we discuss methods to characterize the polymer material and present polymer measurements. Image processing techniques are introduced as a method to abate chatter artifacts in the volumetric data that has already been obtained. Ultra-precise machining techniques, using (1) free-form nanomachining and (2) an oscillating knife, are introduced as potential ways to acquire chatter-free higher-resolution volumetric data in less time. Finally, conclusions of our study and future work conclude the thesis. In this thesis, we conclude that to achieve ultrathin sectioning and high-resolution imaging, embedded plastic should be soft. To overcome the machining defects of soft plastics, we suggested free-form nanomachining and sectioning with an oscillating knife.

Thesis (M.S.)--Miami University, Dept. of Physics, 2009. / Title from first page of PDF document. Includes bibliographical references (p. 57-61).

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Optical scanning holography (OSH) [1] has the benefit of recording the entire three-dimensional (3-D) volume of a specimen in the form of a two-dimensional (2-D) hologram. Reconstruction of the original volume can be accomplished by applying digital reconstruction or decoding techniques to the recorded hologram. Accurate reconstruction of the 3-D volume and more specifically, the individual 2-D optical sections without artifacts such as out-of-focus haze from adjacent sections has been the focus of much work including algorithms, optical techniques, and combinations of the two. This dissertation presents several different techniques for enhancing the reconstruction of a recorded specimen and its optical sections including the use of optical coding and phase filtering techniques in the traditional OSH optical system. / Ph. D.

This thesis concerns the experimental application of the technique of optical sectioning in the aberration-corrected scanning transmission electron microscope (STEM). Another aim was to perform optical sectioning experiments on the still relatively new scanning confocal electron microscope (SCEM). To test the feasibility of this technique, experiments were performed on a variety of samples to measure the achievable depth response. Deconvolution methods were explored in an attempt to further improve the depth response. Finally, some of the first optical sectioning experiments were performed in the SCEM using both elastic and inelastically scattered electrons. The results showed a clear need to investigate confocal electron microscopy due to the missing cone problem for incoherent imaging in the STEM. This is particularly evident when imaging objects of greater width than the STEM probe. Confocal electron microscopy using inelastic electrons appeared to be a promising imaging mode for the future with this thesis consisting of early work in the field.

Les modèles basés sur la mécanique des milieux continus prévoient généralement une déformation à la rupture plus élevée, ainsi qu'une durée de vie en fluage beaucoup plus longue que les valeurs observées expérimentalement. Cette thèse met en évidence deux aspects de cette problématique en analysant l’endommagement à l'aide de tomographie in situ à rayons X de synchrotron et reconstruction 3D de la structure polycristalline par polissages successifs.L’endommagement en termes de fraction surfacique des cavités a été identifié dans les couches de reconstructions tomographiques perpendiculairement à l’axe de déformation. L'évolution de la fraction surfacique des cavités a été comparée avec le modèle de prédiction de Cocks et Ashby. Ce dernier surestime la durée de vie en fluage et sous-estime l’état de l’endommagement. L'importance de l'hétérogénéité initiale de l’endommagement et l’effet de localisation de l’endommagement est également souligné. L'amplitude de la plus grande fluctuation surfacique augmente de façon parabolique en fonction de la fraction surfacique moyenne.Une méthode de sectionnement sériel améliorée basée sur la profilométrie de surface a été développée. Elle permet la mesure précise de l'épaisseur du matériau enlevée localement. Les analyses ont montré que l'emplacement des cavités par rapport aux joints de grains et l’orientation cristallographique des grains au voisinage est similaire pour les échantillons déformé par différents mécanismes de fluage. La population relative des cavités de fluage présente aux joints de grains simples est supérieure à celle présente aux joints triples. Les cavités trouvées aux joints triples, cependant, sont plus grandes. / Power law creep damage is one of the most intriguing unsolved phenomena of materials science. Models based on continuum mechanics generally predict a much higher strain to failure, as well as a much longer creep lifetime than experimentally observed values. This thesis highlights two aspects of this problematic by analyzing creep damage in copper using in situ synchrotron tomography and 3D reconstruction of the damaged polycrystal structure by serial sectioning.Damage in terms of the area fraction of voids was first identified in slices of tomographic reconstructions of creep deformed copper. The local and global evolution of cavities area fraction was checked against the Cocks and Ashby model and it was found that the model overestimates creep lifetime and underestimates damage development. The importance of the initial damage heterogeneity and the role of damage localization are also emphasized. It was found that the amplitude of the largest damage fluctuation increases parabolically as a function of cavity’s mean area fraction.An improved serial sectioning method based on surface profilometry was developed, which allows the accurate measurement of the removed local material thickness. The 3D reconstructions enabled identifying the creep voids and the grains of the polycrystal. It was shown that with the exception of the void shape, the relationship between void location at a given grain boundary and crystallographic orientation of the neighbor grains is similar in samples deformed by different creep mechanisms. The relative population of creep voids is higher at simple grain boundaries than at triple junctions. Voids found at a triple boundary, however, are larger.

<p>In 2002 an amendment was added to the International Convention for the Safety of Life at Sea (SOLAS) which opened up for shipbuilders to replace steel with lightweight materials in the superstructures. However, SOLAS requires equal fire safety compared to ships with steel superstructures.</p><p> </p><p>LASS-c is a cross-organizational project with the aim to find a method to build cruise ships with part of the superstructure made in lightweight materials. As a part of the LASS-c project the purpose of this thesis has been to develop an application in Java (FISPAT). The tool has been designed to find fire sensitive areas in structures such as cruise vessels. A second aim with the thesis has been to evaluate the cruise ship Norwegian Gem with respect to fire sensitive areas.   </p><p> </p><p>In FISPAT the user can make a model of a structure. The model is built up by rooms, networks and devices. With the model, FISPAT can simulate fire spread and the effects on the networks included in the model. The user can then analyze the results to find fire sensitive parts.</p><p> </p><p>One of the main results in this thesis is the tool itself together with this report which also serves as a manual to FISPAT. An evaluation of Norwegian Gem was also made which points to some critical parts of the ship. One example is the main water supply pipe to the sprinklers which has no redundant systems and all sectioning valves are manually operated, hence it is vulnerable to faults. The electrical feed to the three pump units is also a vulnerable point on the vessel. The pumps have redundant electrical networks, but the wires are drawn on the same paths, making it possible to take out both systems with one fire.</p>

In 2002 an amendment was added to the International Convention for the Safety of Life at Sea (SOLAS) which opened up for shipbuilders to replace steel with lightweight materials in the superstructures. However, SOLAS requires equal fire safety compared to ships with steel superstructures.   LASS-c is a cross-organizational project with the aim to find a method to build cruise ships with part of the superstructure made in lightweight materials. As a part of the LASS-c project the purpose of this thesis has been to develop an application in Java (FISPAT). The tool has been designed to find fire sensitive areas in structures such as cruise vessels. A second aim with the thesis has been to evaluate the cruise ship Norwegian Gem with respect to fire sensitive areas.      In FISPAT the user can make a model of a structure. The model is built up by rooms, networks and devices. With the model, FISPAT can simulate fire spread and the effects on the networks included in the model. The user can then analyze the results to find fire sensitive parts.   One of the main results in this thesis is the tool itself together with this report which also serves as a manual to FISPAT. An evaluation of Norwegian Gem was also made which points to some critical parts of the ship. One example is the main water supply pipe to the sprinklers which has no redundant systems and all sectioning valves are manually operated, hence it is vulnerable to faults. The electrical feed to the three pump units is also a vulnerable point on the vessel. The pumps have redundant electrical networks, but the wires are drawn on the same paths, making it possible to take out both systems with one fire.