Developing Methods and Tools for Three-Dimensional Computational Reconstructions in X-ray and Visible Light Microscopy
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- Institutt for fysikk 
In this thesis possibilities for further developments in microscopy have been explored. This was done through two sub-projects: The first project was on small-angle X-ray (SAXS) tomography, and the second revolved around optical microscopy combined with computations. Both projects make use of numerical methods to computationally reconstruct sample properties in three dimensions. Even though the projects are concerned with different ranges of the electromagnetic spectrum, they both have relevance for X-ray microscopy. In the project on SAXS tomography it was investigated if the orientation distribution of talc particles in a sample of injection molded isotactic poly-propylene could be retrieved by using the scattering patterns from tomography experiments. In traditional computational tomography (CT) attenuation contrast can be used to reconstruct the attenuation properties of a sample. New synchrotron and detector technologies have made it possible to observe scattering contrast from sub-micron scale objects. Currently no method exists to retrieve the spatially varying three-dimensional orientation distribution of these objects if the scattering contrast depend on their orientation, without physically cutting the sample. To retrieve the orientation distribution of the talc particles the numerical method of simulated annealing was used. By utilising prior knowledge of the sample and the scattering patterns, various alterations of the energy function have been investigated as possibilities to improve the results. The main features of the orientation distribution were obtained, with some of the finer details that have previously been observed in experiments on a physically cut sample. This shows great promise for further studies on SAXS tomography, and the results achieved in this thesis will be published. In the other sub-project, dealing with light microscopy, a varied-illumination microscope to be used as a research and educational tool, was constructed. Developments of new advanced techniques in microscopy often make demands of increasingly complex and expensive high-quality equipment. In X-ray microscopy this often means the experiments have to be carried out at large synchrotrons, where higher brilliance and coherence can be achieved. Recent developments in visible light microscopy have shown that it is possible to create a small microscope with a wide range of imaging capabilities, by replacing the conventional back light illumination scheme with a programmable LED array, combined with computer based image processing, post exposure. Of particular interest is its ability of Fourier Ptychography, which is an adaptation of Ptychography which is increasingly used with X-ray microscopes. Our microscope is demonstrated to be able to form bright and dark field images, by post processing on the same data set. By utilising the variable-illumination features of the microscope, images deliberately taken out of focus have successfully been digitally refocused by computational reconstructions. The microscope offers highly versatile hardware and software, with already planned future projects on Fourier Ptychography and three-dimensional surface reconstruction of polymer micro-beads during mechanical compression in mind.