Tomography in soft X-ray microscopy is an emerging technique for obtaining quantitative 3D structural information about cells. One of its strengths, compared with other techniques, is that it can image intact cells in their near-native state at a few 10 nm’s resolution, without staining. However, the methods for reconstructing 3D-data rely on algorithms that assume projection data, which the images are generally not due to the imaging systems’ limited depth of focus. To bring out the full potential of tomography in soft X-ray microscopy an improved understanding of the image formation is desired. This Thesis reviews zone plate-based X-ray microscopy for biological imaging and the theory necessary for a numerical implementation of a 3D image formation model. Furthermore, a novel reconstruction approach is proposed that improves the overall resolution in a reconstruction of a tomographically imaged object. This is demonstrated by simulations and experiments. Finally, this Thesis covers work on the Stockholm X-ray microscope, including an upgrade of the X-ray source yielding unprecedented brightness for a compact system. With this upgrade it was possible to do high-quality imaging of cells in their near-native state with only 10 second exposures. / Tomografi i mjukröntgenmikroskopi är en ny teknik för att få ut kvantitativ strukturell 3D information om celler. Dess styrka jämfört med andra tekniker är att den kan avbilda intakta celler i deras nära naturliga tillstånd med ett par 10 nm upplösning, utan omfattande preparering. Dock är metoderna för att rekonstruera 3D-data beroende av algoritmer som antar projektionsdata, vilket bilderna i allmänhet inte är på grund av avbildningsystemens begränsade skärpedjup. För att få ut den fulla potentialen av tomografi i röntgenmikroskopi behövs en ökad förståelse för avbildningsprocessen. Denna avhandling behandlar zonplatte-baserad röntgenmikroskopi för biologisk avbildning och den nödvändiga teorin för en numerisk implementering av en avbildningsmodell i 3D. En ny rekonstruktionsmetod föreslås som förbättrar upplösningen i rekonstruktionen för ett tomografiskt avbildat objekt. Detta visas i simuleringar och experiment. Slutligen omfattar denna avhandling arbete på Stockholms mjukröntgenmikroskop, inklusive en uppgradering av röntgenkällan som ger oöverträffad ljusstyrka för ett kompakt system. Denna uppgradering möjliggör högkvalitativ avbildning av celler i deras nästan naturliga tillstånd med endast 10 sekunders exponering. / <p>QC 20160324</p>

This master’s thesis develops a novel method of digital holography, from recent studies known as Fresnel Incoherent Correlation Holography (FINCH). The method enables the reconstruction of the correlation records of three-dimensional objects, captured under quasi-monochromatic, incoherent illumination. The experimental system is based on an action of a Spatial Light Modulator, driven by computer generated holograms to create mutually correlated beams. Both optical and digital parts of the experiment can be carried out using procedures of classical holography, diffractive optics and digital holography. As an important theoretical result of the master’s thesis, a new computational model was proposed, which allows to describe the experiment completely with respect to its two basic phases. The proposed model allows to understood the method intuitively and can be used additionally for analysis and interpretation of the imaging parameters and the system optimalization. The theoretical part of the master’s thesis also presents a detailed description of the correlation imaging based on an appropriate reconstruction process. Computational models were developed for both monochromatic and quasi-monochromatic illumination. In experimental part, all theoretical results were verified. The imaging parameters were examined using standard resolution target tests and appropriate biological samples. As an original experimental result, spiral modification of the system resulting in a vortex imaging was proposed and realized. Here, a selective edge enhancement of three-dimensional objects is possible, resulting in a significant extension of possible applications of the method.