Segmentation of micro-CT Scans of Biomaterials and steps towards their Join Reconstruction and Segmentation

The delivery of vaccines through oral administration is becoming popular, due to the low cost, the convenient distribution as well as the unnecessary contact between the health provider and the patient. Toxoids are used as vaccines, but here, we note that after vaccination, an immunological response is formed against the molecular markers of the toxoid without resulting in toxin-induced illness. Such preparation is also known as an anatoxin. In this study, we worked with Diphtheria anatoxin (DT) and Tetanus anatoxin (TT). Due to the harsh environment of the gastrointestinal tract, the immunological response is difficult to be achieved from the anatoxins. A promising adjuvant, i.e toxoid carrier, for the oral delivery of vaccines is the Santa Barbara Amorphous-15 (SBA-15). The key feature of SBA-15 effectiveness is the determination of the anatoxin agglomeration in the carrier, which constitutes the central interest of this work. X-ray micro-CT data were acquired to determine the way that different morphologies of SBA-15 affect the incorporation. The analysis of the data was performed using Analytical Reconstruction Techniques (ANRT) and Iterative Segmentation Techniques (IST). The thesis is separated into two parts. The first half is centered on a series of implementations for computing solutions to discretized inverse problems. The area of application is the territory of Computed Tomography (CT). Iterative Reconstruction Techniques (IRT) were studied, derived from the Kaczmarz iterative solver. IRT are responsible for the restoration and reconstruction of the obtained signals, and often provide better results compared to ANRT. Segmentation techniques, which are the cornerstone of the analysis of the samples, will be discussed subsequently. The chosen IST were built from spatial regularisation and K-means clustering. The second part focuses on IST that were employed to extract information about the agglomeration of the anatoxins inside the hierarchical structure