Metal Artifact Reduction in Sinograms of Dental Computed Tomography

Use of metal objects such as dental implants, fillings, crowns, screws, nails, prosthesis and plates have increased in dentistry over the past 20 years, which raised a need for new methods for reducing the metal artifacts in medical images. Although there are several algorithms for metal artifact reduction, none of these algorithms are efficient enough to recover the original image free of all artifacts. This thesis presents two approaches for reducing metal artifacts through accurate segmentation of metal objects on dental computed tomography images. First approach was based on construction and tilting of a 3D jaw phantom, aiming to obtain fewer metals on each slice. 3D jaw phantom included the main anatomical structures of a jaw, and multiple metal fillings inserted on the teeth. Each jaw slice on the 3D phantom was tilted in order to mimic the (1) nodding movement, and (2) mouth opening/closing. Second approach was to segment the metals on an experimental dataset, consisting of a Cone-Beam Computed Tomography image, by using different segmentation algorithms. K-means clustering, Otsu’s thresholding method and logarithmic enhancement were used for extracting the metals from a real dental CT slice. Once the metal fillings on the jaw phantom were segmented out from the image, they were compensated by gap filling methods; Discrete Cosine Domain Gap Filling and inpainting. Qualitative and quantitative analyses were carried out for evaluating the performance of implemented segmentation methods. Efficiency of tilting alternatives on the segmentation of metal fillings was compared. In conclusion, jaw opening/closing movement between 24º-30º suggested a significant enhancement in segmentation, thus, metal artifact reduction on the jaw phantom. Inpainting method showed a better performance for both simulated and experimental dataset over the DCT domain gap filling method. Moreover, merging the logarithmic enhancement and inpainting showed superior results over other metal artifact reduction alternatives

Optical imaging methods for the study of disease models from the nano to the mesoscale

The visualisation of disease phenotypes allows scientists to study fundamental mechanisms of disease. Optical imaging methods are useful not only to observe anatomical features of biological samples, but also to infer interactions between molecular species using fluorescence labelling. This thesis presents the development of imaging and analysis tools to study biological questions in three models of disease, with samples ranging from the sub-cellular to the organ scale. First, the role of the alpha-synuclein (a-syn) protein, whose dysfunction is a hallmark of Parkinson’s Disease, was studied with respect to vesicle trafficking at the synapse. Synaptic vesicles are ∼40 nm in diameter; imaging vesicles therefore requires methods with resolution below the diffraction limit. Single-molecule localisation microscopy (SMLM), which circumvents the diffraction limit by separating fluorophore emission in time to localise individual molecules in space with ∼20 nm precision, was thus implemented to study a-syn in purified synaptic boutons. A software package was developed to analyse the colocalisation of a-syn with internalised vesicles, and the clustering of a-syn under differing synaptic calcium levels. The colocalisation of a-syn and internalised vesicles was found to be temperature independent, suggesting that a-syn is involved in non-canonical trafficking mechanisms. Ground truth simulations from a synaptosome model were used to benchmark two cluster analysis methods. Both methods applied on the experimental data showed that a-syn becomes less clustered at low synaptic calcium levels. Second, the spatiotemporal association of ESCRT-II, a protein complex whose role in the budding of the human immunodeficiency virus (HIV) was previously considered dispensable, and the HIV polyprotein Gag was studied during viral egress using novel image analysis tools. A nearest-neighbour analysis showed the ESCRT-II protein EAP45 colocalises with Gag similarly to ALIX, a protein well known to be involved in HIV budding. However, upon deletion of EAP45’s N-terminus, its colocalisation with Gag was significantly impaired, highlighting the importance of this EAP45 domain in linking to Gag. Single particle tracking was used to trace the trajectories of EAP45 and Gag in live cells, and an algorithm was developed to visualise the simultaneous motion of two particles; these analyses revealed three types of potential dynamic interaction between EAP45 and Gag. Finally, an open-source instrument to visualise phenotypes from large organs in 3D was developed for the study of chronic obstructive pulmonary disease (COPD) models. The instrument implements Optical Projection Tomography, a technique which can reconstruct cross-sectional slices of a transparent object from its orthographic projections, using off-the- shelf components and novel ImageJ plugins for artefact correction and volume reconstructions. Excised and cleared mouse lungs were imaged in which high order airways can be discerned with 50 μm resolution. The raw lung data, instructions for building the instrument, the free ImageJ plugins, and a detailed software manual are available in an online repository to encourage the widespread use of OPT for imaging large samples.Gates Cambridg