Digital pathology has the potential to transform the practice of histopathology, but there are significant barriers to the full clinical adoption of the technology. Amongst these the inefficiency of virtual slides is a particularly important factor, one which has been largely overlooked by the digital pathology community. Previous work by the author has shown that diagnostic tasks take significantly longer with virtual slides than with the microscope (on average 67% longer). This has a serious negative impact on pathologists' acceptance of the technology, the cost-benefit ratio of clinical adoption, and the willingness of pathologists to undertake large scale evaluations and validation studies of digital pathology. The inefficiency of virtual slides is caused by the inferior performance of current digital pathology software compared to the microscope. In this thesis, a comprehensive and methodical approach to designing and evaluating a better digital pathology workstation is described. In chapter 2, detailed and systematic study of the work done in the pathologist's office and the use of the microscope is described. From this, a list of requirements for a digital pathology workstation is generated. In chapter 3, these requirements are summarised and designs for an optimum digital pathology workstation are presented. In chapter 4, several prototype digital pathology workstations are evaluated experimentally. These prototypes focus on the single most significant improvement that can be made to the workstation to better support the work of the pathologist - increasing the resolution of the display and the speed of image delivery. Experimental comparison of these prototypes against the microscope is carried out to measure their performance and identify areas for improvement. After an iterative process of evaluation and development, an evaluation of the final digital pathology workstation prototype shows equivalent performance to the microscope in both diagnostic areas evaluated. Several areas for further improvement and future work are described.

Salmonella enterica subspecies enterica can infect both humans and animals alike, with the most common route being the ingestion of food/water/faecal matter contaminated with Salmonella bacterium. As Salmonella can comfortably survive and replicate within the intestinal tracts of all domestic meat producing animals it is important to control the Salmonella prevalence in such animals and to ensure they are slaughtered and processed in a correct safe and hygienic fashion. This, in turn, should limit the possible contamination of the final meat product. This thesis attempts to assess the prevalence and diversity of Salmonella serovars within pork and pigs slaughtered in Northern Ireland. This study of abattoir pigs and pork conducted between January 2006 and July 2007 determined Salmonella Typhimurium (41) and Salmonella Rissen (29) as the most prevalent Salmonella enterica serovar within the NI pig population. Salmonella serovars Derby, Panama, Orion, Dublin and Meleagridis were also isolated throughout the sampling period. S Typhimurium phage typing analysis identified six distinctive types within the 41 S Typhimurium consisting of phage types; DTl93, DTI04, U288, DT104b, DT120, DTIIO and one S Typhimurium that proved to be untypable. Overall 85.4% of all S Typhimurium were classified as multidrug resistant while Xba1-PFGE analysis subdivided select S. Typhimurium into three distinct clusters. Antibiotic resistance was established to be low amongst S Rissen with all 29 isolates displaying resistance to tetracycline. A combination of XbaI -PFGE and plasmid profiling subdivided the 29 S Rissen into three distinct genotypes. The characteristics of S Typhimurium and S Rissen were investigated by both adhesion and invasion assays while the effect of environmental stresses (temperature, pH, high osmolarity and starvation) had on antibiotic resistance was assessed for three clinical important antibiotics (tetracycline, streptomycin and trimethoprim/sulfamethoxazole). The adhesion and invasion assays concluded that although S. Rissen adhered to Caco-2 tissue culture cells in greater 11lU11bers that S. Typhimurium DTI04 invasion was significantly lower. The environmental stress analysis identified starvation as the stress factor that had the greatest effect on the susceptibility to the three test antibiotics and that of three antibiotics tested the effectiveness of streptomycin was most reduced when applied to the environmentally stressed test Salmonella.

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