Interventional magnetic resonance imaging (iMRI) is being increasingly used for performing imageguided neurosurgical procedures. Intermittent imaging through iMRI can help a neurosurgeon visualise the target and eloquent brain areas during neurosurgery and lead to better patient outcome. MRI plays an important role in planning and performing neurosurgical procedures because it can provide highresolution anatomical images that can be used to discriminate between healthy and diseased tissue, as well as identify location and extent of functional areas. This is of significant clinical utility as it helps the surgeons maximise target resection and avoid damage to functionally important brain areas. There is clinical interest in propagating the pre-operative surgical information to the intra-operative image space as this allows the surgeons to utilise the pre-operatively generated surgical plans during surgery. The current state of the art neuronavigation systems achieve this by performing rigid registration of pre-operative and intra-operative images. As the brain undergoes non-linear deformations after craniotomy (brain shift), the rigidly registered pre-operative images do not accurately align anymore with the intra-operative images acquired during surgery. This limits the accuracy of these neuronavigation systems and hampers the surgeon’s ability to perform more aggressive interventions. In addition, intra-operative images are typically of lower quality with susceptibility artefacts inducing severe geometric and intensity distortions around areas of resection in echo planar MRI images, significantly reducing their utility in the intraoperative setting. This thesis focuses on development of novel methods for an image processing workflow that aims to maximise the utility of iMRI in neurosurgery. I present a fast, non-rigid registration algorithm that can leverage information from both structural and diffusion weighted MRI images to localise target lesions and a critical white matter tract, the optic radiation, during surgical management of temporal lobe epilepsy. A novel method for correcting susceptibility artefacts in echo planar MRI images is also developed, which combines fieldmap and image registration based correction techniques. The work developed in this thesis has been validated and successfully integrated into the surgical workflow at the National Hospital for Neurology and Neurosurgery in London and is being clinically used to inform surgical decisions.

Systemic lupus erythematosus (SLE) carries a significantly enhanced risk of developing cardiovascular disease (CVD) and remains a leading cause of death in these patients, accounting for ~25% of all causes of mortality. Although there is clear evidence li nking accelerated atherosclerosis to SLE (and consequently an increase in cardiovascular events), another factor that may contribute to CVD related morbidity and mortality is reperfusion injury that occurs post - ischaemia. This is termed ischaemic / reperfu sion (I/R) injury and is a known important contributor to the size of the eventual infarct in the heart, which in animal studies has been shown to account for up to 40 - 50% of the final infarct size. Hydroxychloroquine (HCQ), originally an anti - malarial dr ug, is now used to treat autoimmune disorders, including SLE. HCQ has been shown to modulate inflammation in rheumatic diseases such as SLE and rheumatoid arthritis as well as have potential cardiovascular benefits in these patients. One of the keys aims o f this thesis was to explore the potential use of HCQ in reducing cardiac I/R injury. HCQ was found to be cardioprotective in an in vitro neonatal cardiomyocytes simulated I/R injury model as well as in an in vivo cardiac I/R injury model. This was found to be through an ERK - dependent mechanism which was blocked in the presence of the ERK inhibitor U0126 both in vitro and in vivo . Another relevant question addressed in this thesis was if I/R injury is enhanced in lupus. There is evidence from an autoimmune prone mouse model that lupus IgG are pathogenic in mesenteric I/R injury . However, no study as yet has investigated human lupus IgG in a heart model. IgG was purified from the serum of SLE patients (aPL +ve vs aP L – ve), antiphospholipid syndrome (APS) patients, juvenile onset SLE (JSLE) patients and healthy volunteers. The pre - treatment of neonatal rat cardiomyocytes with IgG from all 3 patient groups enhanced simulated I/R injury. However, the most pathogenic wer e those who were aPL positive. Interestingly, JSLE patients who were all aPL negative, enhanced I/R injury to similar levels as those who tested positive in the adult patient cohort. An enhanced p38 MAPK phosphorylation was observed in the presence of aPL positive IgG and this pathogenic effect was blocked in the presence of the p38 inhibitor SB23580. The results ob tained in this thesis have identified a potential role for HCQ in the cardiovascular field as a cardioprotective therapeutic in myocardial I/R injury. Additionally , IgG purified from patients with SLE , APS and JSLE have been shown to accelerate myocardial I/R injury.

Multispectral imaging is a method for acquiring image data over a series of wavelengths across the light spectrum. In combination with several image processing methods, it has become a valuable tool for the enhancement and recovery of information from cultural heritage documents. It enables the identification of distinct physical characteristics of the document and its material components by measuring their interaction with light. In this dissertation I describe an approach to evaluate multispectral imaging processing methods in the context of cultural heritage documents. I begin by framing a digital model, or phantom, of multispectral images of a document composed of interacting layers of text and other materials. Further, I apply a series of image processing methods to the phantom in order to extract and separate those interacting layers and I qualitatively assess the results of each of those methods. I proceed then to propose and apply a quantitative method, based on mutual information, to evaluate the efficacy of those image processing methods. Next, I describe the administration of a series of treatments that degrade the writing or otherwise degrade samples from a real document, and the acquisition of multispectral images from those samples. Finally, I report on the recovery of information via image processing of the acquired experimental data. The results of the image processing of the experimental data are then quantitatively evaluated using the proposed method, and qualitatively described. As multispectral imaging in combination with image processing methods become increasingly used in cultural heritage documents, we need a deeper understanding of how these methods perform in the analysis of this particular data. I contribute to this understanding in two important ways: I introduce a formal methodology to study the methods involved in processing and analysing the multispectral data, and provide a framework to continue testing and developing new methods.

Streptococcus pneumoniae is an important respiratory pathogen and a leading cause of community-acquired pneumonia. As well as invasive disease S. pneumoniae also colonises the nasopharynx. Colonisation with S. pneumoniae is nearly universal in infants, dropping to 10% in adulthood. This frequent exposure has potential for developing and boosting natural adaptive immune responses. However naturally-acquired immune responses that protect against subsequent lung infection with S. pneumoniae are not fully understood. This thesis investigates the targets and function of naturally-acquired IgG to S. pneumoniae in humans and additionally the mechanisms of protection from lung infection following experimental colonisation in mice. The target and function of naturally-acquired IgG in human sera and pooled intravenous immunoglobulin (IVIG) preparations was assessed. IVIG, pooled from >1000 adult donors provides a tool to investigate the natural antibody responses to S. pneumoniae within a population. Data indicate that naturally-acquired human IgG predominantly binds to non-capsular antigens on the surface of S. pneumoniae and can target surface exposed protein antigens. In vitro assays indicate that antibodies to non-capsular targets may be functional, enhancing phagocytosis and killing of S. pneumoniae. In vivo human IgG protected against lung infection. Cellular depletion demonstrated that protection within the lung required neutrophils and clearance of S. pneumoniae from the blood required macrophages. A model of lung infection in the absence of bacteraemia using S. pneumoniae strain EF3030 was developed. This model allowed assessment of the immune responses to S. pneumoniae colonisation of the nasopharynx that protect against re-infection specifically within the lung. Prior nasal colonisation with S. pneumoniae EF3030 was protective against subsequent lung infection. Cellular depletion strategies and challenge in antibody-deficient mice demonstrated that protection against lung infection required the development of both humoral and cell-mediated immunity.

The objectives of this study were to compare different culture conditions and methods used to assess preimplantation embryos. Both invasive and non-invasive markers including the blastocyst formation rate, DNA damage and aneuploidy were investigated. The first aim was to study the relationship between the metabolic profile and embryo development, morphology and aneuploidy in human embryos. The amino acid profile of 15 frozen-thawed human embryos was analysed by HPLC and the turnover of certain amino acid was significantly correlated to their developmental potential. However no relation was found between embryo morphology and its amino acid profile. The second aim was to compare murine in vitro cultured blastocysts to in vivo developed blastocysts for aneuploidy and DNA fragmentation. Two-cell stage embryos were cultured in vitro until the blastocyst stage. In vivo embryos were obtained on day 2 and day 5 following superovulation without further in vitro culture. DNA fragmentation and mosaicism increased with embryo development with higher rates for in vitro developed blastocysts compared to in vivo. The third aim was to evaluate the use of the morphokinetic parameters of EmbryoScope™ as predictors of embryo development, DNA fragmentation, aneuploidy and to assesses the effect of GM-CSF. Two-cell stage embryos were cultured until the blastocyst stage in the Embryoscope™ with and without GM-CSF. No progress in the growth rate of the GM-CSF cultured embryos was recorded. The detailed analysis of the lengths of early cleavages was informative in defining developmental potential but with no relationship with the rate of mosaicism and DNA fragmentation. The relationship between embryo viability, development, DNA fragmentation and chromosomal status is clearly complex as embryos with good morphology may reach the blastocyst stage but be chromosomally abnormal or with high DNA fragmentation. Embryo selection should be established on more than one criterion permitting the selection and transfer of one embryo with the highest implantation potential.

Emission tomographic imaging is framed in the Bayesian and information theoretic framework. The first part of the thesis is inspired by the new possibilities offered by PET-MR systems, formulating models and algorithms for 4-D tomography and for the integration of information from multiple imaging modalities. The second part of the thesis extends the models described in the first part, focusing on the imaging hardware. Three key aspects for the design of new imaging systems are investigated: criteria and efficient algorithms for the optimisation and real-time adaptation of the parameters of the imaging hardware; learning the characteristics of the imaging hardware; exploiting the rich information provided by depthof- interaction (DOI) and energy resolving devices. The document concludes with the description of the NiftyRec software toolkit, developed to enable 4-D multi-modal tomographic inference.

This thesis investigated the ultrasound assessment of the endometrial-myometrial junction (EMJ) and its clinical relevance to the uterine diseases, adenomyosis and endometrial cancer. The inter- and intraobserver variability in the classification of EMJ visualisation using three-dimensional ultrasound was assessed and a high level of agreement was found. Endometrial thickness and parity were found to be significantly associated with the quality of EMJ visualisation. Seven recognised ultrasound features of adenomyosis, including an irregular endometrial-myometrial junction, were investigated for their role in the ultrasound diagnosis of adenomyosis. The other features were an asymmetrically thickened myometrium, parallel shadowing, linear striations, myometrial cysts, hyperechoic lesions and adenomyomas. The presence of any of these features was considered diagnostic of adenomyosis. The inter- and intraobserver variability of ultrasound diagnosis of adenomyosis was also investigated and a good level of agreement was found. This was the case when real-time ultrasound assessments were compared with assessments made from stored uterine volumes, as well as when both assessments were made from stored volumes. Transvaginal ultrasound was used to assess the prevalence of adenomyosis in women attending a general gynaecology clinic in a large prospective observational study. Women were considered to have adenomyosis if one or more ultrasound feature of adenomyosis was found. Using this criterion, the prevalence was estimated to be 20.9% with 7.6% of women being excluded from the data analysis. It was also found that age, gravidity and pelvic endometriosis were all significantly associated with the presence of adenomyosis. Menorrhagia was evaluated in order to assess if it was associated with adenomyosis. Multivariable analysis revealed that while adenomyosis was not significantly associated with menorrhagia when assessed as a binary outcome, when severity of disease was taken into account, there was a significant association. A similar analysis found that adenomyosis was significantly associated with dysmenorrhoea. A second-stage ultrasound test that incorporated assessment of the EMJ was investigated for its use in the diagnosis of endometrial cancer in women presenting with post-menopausal bleeding. It was found to significantly increase the specificity of ultrasound in the diagnosis of endometrial cancer while having a minimal impact on sensitivity.

Quantitative MRI offers the possibility to produce objective measurements of tissue physiology at different scales. Such measurements are highly valuable in applications such as drug development, treatment monitoring or early diagnosis of cancer. From microstructural information in diffusion weighted imaging (DWI) or local perfusion and permeability in dynamic contrast (DCE-) MRI to more macroscopic observations of the local intestinal contraction, a number of aspects of quantitative MRI are considered in this thesis. The main objective of the presented work is to provide pre-processing techniques and model modification in order to improve the reliability of image analysis in quantitative MRI. Firstly, the challenge of clinical DWI signal modelling is investigated to overcome the biasing effect due to noise in the data. Several methods with increasing level of complexity are applied to simulations and a series of clinical datasets. Secondly, a novel Robust Data Decomposition Registration technique is introduced to tackle the problem of image registration in DCE-MRI. The technique allows the separation of tissue enhancement from motion effects so that the latter can be corrected independently. It is successfully applied to DCE-MRI datasets of different organs. This application is extended to the correction of respiratory motion in small bowel motility quantification in dynamic MRI data acquired during free breathing. Finally, a new local model for the arterial input function (AIF) is proposed. The estimation of the arterial blood contrast agent concentration in DCE-MRI is augmented using prior knowledge on local tissue structure from DWI. This work explores several types of imaging using MRI. It contributes to clinical quantitative MRI analysis providing practical solutions aimed at improving the accuracy and consistency of the parameters derived from image data.

Photoacoustic tomography (PAT) is showing its potential as a non-invasive biomedical imaging modality, and interest in the field is growing rapidly. The images possess excellent contrast, high spatial resolution and good specificity, however, they are largely qualitative and not directly representative of the optically absorbing structures of interest. Quantitative PAT (QPAT) aims to determine quantitatively accurate spatial maps of the underlying tissue chromophores, in order to obtain highly-resolved images of functional information such as blood oxygen saturation and haemoglobin concentration. PAT images are inherently three-dimensional (3D), and their high resolution means that the data sets are of an extremely large scale; a typical problem can easily possess 10⁷ unknowns. Existing methods for QPAT have failed to address their applicability to real, 3D PAT images, either by making restrictive approximations to the light model or by using computational intensive techniques which are impractical for large-scale data sets. This thesis develops a practical inversion method for the full and general QPAT problem, in which the tissue geometry is arbitrary, the optical coefficients are unknown and the data is large-scale. The accuracy of the inversion method is ensured by use of the radiative transfer equation (RTE), which provides a highly accurate description of the propagation of light within biological tissue. Using the RTE, a thorough investigation into the effects of errors in the scattering coefficient on the reconstructed absorption coefficient is performed. Computational efficiency in the inversion is provided through an adjoint-assisted, gradient-based minimisation scheme, which iteratively adjusts the parameters of interest until the model prediction matches the measured data. Since the RTE proves too computationally intensive for large data sets, an extension to 3D simulated data is facilitated by the incorporation of the δ-Eddington approximation, thereby providing an accurate, efficient inversion method for QPAT that may be readily applied to experimental data.

Subsets of morbidly obese patients do not appear to exhibit the expected comorbidities, as well as the fact that heightened sympathetic nervous system (SNS) activity has been known to affect metabolism. In this study, Neuropeptide Y (NPY), an SNS co-transmitter is explored as a possible biomarker for unhealthy obesity. The aims of the study were to identify a normoinsulinemic/insulin sensitive morbidly obese Caucasian patient cohort, compare differences in NPY levels in the circulation and adipose tissue between the normoinsulinemic and hyperinsulinemic subjects. I explored the hypothesis that elevated circulating peripheral NPY causes metabolic abnormalities by mediating changes in the normal function of brain stem regulatory mechanisms via inflammation of astrocytes as shown in an in vitro model of primary cell line of human fetal brain stem astrocyte cell line. Blood and abdominal adipose tissue samples were obtained from consenting, morbidly obese patients awaiting bariatric surgery for recruitment in the study. Adipokines and NPY were measured as well as gene and protein expression by real-time PCR and histology. Effect of NPY was determined on a human brainstem astrocytic primary cell-line using immunohistochemistry, real time PCR, cytokine ELISA, intracellular secondary messengers via ELISA and fluorescence microscopy. Secreted lactate levels were measured by calorimetric assays. Differences were found between metabolically healthy obese (MHO) and pathologically obese (PO)/diabetic groups in certain adipokines and insulin sensitivity, which were maintained after surgical weight loss. Differences in adipocyte cell size were visible between the two groups both in subcutaneous and omental adipose tissue depots but inflammatory cell infiltration was not different. Brain stem astrocytes expressed NPY receptors and IL-6 secretion from the astrocytes increased when exposed to a combination of NPY and noradrenaline, reflected by changes in intracellular cAMP. Cytokine array showed increases in various inflammatory cytokines under the same treatment. IL-6 treatment increased astrocyte lactate levels. In astrocytes there was greater level of adrenergic signalling and secretion of IL-6 and lactate by the cells, which could mean different metabolic balance of astrocytes and long-term effects on astrocyte chemosensing function. These findings suggest differences in susceptibility to obesity associated pathologies linked to a synergistic modulation between the intracellular signalling pathways of astrocytes, being regulated at least partially by components of the CNS and having a direct effect on the cells. Perhaps these would pave the way for targeted treatment modalities. In vivo studies in an analogous animal model would further clarify the connection between elevated peripheral NPY and its central effects on the brainstem astrocytes in mediating metabolic disease.