Quantitative lung CT analysis for the study and diagnosis of Chronic Obstructive Pulmonary Disease

The importance of medical imaging in the research of Chronic Obstructive Pulmonary Dis- ease (COPD) has risen over the last decades. COPD affects the pulmonary system through two competing mechanisms; emphysema and small airways disease. The relative contribu- tion of each component varies widely across patients whilst they can also evolve regionally in the lung. Patients can also be susceptible to exacerbations, which can dramatically ac- celerate lung function decline. Diagnosis of COPD is based on lung function tests, which measure airflow limitation. There is a growing consensus that this is inadequate in view of the complexities of COPD. Computed Tomography (CT) facilitates direct quantification of the pathological changes that lead to airflow limitation and can add to our understanding of the disease progression of COPD. There is a need to better capture lung pathophysiology whilst understanding regional aspects of disease progression. This has motivated the work presented in this thesis. Two novel methods are proposed to quantify the severity of COPD from CT by analysing the global distribution of features sampled locally in the lung. They can be exploited in the classification of lung CT images or to uncover potential trajectories of disease progression. A novel lobe segmentation algorithm is presented that is based on a probabilistic segmen- tation of the fissures whilst also constructing a groupwise fissure prior. In combination with the local sampling methods, a pipeline of analysis was developed that permits a re- gional analysis of lung disease. This was applied to study exacerbation susceptible COPD. Lastly, the applicability of performing disease progression modelling to study COPD has been shown. Two main subgroups of COPD were found, which are consistent with current clinical knowledge of COPD subtypes. This research may facilitate precise phenotypic characterisation of COPD from CT, which will increase our understanding of its natural history and associated heterogeneities. This will be instrumental in the precision medicine of COPD

Open-source virtual bronchoscopy for image guided navigation

This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance

Bronchoscopic lung volume reduction for Emphysema: physiological and radiological correlations

Introduction: Patient selection in lung volume reduction (LVR) plays a pivotal role in achieving meaningful clinical outcomes. Currently, LVR patients are selected based on three established criteria: heterogeneity index, percentage of low attenuation area (%LAA), and fissure integrity score. Quantitative computed tomography (QCT) has been developed to quantify lung physiological indices at the lobar level and could potentially revolutionise patient selection in LVR procedures. We developed an in-house QCT software, LungSeg, and used its radiological indices for the purposes of this thesis. The aim of this thesis is to discover potential physiological and radiological indices that could serve as predictors for superior LVR outcomes for better patient selection. Methods: This thesis took two studies and analysed them using LungSeg. The first study was the long-term coil study, a randomised controlled study that had the control group crossing over to the treatment arm at 12 months. At 12 months post-procedure the baseline measurements were assessed against the 12-months post-procedural measurements. The second study was the short-term valve study which was another randomised controlled study that compared the primary and secondary endpoints between the control and the valve-treated group at three months post-procedure. Results: In the long-term coil study, we found that the best statistically significant combination of predictors for change in target lobar volume at inspiration was found to be the combination of baseline target LV at inspiration, -950HU EI at inspiration, and TLCabs with a model adjusted R2 of 0.407 (p = 0.0001). In a subsequent multivariate analysis using ≥45% LAA on the -950HU at Inspiration, the R2 of the same prediction model did improve to 0.493 (P-value = 0.002). Meanwhile, the best statistically significant combination of predictors for change in target lobar volume at inspiration following valve treatment was found to be the combination of baseline target LV at inspiration, target lobar fissure integrity and baseline FEV1abs with a model adjusted R2 of 0.193 (p = 0.105). Conclusion: Using QCT, we have improved the proposed patient selection algorithm for LVR procedures based on the best QCT and lung function predictors.Open Acces

Faculty Impact Statements, 2007

Each issue [in the Research Series] has a distinctive titl

Optical Methods in Sensing and Imaging for Medical and Biological Applications

The recent advances in optical sources and detectors have opened up new opportunities for sensing and imaging techniques which can be successfully used in biomedical and healthcare applications. This book, entitled ‘Optical Methods in Sensing and Imaging for Medical and Biological Applications’, focuses on various aspects of the research and development related to these areas. The book will be a valuable source of information presenting the recent advances in optical methods and novel techniques, as well as their applications in the fields of biomedicine and healthcare, to anyone interested in this subject

CT Scanning

Since its introduction in 1972, X-ray computed tomography (CT) has evolved into an essential diagnostic imaging tool for a continually increasing variety of clinical applications. The goal of this book was not simply to summarize currently available CT imaging techniques but also to provide clinical perspectives, advances in hybrid technologies, new applications other than medicine and an outlook on future developments. Major experts in this growing field contributed to this book, which is geared to radiologists, orthopedic surgeons, engineers, and clinical and basic researchers. We believe that CT scanning is an effective and essential tools in treatment planning, basic understanding of physiology, and and tackling the ever-increasing challenge of diagnosis in our society

Biomarkers of neurological tissue injury and inflammation in paediatric tuberculous meningitis

Includes bibliographical references.[Background] Tuberculous meningitis (TBM) in children has high mortality and neurological morbidity rates. The assessment of disease severity and prognostication are difficult because several factors influence initial presentation, and advanced tools for these are lacking. Biomarkers of neurological injury could help to assess severity and to prognosticate, but have not been assessed in paediatric TBM. This study examined serum and cerebrospinal fluid (CSF) biomarkers of neurological injury in paediatric TBM in association with clinical and physiological data, radiology, inflammatory markers, and outcome. [ Methods ] Serum and CSF (ventricular and lumbar) samples were taken on admission and over 3 weeks in children with probable TBM and hydrocephalus. These were analysed with ELISA for neuromarkers S100B, neuron-specific enolase (NSE) and glial fibrillary acidic protein (GFAP), and with Luminex multianalyte array assay for a panel of inflammatory markers. Results were compared with 2 controls groups. Computerized tomography was done on admission and magnetic resonance imaging (brain, spine and magnetic resonance angiography) at 3 weeks. Brain oxygenation was monitored invasively and non-invasively in selected patients. Clinical and neurodevelopmental outcomes were assessed at 6 months. Data were analysed with various statistical tools, including principal component analysis. [ Results ] Data were collected from 44 children. Of these, 16% died and 36% had disability (25% mildmoderate, 11% severe). S100B, NSE, GFAP and inflammatory markers were elevated in CSF on admission and for up to 3 weeks, but not in serum. Elevated neuromarkers were significantly associated with poor outcome and increased over time in patients who died, although combined inflammatory biomarkers decreased. Cerebral infarcts occurred in 66% of patients and were associated with neuromarker elevation. Novel findings on spinal MRI were the high frequency of asymptomatic disease. Cerebral vascular pathology was documented frequently on imaging but did not predict infarcts. Low brain oxygenation was common and in keeping with physiological events and outcome. [ Conclusion ] CSF neuro- and inflammatory markers are elevated in TBM. Neuromarkers were prognostic of clinical and radiological outcome and an increasing trend suggested ongoing injury. This does not appear to be related to ongoing inflammation as measured by cytokines but may reflect the ongoing secondary injury processes initiated by inflammation

Methods for Analysing Endothelial Cell Shape and Behaviour in Relation to the Focal Nature of Atherosclerosis

The aim of this thesis is to develop automated methods for the analysis of the spatial patterns, and the functional behaviour of endothelial cells, viewed under microscopy, with applications to the understanding of atherosclerosis. Initially, a radial search approach to segmentation was attempted in order to trace the cell and nuclei boundaries using a maximum likelihood algorithm; it was found inadequate to detect the weak cell boundaries present in the available data. A parametric cell shape model was then introduced to fit an equivalent ellipse to the cell boundary by matching phase-invariant orientation fields of the image and a candidate cell shape. This approach succeeded on good quality images, but failed on images with weak cell boundaries. Finally, a support vector machines based method, relying on a rich set of visual features, and a small but high quality training dataset, was found to work well on large numbers of cells even in the presence of strong intensity variations and imaging noise. Using the segmentation results, several standard shear-stress dependent parameters of cell morphology were studied, and evidence for similar behaviour in some cell shape parameters was obtained in in-vivo cells and their nuclei. Nuclear and cell orientations around immature and mature aortas were broadly similar, suggesting that the pattern of flow direction near the wall stayed approximately constant with age. The relation was less strong for the cell and nuclear length-to-width ratios. Two novel shape analysis approaches were attempted to find other properties of cell shape which could be used to annotate or characterise patterns, since a wide variability in cell and nuclear shapes was observed which did not appear to fit the standard parameterisations. Although no firm conclusions can yet be drawn, the work lays the foundation for future studies of cell morphology. To draw inferences about patterns in the functional response of cells to flow, which may play a role in the progression of disease, single-cell analysis was performed using calcium sensitive florescence probes. Calcium transient rates were found to change with flow, but more importantly, local patterns of synchronisation in multi-cellular groups were discernable and appear to change with flow. The patterns suggest a new functional mechanism in flow-mediation of cell-cell calcium signalling