Multi-dimensional local binary pattern texture descriptors and their application for medical image analysis

Texture can be broadly stated as spatial variation of image intensities. Texture analysis and classification is a well researched area for its importance to many computer vision applications. Consequently, much research has focussed on deriving powerful and efficient texture descriptors. Local binary patterns (LBP) and its variants are simple yet powerful texture descriptors. LBP features describe the texture neighbourhood of a pixel using simple comparison operators, and are often calculated based on varying neighbourhood radii to provide multi-resolution texture descriptions. A comprehensive evaluation of different LBP variants on a common benchmark dataset is missing in the literature. This thesis presents the performance for different LBP variants on texture classification and retrieval tasks. The results show that multi-scale local binary pattern variance (LBPV) gives the best performance over eight benchmarked datasets. Furthermore, improvements to the Dominant LBP (D-LBP) by ranking dominant patterns over complete training set and Compound LBP (CM-LBP) by considering 16 bits binary codes are suggested which are shown to outperform their original counterparts. The main contribution of the thesis is the introduction of multi-dimensional LBP features, which preserve the relationships between different scales by building a multi-dimensional histogram. The results on benchmarked classification and retrieval datasets clearly show that the multi-dimensional LBP (MD-LBP) improves the results compared to conventional multi-scale LBP. The same principle is applied to LBPV (MD-LBPV), again leading to improved performance. The proposed variants result in relatively large feature lengths which is addressed using three different feature length reduction techniques. Principle component analysis (PCA) is shown to give the best performance when the feature length is reduced to match that of conventional multi-scale LBP. The proposed multi-dimensional LBP variants are applied for medical image analysis application. The first application is nailfold capillary (NC) image classification. Performance of MD-LBPV on NC images is highest, whereas for second application, HEp-2 cell classification, performance of MD-LBP is highest. It is observed that the proposed texture descriptors gives improved texture classification accuracy

The Characterisation and Treatment of Resistant Hypertension

Hypertension is a highly prevalent condition and, as a risk factor for vascular disease in particular, a leading contributory cause of death worldwide. Recent consensus guidelines suggest that moderate and severe (grade II and III) hypertension should be treated rapidly to achieve targets though, prior to the inception of this thesis, the evidence for the safety and efficacy of this approach, together with the physiological consequences of rapid hypertension treatment in moderate and severe disease, was limited. This thesis explores the clinical consequences of an 18-week treatment programme for individuals with grade II and III hypertension, using guideline- recommended pharmacological treatment, delivered over an accelerated timeframe. The blood pressure response to treatment is reported, together with the tolerance and safety of the protocol, as defined by the protocol completion rate, frequency of medication side effects and clinically significant adverse events. The programme also provided an opportunity to study health-rated quality of life in patients with moderate and severe hypertension and the effect of rapid treatment on health-related quality of life. This allowed for the first validation (according to modern standards) of an English language disease-specific instrument for measuring health-related quality of life in hypertension, following translation of the original MINICHAL disease-specific instrument from the original Spanish. In addition, the clinical treatment programme provided an opportunity to study the microvascular response to rapid treatment of moderate and severe hypertension, particularly with relevance to the rarefaction of hypertension and its reversal with treatment. Moreover, the morphological and functional myocardial consequences of treatment were determined, using cardiac MR imaging. Accordingly, this thesis presents evidence supporting the rapid treatment of moderate and severe hypertension, providing an opportunity for this to be studied in future investigations, with the aim of exploring whether this approach is prognostically advantageous for patients

Characterising pattern asymmetry in pigmented skin lesions

Abstract. In clinical diagnosis of pigmented skin lesions asymmetric pigmentation is often indicative of melanoma. This paper describes a method and measures for characterizing lesion symmetry. The estimate of mirror symmetry is computed first for a number of axes at different degrees of rotation with respect to the lesion centre. The statistics of these estimates are the used to assess the overall symmetry. The method is applied to three different lesion representations showing the overall pigmentation, the pigmentation pattern, and the pattern of dermal melanin. The best measure is a 100% sensitive and 96% specific indicator of melanoma on a test set of 33 lesions, with a separate training set consisting of 66 lesions

Optical Diagnostics in Human Diseases

Optical technologies provide unique opportunities for the diagnosis of various pathological disorders. The range of biophotonics applications in clinical practice is considerably wide given that the optical properties of biological tissues are subject to significant changes during disease progression. Due to the small size of studied objects (from μm to mm) and despite some minimum restrictions (low-intensity light is used), these technologies have great diagnostic potential both as an additional tool and in cases of separate use, for example, to assess conditions affecting microcirculatory bed and tissue viability. This Special Issue presents topical articles by researchers engaged in the development of new methods and devices for optical non-invasive diagnostics in various fields of medicine. Several studies in this Special Issue demonstrate new information relevant to surgical procedures, especially in oncology and gynecology. Two articles are dedicated to the topical problem of breast cancer early detection, including during surgery. One of the articles is devoted to urology, namely to the problem of chronic or recurrent episodic urethral pain. Several works describe the studies in otolaryngology and dentistry. One of the studies is devoted to diagnosing liver diseases. A number of articles contribute to the studying of the alterations caused by diabetes mellitus and cardiovascular diseases. The results of all the presented articles reflect novel innovative research and emerging ideas in optical non-invasive diagnostics aimed at their wider translation into clinical practice

Investigation of factors controlling cutaneous circulation in flaps

The aim of this research was to investigate the blood supply to the lower abdomen. This is a commonly used donor site for autologous reconstruction following breast cancer and the flap of tissue used is based on the deep inferior epigastric circulation (DIEP flap) or the superficial inferior epigastric circulation (SIEA flap). A pilot study investigated the feasibility of assessing the vascular territory of multiple blood vessels in the lower abdomen, and also observed the timing of changes in skin blood supply after free flap transfer. Further studies included sampling using microdialysis catheters, from different areas of the flap, around the theoretical time of opening of choke vessels between angiosomes. Manipulation of skin blood flow was initially investigated using capillary malformations as a model, observing current clinical use of EMLA and AMETOP topical anaesthetic pre-laser treatment

The Role of Fluorescence and Human Factors in Quantitative Transdermal Blood and Tissue Analysis Using NIR Raman Spectroscopy

This research is part of an ongoing project aimed at the application of combined near infrared (NIR) Raman and fluorescence spectroscopy to noninvasive in vivo blood analysis including but not limited to glucose monitoring. Coping with practicalities of human factors and exploring ways to obtain and use knowledge gained about autofluorescence to improve algorithms for blood and tissue analysis are the general goals of this research. Firstly, the study investigated the various sources of human factors pertinent to our concerns, such as fingerprints, turgor, skin hydration and pigmentation. We then introduced specialized in vivo apparatus including means for precise and reproducible placement of the tissues relative to the optical aperture, i.e., the position detector pressure monitor (PDPM). Based on solid instrumental performances, appropriate methodology is now provided for applying and maintaining pressure to keep surface tissues immobile during experiments while obtaining the desired blood content and flow. Secondly, in vivo human fingertip skin autofluorescence photobleaching under 200 mW 830 nm NIR irradiation is observed and it is characterized that: i) the majority of the photobleached fluorescence originates from static tissue not blood, ii) the bleaching (1/e point) occurs in 101-102 sec timescale, and also iii) a photobleached region remains bleached for at least 45 min but recovers completely within several hours. A corresponding extensive but not exhaustive in vitro systematic study narrowed down the major contributors of such fluorescence and bleaching to collagen, melanin, plasma and hemoglobin: two major static tissue constituents and two major blood proteins. Thirdly, we established that measuring the inelastic and elastic emissions simultaneously leads to a sensitive probe for volume changes of both red blood cells and plasma. An algorithm based on measurements obtained while performing research needed for this thesis, as well as some empirical calibration approaches, was presented. The calibrated algorithm showed real potential to track hematocrit variations in cardiac pulses, centrifugal loading, blood vessel blockage using tourniquet, and even during as subtle an occurrence as in a Valsalva maneuver. Finally, NIR fluorescence and photochemistry of pentosidine, a representative of the advanced glycation endproducts (AGEs) which accumulate with age and hyperglycemia, was studied. The results indicate that oxygen plays a pivotal role in its photobleaching process. We hypothesized and offered proofs showing that pentosidine is a 1O2 sensitizer that is also subject to attack by the 1O2 resulting in the photobleaching that is observed when probing tissue using NIR. The photobleaching reaction is kinetically first order in pentosidine and ground state oxygen, and in vivo effectively first order with NIR irradiation also

Investigating the pathological mechanism of neuropathy in POEMS syndrome

POEMS syndrome (Polyneuropathy, Organomegaly, Endocrinopathy, Monoclonal gammopathy, Skin disorder) is a rare disease characterised by an inflammatory polyneuropathy an a monoclonal plasma cell dyscrasia. POEMS syndrome causes some of the most significant disability and mortality of any inflammatory neuropathy. The pathophysiology is unknown but recognised to be cytokine mediated, notably driven by vascular endothelial growth factor, however little is known about the other mediators at play. This thesis collates clinical data from the largest POEMS cohorti in Europe in order to study the characteristic disease features, optimise therapies and identify factors that influence outcome. Utilising our POEMS sample biobank, we carry out highly sensitive immunoassays to study the cytokines released in POEMS syndrome, and whether they correlate with disease activity. We go on to study the proteome of POEMS syndrome through mass spectrometry, to uncover the biological pathway involved and identify a number of novel, potentially pathogenic molecules. Fluid biomarkers of neuropathy in POEMS syndrome and related neuropathies are additionally explored. The development and optimisation of a homebrew immunoassay for peripherin, a peripheral nerve specific biomarker is detailed. The potential clinical utility of this biomarker is compared against that of serum neurofilament light. Finally, we attempt to model the neuropathogenesis of POEMS neuropathy in vitro using a novel human induced pleuripotent stem cell derived neuronal culture system