Medical image segmentation using edge-based active contours.

The main purpose of image segmentation using active contours is to extract the object of interest in images based on textural or boundary information. Active contour methods have been widely used in image segmentation applications due to their good boundary detection accuracy. In the context of medical image segmentation, weak edges and inhomogeneities remain important issues that may limit the accuracy of any segmentation method formulated using active contour models. This thesis develops new methods for segmentation of medical images based on the active contour models. Three different approaches are pursued: The first chapter proposes a novel external force that integrates gradient vector flow (GVF) field forces and balloon forces based on a weighting factor computed according to local image features. The proposed external force reduces noise sensitivity, improves performance over weak edges and allows initialization with a single manually selected point. The next chapter proposes a level set method that is based on the minimization of an objective energy functional whose energy terms are weighted according to their relative importance in detecting boundaries. This relative importance is computed based on local edge features collected from the adjacent region inside and outside of the evolving contour. The local edge features employed are the edge intensity and the degree of alignment between the images gradient vector flow field and the evolving contours normal. Finally, chapter 5 presents a framework that is capable of segmenting the cytoplasm of each individual cell and can address the problem of segmenting overlapping cervical cells using edge-based active contours. The main goal of our methodology is to provide significantly fully segmented cells with high accuracy segmentation results. All of the proposed methods are then evaluated for segmentation of various regions in real MRI and CT slices, X-ray images and cervical cell images. Evaluation results show that the proposed method leads to more accurate boundary detection results than other edge-based active contour methods (snake and level-set), particularly around weak edges

Smart markers for watershed-based cell segmentation

Ankara : The Department of Computer Engineering and the Graduate School of Engineering and Science of Bilkent University, 2012.Thesis (Master's) -- Bilkent University, 2012.Includes bibliographical refences.Automated cell imaging systems facilitate fast and reliable analysis of biological events at the cellular level. In these systems, the first step is usually cell segmentation that greatly affects the success of the subsequent system steps. On the other hand, similar to other image segmentation problems, cell segmentation is an ill-posed problem that typically necessitates the use of domain specific knowledge to obtain successful segmentations even by human subjects. The approaches that can incorporate this knowledge into their segmentation algorithms have a potential to greatly improve the segmentation results. In this study, we propose a new approach for the effective segmentation of live cells from phase-contrast microscopy. This approach introduces a new set of “smart markers” for a marker-controlled watershed algorithm, for which the identification of its markers is critical. The proposed approach relies on using domain specific knowledge, in the form of visual characteristics of the cells, to define the markers. We evaluate our approach on a total of 1954 cells. The experimental results demonstrate that the proposed approach is quite effective in identifying better markers compared to its counterparts. This will in turn be effective in improving the segmentation performance of a marker-controlled watershed algorithm.Koyuncu, Can FahrettinM.S

Simulation and control of stationary crossflow vortices

Turbulent flow and transition are some of the most important phenomena of fluid mechanics and aerodynamics and represent a challenging engineering problem for aircraft manufacturers looking to improve aerodynamic efficiency. Laminar flow technology has the potential to provide a significant reduction to aircraft drag by manipulating the instabilities within the laminar boundary layer to achieve a delay in transition to turbulence. Currently prediction and simulation of laminar-turbulent transition is con- ducted using either a low-fidelity approach involving the stability equations or via a full Direct Numerical Simulation (DNS). The work in this thesis uses an alternative high-fidelity simulation method that aims to bridge the gap between the two simulation streams. The methodology uses an LES approach with a low-computational cost sub-grid scale model (WALE) that has inherent ability to reduce its turbulent viscosity contribution to zero in laminar regions. With careful grid spacing the laminar regions can be explicitly modelled as an unsteady Navier-Stokes simulation while the turbulent and transitional regions are simulated using LES. The methodology has been labelled as an unsteady Navier-Stokes/Large Eddy Simulation (UNS/LES) approach. Two test cases were developed to test the applicability of the method to simulate and control the crossflow instability. The first test case replicated the setup from an experiment that ran at a chord-based Reynolds number of 390, 000. Two methods were used to generate the initial disturbance for the crossflow vortices, firstly using a continuous suction hole and secondly an isolated roughness element. The results for this test case showed that the approach was capable of modelling the full transition process, from explicitly modelling the growth of the initial amplitude of the disturbances to final breakdown to turbulence. Results matched well with the available experimental data. The second test case replicated an experimental setup using a custom- designed aerofoil run at a chord-based Reynolds number of 2.4 million. The test case used Distributed Roughness Elements (DRE) to induce crossflow vortices at both a critical and a control wavelength. By forcing the crossflow vortices at a stable (control) wavelength a delay in laminar-turbulent transition can be achieved. The results showed that the UNS/LES approach was capable of capturing the initial disturbance amplitudes due to the roughness elements and their growth rates matched well with experimental data. Finally, downstream a transitional region was assessed with low-freestream turbulence provided using a modified Synthetic Eddy Method (SEM). The full laminar-turbulent transition pro- cess was simulated and results showed significant promise. In conclusion, the method employed in this thesis showed promising results and demonstrated a possible route to high-fidelity transition simulation run at more realistic flow conditions and geometries than DNS. Further work and validation is required to test the secondary instability region and the final breakdown to turbulence

Magnetic resonance guided focused ultrasound surgery - a novel treatment for uterine fibroids

Uterine fibroids are the most common tumour of the reproductive tract in women of reproductive age. Although they are benign tumours that are often asymptomatic, they may cause debilitating symptoms in many women, such as abnormal uterine bleeding, abdominal pain, increased abdominal girth, urinary frequency, constipation, pregnancy loss, dyspareunia, and in some cases infertility. Several approaches are available for the treatment of uterine fibroids. These include pharmacologic options, such as hormonal therapies and gonadotropinreleasing hormone agonists; surgical approaches, such as hysterectomy, myomectomy; myolysis, laparoscopic uterine artery occlusion, uterine artery embolisation and magnetic resonance imaging-guided focused ultrasound surgery. The choice of approach may be dictated by factors such as the patient’s desire to become pregnant in the future, the importance of uterine preservation, symptom severity, and tumour characteristics. There is however, no widely agreed therapeutic strategy. There is a widespread view that hysterectomy is overused in the UK; the Chief Medical Officer in his annual report ‘On the state of public health’ in 2005, highlighted that hysterectomy in younger women is associated with complications, hospital stays, procedure-related interference with normal life and is costly. In addition he outlined the need to reduce the number of hysterectomies. This, along with the change in cultural attitudes amongst patients, who are becoming increasingly reluctant to undergo these conventional invasive procedures, has increased the need for new treatment options. Ideally new treatment options for uterine fibroids would be minimally invasive, have long-term data demonstrating efficacy and safety, have minimal or no incidence of fibroid recurrence, be easy to perform, preserve fertility, and be cost effective. New treatment approaches are under investigation, with the goals of being effective, safe, and less invasive. MRgFUS is a non-invasive thermo-ablative hybrid technique which uses both MR and ultrasound to destroy tumours. It is an outpatient procedure, which avoids the need for an anaesthetic, has a short recovery period, and is uterine sparing. The main objective of this work was to set out the rationale for using Magnetic Resonance guided Focused Ultrasound Surgery (MRgFUS) for the treatment of uterine fibroids. In order to achieve this aim, four main bodies of work are necessary; 1) Identifying patient selection criteria and investigating mitigating techniques to increase the pool of women for whom this treatment can be offered. 2) Investigating a method designed to overcome the problem of safely treating women with abdominal scars for whom this treatment can cause potential morbidity. 3) Investigating the potentiality of using MRgFUS to prolong the tumour shrinkage effect of GnRH analogue injections. 4) Investigating the safety of MRgFUS in treating symptomatic women who wish to preserve fertility. Results: the first aim of this project was to identify patient selection criteria and to investigate methods to widen the selection criteria. In our retrospective review it was found that 74% of women presenting were deemed technically suitable to proceed with treatment and several mitigating techniques that solved current technical difficulties were identified and allowed for less restrictive MRgFUS selection criteria for treatment of symptomatic uterine fibroids. These less restrictive criteria are expected to expand the pool of patients for whom MRgFUS is a viable treatment option for uterine fibroid symptoms. The second aim was to identify a method of overcoming the problem of treating women with previous abdominal scars safely. We identified a unique method of highlighting the scar by painting it with a paramagnetic iron oxide material which clearly outlined the scar on MR scanning allowing complete avoidance of the scar using MR guidance. In this small pilot study, all women were treated safely with no skin burns. The third aim of this project looked at the potentiality of prolonging the shrinkage effect of GnRH analogues by following a course of 3 injections with MRgFUS treatment. In this prospective study of fifty women, there was a 50% reduction in the mean symptoms severity score at 6 months which was maintained for 24 months post treatment. There was an average reduction in target fibroid volume which was maintained for 24 months. The final aim of the project was to investigate the safety of using MRgFUS as a treatment option for those women who wished to preserve their fertility. In this multicentre international study, One hundred and sixteen women were recruited from five centres. There were sixty four reported pregnancies in Sixty one women, with 30 completed deliveries. There were no reported cases of uterine rupture, premature labour, abnormal placentation or placental abruption. Conclusion: There is a growing body of data from clinical trials and more than four years of clinical experience to validate the safety and efficacy of MRgFUS for the treatment of uterine fibroids. MRgFUS is a totally non-invasive outpatient procedure that is not associated with the typical surgical risks of bleeding, infection and has minimal recovery time. Additionally, the procedure allows women to address their symptoms whilst preserving the uterus. Consequently, MRgFUS is an alternative treatment option for suitable patients who have refused other interventions due to concerns about lost productivity, risks of surgical complications or future fertility

Dosimetric and radiobiological evaluation of combined course of radiation therapy for locally advanced cervical cancer based on different techniques for dose delivery

Рак шейки матки является четвертым наиболее распространенным злокачественным заболеванием у женщин во всем мире. Брахитерапия (БТ) - это шаг в лучевой терапии локально распространенного рака шейки матки, но для некоторых пациентов БТ не подходит по медицинским, религиозным или этическим причинам. Для этих пациентов весь курс лечения должен проводиться с использованием только EBRT, поэтому в этом исследовании предпринята попытка оценить различные методы комбинированной лучевой терапии - не включая BT - для лечения рака шейки матки, чтобы определить лучшую технику среди российских пациентов в Томске.Cervical cancer is the fourth most common malignancy in females worldwide. Brachytherapy (BT) is step in radiotherapy of locally advanced cervical cancer, but for some patients BT not an option due to medical, religious or ethical reasons. For these patients, the whole treatment course should be given using only EBRT, so this study tries to evaluate different techniques of combined Radiotherapy -not include BT- for cervical cancer to detect the best technique among Russian patients at Tomsk

Orogenic lithosphere and slabs in the greater Alpine area – interpretations based on teleseismic P-wave tomography

Based on recent results of AlpArray, we propose a new model of Alpine collision that involves subduction and detachment of thick (∼ 180 km) European lithosphere. Our approach combines teleseismic P-wave tomography and existing local earthquake tomography (LET), allowing us to image the Alpine slabs and their connections with the overlying orogenic lithosphere at an unprecedented resolution. The images call into question the conventional notion that downward-moving lithosphere and slabs comprise only seismically fast lithosphere. We propose that the European lithosphere is heterogeneous, locally containing layered positive and negative Vp anomalies of up to 5 %–6 %. We attribute this layered heterogeneity to seismic anisotropy and/or compositional differences inherited from the Variscan and pre-Variscan orogenic cycles rather than to thermal anomalies. The lithosphere–asthenosphere boundary (LAB) of the European Plate therefore lies below the conventionally defined seismological LAB. In contrast, the lithosphere of the Adriatic Plate is thinner and has a lower boundary approximately at the base of strong positive Vp anomalies at 100–120 km. Horizontal and vertical tomographic slices reveal that beneath the central and western Alps, the European slab dips steeply to the south and southeast and is only locally still attached to the Alpine lithosphere. However, in the eastern Alps and Carpathians, this slab is completely detached from the orogenic crust and dips steeply to the north to northeast. This along-strike change in attachment coincides with an abrupt decrease in Moho depth below the Tauern Window, the Moho being underlain by a pronounced negative Vp anomaly that reaches eastward into the Pannonian Basin area. This negative Vp anomaly is interpreted as representing hot upwelling asthenosphere that heated the overlying crust, allowing it to accommodate Neogene orogen-parallel lateral extrusion and thinning of the ALCAPA tectonic unit (upper plate crustal edifice of Alps and Carpathians) to the east. A European origin of the northward-dipping, detached slab segment beneath the eastern Alps is likely since its down-dip length matches estimated Tertiary shortening in the eastern Alps accommodated by originally south-dipping subduction of European lithosphere. A slab anomaly beneath the Dinarides is of Adriatic origin and dips to the northeast. There is no evidence that this slab dips beneath the Alps. The slab anomaly beneath the Northern Apennines, also of Adriatic origin, hangs subvertically and is detached from the Apenninic orogenic crust and foreland. Except for its northernmost segment where it locally overlies the southern end of the European slab of the Alps, this slab is clearly separated from the latter by a broad zone of low Vp velocities located south of the Alpine slab beneath the Po Basin. Considered as a whole, the slabs of the Alpine chain are interpreted as highly attenuated, largely detached sheets of continental margin and Alpine Tethyan oceanic lithosphere that locally reach down to a slab graveyard in the mantle transition zone (MTZ)

The effects of shadow visibility on image interpretability

An empirical approach to measuring and predicting the effects of target scene shadows on image interpretability is described. A simulated aerial imagery data base is utilized to quantify image interpretability and computed graphics form the basis of the predictor algorithms. A technique to quantify the relative visibilities of individual line segment images is developed. Three categories of predictors are proposed and utilize line segment visibility to predict image interpretability. The success of the algorithms are tested using regression analysis procedures