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  • 1.
    Jaque, Cassandra
    et al.
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Johansson, Anders
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    Kromatografi av polära läkemedel och metaboliter med HILIC-teknik2013Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The purpose of this project was to investigate if retention of polar compounds that are given to treat tuberculosis, diabetes, inflammatory bowel disease and childhood leukemia could be obtained with HILIC separation. By varying different parameters for different types of columns the compounds were analyzed with the aim of finding guidelines for future method optimizations. To perform these analyzes three different columns were tested – ZIC-HILIC (silica-based with zwitterions), ZIC-pHILIC (polymer-based with zwitterions) and XBridge Amide (amide functions). The results were evaluated with selected quality measures. The parameters being varied were pH, temperature, flow rate, type of buffer and ionic strength. In addition, comparisons between isocratic and gradient separations were performed.

     

    Over 1 000 analyzes were conducted in which retention of 16 of total 18 substances were successfully obtained with HILIC. The columns that generated the best results in terms of greatest number of identified compounds were ZIC-HILIC and XBridge Amide. ZIC-pHILIC offered a wide pH range but generally gave inferior chromatography. The influence of the different parameters on the results has not been investigated in sufficient scope. This means that no specific methods for the different drug groups can be reported.

  • 2.
    Tardif, Jean-Claude
    et al.
    Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada.
    Rhéaume, Eric
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Lemieux Perreault, Louis-Philippe
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Grégoire, Jean C
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Feroz Zada, Yassamin
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Asselin, Géraldine
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Provost, Sylvie
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Barhdadi, Amina
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Rhainds, David
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    L'Allier, Philippe L
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Ibrahim, Reda
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Upmanyu, Ruchi
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Niesor, Eric J
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Benghozi, Renée
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Suchankova, Gabriela
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Laghrissi-Thode, Fouzia
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Guertin, Marie-Claude
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Olsson, Anders G
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Mongrain, Ian
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Schwartz, Gregory G
    University of Colorado, Denver, USA and F. Hoffmann-La Roche, Basel, Switzerland.
    Dubé, Marie-Pierre
    Université de Montréal Beaulieu-Saucier Pharmacogenomics, Centre Montreal, Quebec, Canada.
    Pharmacogenomic determinants of the cardiovascular effects of dalcetrapib.2015In: Circulation: Cardiovascular Genetics, ISSN 1942-325X, E-ISSN 1942-3268, Vol. 8, no 2, 372-382 p.Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Dalcetrapib did not improve clinical outcomes, despite increasing high-density lipoprotein cholesterol by 30%. These results differ from other evidence supporting high-density lipoprotein as a therapeutic target. Responses to dalcetrapib may vary according to patients' genetic profile.

    METHODS AND RESULTS: We conducted a pharmacogenomic evaluation using a genome-wide approach in the dal-OUTCOMES study (discovery cohort, n=5749) and a targeted genotyping panel in the dal-PLAQUE-2 imaging trial (support cohort, n=386). The primary endpoint for the discovery cohort was a composite of cardiovascular events. The change from baseline in carotid intima-media thickness on ultrasonography at 6 and 12 months was evaluated as supporting evidence. A single-nucleotide polymorphism was found to be associated with cardiovascular events in the dalcetrapib arm, identifying the ADCY9 gene on chromosome 16 (rs1967309; P=2.41×10(-8)), with 8 polymorphisms providing P<10(-6) in this gene. Considering patients with genotype AA at rs1967309, there was a 39% reduction in the composite cardiovascular endpoint with dalcetrapib compared with placebo (hazard ratio, 0.61; 95% confidence interval, 0.41-0.92). In patients with genotype GG, there was a 27% increase in events with dalcetrapib versus placebo. Ten single-nucleotide polymorphism in the ADCY9 gene, the majority in linkage disequilibrium with rs1967309, were associated with the effect of dalcetrapib on intima-media thickness (P<0.05). Marker rs2238448 in ADCY9, in linkage disequilibrium with rs1967309 (r(2)=0.8), was associated with both the effects of dalcetrapib on intima-media thickness in dal-PLAQUE-2 (P=0.009) and events in dal-OUTCOMES (P=8.88×10(-8); hazard ratio, 0.67; 95% confidence interval, 0.58-0.78).

    CONCLUSIONS: The effects of dalcetrapib on atherosclerotic outcomes are determined by correlated polymorphisms in the ADCY9 gene.

    CLINICAL TRIAL INFORMATION: URL: http://www.clinicaltrials.gov. Unique identifiers: NCT00658515 and NCT01059682.

  • 3.
    Fernlund, Eva
    et al.
    Region Östergötland, Center of Paediatrics and Gynaecology and Obstetrics, Department of Paediatrics in Linköping. Lund University, Sweden.
    Schlegel, Todd T.
    Karolinska Institute, Sweden; Karolinska University Hospital, Sweden.
    Platonov, Pyotr G.
    Lund University, Sweden.
    Carlson, Jonas
    Lund University, Sweden.
    Carlsson, Marcus
    Lund University, Sweden.
    Liuba, Petru
    Lund University, Sweden.
    Peripheral microvascular function is altered in young individuals at risk for hypertrophic cardiomyopathy and correlates with myocardial diastolic function2015In: American Journal of Physiology. Heart and Circulatory Physiology, ISSN 0363-6135, E-ISSN 1522-1539, Vol. 308, no 11, H1351-H1358 p.Article in journal (Refereed)
    Abstract [en]

    Hypertrophic cardiomyopathy (HCM) is a major cause of sudden cardiac death in the young. Based on previous reports of functional abnormalities in not only coronary but also peripheral vessels in adults with HCM, we aimed to assess both peripheral vascular and myocardial diastolic function in young individuals with an early stage of HCM and in individuals at risk for HCM. Children, adolescents, and young adults (mean age: 12 yr) with a family history of HCM who either had (HCM group; n = 36) or did not have (HCM-risk group; n = 30) echocardiography-documented left ventricular (LV) hypertrophy as well as healthy matched controls (n = 85) and healthy young athletes (n = 12) were included in the study. All underwent assessment with 12-lead electrocardiography, two-dimensional echocardiography, tissue Doppler imaging and laser Doppler with transdermal iontophoresis of ACh and sodium nitroprusside. LV thickness and mass were increased in HCM and athlete groups compared with control and HCM-risk groups. The mitral E-to-e ratio, measured via tissue Doppler, was increased in HCM (P less than 0.0001) and HCM-risk (P less than 0.01) groups compared with control and athlete groups, as were microvascular responses to ACh (HCM group: P less than 0.045 and HCM- risk group: P less than 0.02). Responses to ACh correlated with the E-to-e ratio (r = 0.5, P = 0.001). Microvascular responses to sodium nitroprusside were similar in all groups (P = 0.2). HCM-causing mutations or its familial history are associated with changes in cardiac diastolic function and peripheral microvascular function even before the onset of myocardial hypertrophy. Tissue Doppler can be used to differentiate HCM from physiological LV hypertrophy in young athletes.

  • 4.
    Renström, Klara
    Linköping University, Department of Biomedical Engineering, Medical Informatics. Linköping University, Faculty of Science & Engineering.
    Automatic age estimation of children based on brain matter composition using quantitative MRI2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The development of a child can be monitored by studying the changes in physical appearance or the development of capabilities e.g. walking and talking. But is it possible to find a quantitative measure for brain development? The aim of this thesis work is to investigate that possibility using quantitative magnetic resonance imaging (qMRI) images by answering the following questions:

    • Can brain development be determined using qMRI? If so, what properties of the brain can be used?
    • Can the age of a child be automatically detected with an algorithm? If so, how can this algorithm function? With what accuracy?

    Previous studies have shown that it is possible to detect properties in the brain changing with age, based on MRI images. These properties have e.g. been changes in T1 and T2 relaxation time, i.e. properties in water signal behavior that can be measured using multiple MR acquisitions. In the literature this was linked to a rapid myelination process that occurs after birth. Furthermore the organization and growth of the brain is a property that can be measured and monitored.

    This thesis have investigated several different properties in the brain based on qMRI images in order to identify those who have a strong correlation with age in the range 0-20 years. The properties that were found to have a high correlation were:

    • Position of the first histogram peak in T1 weighted qMRI images,
    • Fraction of white matter in the brain,
    • Mean pixel value of PD weighted qMRI images,
    • Volume of white matter in the brain,

    Curves on the form f(x) = ae^(-bx) +c are fitted to the data sets and confidence intervals are calculated to frame the statistical insecurity of the curve. The mean error in percent for the different properties can be seen in the list below:

    Property, Mean error [%] 0-20 years, Mean error [%] 0-3 years

    Peak position: 53.84, 98.17

    Fraction of WM: 118.97, 71.67

    Mean pixel value: 200.89, 126.28

    Volume of WM: 241.72, 72.58

    The conclusions drawn based on the presented results are that there are properties in the brain that correlates well to aging, but the error is too large for making a valid prediction of age over the entire range of 0-20 years. When decreasing the age range to 0-3 years the mean error becomes smaller, but it is still too large. More data is needed to evaluate and improve this result.

  • 5.
    Rehn, Emelie
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Medicine and Health Sciences.
    Modeling of scatter radiation during interventional X-ray procedures2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    During catheterized x-ray interventions the patient and medical staff is exposed to scatter radiation, as a consequence of tissue interactions. Ionizing radiation for medical purpose is potentially dangerous and can cause malignancy, skin damage and more. Studies have suggested an increase in the prevalence of eye lens cataract, thyroid cancer and left sided brain tumors in doctors. Therefore, it is mandatory to reduce the radiation dose in medicine, a principle known as ALARA (as low as Reasonably Achievable). Lead aprons, collars and shieldings are safety precautions to protect the team in the operating room. The x-ray equipment and surgical techniques are constantly evolving and the interventions become more complex which may increase the x-ray dose. Although x-ray imaging is required in interventional procedures endeavors of reducing radiation exposure to staff is of high interest. There is a need to increase the awareness about scatter radiation and radiation protection efforts are gaining momentum. Initiative to train a dose reducing behavior by education and awareness are key documents within the European Union’s guidelines on Radiation protection.

    The aims of this thesis were to create a 3D model for representation of real-time exposure and accumulated scatter radiation to staff performing interventional x-ray procedures and identify parameters that affect the scatter radiation.

    Extensive measurements were made with real time dosimeters while irradiating an anthropomorphic phantom. For five lateral C-arm projections, 68 - 80 data points each were used to measure scatter dose distribution around the patient. In the typical operator position, the effect of craniocaudal projection angle, patient size, field size, image detector height and pulse rate on scatter radiation dose was also investigated.

    It was possible to create a 3D model from interpolated measurement data that can generate dose rate with promising results. Six out of eight modelled doses deviated +/- 26.6 % from the validation cases. A model that delivers relative dose is an intuitive approach in education for interventional x-ray radiation safety. The staff position in relation to the x-ray source and the patient size have a significant correlation to the dose rate. Additional measurements are needed to ensure the reliability of the model. This work completes the effect of scatter radiation distribution around the patient table, which is not yet evaluated as thoroughly by other authors.

  • 6.
    Säberg, Alexander
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, Faculty of Science & Engineering.
    Synthesis of a clickable FDG precursor for PET in vivo imaging2015Independent thesis Basic level (degree of Bachelor), 10,5 credits / 16 HE creditsStudent thesis
    Abstract [en]

    The thesis of this study describes a synthesis way to produce an alkyne equipped clickable precursor of 2-deoxy-2-fluoro-D-glucose (FDG) with a beta-configuration. This FDG-derivate is produced with a clickable link in purpose to be used in PET in vivo imaging. The product was synthesized by acetylation protection and further epoxidation on the glucose analog D-Glucal. Glycosylation occurred by electrophilic reaction of propargyl alcohol and configuration of the product was ensured during Lattrell-Dax inversion.

  • 7.
    Axelsson, Viktor
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Automatisk segmentering och maskering av implantat i mammografibilder2014Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    A report on my thesis developing an algorithm to automatically classify a mammogram image as containing an implant or not and segmenting and masking any present breast implant in the image.

  • 8.
    Kardell, Martin
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Automatic Segmentation of Tissues in CT Images of the Pelvic Region2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In brachytherapy, radiation therapy is performed by placing the radiation source into or very close to the tumour. When calculating the absorbed dose, water is often used as the radiation transport and dose scoring medium for soft tissues and this leads to inaccuracies. The iterative reconstruction algorithm DIRA is under development at the Center for Medical Imaging Science and Visualization, Linköping University. DIRA uses dual-energy CT to decompose tissues into different doublets and triplets of base components for a better absorbed dose estimation. To accurately determine mass fractions of these base components for different tissues, the tissues needs to be identified in the image. The aims of this master thesis are: (i) Find an automated segmentation algorithm in CT that best segments the male pelvis. (ii) Implement a segmentation algorithm that can be used in DIRA. (iii) Implement a fully automatic segmentation algorithm.

    Seven segmentation methods were tested in Matlab using images obtained from Linköping University Hospital. The methods were: active contours, atlas based registration, graph cuts, level set, region growing, thresholding and watershed. Four segmentation algorithms were selected for further analysis: phase based atlas registration, region growing, thresholding and active contours without edges. The four algorithms were combined and supplemented with other image analysis methods to form a fully automated segmentation algorithm that was implemented in DIRA.

    The newly developed algorithm (named MK2014) was sufficiently stable for pelvic image segmentation with a mean computational time of 45.3 s and a mean Dice similarity coefficient of 0.925 per 512×512 image. The performance of MK2014 tested on a simplified anthropomorphic phantom in DIRA gave promising result. Additional tests with more realistic phantoms are needed to confirm the general applicability of MK2014 in DIRA.

  • 9.
    Athanasiou, Vasileios
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Health Sciences.
    Estimation and modelling of fMRI BOLD response2014Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    One of the current topics of research in neuroimaging techniques is related to explaining and modelling the Blood Oxygen Level Dependent (BOLD) responses. BOLD responses are estimated by processing functional Magnetic Resonance Imaging (fMRI) data. BOLD responses are caused by hemodynamic responses to neural activity which alter the levels of blood oxygenation at local brain regions. The main aims of the current thesis were to i) develop and examine methods regarding BOLD response estimation from the visual cortex and the frontal cortex of human brain and to ii) develop a model in order to explain the physiological mechanisms which cause the estimated BOLD responses.

    In order to satisfy the main aims, fMRI data were provided by the Center of Medical Imaging and Visualization (CMIV). The provided fMRI data consist of fMRI brain measurements of twelve healthy human subjects who were subjected to visual stimulation. By processing the fMRI data, Regions Of Interest (ROIs) were extracted at the anatomical sites of the visual cortex and the frontal cortex. Afterwards, the fMRI data were manipulated in order to extract BOLD responses from the visual cortex and the frontal cortex. Various methods were developed and compared in terms of which technique provided well representative BOLD responses.       

    Subsequently, a model was developed by using software Wolfram Mathematica 9 in order to explain the physiological mechanisms of the estimated BOLD responses at the visual and the frontal cortex. The model aimed to solve for oxygen concentration in blood plasma as blood flows from the arterial part to the venous part of the blood circulation system through a capillary. Oxygen outward diffusion through the capillary wall and oxygen concentration at the extravascular environment were modelled as well. Blood plasma oxygen concentration was turned into hemoglobin oxygen saturation (Sa ) through hemoglobin oxygen dissociation curve and Henry’s law for gases. As a result, the Sa  was estimated through modelling for oxygen concentration in blood plasma. Finally, the developed model ended to a system with input the fractional change of Cerebral Blood Flow (CBF) velocity and Cerebral Metabolic Rate of Oxygen (CMR ) and as output a proportional signal to the BOLD response. By simulating for different scenarios of fractional changes of CBF velocity and CMR  and by comparing the resulted BOLD responses to the estimated ones, it was attempted to explain for the physiological mechanisms which caused the BOLD responses at the anatomical sites of the visual and frontal cortex.

  • 10.
    Riseby, Emil
    et al.
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Svensson, Alexander
    Linköping University, Department of Science and Technology, Media and Information Technology. Linköping University, The Institute of Technology.
    Multispectral Imaging for Surveillance Applications2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Silicon based sensors is a commonly used technology in digital cameras today. That has made such cameras relatively cheap and widely used. Unfortunately they are constructed to capture and represent image quality for humans. Several image applications work better without the restrictions of the visible spectrum. Human visual restrictions are often indirectly put on technology by using images showing only visible light. Thinking outside the box in this case is seeing beyond the visible spectrum.

  • 11.
    Perkiö, Mattias
    Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Assessment of Pulse Wave Velocity in the Aorta by using 4D Flow MRI2014Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The purpose of this master thesis was to evaluate the estimation of pulse wave velocity (PWV) in the aorta using 4D flow MRI. PWV is the velocity of the pressure wave generated by the heart during systole and is a marker of arterial stiffness and a predictor of cardiovascular disease (CVD). PWV can in principle be estimated based on the time (travel-time) it takes for the pulse wave to travel a fixed distance (travel-distance), or based on the distance the pulse wave travels during a fixed time. In the commonly used time-to-travel-a-fixed-distance approach, planes are placed at two or more locations along the aorta. The travel-time is found by studying velocity waveforms at these pre-defined locations over time and thereby by estimating the time-difference for the pressure wave to reach each of these locations. In the distance-travelled-in-a-fixed-time approach, the pulse wave is located by studying at the velocity along the aorta at pre-defined instances in time. The travel-distance for the pulse wave between two instances in time is set as the difference in location of the pulse wave, where the location is identified as the location when the velocity has reached a predefined baseline. The specific aims of this thesis was to investigate the effect of using multiple locations as well as the effects of temporal and spatial resolution in the time-to-travel-a-fixed-distance approach, and to evaluate the possibility of using the distance-travelled-in-a-fixed-time approach. Additionally, the possibility of combining the two approaches was investigated. The study of using multiple locations revealed that more planes reduces the uncertainty of PWV estimation. Temporal resolution was found to have a major impact on PWV estimation, whereas spatial resolution had a more minor effect. A method for estimating PWV using 4D flow MRI using the distance-travelled-in-a-fixed-time approach was presented. Values obtained were compared favourably against previous findings and reference values, in the case of healthy young volunteers. The combination of the time-to-travel-a-fixed-distance and distance-travelled-in-a-fixed-time approaches appears feasible.

  • 12.
    Tuvhag, Ellinor
    Linköping University, Department of Medical and Health Sciences. Linköping University, Faculty of Health Sciences.
    Undersökning av koppars effekt som antibakteriellt agens i tyg2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The purpose of this study was to test the antibacterial effect of thin copper treads woven into a polyester fabric. The investigation was done by inoculation of Staphylococcus aureus strain ATCC 6538 to the fabric and evaluation of the number of viable cells post exposure by viable count. The issue to be answered was whether the copper fabric had a bactericide or bacteriostatic effect? The fabric is still in prototype stage, and if proven to have antibacterial properties the aim is to use it to prevent bacterial growth in wounds and other vulnerable locations in clinical care. Copper is an essential trace element, but also has antimicrobial properties through a wide range of mechanisms where cell membrane damage is one of the more important. Methods used for inoculation was the absorption method, where a nutrient broth containing S. aureus was pipetted on to the fabric specimens, and the transfer method where the fabric specimens were pressed onto an agar plate that had previously been spread with peptone salt solution containing S. aureus. Total number of bacteria per fabric specimen after short contact (<1 min) and incubation (18-24 h at 37±2°C) was calculated. Incubation showed significant difference in total number of bacteria between the copper fabric and negative control in three of four tests. Short contact showed a tendency of antibacterial effect. The conclusion was that the copper fabric harmed and killed bacteria during incubation but that more records would be needed to be sure about the effects of short contact on bacteria.

  • 13.
    Ottosson, Marie-Louise
    Linköping University, Faculty of Health Sciences.
    Visualisering av basalcellscancer med Tissue Viability Imaging - ett icke-invasivt diagnostiskt alternativ2014Independent thesis Basic level (degree of Bachelor), 180 HE creditsStudent thesis
    Abstract [en]

    Basal cell carcinoma (BCC) is the most common non-melanoma skin cancer. It can be divided in different subtypes. The most common type is superficial and is most frequently occurring on the trunk and on the face. In severe cases it can be difficult to differentiate basal cell carcinoma from other skin tumors, therefore a skin biopsy is conclusive diagnostic method. In terms of treatment, curettage is a common non-surgical treatment of basal cell carcinoma. However, being superficial, curettage increases the risk of recurrence. Between 30-40 % of most recurrences occur within five years.

    Tissue Viability Imaging or TiVi is a diagnostic method used by the Department of Dermatology at the University Hospital in Linköping. The technology allows the investigator to see through the top layer of the skin (epidermis) and map the skin skin blood circulation in the dermal area.

    The aim of this study was to investigate whether histological features of present basal cell carcinoma, inflammation, stroma and microvessels, correlates with the presence of the tumour visualized by Tissue Viability Imaging technique.

    The hypothesis is, that by visualizing BCC recurrence at the first visit at the clinic by using TiVi technique, we can diagnose BCC and treat patients in one step, thus reducing the amount of discomfort for the patient and also reduce the cost of care.

    In this pilot-study, patient material involving two basal cell carcinomas from one patient were used. The results show that microscopic examination of the tumor and blood vessels correlate with visualizing basal cell carcinoma with TiVi, although furthermore studies of existing basal cell carcinoma and several tumours are required to ensure correlation before TiVi can be used to replace skin biopsy.

  • 14.
    Willén, Daniel
    Linköping University, Department of Physics, Chemistry and Biology, Organic Chemistry. Linköping University, The Institute of Technology.
    Synthesis of azidoethyl 3,4,6-tri-O-acetyl-α-D-mannopyranoside for future bioconjugation in PET studies2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Positron emission tomography is a powerful imaging method capable of diagnosing and studyingdiseases at atomic levels. The following thesis involves the synthesis of a 2 -deoxy-2 -[18F]uoro-D-glucose derivative able to participate in click chemisty conjugation. The synthesis involves six stepswith D-mannopyranose as starting material; regioselective acetylation and protection of the hydroxylgroup on C-2 of the monosaccharide, glycosylation with 2-azidoethanol, removal of the selectiveprotecting group and substitution of the hydroxyl group on C-2 with uorine. The potential toconjugate the glycoside to other biomolecules and obtain PET data might have uses in diagnosticaland medicinal chemistry.

  • 15.
    Shayeghpour, Omid
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    Improving information perception from digital images for users with dichromatic color vision2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Color vision deficiency (CVD) is the inability or limited ability to recognize colors and discriminate between them. A person with this condition perceives a narrower range of colors compared to a person with a normal color vision. A growing number of researchers are striving to improve the quality of life for CVD patients. Finding cure, making rectification equipment, providing simulation tools and applying color transformation methods are among the efforts being made by researchers in this field. In this study we concentrate on recoloring digital images in such a way that users with CVD, especially dichromats, perceive more details from the recolored images compared to the original image. The main focus is to give the CVD user a chance to find information within the picture which they could not perceive before. However, this transformed image might look strange or unnatural to users with normal color vision. During this color transformation process, the goal is to keep the overall contrast of the image constant while adjusting the colors that might cause confusion for the CVD user. First, each pixel in the RGB-image is converted to HSV color space in order to be able to control hue, saturation and intensity for each pixel and then safe and problematic hue ranges need to be found. The method for recognizing these ranges was inspired by a condition called “unilateral dichromacy” in which the patient has normal color vision in one eye and dichromacy in another. A special grid-like color card is designed, having constant saturation and intensity over the entire image, while the hue smoothly changes from one block to another to cover the entire hue range. The next step is to simulate the way this color card is perceived by a dichromatic user and finally to find the colors that are perceived identically from two images and the ones that differ too much. This part makes our method highly customizable and we can apply it to other types of CVD, even personalize it for the color vision of a specific observer. The resulting problematic colors need to be dealt with by shifting the hue or saturation based on some pre-defined rules. The results for the method have been evaluated both objectively and subjectively. First, we simulated a set of images as they would be perceived by a dichromat and compared them with simulated view of our transformed images. The results clearly show that our recolored images can eliminate a lot of confusion from user and convey more details. Moreover, an online questionnaire was created and 39 users with CVD confirmed that the transformed images allow them to perceive more information compared to the original images.

  • 16.
    Peterson, Erika
    Linköping University, Department of Medical and Health Sciences, Division of Radiological Sciences. Linköping University, Faculty of Health Sciences.
    Synthetic MRI for visualization of quantitative MRI2013Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Magnetic resonance imaging (MRI) is an imaging technique that is used in hospitals worldwide. The images are acquired through the use of an MRI scanner and the clinical information is provided through the image contrast, which is based on the magnetic properties in biological tissue. By altering the scanner settings, images with different contrast properties can be obtained. Conventional MRI is a qualitative imaging technique and no absolute measurements are performed. At Center for Medical Imaging and Visualization (CMIV) researchers are developing a new MRI technique named synthetic MRI (SyMRI). SyMRI is based on quantitative measurements of data and absolute values of the magnetic properties of the biological tissue can be obtained.

    The purpose of this master thesis has been to take the development of SyMRI a step further by developing and implementing a visualization studio for SyMRI imaging of the human brain. The software, SyMRI Brain Studio, is intended to be used in clinical routine. Input from radiologists was used to evaluate the imaging technique and the software. Additionally, the requirements of the radiologists were converted into technical specifications for the imaging technique and SyMRI Brain Studio. Additionally, validation of the potential in terms of replacing conventional MRI with SyMRI Brain Studio was performed.

    The work resulted in visualization software that provides a solid formation for the future development of SyMRI Brain Studio into a clinical tool that can be used for validation and research purposes. A list of suggestions for the future developments is also presented. Future clinical evaluation, technical improvements and research are required in order to estimate the potential of SyMRI and to introduce the technique as a generally used clinical tool.

  • 17.
    Wahham, Atheer
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    Multispectral Image Acquisition2006Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The purpose of this project was to develop control software for a multi-spectral imaging system. The multi-spectral imaging system used by the colour Lab consists of a camera (Alta USB camera) and a filter (VariSpec liquid crystal tuneable filter). The camera and the filter were delivered by two different manufacturers and therefore have two separate stand-alone control programs.

    The fact that the hardware had to be controlled by two separate pieces of software meant that the image capturing procedure was very time-consuming and needed an unrealistic amount of user input.

    The project resulted in a C++ console program with all the required and necessary functionsas those provided by the individual software, camera and filter; and operated both the camera and the filter simultaneously and conveniently. The project was performed at the Norwegian colour Laboratory in Gjøvik University College.

  • 18.
    Engström, Philip
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    Interactive GPU-based Volume Rendering2006Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Modern GPUs possess enormous computational capabilities, power that has just become available for general purpose programming via the development of highly programmable shaders. This thesis investigates ways to use this power for the purpose of medical visualization.

    The project was carried out in collaboration with Sectra Imtec, a Linköpingbased medical imaging company. The problem to be solved was how best to render high quality images at interactive frame rates for the purpose of previewing a medical data set. Two different GPU-accelerated volume rendering approaches were investigated and implemented. One approach based on textured slices of proxy geometry, and one based on ray casting.

    It is shown that the ray casting implementation presented far superior image quality. Because of this, most of the work during the project concerned improving the method enough to make the visualization interactive. In particular, an empty space skipping method via a complex bounding geometry was implemented and is described in detail.

    This report also presents important background facts regarding volume rendering and modern graphics cards, so that it is accessible for any reader with basic computer graphics knowledge.

  • 19.
    Safarzadeh Khooshabi, Ghazaleh
    Linköping University, Department of Biomedical Engineering. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Segmentation Validation Framework2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Many segmentation algorithms have been published in literature. Accurate assessment of these algorithms is needed in order to gain acceptance in the clinical practice or compare different algorithms. However in medical imaging segmentation field, there is usually a lack of gold standard method. In many studies, the manual segmentation from expert raters is regarded as the gold standard. Even though these manual denotation methods suffer from high inter-rater and intra-rater variability.

    In this thesis, a relatively complete segmentation validation framework was developed, which uses the “Simultaneous Truth and Performance Level Estimation” (STAPLE) method to produce the ground truth from a set of manual expert segmentations, and performs a set of quantitative validation metrics measurement to assess the automated segmentation versus the ground truth given by STAPLE. It is also designed to be easy-to-use and cover most common image formats and popular operating systems. A number of tests using synthetic data have proved the accuracy of the proposed framework. In addition, some examples of how this framework can be used to evaluate the performance of different segmentation algorithm are also presented.

  • 20.
    Nilsson, Andreas
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    IBL in GUI for mobile devices2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Mobile phones are here to stay, and the interaction with them is an evolving process. Designing software for mobile devices poses new challenges not seen in desktop computer environments. Screen size, performance and inputs, are just a few areas where they significantly differ. Although, intriguingly the gap between them is narrowing. Devices are now able to do things previously only restricted to PCs. The graphics chip integrated with high-end devices of today and tomorrow has capabilities worth exploring. With more power and advanced shader support, techniques such as image based lighting becomes worth exploring.

    To solve the problem described in this thesis I built a framework for image processing. This framework is further described indirectly throughout the report and is available upon request. The framework is never the focus of the report since any framework should suffice and the developed framework should not hinder the reader’s own experimentations.

    The purpose of this thesis is to see whether image based lighting (IBL) and image based rendering (IBR) is feasible with a mobile phone, as well as explore which applications it would suit for. Also, examining if it can be combined with high dynamic range imaging (HDRI) to enhance the user experience. Both IBL/IBR and HDRI might be new terms for the reader; if so I encourage you to read 2.2 for a deeper understanding.

  • 21.
    Sievert, Andreas
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    Tools and Algorithms for Classification in Volume Rendering of Dual Energy Data Sets2008Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In the last few years, technology within the medical imaging sector has made many advances, which in turn has opened many new possibilities. One such recent advance is the development of imaging with data from dual energy computed tomography, CT, scanners. However, with new possibilities come new challenges.

    One challenge, that is discussed in this thesis, is rendering of images created from two volumes in an efficient way with respect to the classification of the data. Focus lies on investigating how dual energy data sets can be classified in order to fully use the potential of having volumes from two different energy levels. A critical asset in this investigation is the ability to utilize a transfer function description that extends into two dimensions. One such transfer function description is presented in detail.

    With this two-dimensional description comes the need for a new way to interact with the transfer function. How the interaction between a user and the transfer function description is implemented for Siemens Corporate Research in Princeton, NJ will also be discussed in this thesis as well as the classification results of rendering dual energy data. These results show that it is possible to classify blood vessels correctly when rendering dual energy computed tomography angiography, CTA, data.

  • 22.
    Wahlbom Hellström, Victoria
    et al.
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics. Linköping University, The Institute of Technology.
    Alenius, Frida
    Linköping University, Department of Management and Engineering, Applied Thermodynamics and Fluid Mechanics. Linköping University, The Institute of Technology.
    Investigation of Scale Adaptive Simulation (SAS) Turbulence Modelling for CFD-Applications2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Fluid dynamics simulations generally require large computational recourses in form of computer power and time. There are different methods for simulating fluid flows that are more or less demanding, but also more or less accurate. Two well known computational methods are the Reynolds Averaged Navier-Stokes (RANS) and Large Eddy Simulation (LES). RANS computes the timeaveraged flow properties, while LES resolve the large structures (eddies) of the flow directly and model the small ones. Hybrid models are combinations of these two models which have been developed to improve the RANS solutions and shorten the simulation time compared to LES computations. One such model is the Scale Adaptive Simulation (SAS) model which uses the RANS model in steady flow regions, such as close to walls, and a LES like model in unsteady regions with large fluctuations.

    This study was done for evaluating the SAS model compared to Unsteady RANS (URANS) and LES and their performance compared to measurements from an engineering point of view. This was done by running simulations on two different test cases, one external and one internal flow situation. The first one was flow around a wall-mounted cylinder and the second one was flow through an aorta with a coarctation in the descending aorta. The first test case was used to thoroughly evaluate the SAS model by running many simulations with URANS, SAS and LES with different element types, element sizes and flow parameters. The element types that have been analyzed are; tetrahedral, hexahedral and polyhedral. The results were compared with experiments done by Sumner et al. [7, 8, 9, 10]. The second test case was used for evaluating the SAS model even further on another flow situation. For this test case, only two SAS simulations were performed on two different grids; a structured hexahedral and an unstructured polyhedral. These results were compared with Magnetic Resonance Imaging (MRI) measurements obtained from Linköping University.

    No conclusion of which one of the simulated cases gives the best overall agreement with experimental results could be concluded from the obtained results. The best prediction of the drag coefficient for the cylinder was obtained for the coarsest polyhedral mesh that was run with LES, with the disagreement 0.4 percent. The best prediction of the Strouhal number was obtained for a URANS simulation performed on the coarsest mesh with an improved grid close to the cylinder surface, generating less than one, with a disagreement of 3 percent compared to measurements. For the meshes used, it was found that the polyhedral mesh gave the best overall results and the tetrahedral mesh gave the worst results for the cylinder case. For the aorta case the SAS model produced velocity components that had acceptable agreement with the MRI-measurements, but gave very poor results for the turbulent kinetic energy. The main conclusion of this thesis was that the SAS model performed better than URANS, but took longer time to compute simulations than LES, which was the model that generated the best overall results.

  • 23.
    Strandell, Ebbe
    Linköping University, Department of Science and Technology. Linköping University, The Institute of Technology.
    Computational Geometry and Surface Reconstruction from Unorganized Point Clouds2007Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This thesis addresses the problem of constructing virtual representations of surfaces only known as clouds of unstructured points in space. This problem is related to many areas including computer graphics, image processing, computer vision, reverse engineering and geometry studies. Data sets can be acquired from a wide range of sources including Computer Tomography (CT), Magnetic Resonance Imaging (MRI), medical cryosections, laser range scanners, seismic surveys or mathematical models. This thesis will furthermost focus on medical samples acquired through cryosections of bodies.

    In this thesis report various computational geometry approaches of surface reconstruction are evaluated in terms of adequateness for scientific uses. Two methods called “γ-regular shapes” and “the Power Crust” are implemented and evaluated. The contribution of this work is the proposal of a new hybrid method of surface reconstruction in three dimensions. The underlying thought of the hybrid solution is to utilize the inverse medial axis transformation, defined by the Power Crust, to recover holes that may appear in the three dimensional γ-regular shapes.

  • 24.
    Eriksson, Peter
    Linköping University, Department of Physics, Chemistry and Biology. Linköping University, The Institute of Technology.
    A new synthesis of nanoparticles designed for Biomedical Imaging. A pilot study.2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This thesis presents a new procedure for synthesizing nanoparticles with fluorescent and MRI contrast enhancement properties. The produced nanoparticles consist of mixtures between two well-known materials; zinc oxide and gadolinium oxide. Zinc oxide is a well-known semiconductor with visible fluorescence and gadolinium oxide is a paramagnetic material exhibiting excellent magnetic properties for enhancing contrast in MRI. 

    The presented synthesis is based on a recently published protocol by Zhang et al [1], for synthesis of pure zinc oxide nanoparticles. The procedure includes a precursor synthesis where respectively metal is dissolved in a solution of water and methacrylic acid. Thereafter the precursors are mixed and dissolved in TEG for a combined nucleation and in-situ polymerization step.

    The work in this thesis is multidisciplinary involving molecular design, chemical synthesis, nanoparticle preparation, purification, characterization and also biological applications. The first rounds of nanoparticles were readily dispersible in water, had adequate fluorescent properties, were in a size range suited for in vivo applications and had better relaxivity properties compared to commonly used contrast agent. These results motivate future work including further optimizations of the protocol. This new nanomaterial has high potential as contrast agent for biomedical imaging.

  • 25.
    Dadi, Kamalaker Reddy
    Linköping University, Department of Biomedical Engineering. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Circadian Rhythms in the Brain - A first step2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Circadian Rhythms (CR) are driven by a biological clock called as suprachiasmaticnucleus (SCN), located in a brain region called the hypothalamus. These rhythms are very much necessary in maintaining the sleep and wake cycle at appropriate times in a day. As a starting step towards non-invasive investigation of CR, aim is to study changes in the physiological processes of two Regions of Interest (ROI), the hypothalamus and the visual cortex. This was studied using a functional Magnetic Resonance Imaging (fMRI) technique to investigate for any changes or differences in the Blood Oxygen Level Dependent (BOLD)signals extracted from the ROI during a visual stimulation. We acquired and processed fMRI data to extract BOLD signals from ROI and the extracted signals are again further used to study the correlation with the experimental ON-OFF design paradigm.

    The extracted BOLD signals varied a lot between the two specified brain regions within the same subject and between three types of fMRI data. These variations were found in terms of number of activated voxels and also Signal to Noise ratio(SNR) level present in the signals. The number of activated voxels and SNR werehigh in visual cortex whereas low number of activated voxels and low SNR were found in hypothalamus. The correlation between BOLD responses from primaryvisual cortex were shown as positive with the experimental stimulation whereas BOLD responses extracted from hypothalamus have shown a negative correlation in time with the experimental stimulation.

    As a start up of the project, these BOLD responses can provide references for a future use in research studies, especially to further study about change in phase of the BOLD signal extracted exactly from the SCN. These phase responses can then be used to study physiological processing in subjects affected by sleep disorders.

  • 26.
    Kus, Emre
    Linköping University, Department of Biomedical Engineering. Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, The Institute of Technology.
    Estimation and visualization of relative pressure fields in the human heart from time resolved MRI flow data2013Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Heart diseases are the leading cause of death in developed countries, hence, understanding of the hemodynamics of the heart is critically important to enable methods for cardiovascular diagnosis. Assessment of intracardiac blood pressure is highly interesting as blood flow is driven by the pressure differences.

    Phase-contrast magnetic resonance imaging (PC-MRI) is a tool for measuring blood flow and has a wide range of cardiovascular applications. Based on previous studies, an approach to estimate the relative pressure fields in the human heart from three-dimensional time-resolved PC-MRI velocity data was implemented and evaluated. The relative pressure fields were obtained by solving the pressure Poisson equation, using a multi-grid approach. The method was evaluated on a numerical phantom and on PC-MRI data from one healthy subject and one patient with dilated cardiomyopathy. The pressure field was visualized in combination with blood flow data and morphological images.

    Results indicate that the used approach works well for cardiac relative pressure estimation and are in agreement with findings from previous research. The complete spatial and temporal coverage of relative pressure enables a higher understanding of physiology and pathophysiology of the human heart and is expected to give new insights for clinical investigations.

  • 27.
    Ross, Steffen
    et al.
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Faculty of Health Sciences.
    Ebner, Lukas
    University of Bern, Switzerland .
    Flach, Patricia
    University Hospital of Zürich, Switzerland and University of Zurich, Switzerland .
    Brodhage, Rolf
    Roentgen Institut Brunnhof, Bern, Switzerland.
    Bolliger, Stephan A.
    University of Bern, Switzerland .
    Christe, Andreas
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Faculty of Health Sciences.
    Thali, Michael J.
    University of Zurich, Switzerland .
    Postmortem Whole-Body MRI in Traumatic Causes of Death2012In: American Journal of Roentgenology, ISSN 0361-803X, E-ISSN 1546-3141, Vol. 199, no 6, 1186-1192 p.Article in journal (Refereed)
    Abstract [en]

    OBJECTIVE:

    The aim of this study was to determine the sensitivity and specificity of postmortem whole-body MRI for typical injuries resulting from traumatic causes of death.

    MATERIALS AND METHODS:

    Forty cases of accidental death were evaluated with postmortem whole-body MRI. Imaging was conducted according to a standard protocol, and each examination had an average duration of 90 minutes. The imaging findings were correlated with the autopsy findings, which served as the reference standard.

    RESULTS:

    MRI showed the main pathologic process leading to death in 39 of the 40 cases. The sensitivity of postmortem MRI ranged from 100% (pneumothorax) to 40% (fractures of the upper extremities). In general, MRI had a high level of performance for depicting soft-tissue lesions, such as subcutaneous hematoma (e.g., galeal hematoma with a sensitivity 95%). The sensitivity of MRI was remarkably lower for lesions of the upper abdominal organs (liver, 80%; spleen, 50%; pancreas, 60%; kidneys, 66%).

    CONCLUSION:

    Postmortem whole-body MRI had overall good performance for depicting traumatic findings in corpses and therefore may serve an important role as an adjunct to classic autopsy for the forensic examination of cases of traumatic cause of death. However, the reduced sensitivity of postmortem MRI for lacerations of the upper abdominal organs and the observed superimposition of antemortem findings and postmortem findings (e.g., in the pulmonary tissue) in this retrospective study suggest that whole-body postmortem MRI not be recommended as a replacement for classic autopsy.

  • 28.
    Budde, Kiran Kumar
    Linköping University, Department of Electrical Engineering, Computer Vision.
    A Matlab Toolbox for fMRI Data Analysis: Detection, Estimation and Brain Connectivity2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Functional Magnetic Resonance Imaging (fMRI) is one of the best techniques for neuroimaging and has revolutionized the way to understand the brain functions. It measures the changes in the blood oxygen level-dependent (BOLD) signal which is related to the neuronal activity. Complexity of the data, presence of different types of noises and the massive amount of data makes the fMRI data analysis a challenging one. It demands efficient signal processing and statistical analysis methods.  The inference of the analysis is used by the physicians, neurologists and researchers for better understanding of the brain functions.

         The purpose of this study is to design a toolbox for fMRI data analysis. It includes methods to detect the brain activity maps, estimation of the hemodynamic response (HDR) and the connectivity of the brain structures. This toolbox provides methods for detection of activated brain regions measured with Bayesian estimator. Results are compared with the conventional methods such as t-test, ordinary least squares (OLS) and weighted least squares (WLS). Brain activation and HDR are estimated with linear adaptive model and nonlinear method based on radial basis function (RBF) neural network. Nonlinear autoregressive with exogenous inputs (NARX) neural network is developed to model the dynamics of the fMRI data.  This toolbox also provides methods to brain connectivity such as functional connectivity and effective connectivity.  These methods are examined on simulated and real fMRI datasets.

  • 29.
    Morren, Geert
    et al.
    Department of General Surgery, University of Maastricht, Maastricht, The Netherlands.
    Beets-Tan, R. G. H.
    Department of Radiology, University of Maastricht, Maastricht, The Netherlands.
    van Engelshoven, J. M. A.
    Department of Radiology, University of Maastricht, Maastricht, The Netherlands.
    Anatomy of the anal canal and perianal structures as defined by phased-array magnetic resonance imaging2001In: British Journal of Surgery, ISSN 0007-1323, E-ISSN 1365-2168, Vol. 88, no 11, 1506-1512 p.Article in journal (Refereed)
    Abstract [en]

    Background:

    The anatomy of the anal canal and perianal structures has been imaged using endoluminal magnetic resonance imaging (MRI). Phased-array MRI avoids the use of an endoluminal coil that may distort anatomy. The aim of this study was to describe the anatomy of the anal canal and perianal structures using phased-array MRI.

    Methods:

    Imaging was performed in 14 men and 19 nulliparous women. The dimensions of the anal canal, puborectalis, external anal sphincter, perineal body, superficial transverse perineal muscle, bulbospongiosus, ischiocavernosus and anococcygeal body were measured in different planes, and sex differences were calculated.

    Results:

    The lateral canal was significantly longer than its anterior and posterior part (P < 0·001). The anterior external anal sphincter was shorter in women than in men (P = 0·01) and occupied, respectively, 30 and 38 per cent of the anal canal length (P = 0·001). The caudal ends of the external anal sphincter formed a double layer. The perineal body was thicker in women than in men (P < 0·001) and easier to define. The superficial transverse muscles had a lateral and caudal extension to the ischiopubic bones. The bulbospongiosus was thicker in men than in women (P < 0·001). The ischiocavernosus and anococcygeal body had the same dimensions in both sexes.

    Conclusion:

    Phased-array MRI is a non-invasive technique that allows an accurate description of the normal anatomy of the anal canal and perianal structures.

  • 30.
    Baeza Ortega, José Antonio
    Linköping University, Center for Medical Image Science and Visualization, CMIV. Linköping University, Department of Biomedical Engineering. Linköping University, The Institute of Technology.
    Combined Visualization of Intracardiac Blood Flow and Wall Motion Assessed by MRI2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    MRI is a well known and widely spread technique to characterize cardiac pathologies due to its high spatial resolution, its accessibility and its adjustable contrast among soft tissues.

    In attempt to close the gap between blood flow, myocardial movement and the cardiac fucntion, researching in the MRI field addresses the quantification of some of the most relevant blood and myocardial parameters.

    During this proyect a new tool that allows reading, postprocessing, quantifying and visualizing 2D motion sense MR data has been developed. In order to analyze intracardiac blood flow and wall motion, the new tool quantifies velocity, turbulent kinetic energy, pressure and strain.

    In the results section the final tool is presented, describing the visualization modes, which represent the quantified parameters both individually and combined; and detailing auxiliary tool features as masking, thresholding, zooming, and cursors.

    Finally, thecnical aspects as the convenience of two dimensional examinations to create compact tools, and the challenges of masking as part of the relative pressure calculation, among others, are discussed; ending up with the proposal of some future developments.

  • 31.
    Wondim, Yonas kassaw
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Hyperspectral Image Analysis Algorithm for Characterizing Human Tissue2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    AbstractIn the field of Biomedical Optics measurement of tissue optical properties, like absorption, scattering, and reduced scattering coefficient, has gained importance for therapeutic and diagnostic applications. Accuracy in determining the optical properties is of vital importance to quantitatively determine chromophores in tissue.There are different techniques used to quantify tissue chromophores. Reflectance spectroscopy is one of the most common methods to rapidly and accurately characterize the blood amount and oxygen saturation in the microcirculation. With a hyper spectral imaging (HSI) device it is possible to capture images with spectral information that depends both on tissue absorption and scattering. To analyze this data software that accounts for both absorption and scattering event needs to be developed.In this thesis work an HSI algorithm, capable of assessing tissue oxygenation while accounting for both tissue absorption and scattering, is developed. The complete imaging system comprises: a light source, a liquid crystal tunable filter (LCTF), a camera lens, a CCD camera, control units and power supply for light source and filter, and a computer.This work also presents a Graphic processing Unit (GPU) implementation of the developed HSI algorithm, which is found computationally demanding. It is found that the GPU implementation outperforms the Matlab “lsqnonneg” function by the order of 5-7X.At the end, the HSI system and the developed algorithm is evaluated in two experiments. In the first experiment the concentration of chromophores is assessed while occluding the finger tip. In the second experiment the skin is provoked by UV light while checking for Erythema development by analyzing the oxyhemoglobin image at different point of time. In this experiment the melanin concentration change is also checked at different point of time from exposure.It is found that the result matches the theory in the time dependent change of oxyhemoglobin and deoxyhemoglobin. However, the result of melanin does not correspond to the theoretically expected result.

  • 32.
    Narasimha Reddy, Vaka
    Linköping University, Department of Biomedical Engineering, Biomedical Instrumentation. Linköping University, The Institute of Technology.
    Comparison and Optimization of Insonation Strategies for Contrast Enhanced Ultrasound Imaging2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Evolution of vulnerable carotid plaques are crucial reason for cerebral ischemic strokes and identifying them in the early stage can become very important in avoiding the risk of stroke. In order to improve the identification and quantification accuracy of infancy plaques better visualization techniques are needed. Improving the visualization and quantification of neovascularization in carotid plaque using contrast enhanced ultrasound imaging still remains a challenging task. In this thesis work, three optimization techniques are proposed, which showed an improvement in the sensitivity of contrast agents when compared to the conventional clinical settings and insonation strategies. They are as follows:1) Insonation at harmonic specific (2nd harmonic) resonance frequency instead of resonance frequency based on maximum energy absorption provides enhanced nonlinear contribution.2) At high frequency ultrasound imaging, shorter pulse length will provide improved harmonic signal content when compared to longer pulse lengths. Applying this concept to multi- pulse sequencing (Pulse Inversion and Cadence contrast pulse sequencing) resulted in increased magnitude of the remaining harmonic signal after pulse summations.3) Peak negative pressure optimization of Pulse Inversion and Cadence contrast pulse sequencing was showed to further enhance the nonlinear content of the backscattered signal from contrast microbubbles without increasing the safety limits, defined by the mechanical index.The results presented in this thesis are based on computational modeling (Bubblesim software) and as a future continuation we plan to verify the simulation results with vitro studies.

  • 33.
    Forsgren, Mikael Fredrik
    Linköping University, Department of Medical and Health Sciences, Radiation Physics. Linköping University, Faculty of Health Sciences.
    Human Whole Body Pharmacokinetic Minimal Model for the Liver Specific Contrast Agent Gd-EOB-DTPA2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Magnetic resonance imaging (MRI) of the liver is an important non-invasive tool for diagnosing liver disease. A key application is dynamic contrast enhanced magnetic resonance imaging (DCE-MRI). With the use of the hepatocyte specific contrast agent (CA) Gd-EOB-DTPA it is now possible to evaluate the liver function. Beyond traditional qualitative evaluation of the DCE-MRI images, parametric quantitative techniques are on the rise which yields more objective evaluations. Systems biology is a gradually expanding field using mathematical modeling to gain deeper mechanistic understanding in complex biological systems. The aim of this thesis to combine these two fields in order to derive a physiologically accurate minimal whole body model that can be used to quantitatively evaluate liver function using clinical DCE-MRI examinations. 

    The work is based on two previously published sources of data using Gd-EOB-DTPA in healthy humans; i) a region of interest analysis of the liver using DCE-MRI ii) a pre-clinical evaluation of the contrast agent using blood sampling.  The modeling framework consists of a system of ordinary differential equations for the contrast agent dynamics and non-linear models for conversion of contrast agent concentrations to relaxivity values in the DCE-MRI image volumes.

    Using a χ2-test I have shown that the model, with high probability, can fit the experimental data for doses up to twenty times the clinically used one, using the same parameters for all doses. The results also show that some of the parameters governing the hepatocyte flux of CA can be numerically identifiable. Future applications with the model might be as a basis for regional liver function assessment. This can lead to disease diagnosis and progression evaluation for physicians as well as support for surgeons planning liver resection.

  • 34.
    Samuelsson, Johanna
    Linköping University, Department of Medical and Health Sciences.
    Visualization of Regional Liver Function with Hepatobiliary Contrast Agent Gd-EOB-DTPA2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Liver biopsy is a very common, but invasive procedure for diagnosing liver disease. However, such a biopsy may result in severe complications and in some cases even death. Therefore, it would be highly desirable to develop a non-invasive method which would provide the same amount of information on staging of the disease and also the location of pathologies. This thesis describes the implementation of such a non-invasive method for visualizing and quantifying liver function by the combination of MRI (Magnetic Resonance Imaging), image reconstruction, and image analysis, and pharmacokinetic modeling. The first attempt involved automatic segmentation, functional clustering (k-means) and classification (kNN) of in-data (liver, spleen and blood vessel segments) in the pharmacokinetic model. However, after implementing and analyzing this method some important issues were identified and the image segmentation method was therefore revised. The segmentation method that was subsequently developed involved a semi-automatic procedure, based on a modified image forest transform (IFT). The data were then simulated and optimized using a pharmacokinetic model describing the pharmacokinetics of the liver specific contrast agent Gd-EOB-DTPA in the human body. The output from the modeling procedure was then further analyzed, using a least-squares method, in order to assess liver function by estimating the fractions of hepatocytes, extracellular extravascular space (EES) and blood plasma in each voxel of the image. The result were in fair agreement with literature values, although further analyses and developments will be required in order to validate and also to confirm the accuracy of the method.

  • 35.
    Ahlman, Gustav
    Linköping University, Department of Electrical Engineering, Computer Vision.
    Improved Temporal Resolution Using Parallel Imaging in Radial-Cartesian 3D functional MRI2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    MRI (Magnetic Resonance Imaging) is a medical imaging method that uses magnetic fields in order to retrieve images of the human body. This thesis revolves around a novel acquisition method of 3D fMRI (functional Magnetic Resonance Imaging) called PRESTO-CAN that uses a radial pattern in order to sample the (kx,kz)-plane of k-space (the frequency domain), and a Cartesian sample pattern in the ky-direction. The radial sample pattern allows for a denser sampling of the central parts of k-space, which contain the most basic frequency information about the structure of the recorded object. This allows for higher temporal resolution to be achieved compared with other sampling methods since a fewer amount of total samples are needed in order to retrieve enough information about how the object has changed over time. Since fMRI is mainly used for monitoring blood flow in the brain, increased temporal resolution means that we can be able to track fast changes in brain activity more efficiently.The temporal resolution can be further improved by reducing the time needed for scanning, which in turn can be achieved by applying parallel imaging. One such parallel imaging method is SENSE (SENSitivity Encoding). The scan time is reduced by decreasing the sampling density, which causes aliasing in the recorded images. The aliasing is removed by the SENSE method by utilizing the extra information provided by the fact that multiple receiver coils with differing sensitivities are used during the acquisition. By measuring the sensitivities of the respective receiver coils and solving an equation system with the aliased images, it is possible to calculate how they would have looked like without aliasing.In this master thesis, SENSE has been successfully implemented in PRESTO-CAN. By using normalized convolution in order to refine the sensitivity maps of the receiver coils, images with satisfying quality was able to be reconstructed when reducing the k-space sample rate by a factor of 2, and images of relatively good quality also when the sample rate was reduced by a factor of 4. In this way, this thesis has been able to contribute to the improvement of the temporal resolution of the PRESTO-CAN method.

  • 36.
    Frånlund, Ebba
    Linköping University, Department of Physics, Chemistry and Biology.
    Exon sequencing of the gene encoding UCMA/GRP in healthy and clinical subjects2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Mineralization of soft tissues can cause significantly increased morbidity and mortality. The mechanism for this process is still unknown; however, patients with chronic kidney disease (CKD) are at high risk of developing vascular calcifications. Coronary artery calcification occurs faster in CKD patients undergoing dialysis in comparison with the general population. The pathological process of vascular calcification is the leading cause of death in patients with CKD.

     

    Upper zone of growth plate and cartilage matrix associated protein (UCMA) is a novel vitamin-K dependent (VKD) protein expressed in bone and the vascular system. The UCMA protein contains 15 γ-carboxyglutamic acid (Gla) residues in its 138 residue sequence which is the highest ratio between the number of Gla-residues and the size of the mature protein found in any protein so far. These Gla-residues form a domain that gives unique calcium binding properties for UCMA with high affinity for calcium phosphate crystals (i.e., hydroxyapatite). Even though the function of UCMA remains to be elucidated, it has been speculated that UCMA inhibits calcification of soft tissues and could therefore have a protective function against vascular calcification. Any mutations in the gene coding for UCMA might lead to a diminished function or defective protein.

     

    The aim of this study was to determine whether the gene encoding UCMA in patients with the most progressed stage of CKD (stage 5 CKD) contained any mutations. This was accomplished by performing a full re-sequencing of all five exons with dideoxy sequencing in 16 patients with stage 5 CKD on heamodialysis. If any mutations were discovered, pyrosequencing would be performed on 98 healthy control individuals. This would help to determine if the mutation was exclusive for the patients or existed in the general population as well.

     

    Genomic DNA was extracted from whole blood originating from 16 patients with CKD on haemodialysis. Each of UCMAs five exons were amplified with PCR and the results were visualized using gel electrophoresis. Each exon was re-sequenced and pyrosequencing was performed on 98 healthy control samples. The acquired results were compared with the sequence of the UCMA gene identified at NCBI-GenBank (NCBI, build 37.2, NM_145314.1, Gene ID: 221044) and the Ensemble genome browser (ENSG00000165623). In addition, the frequencies of each SNP were calculated and compared with a study at the Ensemble database originating from the 1000 genomes project (1000GENOMES:low_coverage: CEU).

     

    Because the population of our study group was too small to yield appropriate power for statistical calculations, no definite conclusions could be drawn from the acquired results. Nevertheless, this is the first patient group with CKD ever studied and should thus be regarded as a pilot study due to the limited size. However, no indication was found that UCMA had major defects in the investigated patients. Instead, a heterozygous transversion mutation was found in SNP rs4750328, indicating that the site of this SNP is subject to other modifications. Furthermore, a novel SNP was discovered which has not been described in other populations to our knowledge. The novel SNP is non-synonymous (i.e., causes an amino acid exchange) and located at the carboxyl-terminal of the protein. A serine is incorporated instead of threonine giving a 138Thr>Ser change since the last ACC codon in exon 5 (adjacent to the stop codon) is altered to an AGC codon. The UCMA 138Thr>Ser polymorphism was submitted to the dbSNP database and has been assigned the accession number ss283927876, which will be publicly available upon the release of the next dbSNP Build, B134. In order to determine the physiological significance of the discovered SNP, functional studies are required on both the wild-type and mutated UCMA variants.

  • 37.
    Thomasson, Viola
    Linköping University, Department of Electrical Engineering, Computer Vision.
    Liver Tumor Segmentation Using Level Sets and Region Growing2011Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Medical imaging is an important tool for diagnosis and treatment planning today. However as the demand for efficiency increases at the same time as the data volumes grow immensely, the need for computer assisted analysis, such as image segmentation, to help and guide the practitioner increases.

    Medical image segmentation could be used for various different tasks, the localization and delineation of pathologies such as cancer tumors is just one example. Numerous problems with noise and image artifacts in the generated images make the segmentation a difficult task, and the developer is forced to choose between speed and performance. In clinical practise, however, this is impossible as both speed and performance are crucial. One solution to this problem might be to involve the user more in the segmentation, using interactivite algorithms where the user might influence the segmentation for an improved result.

    This thesis has concentrated on finding a fast and interactive segmentation method for liver tumor segmentation. Various different methods were explored, and a few were chosen for implementation and further development. Two methods appeared to be the most promising, Bayesian Region Growing (BRG) and Level Set.

    An interactive Level Set algorithm emerged as the best alternative for the interactivity of the algorithm, and could be used in combination with both BRG and Level Set. A new data term based on a probability model instead of image edges was also explored for the Level Set-method, and proved to be more promising than the original one. The probability based Level Set and the BRG method both provided good quality results, but the fastest of the two was the BRG-method, which could segment a tumor present in 25 CT image slices in less than 10 seconds when implemented in Matlab and mex-C++ code on an ACPI x64-based PC with two 2.4 GHz Intel(R) Core(TM) 2CPU and 8 GB RAM memory. The interactive Level Set could be succesfully used as an interactive addition to the automatic method, but its usefulness was somewhat reduced by its slow processing time ( 1.5 s/slice) and the relative complexity of the needed user interactions.

  • 38.
    Andersson, Ida
    Linköping University, Department of Computer and Information Science.
    Design of Hosted ASP Solution for an Imaging Informatics System2011Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    PACS (Picture Archiving and Communication System) are IT systems used for distributing, viewing and archiving digital images in radiology. Sectra Imtec AB develops and markets Sectra's PACS systems as large enterprise solutions where the customers pay for hardware, software licenses and support.

    The background to the study was that interesting business opportunities lies in providing Sectra PACS as a hosted ASP (Application Service Provider) solution through the Internet. This solution would make it possible to run PACS clients connected to the same server on many different sites, requiring only an internet connection. It would decrease the need of on-site hardware, software and service. The purpose of the study is to investigate obstacles and opportunities for development, adaptation and integration of a hosted ASP solution for the current Sectra PACS and to develop a prototype based on these investigations.

    The method Case Study Research is used to develop a lo-fi (low fidelity) prototype for hosted ASP solution for Sectra PACS. User analysis is made through PACT (People, Activities, Contexts and Technologies) analysis, the stakeholder model and by visiting a clinic.

    Focus has been on developing a prototype where changes to the current Sectra PACS are kept on a minimum level. This has resulted in that the hosted ASP solution could be implemented without a lot of new development, only small changes in the current Sectra PACS are necessary. The lo-fi prototype provides an overview of the hosted ASP solution and covers different areas; from server configurations to client configuration and legal aspects.

  • 39.
    Wallstedt, Maria
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics .
    Evaluation of blood interactions with a drug loaded protein matrix2011Independent thesis Advanced level (degree of Master (One Year)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Many things might happen in the body when a titanium implant is inserted into bone. Examples are activation of the immune system and imbalance between bone formation and bone resorption, which might lead to damaged bone around the implant and at worse, loosening of the implant.

    Bisphosphonates, BP’s, is a class of drugs that is able to decrease the osteoclast (bone resorption cell) activity and thereby strengthen the bone. FibMat2.0 is a fibrinogen matrix and consists of a thin protein layer which can be applied on an implant and act as a local drug delivery system.

    The work in this thesis was divided into two parts where aim of the first part was to study FibMat2.0 with integrated BP’s, and their effect in the presence of blood. The aim for the second part was to determine whether it was possible to incorporate antithrombotic drugs into the fibrinogen matrix. No detection method for the amount of drugs incorporated into the fibrinogen matrix was used but the fact that the drugs gave effect was verifying that it is possible to integrate other drugs than BP’s into FibMat2.0. Methods that have been used in the experiments in presence of blood are imaging of coagulation, fluorescence microscopy and cone-and-plate.

    For the first part, the results showed that surfaces incubated with fibrinogen and fibrinogen with integrated BP’s act alike in regard to coagulation and platelet adhesion. Compared to titanium, which is known to be a biocompatible material, the surfaces with fibrinogen and fibrinogen with BP’s behave similar in regard to platelet adhesion. When it comes to coagulation, the surfaces coated with fibrinogen with or without an addition of BP’s have shown a longer coagulation time compared to the clean titanium surface.

    For the second part, some conclusions have been drawn according to the results. Heparin and hirudin have shown anticoagulant effects when integrated in the matrix. The platelet inhibitor cangrelor seemed to have better effect when added in blood and incubated compared to incubation with the platelet inhibitor on the surface before incubation in blood. Finally, when combining heparin and cangrelor, very clear differences in regard to formation of fibrin network could be seen. It seems promising to be able to load different kind of drugs in FibMat2.0.

  • 40.
    Dahlbom, Gro
    Linköping University, Department of Computer and Information Science.
    The art of saving life: Interaction of the initial trauma care system from a cognitive science persepctive2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Trauma care is the treatment of patients with injuries caused by external forces, for instance car crashes, assaults or fall accidents. These urgent patients typically arrive at the hospital’s Emergency Department, where they are treated by an interdisciplinary team of physicians and nurses, who collaborate to identify and address life-threatening injuries.

    In this thesis, the urgent phase of trauma care has been explored through observations of trauma calls and interviews with trauma care professionals, with the purpose of mapping the workflow and providing a basis for a discussion of IT systems within trauma radiology. The professionals, procedures and tools involved are collectively described as the initial trauma care system. There has been a focus on interaction between the units of this system, as well as on how decisions regarding treatment are made, often with the help of medical imaging.

    The initial trauma care system functions under significant time pressure, striving towards the well-defined objective of saving the life of the patient. To a great extent the system relies on standardized procedures, aiming for screening life-threatening injuries. The trauma team features a clear hierarchy and distinct roles, where the team leader role is considered vital for the team’s performance. Experience is valued and important for everyone, especially since the team often makes decisions, that may affect the future of the patient, based on incomplete information about the situation. Therefore, CT (computed tomography) images offer valuable decision-making support.

    The respondents are fairly satisfied with the current tools for viewing and manipulating radiological images. Little support for the need of improved or novel IT systems in trauma radiology is found, as is the use for 3D visualization of radiological images in this domain. Informants recognize communication failures and lacking teamwork as the major problems in trauma care. Difficulties like this may be decreased by education and training regarding these issues.

  • 41.
    Salomonsson, Stefan
    Linköping University, Department of Electrical Engineering, Information Coding.
    Simulation of Temperature Distribution in IR Camera Chip2011Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The thesis investigates the temperature distribution in the chip of an infrared camera caused by its read out integrated circuit. The heat from the read out circuits can cause distortions to the thermal image. Knowing the temperature gradient caused by internal heating, it will later be possible to correct the image by implementing algorithms subtracting temperature contribution from the read out integrated circuit.

    The simulated temperature distribution shows a temperature gradient along the edges of the matrix of active bolometers. There are also three hot spots at both the left and right edge of the matrix, caused by heat from the chip temperaturesensors and I/O pads. Heat from the chip temperature sensors also causes an uneven temperature profile in the column of reference pixels, possibly causing imperfections in the image at the levels of the sensors.

    Simulations of bolometer row biasing are carried out to get information about how biasing affects temperatures in neighbouring rows. The simulations show some row-to-row interference, but the thermal model suffers from having biasing heat inserted directly onto the top surface of the chip, as opposed to having heat originate from the bolometers. To get better simulation results describing the row biasing, a thermal model of the bolometers needs to be included.

    The results indicate a very small temperature increase in the active pixel array, with temperatures not exceeding ten millikelvin. Through comparisons with another similar simulation of the chip, there is reason to believe the simulated temperature increase is a bit low. The other simulation cannot be used to draw any conclusions about the distribution of temperature.

  • 42.
    Larsson, Emanuel
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology .
    Quantitative Analysis of Bone Tissue Engineering Scaffolds and Skull Bones by means of Synchrotron and Conventional X-ray Computed Microtomography2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The study of internal structure of materials has always been an essential issue in a variety of application fields, from the medical radiology to the materials science. X-ray computed microtomography (with both conventional and synchrotron radiation sources) has a great potential for these purposes because its three-dimensional and non destructive nature as well as the fact that it does not require any sample preparation and it allows to study samples under stress or after consecutive treatments.

    The recent developments of new X-ray sources with innovative imaging techniques, as well as novel high resolution detectors, allow moving forward the maximum achievable resolution of this technique to a few micrometers or even less. This contributed to increase its application in biomedical purposes, but also to raise the need for quantitative analysis of the reconstructed data.

    Indeed in most of the cases a quantitative characterization of the samples microstructures is needed to better understand their physical and chemical behavior, the effects of manufacturing process or the response to stress. Dedicated software packages have been developed to perform a geometrical and morphological characterization of the samples texture and to evaluate some typical parameters commonly used to classify porous media such as porosity, cell size distribution, connectivity and anisotropy.

    In this work two case studies have been considered for the application of a quantitative analysis approach to microtomography datasets: the first concerns the characterization of bone ingrowth within tissue engineering scaffolds, while the second is related to the extraction of morphological descriptors for the architecture of human skull bones.

    It will be shown how suitable image processing and analysis techniques are able to effectively quantify significant parameters such as the trabecular thickness of the skull bones as well as the porosity and the degree of connectivity of bone tissue engineering scaffolds. Similar quantitative analysis methods applied to microtomography images have to be considered as an effective methodology for a comprehensive characterization of other biomedical samples.

  • 43.
    Helmersson, Teresa
    Linköping University, Department of Medical and Health Sciences.
    Evaluation of Synthetic MRI for Clinical Use2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Conventional Magnetic Resonance Imaging (MRI) is a qualitative method for obtaining images of softtissues in patients. Conventional MRI is the standard method used today and it results in gray-scaleimages in which the different magnetic properties of biological tissues determine the image contrast. However, the magnitude of the measured signal is only relative and therefore not directlycomparable between images. Synthetic MRI is a relatively new technique which can be used to postsynthesizedifferent images based on absolute measurement of several magnetic properties oftissues. Synthetic MRI can therefore provide quantitative information together with the contrastimages.

    In order to use synthetic MRI clinically an evaluation of the image quality and diagnostic ability isrequired. The purpose of this thesis is to evaluate if synthetic MRI and conventional MRI produceimages with equal contrast.

    A study was designed and conducted for statistical evaluation of contrast and Contrast-to-Noise Ratio(CNR) generated with different imaging methods. A total of 22 patients were examined using bothconventional MRI and synthetic MRI and the results were pairwise analyzed.

    The contrast and CNR could not be stated as equal for the imaging methods. Typically the contrastwas higher in the synthetic images for the T1 and T2 weighted images. This was not observed withCNR which suggests that the noise is higher in the synthetic images. The higher contrast obtained insynthetic images resulted in a better separation of different tissues using synthetic MRI. Thesynthetic T2 FLAIR images contained artifacts that are not good for clinical use. However the fact thatthe different imaging methods produce different image quality is not proven to be clinically decisive.

  • 44.
    Richter, Maja
    Linköping University, Department of Physics, Chemistry and Biology, Applied Physics .
    Study of immune and haemostatic response induced by protein multilayers.2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    FibMat2.0 is a fibrinogen multilayer developed by AddBIO. Other proteins such as immunoglobulin G (IgG) and human serum albumin (HSA) can also be used to build multilayers with the same technique. The aim of this study of FibMat2.0 was to investigate if the manufacturing of the protein multilayer would induce an immune or haemostatic response in the body. The multilayers of IgG and HSA were also studied. Methods such as null ellipsometry, imaging of coagulation and the cone-and-plate setup were used to study immune reactions, activation of the coagulation cascade, and stability of the multilayers.

    Small amounts of plasma proteins were adsorbed to fibrinogen multilayers, but complement proteins adsorbed only to the IgG matrix and high molecular weight kininogen (HMWK) adsorbed only to the HSA monolayer. The imaging of coagulation method indicated that the titanium surface and the HSA monolayer activate surface induced coagulation rapidly, whereas fibrinogen and IgG multilayers demonstrated longer coagulation times. Platelets and a few white blood cells were bound to titanium surfaces and fibrinogen multilayers, but not to IgG multilayers or HSA monolayers.

    A conclusion in this study is that the surface of an implant can be coated with FibMat2.0 without any risks, but more studies are needed to better understand the interactions between the surfaces prepared in the present study and the immune and the haemostatic systems of the human body.

  • 45.
    Larsson, Jonatan
    Linköping University, Department of Biomedical Engineering, Medical Informatics.
    Implementation and evaluation of motion correction for quantitative MRI2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Image registration is the process of aligning two images such that their mutual features overlap. This is of great importance in several medical applications. In 2008 a novel method for simultaneous T1, T2 and proton density quantification was suggested. The method is in the field of quantitative Magnetic Resonance Imaging or qMRI. In qMRI parameters are quantified by a pixel-to-pixel fit of the image intensity as a function of different MR scanner settings. The quantification depends on several volumes of different intensities to be aligned. If a patient moves during the data aquisition the datasets will not be aligned and the results are degraded due to this. Since the quantification takes several minutes there is a considerable risk of patient movements. In this master thesis three image registration methods are presented and a comparison in robustness and speed was made. The phase based algorithm was suited for this problem and limited to finding rigid motion. The other two registration algorithms, originating from the Statistical Parametrical Mapping, SPM, package, were used as references. The result shows that the pixel-to-pixel fit is greatly improved in the datasets with found motion. In the comparison between the different methods the phase based algorithm turned out to be both the fastest and the most robust method.

  • 46.
    Skallberg, Andreas
    Linköping University, Department of Physics, Chemistry and Biology.
    Synthesis and functionalization of Gd-based nanoparticles for MRI contrast enhancement2011Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Magnetic metal oxide nanoparticles for contrast enhancement in Magnetic Resonance Imaging (MRI) have proven to be one of the most promising applications in diagnostic science. The nanoparticles can provide better and more accurate diagnosis by their capability to enhance the contrast between different soft tissues. New and better contrast agents need to be developed, to further improve this contrast enhancement. This thesis is focused on biofunctionalization of gadolinium oxide (Gd2O3) nanoparticles to obtain specific properties for further functionalization with the long term goal to improve the biocompatibility and the biomolecular recognition.

    Gd2O3 nanoparticles have been synthesized by a polyol synthesis and characterized with Transmission Electron Microscopy (TEM), X-ray Photoelectron Spectroscopy (XPS) and Dynamic Light Scattering (DLS).

    Three different capping procedures of Gd2O3 nanoparticles was investigated to obtain improved stability and to present functional groups for further functionalization. Capping molecules used was oleic acid, citric acid and 3-aminopropyl-triethoxysilane (APTES).

    The presence of oleic acid and citric acid was examined with Fourier Transform Infrared Transmission (FT-IR) and XPS. The crystalline nature of Gd2O3 when capped with oleic acid and citric acid was also examined using X-ray powder diffraction (XRPD) and TEM. The capping layer from APTES was examined using XPS and DLS.

    Dialysis and filtration has a crucial role in decreasing the risk of aggregation and increasing the possibilities for functionalization of the Gd2O3 nanoparticles. Diafiltration procedure was studied which may lead to better and quicker filtration.

  • 47.
    Thyr, Per
    Linköping University, Department of Electrical Engineering, Computer Vision. Linköping University, The Institute of Technology.
    Method for Acquisition and Reconstruction of non-Cartesian 3-D fMRI2008Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The PRESTO sequence is a well-known 3-D fMRI imaging sequence. In this sequence the echo planar imaging technique is merged with the echo-shift technique. This combination results in a very fast image acquisition, which is required for fMRI examinations of neural activation in the human brain. The aim of this work was to use the basic Cartesian PRESTO sequence as a framework when developing a novel trajectory using a non-Cartesian grid.

    Our new pulse sequence, PRESTO CAN, rotates the k-space profiles around the ky-axis in a non-Cartesian manner. This results in a high sampling density close to the centre of the k-space, and at the same time it provides sparser data collection of the part of the k-space that contains less useful information. This "can- or cylinder-like" pattern is expected to result in a much faster k-space acquisition without loosing important spatial information.

    A new reconstruction algorithm was also developed. The purpose was to be able to construct an image volume from data obtained using the novel PRESTO CAN sequence. This reconstruction algorithm was based on the gridding technique, and a Kaiser-Bessel window was also used in order to re-sample the data onto a Cartesian grid. This was required to make 3-D Fourier transformation possible. In addition, simulations were also performed in order to verify the function of the reconstruction algorithm. Furthermore, in vitro tests showed that the development of the PRESTO CAN sequence and the corresponding reconstruction algorithm were highly successful.

    In the future, the results can relatively easily be extended and generalized for in vivo investigations. In addition, there are numerous exciting possibilities for extending the basic techniques described in this thesis.

  • 48.
    Hedberg, Rikard
    Linköping University, Department of Electrical Engineering.
    Tree species classification using support vector machine on hyperspectral images2010Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    For several years, FORAN Remote Sensing in Linköping has been using pulseintense laser scannings together with multispectral imaging for developing analysismethods in forestry. One area these laser scannings and images are used for is toclassify the species of single trees in forests. The species have been divided intopine, spruce and deciduous trees, classified by a Maximum Likelihood classifier.This thesis presents the work done on a more spectrally high-resolution imagery,hyperspectral images. These images are divided into more, and finer gradedspectral components, but demand more signal processing. A new classifier, SupportVector Machine, is tested against the previously used Maximum LikelihoodClassifier, to see if it is possible to increase the performance. The classifiers arealso set to divide the deciduous trees into aspen, birch, black alder and gray alder.The thesis shows how the new data set is handled and processed to the differentclassifiers, and shows how a better result can be achieved using a Support VectorMachine.

  • 49.
    Mollén, Albert
    Linköping University, Department of Physics, Chemistry and Biology.
    Investigation of Ageing effects and Image stability in Hybrid Photon Pixel detectors at the LHCb experiment CERN2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The world’s largest particle accelerator, Large Hadron Collider, located at CERN outside Geneva performed its first proton-proton collisions in November 2009. One of the four main experiments is LHCb, studying rare decays of hadrons containing the beauty quark. An essential part of the particle identification in LHCb is made by the two Ring Imaging Cherenkov detectors. These detectors use pixel Hybrid Photon Detectors for detection and imaging of Cherenkov rings. This paper reports on measurements carried out on the Hybrid Photon Detectors, including a discussion of the results. In particular, ageing effect and image stability are studied. A fraction of the photon detectors show a degradation in performance within these fields.

  • 50.
    Sterner, Olof
    Linköping University, Department of Physics, Chemistry and Biology.
    Swelling and protein adsorption characteristics of stimuli-responsive hydrogel gradients2010Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    In this work, a gradient of interpenetrating polymer networks, consisting of anionic and cationic polymers, has been investigated with respect to protein resistant properties and swelling characteristics at different pH and ionic strength conditions.

    The swelling and protein adsorption have been studied using \emph{in situ} spectroscopic ellipsometry(SE) and imaging surface plasmon resonance(iSPR) respectively. It has been shown that, by altering the buffer pH, the region of lowest protein adsorption on the surface could be moved laterally. The swelling has similarly been shown to respond to both changes in pH and ionic strength. Additionally, the arise of surface charge and the polymer swelling in solution, both a consequence of the ionisation of fixed charges on the polymer, have been indicated to occur at different buffer pH.

    The studied polymer systems show promising properties for future applications in, for example, the biosensor area, where the surface chemistry can be tailor-made to work optimally in a given environment.

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