Retinal Image Analysis Using Machine Vision

The topic of this thesis is studying how lesions in retina caused by diabetic retinopathy can be detected from color fundus images by using machine vision methods. Methods for equalizing uneven illumination in fundus images, detecting regions of poor image quality due toinadequate illumination, and recognizing abnormal lesions were developed duringthe work. The developed methods exploit mainly the color information and simpleshape features to detect lesions. In addition, a graphical tool for collecting lesion data was developed. The tool was used by an ophthalmologist who marked lesions in the images to help method development and evaluation. The tool is a general purpose one, and thus it is possible to reuse the tool in similar projects.The developed methods were tested with a separate test set of 128 color fundus images. From test results it was calculated how accurately methods classify abnormal funduses as abnormal (sensitivity) and healthy funduses as normal (specificity). The sensitivity values were 92% for hemorrhages, 73% for red small dots (microaneurysms and small hemorrhages), and 77% for exudates (hard and soft exudates). The specificity values were 75% for hemorrhages, 70% for red small dots, and 50% for exudates. Thus, the developed methods detected hemorrhages accurately and microaneurysms and exudates moderately.

A Graphical Pattern Editor for Java Frameworks

Ohjelmistojen uudelleenkäyttö on hyvin tärkeä käsite ohjelmistotekniikan alueella.Ohjelmistojen uudelleenkäyttötekniikat parantavat ohjelmistokehitysprosessin laatua. Yleisiä ratkaisuja sekä ohjelmiston suunnittelun että arkkitehtuurin uudelleenkäyttöön ovat olio-ohjelmointi ja sovelluskehykset. Tähän asti ei ole ollut olemassa yleisiä tapoja sovelluskehysten erikoistamiseen. Monet nykyääntunnetuista sovelluskehyksistä ovat hyvin suuria ja mutkikkaita. Tällaisten sovelluskehyksien käyttö on monimutkaista myös kokeneille ohjelmoijille. Hyvin dokumentoidut uudelleenkäytettävät sovelluskehyksen rajapinnat parantavat kehyksen käytettävyyttä ja tehostavat myös erikoistamisprosessiakin sovelluskehyksen käyttäjille. Sovelluskehyseditori (framework editor, JavaFrames) on prototyyppityökalu, jota voidaan käyttää yksinkertaistamaan sovelluskehyksen käyttöä. Perusajatus JavaFrames lähestymistavassa ovat erikoistamismallit, joita käytetään kuvamaan sovelluskehyksen uudelleenkäytettäviä rajapintoja. Näihin malleihin perustuen JavaFrames tarjoaa automaattisen lähdekoodi generaattorin, dokumentoinninja arkkitehtuurisääntöjen tarkistuksen. Tämä opinnäyte koskee graafisen mallieditorin kehittämistä JavaFrames ympäristöön. Työssä on laadittu työkalu,jonka avulla voidaan esittää graafisesti erikoistamismalli. Editori sallii uusien mallien luomisen, vanhojen käyttämättä olevien poistamisen, kuten myös yhteyksien lisäämisen mallien välille. Tällainen graafinen tuki JavaFrames ympäristöönvoi huomattavasti yksinkertaistaa sen käyttöä ja tehdä sovellusten kehittämisprosessista joustavamman.

Sleep-Disordered Breathing in Women

Sleep-disordered breathing (SDB) is underdiagnosed in women, probably due to the different gender-related manifestation. We investigated the differences in presentation, symptoms and co-morbidities of SDB in men and in pre- and postmenopausal women by a clinical, retrospective, cross-sectional study of 601 consecutively referred women and 233 age- and BMI-matched male-female pairs studied with the static-chargesensitive bed (SCSB) and an oximeter. Data on the use of nasal CPAP were gathered from the Paimio hospital database, and the co-morbidity information was based on reimbursed medication data from the National Agency for Medicines and the Social Insurance institution. The abnormal breathing episodes at night were more frequent in men than in women, and in postmenopausal women compared to premenopausal ones. Partial upper airway obstruction was the most common type of SDB in both genders but especially in females. BMI and the major symptoms of SDB were similar in pre- and postmenopausal women, and a menopause effect on symptoms was not found. CPAP adherence did not differ between symptomatic patients with partial upper airway obstruction and those presenting with conventional obstructive sleep apnea. Comorbidities were more frequent in SDB patients than in the general Finnish population. Compared to sleep apnea, partial upper airway obstruction was associated with a threefold prevalence of asthma and/or COPD in both genders, and with a 60% reduced prevalence of hypertension in females matched for age and BMI. Our results emphasize that partial upper airway obstruction is not a milder form of SDB but a different entity, the severity of which is underestimated when using the conventional apnea-hypopnea index. It seems clinically relevant to diagnose and treat the co-morbidities and SDB also in patients with partial upper airway obstruction, especially in elderly and symptomatic women.

Evaluation of Bubble Formation and Break Up in Suppression Pools by Using Pattern Recognition Methods

During a possible loss of coolant accident in BWRs, a large amount of steam will be released from the reactor pressure vessel to the suppression pool. Steam will be condensed into the suppression pool causing dynamic and structural loads to the pool. The formation and break up of bubbles can be measured by visual observation using a suitable pattern recognition algorithm. The aim of this study was to improve the preliminary pattern recognition algorithm, developed by Vesa Tanskanen in his doctoral dissertation, by using MATLAB. Video material from the PPOOLEX test facility, recorded during thermal stratification and mixing experiments, was used as a reference in the development of the algorithm. The developed algorithm consists of two parts: the pattern recognition of the bubbles and the analysis of recognized bubble images. The bubble recognition works well, but some errors will appear due to the complex structure of the pool. The results of the image analysis were reasonable. The volume and the surface area of the bubbles were not evaluated. Chugging frequencies calculated by using FFT fitted well into the results of oscillation frequencies measured in the experiments. The pattern recognition algorithm works in the conditions it is designed for. If the measurement configuration will be changed, some modifications have to be done. Numerous improvements are proposed for the future 3D equipment.

Model-View-Controller architectural pattern and its evolution in graphical user interface frameworks

Model-View-Controller (MVC) is an architectural pattern used in software development for graphical user interfaces. It was one of the first proposed solutions in the late 1970s to the Smart UI anti-pattern, which refers to the act of writing all domain logic into a user interface. The original MVC pattern has since evolved in multiple directions, with various names and may confuse many. The goal of this thesis is to present the origin of the MVC pattern and how it has changed over time. Software architecture in general and the MVC’s evolution within web applications are not the primary focus. Fundamen- tal designs are abstracted, and then used to examine the more recent versions. Prob- lems with the subject and its terminology are also presented.

The Role of Oxidative Stress in Environmental Responses of Fennoscandian Animals

All aerobic organisms have to deal with the toxicity of oxygen. Oxygen enables more efficient energy production compared to anaerobic respiration or fermentation, but at the same time reactive oxygen species (ROS) are being formed. ROS can also be produced by external factors such as UV-radiation and contamination. ROS can cause damage to biomolecules such as DNA, lipids and proteins and organisms try to keep the damage as small as possible by repairing biomolecules and metabolizing ROS. All ROS are not harmful, because they are used as signaling molecules. To cope against ROS organism have an antioxidant (AOX) system which consists both enzymatic and non-enzymatic AOX defense. Some AOX are produced by the organism itself and some are gained via diet. In this thesis I studied environmentally caused changes in the redox regulation of different wild vertebrate animals to gain knowledge on the temporal, spatial and pollution-derived-effects on the AOX systems. As study species I used barn swallow, ringed seal and the Baltic salmon. For the barn swallow the main interest was the seasonal fluctuation in the redox regulation and its connection to migration and breeding. The more contaminated ringed seals of the Baltic Sea were compared to seals from cleaner Svalbard to investigate whether they suffered from contaminant induced oxidative stress. The regional and temporal variation in redox regulation and regional variation in mRNA and protein expressions of Baltic salmon were studied to gain knowledge if the salmon from different areas are equally stressed. As a comparative aspect the redox responses of these different species were investigated to see which parts of the AOX system are substantial in which species. Certain parts of AOX system were connected to breeding and others to migration in barn swallows, there was also differences in biotransformation between birds caught from Africa and Finland. The Baltic ringed seal did not differ much from the seals from Svalbard, despite the difference in contaminant load. A possible explanation to this could be the enhanced AOX mechanisms against dive-associated oxidative stress in diving air-breathing animals, which also helps to cope with ROS derived from other sourses. The Baltic salmon from Gulf of Finland (GoF) showed higher activities in their AOX defense enzymes and more oxidative damage than fish from other areas. Also on mRNA and proteomic level, stress related metabolic changes were most profound in in the fish from GoF. Mainly my findings on species related differences followed the pattern of mammals showing highest activities and least damage and birds showing lower activities and most damage, fish being intermediate. In general, the glutathione recycling-related enzymes and the ratio of oxidized and reduced glutathione seemed to be the most affected parameters in all of the species.