Eye Fundus Image Analysis for Automatic Detection of Diabetic Retinopathy

Diabetes is a rapidly increasing worldwide problem which is characterised by defective metabolism of glucose that causes long-term dysfunction and failure of various organs. The most common complication of diabetes is diabetic retinopathy (DR), which is one of the primary causes of blindness and visual impairment in adults. The rapid increase of diabetes pushes the limits of the current DR screening capabilities for which the digital imaging of the eye fundus (retinal imaging), and automatic or semi-automatic image analysis algorithms provide a potential solution. In this work, the use of colour in the detection of diabetic retinopathy is statistically studied using a supervised algorithm based on one-class classification and Gaussian mixture model estimation. The presented algorithm distinguishes a certain diabetic lesion type from all other possible objects in eye fundus images by only estimating the probability density function of that certain lesion type. For the training and ground truth estimation, the algorithm combines manual annotations of several experts for which the best practices were experimentally selected. By assessing the algorithm’s performance while conducting experiments with the colour space selection, both illuminance and colour correction, and background class information, the use of colour in the detection of diabetic retinopathy was quantitatively evaluated. Another contribution of this work is the benchmarking framework for eye fundus image analysis algorithms needed for the development of the automatic DR detection algorithms. The benchmarking framework provides guidelines on how to construct a benchmarking database that comprises true patient images, ground truth, and an evaluation protocol. The evaluation is based on the standard receiver operating characteristics analysis and it follows the medical practice in the decision making providing protocols for image- and pixel-based evaluations. During the work, two public medical image databases with ground truth were published: DIARETDB0 and DIARETDB1. The framework, DR databases and the final algorithm, are made public in the web to set the baseline results for automatic detection of diabetic retinopathy. Although deviating from the general context of the thesis, a simple and effective optic disc localisation method is presented. The optic disc localisation is discussed, since normal eye fundus structures are fundamental in the characterisation of DR.

Spectral retinal image processing and analysis for ophthalmology

Diabetic retinopathy, age-related macular degeneration and glaucoma are the leading causes of blindness worldwide. Automatic methods for diagnosis exist, but their performance is limited by the quality of the data. Spectral retinal images provide a significantly better representation of the colour information than common grayscale or red-green-blue retinal imaging, having the potential to improve the performance of automatic diagnosis methods. This work studies the image processing techniques required for composing spectral retinal images with accurate reflection spectra, including wavelength channel image registration, spectral and spatial calibration, illumination correction, and the estimation of depth information from image disparities. The composition of a spectral retinal image database of patients with diabetic retinopathy is described. The database includes gold standards for a number of pathologies and retinal structures, marked by two expert ophthalmologists. The diagnostic applications of the reflectance spectra are studied using supervised classifiers for lesion detection. In addition, inversion of a model of light transport is used to estimate histological parameters from the reflectance spectra. Experimental results suggest that the methods for composing, calibrating and postprocessing spectral images presented in this work can be used to improve the quality of the spectral data. The experiments on the direct and indirect use of the data show the diagnostic potential of spectral retinal data over standard retinal images. The use of spectral data could improve automatic and semi-automated diagnostics for the screening of retinal diseases, for the quantitative detection of retinal changes for follow-up, clinically relevant end-points for clinical studies and development of new therapeutic modalities.

Pulsatile Blood Flow Simulations in Computed Tomography(CT) Scan-Based and Idealized Geometries of Human Aorta

Blood flow in human aorta is an unsteady and complex phenomenon. The complex patterns are related to the geometrical features like curvature, bends, and branching and pulsatile nature of flow from left ventricle of heart. The aim of this work was to understand the effect of aorta geometry on the flow dynamics. To achieve this, 3D realistic and idealized models of descending aorta were reconstructed from Computed Tomography (CT) images of a female patient. The geometries were reconstructed using medical image processing code. The blood flow in aorta was assumed to be laminar and incompressible and the blood was assumed to be Newtonian fluid. A time dependent pulsatile and parabolic boundary condition was deployed at inlet. Steady and unsteady blood flow simulations were performed in real and idealized geometries of descending aorta using a Finite Volume Method (FVM) code. Analysis of Wall Shear Stress (WSS) distribution, pressure distribution, and axial velocity profiles were carried out in both geometries at steady and unsteady state conditions. The results obtained in thesis work reveal that the idealization of geometry underestimates the values of WSS especially near the region with sudden change of diameter. However, the resultant pressure and velocity in idealized geometry are close to those in real geometry

Application of Computational Fluid Dynamics in Modeling Blood Flow in Human Thoracic Aorta

The aim of this study was to simulate blood flow in thoracic human aorta and understand the role of flow dynamics in the initialization and localization of atherosclerotic plaque in human thoracic aorta. The blood flow dynamics in idealized and realistic models of human thoracic aorta were numerically simulated in three idealized and two realistic thoracic aorta models. The idealized models of thoracic aorta were reconstructed with measurements available from literature, and the realistic models of thoracic aorta were constructed by image processing Computed Tomographic (CT) images. The CT images were made available by South Karelia Central Hospital in Lappeenranta. The reconstruction of thoracic aorta consisted of operations, such as contrast adjustment, image segmentations, and 3D surface rendering. Additional design operations were performed to make the aorta model compatible for the numerical method based computer code. The image processing and design operations were performed with specialized medical image processing software. Pulsatile pressure and velocity boundary conditions were deployed as inlet boundary conditions. The blood flow was assumed homogeneous and incompressible. The blood was assumed to be a Newtonian fluid. The simulations with idealized models of thoracic aorta were carried out with Finite Element Method based computer code, while the simulations with realistic models of thoracic aorta were carried out with Finite Volume Method based computer code. Simulations were carried out for four cardiac cycles. The distribution of flow, pressure and Wall Shear Stress (WSS) observed during the fourth cardiac cycle were extensively analyzed. The aim of carrying out the simulations with idealized model was to get an estimate of flow dynamics in a realistic aorta model. The motive behind the choice of three aorta models with distinct features was to understand the dependence of flow dynamics on aorta anatomy. Highly disturbed and nonuniform distribution of velocity and WSS was observed in aortic arch, near brachiocephalic, left common artery, and left subclavian artery. On the other hand, the WSS profiles at the roots of branches show significant differences with geometry variation of aorta and branches. The comparison of instantaneous WSS profiles revealed that the model with straight branching arteries had relatively lower WSS compared to that in the aorta model with curved branches. In addition to this, significant differences were observed in the spatial and temporal profiles of WSS, flow, and pressure. The study with idealized model was extended to study blood flow in thoracic aorta under the effects of hypertension and hypotension. One of the idealized aorta models was modified along with the boundary conditions to mimic the thoracic aorta under the effects of hypertension and hypotension. The results of simulations with realistic models extracted from CT scans demonstrated more realistic flow dynamics than that in the idealized models. During systole, the velocity in ascending aorta was skewed towards the outer wall of aortic arch. The flow develops secondary flow patterns as it moves downstream towards aortic arch. Unlike idealized models, the distribution of flow was nonplanar and heavily guided by the artery anatomy. Flow cavitation was observed in the aorta model which was imaged giving longer branches. This could not be properly observed in the model with imaging containing a shorter length for aortic branches. The flow circulation was also observed in the inner wall of the aortic arch. However, during the diastole, the flow profiles were almost flat and regular due the acceleration of flow at the inlet. The flow profiles were weakly turbulent during the flow reversal. The complex flow patterns caused a non-uniform distribution of WSS. High WSS was distributed at the junction of branches and aortic arch. Low WSS was distributed at the proximal part of the junction, while intermedium WSS was distributed in the distal part of the junction. The pulsatile nature of the inflow caused oscillating WSS at the branch entry region and inner curvature of aortic arch. Based on the WSS distribution in the realistic model, one of the aorta models was altered to induce artificial atherosclerotic plaque at the branch entry region and inner curvature of aortic arch. Atherosclerotic plaque causing 50% blockage of lumen was introduced in brachiocephalic artery, common carotid artery, left subclavian artery, and aortic arch. The aim of this part of the study was first to study the effect of stenosis on flow and WSS distribution, understand the effect of shape of atherosclerotic plaque on flow and WSS distribution, and finally to investigate the effect of lumen blockage severity on flow and WSS distributions. The results revealed that the distribution of WSS is significantly affected by plaque with mere 50% stenosis. The asymmetric shape of stenosis causes higher WSS in branching arteries than in the cases with symmetric plaque. The flow dynamics within thoracic aorta models has been extensively studied and reported here. The effects of pressure and arterial anatomy on the flow dynamic were investigated. The distribution of complex flow and WSS is correlated with the localization of atherosclerosis. With the available results we can conclude that the thoracic aorta, with complex anatomy is the most vulnerable artery for the localization and development of atherosclerosis. The flow dynamics and arterial anatomy play a role in the localization of atherosclerosis. The patient specific image based models can be used to diagnose the locations in the aorta vulnerable to the development of arterial diseases such as atherosclerosis.

Packaging concept development for an assortment of medical device products

Diplomityön tavoitteena oli kehittää Wipak Oy:n valmistamille sterilointipakkauksille tulevaisuuden pakkauskonsepti. Sterilointipakkaukset luokitellaan lääkelaitedirektiivin mukaan lisätarvikkeiksi luokan 1 lääkelaitteille, ja tämä näkökulma oli vahvasti mukana konseptin kehityksessä. Lähtökohtana pakkauskonseptin suunnittelulle oli tuotteiden arvoketjussa, eli pakata tuotteet siten että pakkausten avulla voidaan tuottaa lisäarvoa arvoketjun toimijoille. Tavoitteena oli parantaa pakkausten viestintää, toimivuutta/tehokkuutta toimitusketjussa sekä vahvistaa brändin imagoa myynti- ja kuljetuspakkauksen avulla. Lääkinnälliset laitteet ja tarvikkeet ovat lainsäädännön ja normien avulla tarkasti säädeltyjä. Näiden normien vaatimukset asettavat perusteet myynti- ja kuljetuspakkausten kehittämiselle. Tämän lisäksi suunnittelussa on huomioitu asiakkaiden toiveet ja kehitystarpeet. Kirjallisuusosuudessa on keskitytty lääkinnällisten laitteiden pakkausyksiköiden toimintoihin sekä niiden kehitysnäkymiin. Pääpaino on ollut pakkausmerkintöjen ja jäljitettävyyden kehittämisellä, koska tietojen automaattisen tunnistuksen hyödyntäminen lääkintälaitteiden pakkausten arvoketjussa on kasvava trendi. Manuaalisesti tehtävät tuotevirtojen kirjaukset ketjun eri toimijoiden osalta lisäävät riskejä jäljitettävyyden kannalta ja aiheuttavat lisätyötä ja – kustannuksia ketjun kaikille osapuolille. Ehdotus uudesta pakkauskonseptista on kehitetty näiden tietojen pohjalta. Ehdotuksessa on huomioitu lainsäädännöstä ja ketjun toimijoilta tulevat tarpeet, sekä alan tulevaisuuden kehitysnäkymät. Ehdotetun pakkauskonseptin avulla saadaan lisättyä myynti- ja kuljetuspakkausten tehokkuutta, parannettua jäljitettävyyttä ja helpotettu arvoketjun alavirran toimijoiden työtä lisäämällä erillinen sisäpakkaus myyntiyksikön sisälle. Työssä on lisäksi selvitetty pakkauskonseptin kustannusvaikutukset tuotteiden hintaan. Lopussa on ehdotettu jatkotoimenpiteet suunnitelman implementoimisesta käytäntöön.

Adopting the Vaadin Java framework to rebuild VTT’s Web Interfaces and Database Applications

With the growth in new technologies, using online tools have become an everyday lifestyle. It has a greater impact on researchers as the data obtained from various experiments needs to be analyzed and knowledge of programming has become mandatory even for pure biologists. Hence, VTT came up with a new tool, R Executables (REX) which is a web application designed to provide a graphical interface for biological data functions like Image analysis, Gene expression data analysis, plotting, disease and control studies etc., which employs R functions to provide results. REX provides a user interactive application for the biologists to directly enter the values and run the required analysis with a single click. The program processes the given data in the background and prints results rapidly. Due to growth of data and load on server, the interface has gained problems concerning time consumption, poor GUI, data storage issues, security, minimal user interactive experience and crashes with large amount of data. This thesis handles the methods by which these problems were resolved and made REX a better application for the future. The old REX was developed using Python Django and now, a new programming language, Vaadin has been implemented. Vaadin is a Java framework for developing web applications and the programming language is extremely similar to Java with new rich components. Vaadin provides better security, better speed, good and interactive interface. In this thesis, subset functionalities of REX was selected which includes IST bulk plotting and image segmentation and implemented those using Vaadin. A code of 662 lines was programmed by me which included Vaadin as the front-end handler while R language was used for back-end data retrieval, computing and plotting. The application is optimized to allow further functionalities to be migrated with ease from old REX. Future development is focused on including Hight throughput screening functions along with gene expression database handling

Critical elements underpinning the emergence of the medical game ecosystem: gamifying traumatic brain injury rehabilitation in Finland

The healthcare sector is currently in the verge of a reform and thus, the medical game research provide an interesting area of research. The aim of this study is to explore the critical elements underpinning the emergence of the medical game ecosystem with three sub-objectives: (1) to seek who are the key actors involved in the medical game ecosystem and identify their needs, (2) to scrutinise what types of resources are required in medical game development and what types of relationships are needed to secure those resources, and (3) to identify the existing institutions (‘the rules of the game’) affecting the emergence of the medical game ecosystem. The theoretical background consists of service ecosystems literature. The empirical study conducted is based on the semi-structured theme interviews of 25 experts in three relevant fields: games and technology, health and funding. The data was analysed through a theoretical framework that was designed based upon service ecosystems literature. The study proposes that the key actors are divided into five groups: medical game companies, customers, funders, regulatory parties and complementors. Their needs are linked to improving patient motivation and enhancing the healthcare processes resulting in lower costs. Several types of resources, especially skills and knowledge, are required to create a medical game. To gain access to those resources, medical game companies need to build complex networks of relationships. Proficiency in managing those value networks is crucial. In addition, the company should take into account the underlying institutions in the healthcare sector affecting the medical game ecosystem. Three crucial institutions were identified: validation, lack of innovation supporting structures in healthcare and the rising consumerisation. Based on the findings, medical games cannot be made in isolation. A developmental trajectory model of the emerging medical game ecosystem was created based on the empirical data. The relevancy of relationships and resources is dependent on the trajectory that the medical game company at that time resides. Furthermore, creating an official and documented database for clinically valdated medical games was proposed to establish the medical game market and ensure an adequate status for the effective medical games. Finally, ecosystems approach provides interesting future opportunities for research on medical game ecosystems.

Critical elements underpinning the emergence of the medical game ecosystem:gamifying traumatic brain injury rehabilitation in Finland

The healthcare sector is currently in the verge of a reform and thus, the medical game research provide an interesting area of research. The aim of this study is to explore the critical elements underpinning the emergence of the medical game ecosystem with three sub-objectives: (1) to seek who are the key actors involved in the medical game ecosystem and identify their needs, (2) to scrutinise what types of resources are required in medical game development and what types of relationships are needed to secure those resources, and (3) to identify the existing institutions (‘the rules of the game’) affecting the emergence of the medical game ecosystem. The theoretical background consists of service ecosystems literature. The empirical study conducted is based on the semi-structured theme interviews of 25 experts in three relevant fields: games and technology, health and funding. The data was analysed through a theoretical framework that was designed based upon service ecosystems literature. The study proposes that the key actors are divided into five groups: medical game companies, customers, funders, regulatory parties and complementors. Their needs are linked to improving patient motivation and enhancing the healthcare processes resulting in lower costs. Several types of resources, especially skills and knowledge, are required to create a medical game. To gain access to those resources, medical game companies need to build complex networks of relationships. Proficiency in managing those value networks is crucial. In addition, the company should take into account the underlying institutions in the healthcare sector affecting the medical game ecosystem. Three crucial institutions were identified: validation, lack of innovation supporting structures in healthcare and the rising consumerisation. Based on the findings, medical games cannot be made in isolation. A developmental trajectory model of the emerging medical game ecosystem was created based on the empirical data. The relevancy of relationships and resources is dependent on the trajectory that the medical game company at that time resides. Furthermore, creating an official and documented database for clinically validated medical games was proposed to establish the medical game market and ensure an adequate status for the effective medical games. Finally, ecosystems approach provides interesting future opportunities for research on medical game ecosystems