Toward integrated management of cerebral aneurysms

In the last few years, some of the visionary concepts behind the virtual physiological human began to be demonstrated on various clinical domains, showing great promise for improving healthcare management. In the current work, we provide an overview of image- and biomechanics-based techniques that, when put together, provide a patient-specific pipeline for the management of intracranial aneurysms. The derivation and subsequent integration of morphological, morphodynamic, haemodynamic and structural analyses allow us to extract patient-specific models and information from which diagnostic and prognostic descriptors can be obtained. Linking such new indices with relevant clinical events should bring new insights into the processes behind aneurysm genesis, growth and rupture. The development of techniques for modelling endovascular devices such as stents and coils allows the evaluation of alternative treatment scenarios before the intervention takes place and could also contribute to the understanding and improved design of more effective devices. A key element to facilitate the clinical take-up of all these developments is their comprehensive validation. Although a number of previously published results have shown the accuracy and robustness of individual components, further efforts should be directed to demonstrate the diagnostic and prognostic efficacy of these advanced tools through large-scale clinical trials.

Comparison of Energy Minimization Methods for 3-D Brain Tissue Classification

This paper presents 3-D brain tissue classificationschemes using three recent promising energy minimizationmethods for Markov random fields: graph cuts, loopybelief propagation and tree-reweighted message passing.The classification is performed using the well knownfinite Gaussian mixture Markov Random Field model.Results from the above methods are compared with widelyused iterative conditional modes algorithm. Theevaluation is performed on a dataset containing simulatedT1-weighted MR brain volumes with varying noise andintensity non-uniformities. The comparisons are performedin terms of energies as well as based on ground truthsegmentations, using various quantitative metrics.

Reconeixement de gestos de la mà amb el sensor Kinect

El reconeixement dels gestos de la mà (HGR, Hand Gesture Recognition) és actualment un camp important de recerca degut a la varietat de situacions en les quals és necessari comunicar-se mitjançant signes, com pot ser la comunicació entre persones que utilitzen la llengua de signes i les que no. En aquest projecte es presenta un mètode de reconeixement de gestos de la mà a temps real utilitzant el sensor Kinect per Microsoft Xbox, implementat en un entorn Linux (Ubuntu) amb llenguatge de programació Python i utilitzant la llibreria de visió artifical OpenCV per a processar les dades sobre un ordinador portàtil convencional. Gràcies a la capacitat del sensor Kinect de capturar dades de profunditat d’una escena es poden determinar les posicions i trajectòries dels objectes en 3 dimensions, el que implica poder realitzar una anàlisi complerta a temps real d’una imatge o d’una seqüencia d’imatges. El procediment de reconeixement que es planteja es basa en la segmentació de la imatge per poder treballar únicament amb la mà, en la detecció dels contorns, per després obtenir l’envolupant convexa i els defectes convexos, que finalment han de servir per determinar el nombre de dits i concloure en la interpretació del gest; el resultat final és la transcripció del seu significat en una finestra que serveix d’interfície amb l’interlocutor. L’aplicació permet reconèixer els números del 0 al 5, ja que s’analitza únicament una mà, alguns gestos populars i algunes de les lletres de l’alfabet dactilològic de la llengua de signes catalana. El projecte és doncs, la porta d’entrada al camp del reconeixement de gestos i la base d’un futur sistema de reconeixement de la llengua de signes capaç de transcriure tant els signes dinàmics com l’alfabet dactilològic.

A rapid and effective vignetting correction for quantitative microscopy

Images acquired using optical microscopes are inherently subject to vignetting effects due to imperfect illumination and image acquisition. However, such vignetting effects hamper accurate extraction of quantitative information from biological images, leading to less effective image segmentation and increased noise in the measurements. Here, we describe a rapid and effective method for vignetting correction, which generates an estimate for a correction function from the background fluorescence without the need to acquire additional calibration images. We validate the usefulness of this algorithm using artificially distorted images as a gold standard for assessing the accuracy of the applied correction and then demonstrate that this correction method enables the reliable detection of biologically relevant variation in cell populations. A simple user interface called FlattifY was developed and integrated into the image analysis platform YeastQuant to facilitate easy application of vignetting correction to a wide range of images.

Hand detection in cluttered scene images using Fourier-Mellin invariant features

This paper proposes an automatic hand detection system that combines the Fourier-Mellin Transform along with other computer vision techniques to achieve hand detection in cluttered scene color images. The proposed system uses the Fourier-Mellin Transform as an invariant feature extractor to perform RST invariant hand detection. In a first stage of the system a simple non-adaptive skin color-based image segmentation and an interest point detector based on corners are used in order to identify regions of interest that contains possible matches. A sliding window algorithm is then used to scan the image at different scales performing the FMT calculations only in the previously detected regions of interest and comparing the extracted FM descriptor of the windows with a hand descriptors database obtained from a train image set. The results of the performed experiments suggest the use of Fourier-Mellin invariant features as a promising approach for automatic hand detection.

Hand detection in cluttered scene images using Fourier-Mellin invariant features

This paper proposes an automatic hand detection system that combines the Fourier-Mellin Transform along with other computer vision techniques to achieve hand detection in cluttered scene color images. The proposed system uses the Fourier-Mellin Transform as an invariant feature extractor to perform RST invariant hand detection. In a first stage of the system a simple non-adaptive skin color-based image segmentation and an interest point detector based on corners are used in order to identify regions of interest that contains possible matches. A sliding window algorithm is then used to scan the image at different scales performing the FMT calculations only in the previously detected regions of interest and comparing the extracted FM descriptor of the windows with a hand descriptors database obtained from a train image set. The results of the performed experiments suggest the use of Fourier-Mellin invariant features as a promising approach for automatic hand detection.

SAR Interferometric phase noise reduction using wavelet transform

The problem of synthetic aperture radar interferometric phase noise reduction is addressed. A new technique based on discrete wavelet transforms is presented. This technique guarantees high resolution phase estimation without using phase image segmentation. Areas containing only noise are hardly processed. Tests with synthetic and real interferograms are reported.

Motion estimation using higher-order statistics

The objective of this paper is to introduce a fourth-order cost function of the displaced frame difference (DFD) capable of estimatingmotion even for small regions or blocks. Using higher than second-orderstatistics is appropriate in case the image sequence is severely corruptedby additive Gaussian noise. Some results are presented and compared to those obtained from the mean kurtosis and the mean square error of the DFD.

A concurrent region growing algorithm guided by circumscribed contours

Image segmentation of natural scenes constitutes a major problem in machine vision. This paper presents a new proposal for the image segmentation problem which has been based on the integration of edge and region information. This approach begins by detecting the main contours of the scene which are later used to guide a concurrent set of growing processes. A previous analysis of the seed pixels permits adjustment of the homogeneity criterion to the region's characteristics during the growing process. Since the high variability of regions representing outdoor scenes makes the classical homogeneity criteria useless, a new homogeneity criterion based on clustering analysis and convex hull construction is proposed. Experimental results have proven the reliability of the proposed approach

Reconeixement de gestos de la mà amb el sensor Kinect

El reconeixement dels gestos de la mà (HGR, Hand Gesture Recognition) és actualment un camp important de recerca degut a la varietat de situacions en les quals és necessari comunicar-se mitjançant signes, com pot ser la comunicació entre persones que utilitzen la llengua de signes i les que no. En aquest projecte es presenta un mètode de reconeixement de gestos de la mà a temps real utilitzant el sensor Kinect per Microsoft Xbox, implementat en un entorn Linux (Ubuntu) amb llenguatge de programació Python i utilitzant la llibreria de visió artifical OpenCV per a processar les dades sobre un ordinador portàtil convencional. Gràcies a la capacitat del sensor Kinect de capturar dades de profunditat d’una escena es poden determinar les posicions i trajectòries dels objectes en 3 dimensions, el que implica poder realitzar una anàlisi complerta a temps real d’una imatge o d’una seqüencia d’imatges. El procediment de reconeixement que es planteja es basa en la segmentació de la imatge per poder treballar únicament amb la mà, en la detecció dels contorns, per després obtenir l’envolupant convexa i els defectes convexos, que finalment han de servir per determinar el nombre de dits i concloure en la interpretació del gest; el resultat final és la transcripció del seu significat en una finestra que serveix d’interfície amb l’interlocutor. L’aplicació permet reconèixer els números del 0 al 5, ja que s’analitza únicament una mà, alguns gestos populars i algunes de les lletres de l’alfabet dactilològic de la llengua de signes catalana. El projecte és doncs, la porta d’entrada al camp del reconeixement de gestos i la base d’un futur sistema de reconeixement de la llengua de signes capaç de transcriure tant els signes dinàmics com l’alfabet dactilològic.

Characterization of fiber and vessel elements in pulp suspension images

The thesis is related to the topic of image-based characterization of fibers in pulp suspension during the papermaking process. Papermaking industry is focusing on process control optimization and automatization, which makes it possible to manufacture highquality products in a resource-efficient way. Being a part of the process control, pulp suspension analysis allows to predict and modify properties of the end product. This work is a part of the tree species identification task and focuses on analysis of fiber parameters in the pulp suspension at the wet stage of paper production. The existing machine vision methods for pulp characterization were investigated, and a method exploiting direction sensitive filtering, non-maximum suppression, hysteresis thresholding, tensor voting, and curve extraction from tensor maps was developed. Application of the method to the microscopic grayscale pulp images made it possible to detect curves corresponding to fibers in the pulp image and to compute their morphological characteristics. Performance of the method was evaluated based on the manually produced ground truth data. An accuracy of fiber characteristics estimation, including length, width, and curvature, for the acacia pulp images was found to be 84, 85, and 60% correspondingly.

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

Urban Detection From Hyperspectral Images Using Dimension-Reduction Model and Fusion of Multiple Segmentations Based on Stuctural and Textural Features

Ce mémoire de maîtrise présente une nouvelle approche non supervisée pour détecter et segmenter les régions urbaines dans les images hyperspectrales. La méthode proposée n ́ecessite trois étapes. Tout d’abord, afin de réduire le coût calculatoire de notre algorithme, une image couleur du contenu spectral est estimée. A cette fin, une étape de réduction de dimensionalité non-linéaire, basée sur deux critères complémentaires mais contradictoires de bonne visualisation; à savoir la précision et le contraste, est réalisée pour l’affichage couleur de chaque image hyperspectrale. Ensuite, pour discriminer les régions urbaines des régions non urbaines, la seconde étape consiste à extraire quelques caractéristiques discriminantes (et complémentaires) sur cette image hyperspectrale couleur. A cette fin, nous avons extrait une série de paramètres discriminants pour décrire les caractéristiques d’une zone urbaine, principalement composée d’objets manufacturés de formes simples g ́eométriques et régulières. Nous avons utilisé des caractéristiques texturales basées sur les niveaux de gris, la magnitude du gradient ou des paramètres issus de la matrice de co-occurrence combinés avec des caractéristiques structurelles basées sur l’orientation locale du gradient de l’image et la détection locale de segments de droites. Afin de réduire encore la complexité de calcul de notre approche et éviter le problème de la ”malédiction de la dimensionnalité” quand on décide de regrouper des données de dimensions élevées, nous avons décidé de classifier individuellement, dans la dernière étape, chaque caractéristique texturale ou structurelle avec une simple procédure de K-moyennes et ensuite de combiner ces segmentations grossières, obtenues à faible coût, avec un modèle efficace de fusion de cartes de segmentations. Les expérimentations données dans ce rapport montrent que cette stratégie est efficace visuellement et se compare favorablement aux autres méthodes de détection et segmentation de zones urbaines à partir d’images hyperspectrales.

The Computation of Color

This thesis takes an interdisciplinary approach to the study of color vision, focussing on the phenomenon of color constancy formulated as a computational problem. The primary contributions of the thesis are (1) the demonstration of a formal framework for lightness algorithms; (2) the derivation of a new lightness algorithm based on regularization theory; (3) the synthesis of an adaptive lightness algorithm using "learning" techniques; (4) the development of an image segmentation algorithm that uses luminance and color information to mark material boundaries; and (5) an experimental investigation into the cues that human observers use to judge the color of the illuminant. Other computational approaches to color are reviewed and some of their links to psychophysics and physiology are explored.