Robust pre-processing techniques for non-ideal iris images

The human iris has been demonstrated to be a very accurate, non-invasive and easy-to-use biometric for personal identification. Most of the current state-of-the-art iris recognition systems require the iris acquisition to be ideal. A lot of constraints are hence put on the user and the acquisition process.;Our aim in this research is to relax these conditions and to develop a pre-processing algorithm, which can be used in conjunction with any matching algorithm to handle the so-called non-ideal iris images. In this thesis we present a few robust techniques to process the non-ideal iris images so as to give a segmented iris image to the matching algorithm. The motivation behind this work is to reduce the false reject rates of the current recognition systems and to reduce the intra-class variability. A new technique for estimating and compensating the angle in non-frontal iris images is presented. We have also developed a novel segmentation algorithm, which uses an ellipse-fitting approach for localizing the pupil. A fast and simple limbus boundary segmentation algorithm is also presented

Low-Quality Fingerprint Classification

Traditsioonilised sõrmejälgede tuvastamise süsteemid kasutavad otsuste tegemisel minutiae punktide informatsiooni. Nagu selgub paljude varasemate tööde põhjal, ei ole sõrmejälgede pildid mitte alati piisava kvaliteediga, et neid saaks kasutada automaatsetes sõrmejäljetuvastuse süsteemides. Selle takistuse ületamiseks keskendub magistritöö väga madala kvaliteediga sõrmejälgede piltide tuvastusele – sellistel piltidel on mitmed üldteada moonutused, nagu kuivus, märgus, füüsiline vigastatus, punktide olemasolu ja hägusus. Töö eesmärk on välja töötada efektiivne ja kõrge täpsusega sügaval närvivõrgul põhinev algoritm, mis tunneb sõrmejälje ära selliselt madala kvaliteediga pildilt. Eksperimentaalsed katsed sügavõppepõhise meetodiga näitavad kõrget tulemuslikkust ja robustsust, olles rakendatud praktikast kogutud madala kvaliteediga sõrmejälgede andmebaasil. VGG16 baseeruv sügavõppe närvivõrk saavutas kõrgeima tulemuslikkuse kuivade (93%) ja madalaima tulemuslikkuse häguste (84%) piltide klassifitseerimisel.Fingerprint recognition systems mainly use minutiae points information. As shown in many previous research works, fingerprint images do not always have good quality to be used by automatic fingerprint recognition systems. To tackle this challenge, in this thesis, we are focusing on very low-quality fingerprint images, which contain several well-known distortions such as dryness, wetness, physical damage, presence of dots, and blurriness. We develop an efficient, with high accuracy, deep neural network algorithm, which recognizes such low-quality fingerprints. The experimental results have been conducted on real low-quality fingerprint database, and the achieved results show the high performance and robustness of the introduced deep network technique. The VGG16 based deep network achieves the highest performance of 93% for dry and the lowest of 84% for blurred fingerprint classes

New algorithms for the analysis of live-cell images acquired in phase contrast microscopy

La détection et la caractérisation automatisée des cellules constituent un enjeu important dans de nombreux domaines de recherche tels que la cicatrisation, le développement de l'embryon et des cellules souches, l’immunologie, l’oncologie, l'ingénierie tissulaire et la découverte de nouveaux médicaments. Étudier le comportement cellulaire in vitro par imagerie des cellules vivantes et par le criblage à haut débit implique des milliers d'images et de vastes quantités de données. Des outils d'analyse automatisés reposant sur la vision numérique et les méthodes non-intrusives telles que la microscopie à contraste de phase (PCM) sont nécessaires. Comme les images PCM sont difficiles à analyser en raison du halo lumineux entourant les cellules et de la difficulté à distinguer les cellules individuelles, le but de ce projet était de développer des algorithmes de traitement d'image PCM dans Matlab® afin d’en tirer de l’information reliée à la morphologie cellulaire de manière automatisée. Pour développer ces algorithmes, des séries d’images de myoblastes acquises en PCM ont été générées, en faisant croître les cellules dans un milieu avec sérum bovin (SSM) ou dans un milieu sans sérum (SFM) sur plusieurs passages. La surface recouverte par les cellules a été estimée en utilisant un filtre de plage de valeurs, un seuil et une taille minimale de coupe afin d'examiner la cinétique de croissance cellulaire. Les résultats ont montré que les cellules avaient des taux de croissance similaires pour les deux milieux de culture, mais que celui-ci diminue de façon linéaire avec le nombre de passages. La méthode de transformée par ondelette continue combinée à l’analyse d'image multivariée (UWT-MIA) a été élaborée afin d’estimer la distribution de caractéristiques morphologiques des cellules (axe majeur, axe mineur, orientation et rondeur). Une analyse multivariée réalisée sur l’ensemble de la base de données (environ 1 million d’images PCM) a montré d'une manière quantitative que les myoblastes cultivés dans le milieu SFM étaient plus allongés et plus petits que ceux cultivés dans le milieu SSM. Les algorithmes développés grâce à ce projet pourraient être utilisés sur d'autres phénotypes cellulaires pour des applications de criblage à haut débit et de contrôle de cultures cellulaires.Automated cell detection and characterization is important in many research fields such as wound healing, embryo development, immune system studies, cancer research, parasite spreading, tissue engineering, stem cell research and drug research and testing. Studying in vitro cellular behavior via live-cell imaging and high-throughput screening involves thousands of images and vast amounts of data, and automated analysis tools relying on machine vision methods and non-intrusive methods such as phase contrast microscopy (PCM) are a necessity. However, there are still some challenges to overcome, since PCM images are difficult to analyze because of the bright halo surrounding the cells and blurry cell-cell boundaries when they are touching. The goal of this project was to develop image processing algorithms to analyze PCM images in an automated fashion, capable of processing large datasets of images to extract information related to cellular viability and morphology. To develop these algorithms, a large dataset of myoblasts images acquired in live-cell imaging (in PCM) was created, growing the cells in either a serum-supplemented (SSM) or a serum-free (SFM) medium over several passages. As a result, algorithms capable of computing the cell-covered surface and cellular morphological features were programmed in Matlab®. The cell-covered surface was estimated using a range filter, a threshold and a minimum cut size in order to look at the cellular growth kinetics. Results showed that the cells were growing at similar paces for both media, but their growth rate was decreasing linearly with passage number. The undecimated wavelet transform multivariate image analysis (UWT-MIA) method was developed, and was used to estimate cellular morphological features distributions (major axis, minor axis, orientation and roundness distributions) on a very large PCM image dataset using the Gabor continuous wavelet transform. Multivariate data analysis performed on the whole database (around 1 million PCM images) showed in a quantitative manner that myoblasts grown in SFM were more elongated and smaller than cells grown in SSM. The algorithms developed through this project could be used in the future on other cellular phenotypes for high-throughput screening and cell culture control applications

Image analysis for gene expression based phenotype characterization in yeast cells

  Image analysis of objects in the microscope scale requires accuracy so that measurements can be used to differentiate between groups of objects that are being studied. This thesis deals with measurements in yeast biology that are obtained through microscope images. We study the algorithms and workflow of image analysis of yeast cells in order to understand and improve the measurement accuracy. The Saccharomyces cerevisiae cell is widely used as a model organism in the life sciences. It is essential to study the gene and protein behaviour within these cells, and consequently making it possible to find treatment and solutions for genetic and hereditary diseases. This is possible since many processes that occurs at the molecular level in this organism are similar to those in human cells. In the research group Imaging and Bioinformatics, we have developed a framework for analysis of yeast cells. This framework is intended to serve as a support for research in yeast biology. The framework is integrated in one application and presented via a GUI. The application integrates modules and algorithms including segmentation, measurement, analysis and visualization.  Erasmus-Mundus, Raymond-Sackler, LSBSLIACS - OU

Biometric Systems

Biometric authentication has been widely used for access control and security systems over the past few years. The purpose of this book is to provide the readers with life cycle of different biometric authentication systems from their design and development to qualification and final application. The major systems discussed in this book include fingerprint identification, face recognition, iris segmentation and classification, signature verification and other miscellaneous systems which describe management policies of biometrics, reliability measures, pressure based typing and signature verification, bio-chemical systems and behavioral characteristics. In summary, this book provides the students and the researchers with different approaches to develop biometric authentication systems and at the same time includes state-of-the-art approaches in their design and development. The approaches have been thoroughly tested on standard databases and in real world applications

Generalizable automated pixel-level structural segmentation of medical and biological data

Over the years, the rapid expansion in imaging techniques and equipments has driven the demand for more automation in handling large medical and biological data sets. A wealth of approaches have been suggested as optimal solutions for their respective imaging types. These solutions span various image resolutions, modalities and contrast (staining) mechanisms. Few approaches generalise well across multiple image types, contrasts or resolution. This thesis proposes an automated pixel-level framework that addresses 2D, 2D+t and 3D structural segmentation in a more generalizable manner, yet has enough adaptability to address a number of specific image modalities, spanning retinal funduscopy, sequential fluorescein angiography and two-photon microscopy. The pixel-level segmentation scheme involves: i ) constructing a phase-invariant orientation field of the local spatial neighbourhood; ii ) combining local feature maps with intensity-based measures in a structural patch context; iii ) using a complex supervised learning process to interpret the combination of all the elements in the patch in order to reach a classification decision. This has the advantage of transferability from retinal blood vessels in 2D to neural structures in 3D. To process the temporal components in non-standard 2D+t retinal angiography sequences, we first introduce a co-registration procedure: at the pairwise level, we combine projective RANSAC with a quadratic homography transformation to map the coordinate systems between any two frames. At the joint level, we construct a hierarchical approach in order for each individual frame to be registered to the global reference intra- and inter- sequence(s). We then take a non-training approach that searches in both the spatial neighbourhood of each pixel and the filter output across varying scales to locate and link microvascular centrelines to (sub-) pixel accuracy. In essence, this \link while extract" piece-wise segmentation approach combines the local phase-invariant orientation field information with additional local phase estimates to obtain a soft classification of the centreline (sub-) pixel locations. Unlike retinal segmentation problems where vasculature is the main focus, 3D neural segmentation requires additional exibility, allowing a variety of structures of anatomical importance yet with different geometric properties to be differentiated both from the background and against other structures. Notably, cellular structures, such as Purkinje cells, neural dendrites and interneurons, all display certain elongation along their medial axes, yet each class has a characteristic shape captured by an orientation field that distinguishes it from other structures. To take this into consideration, we introduce a 5D orientation mapping to capture these orientation properties. This mapping is incorporated into the local feature map description prior to a learning machine. Extensive performance evaluations and validation of each of the techniques presented in this thesis is carried out. For retinal fundus images, we compute Receiver Operating Characteristic (ROC) curves on existing public databases (DRIVE & STARE) to assess and compare our algorithms with other benchmark methods. For 2D+t retinal angiography sequences, we compute the error metrics ("Centreline Error") of our scheme with other benchmark methods. For microscopic cortical data stacks, we present segmentation results on both surrogate data with known ground-truth and experimental rat cerebellar cortex two-photon microscopic tissue stacks.Open Acces