Monitoring mesenchymal stem cell cultures using image processing and pattern recognition techniques

Stem cells have attracted tremendous interest in recent times due to their promise in providing innovative new treatments for a great range of currently debilitating diseases. This is due to their potential ability to regenerate and repair damaged tissue, and hence restore lost body function, in a manner beyond the body's usual healing process. Bone marrow-derived mesenchymal stem cells or bone marrow stromal cells are one type of adult stem cells that are of particular interest. Since they are derived from a living human adult donor, they do not have the ethical issues associated with the use of human embryonic stem cells. They are also able to be taken from a patient or other donors with relative ease and then grown readily in the laboratory for clinical application. Despite the attractive properties of bone marrow stromal cells, there is presently no quick and easy way to determine the quality of a sample of such cells. Presently, a sample must be grown for weeks and subject to various time-consuming assays, under the direction of an expert cell biologist, to determine whether it will be useful. Hence there is a great need for innovative new ways to assess the quality of cell cultures for research and potential clinical application. The research presented in this thesis investigates the use of computerised image processing and pattern recognition techniques to provide a quicker and simpler method for the quality assessment of bone marrow stromal cell cultures. In particular, aim of this work is to find out whether it is possible, through the use of image processing and pattern recognition techniques, to predict the growth potential of a culture of human bone marrow stromal cells at early stages, before it is readily apparent to a human observer. With the above aim in mind, a computerised system was developed to classify the quality of bone marrow stromal cell cultures based on phase contrast microscopy images. Our system was trained and tested on mixed images of both healthy and unhealthy bone marrow stromal cell samples taken from three different patients. This system, when presented with 44 previously unseen bone marrow stromal cell culture images, outperformed human experts in the ability to correctly classify healthy and unhealthy cultures. The system correctly classified the health status of an image 88% of the time compared to an average of 72% of the time for human experts. Extensive training and testing of the system on a set of 139 normal sized images and 567 smaller image tiles showed an average performance of 86% and 85% correct classifications, respectively. The contributions of this thesis include demonstrating the applicability and potential of computerised image processing and pattern recognition techniques to the task of quality assessment of bone marrow stromal cell cultures. As part of this system, an image normalisation method has been suggested and a new segmentation algorithm has been developed for locating cell regions of irregularly shaped cells in phase contrast images. Importantly, we have validated the efficacy of both the normalisation and segmentation method, by demonstrating that both methods quantitatively improve the classification performance of subsequent pattern recognition algorithms, in discriminating between cell cultures of differing health status. We have shown that the quality of a cell culture of bone marrow stromal cells may be assessed without the need to either segment individual cells or to use time-lapse imaging. Finally, we have proposed a set of features, that when extracted from the cell regions of segmented input images, can be used to train current state of the art pattern recognition systems to predict the quality of bone marrow stromal cell cultures earlier and more consistently than human experts.

Non-evolutive pattern recognition techniques: An application in medical image diagnostics

Lo studio dell’intelligenza artificiale si pone come obiettivo la risoluzione di una classe di problemi che richiedono processi cognitivi difficilmente codificabili in un algoritmo per essere risolti. Il riconoscimento visivo di forme e figure, l’interpretazione di suoni, i giochi a conoscenza incompleta, fanno capo alla capacità umana di interpretare input parziali come se fossero completi, e di agire di conseguenza. Nel primo capitolo della presente tesi sarà costruito un semplice formalismo matematico per descrivere l’atto di compiere scelte. Il processo di “apprendimento” verrà descritto in termini della massimizzazione di una funzione di prestazione su di uno spazio di parametri per un ansatz di una funzione da uno spazio vettoriale ad un insieme finito e discreto di scelte, tramite un set di addestramento che descrive degli esempi di scelte corrette da riprodurre. Saranno analizzate, alla luce di questo formalismo, alcune delle più diffuse tecniche di artificial intelligence, e saranno evidenziate alcune problematiche derivanti dall’uso di queste tecniche. Nel secondo capitolo lo stesso formalismo verrà applicato ad una ridefinizione meno intuitiva ma più funzionale di funzione di prestazione che permetterà, per un ansatz lineare, la formulazione esplicita di un set di equazioni nelle componenti del vettore nello spazio dei parametri che individua il massimo assoluto della funzione di prestazione. La soluzione di questo set di equazioni sarà trattata grazie al teorema delle contrazioni. Una naturale generalizzazione polinomiale verrà inoltre mostrata. Nel terzo capitolo verranno studiati più nel dettaglio alcuni esempi a cui quanto ricavato nel secondo capitolo può essere applicato. Verrà introdotto il concetto di grado intrinseco di un problema. Verranno inoltre discusse alcuni accorgimenti prestazionali, quali l’eliminazione degli zeri, la precomputazione analitica, il fingerprinting e il riordino delle componenti per lo sviluppo parziale di prodotti scalari ad alta dimensionalità. Verranno infine introdotti i problemi a scelta unica, ossia quella classe di problemi per cui è possibile disporre di un set di addestramento solo per una scelta. Nel quarto capitolo verrà discusso più in dettaglio un esempio di applicazione nel campo della diagnostica medica per immagini, in particolare verrà trattato il problema della computer aided detection per il rilevamento di microcalcificazioni nelle mammografie.

Analysis of pattern recognition techniques for in-air signature biometrics

As a result of advances in mobile technology, new services which benefit from the ubiquity of these devices are appearing. Some of these services require the identification of the subject since they may access private user information. In this paper, we propose to identify each user by drawing his/her handwritten signature in the air (in-airsignature). In order to assess the feasibility of an in-airsignature as a biometric feature, we have analysed the performance of several well-known patternrecognitiontechniques—Hidden Markov Models, Bayes classifiers and dynamic time warping—to cope with this problem. Each technique has been tested in the identification of the signatures of 96 individuals. Furthermore, the robustness of each method against spoofing attacks has also been analysed using six impostors who attempted to emulate every signature. The best results in both experiments have been reached by using a technique based on dynamic time warping which carries out the recognition by calculating distances to an average template extracted from several training instances. Finally, a permanence analysis has been carried out in order to assess the stability of in-airsignature over time.

Damage detection by using FBGs and strain field pattern recognition techniques

A novel methodology for damage detection and location in structures is proposed. The methodology is based on strain measurements and consists in the development of strain field pattern recognition techniques. The aforementioned are based on PCA (principal component analysis) and damage indices (T 2 and Q). We propose the use of fiber Bragg gratings (FBGs) as strain sensors

Experimental investigation of a wavelet based drive-by bridge inspection system incorporating pattern recognition

This paper presents the results of an experimental investigation, carried out in order to verify the feasibility of a ‘drive-by’ approach which uses a vehicle instrumented with accelerometers to detect and locate damage in a bridge. In theoretical simulations, a simplified vehicle-bridge interaction model is used to investigate the effectiveness of the approach in detecting damage in a bridge from vehicle accelerations. For this purpose, the accelerations are processed using a continuous wavelet transform and damage indicators are evaluated and compared. Alternative statistical pattern recognition techniques are incorporated to allow for repeated vehicle passes. Parameters such as vehicle speed, damage level, location and road roughness are varied in simulations to investigate the effect. A scaled laboratory experiment is carried out to assess the effectiveness of the approach in a more realistic environment, considering a number of bridge damage scenarios.

Pattern recognition analysis on heavy ion reaction data

One of the problems in the analysis of nucleus-nucleus collisions is to get information on the value of the impact parameter b. This work consists in the application of pattern recognition techniques aimed at associating values of b to groups of events. To this end, a support vec- tor machine (SVM) classifier is adopted to analyze multifragmentation reactions. This method allows to backtracing the values of b through a particular multidimensional analysis. The SVM classification con- sists of two main phase. In the first one, known as training phase, the classifier learns to discriminate the events that are generated by two different model:Classical Molecular Dynamics (CMD) and Heavy- Ion Phase-Space Exploration (HIPSE) for the reaction: 58Ni +48 Ca at 25 AMeV. To check the classification of events in the second one, known as test phase, what has been learned is tested on new events generated by the same models. These new results have been com- pared to the ones obtained through others techniques of backtracing the impact parameter. Our tests show that, following this approach, the central collisions and peripheral collisions, for the CMD events, are always better classified with respect to the classification by the others techniques of backtracing. We have finally performed the SVM classification on the experimental data measured by NUCL-EX col- laboration with CHIMERA apparatus for the previous reaction.

Automatic physical activity pattern recognition and meal intake modelling in type 1 diabetes for their inclusion in artificial pancreas systems

La diabetes comprende un conjunto de enfermedades metabólicas que se caracterizan por concentraciones de glucosa en sangre anormalmente altas. En el caso de la diabetes tipo 1 (T1D, por sus siglas en inglés), esta situación es debida a una ausencia total de secreción endógena de insulina, lo que impide a la mayoría de tejidos usar la glucosa. En tales circunstancias, se hace necesario el suministro exógeno de insulina para preservar la vida del paciente; no obstante, siempre con la precaución de evitar caídas agudas de la glucemia por debajo de los niveles recomendados de seguridad. Además de la administración de insulina, las ingestas y la actividad física son factores fundamentales que influyen en la homeostasis de la glucosa. En consecuencia, una gestión apropiada de la T1D debería incorporar estos dos fenómenos fisiológicos, en base a una identificación y un modelado apropiado de los mismos y de sus sorrespondientes efectos en el balance glucosa-insulina. En particular, los sistemas de páncreas artificial –ideados para llevar a cabo un control automático de los niveles de glucemia del paciente– podrían beneficiarse de la integración de esta clase de información. La primera parte de esta tesis doctoral cubre la caracterización del efecto agudo de la actividad física en los perfiles de glucosa. Con este objetivo se ha llevado a cabo una revisión sistemática de la literatura y meta-análisis que determinen las respuestas ante varias modalidades de ejercicio para pacientes con T1D, abordando esta caracterización mediante unas magnitudes que cuantifican las tasas de cambio en la glucemia a lo largo del tiempo. Por otro lado, una identificación fiable de los periodos con actividad física es un requisito imprescindible para poder proveer de esa información a los sistemas de páncreas artificial en condiciones libres y ambulatorias. Por esta razón, la segunda parte de esta tesis está enfocada a la propuesta y evaluación de un sistema automático diseñado para reconocer periodos de actividad física, clasificando su nivel de intensidad (ligera, moderada o vigorosa); así como, en el caso de periodos vigorosos, identificando también la modalidad de ejercicio (aeróbica, mixta o de fuerza). En este sentido, ambos aspectos tienen una influencia específica en el mecanismo metabólico que suministra la energía para llevar a cabo el ejercicio y, por tanto, en las respuestas glucémicas en T1D. En este trabajo se aplican varias combinaciones de técnicas de aprendizaje máquina y reconocimiento de patrones sobre la fusión multimodal de señales de acelerometría y ritmo cardíaco, las cuales describen tanto aspectos mecánicos del movimiento como la respuesta fisiológica del sistema cardiovascular ante el ejercicio. Después del reconocimiento de patrones se incorpora también un módulo de filtrado temporal para sacar partido a la considerable coherencia temporal presente en los datos, una redundancia que se origina en el hecho de que en la práctica, las tendencias en cuanto a actividad física suelen mantenerse estables a lo largo de cierto tiempo, sin fluctuaciones rápidas y repetitivas. El tercer bloque de esta tesis doctoral aborda el tema de las ingestas en el ámbito de la T1D. En concreto, se propone una serie de modelos compartimentales y se evalúan éstos en función de su capacidad para describir matemáticamente el efecto remoto de las concetraciones plasmáticas de insulina exógena sobre las tasas de eleiminación de la glucosa atribuible a la ingesta; un aspecto hasta ahora no incorporado en los principales modelos de paciente para T1D existentes en la literatura. Los datos aquí utilizados se obtuvieron gracias a un experimento realizado por el Institute of Metabolic Science (Universidad de Cambridge, Reino Unido) con 16 pacientes jóvenes. En el experimento, de tipo ‘clamp’ con objetivo variable, se replicaron los perfiles individuales de glucosa, según lo observado durante una visita preliminar tras la ingesta de una cena con o bien alta carga glucémica, o bien baja. Los seis modelos mecanísticos evaluados constaban de: a) submodelos de doble compartimento para las masas de trazadores de glucosa, b) un submodelo de único compartimento para reflejar el efecto remoto de la insulina, c) dos tipos de activación de este mismo efecto remoto (bien lineal, bien con un punto de corte), y d) diversas condiciones iniciales. ABSTRACT Diabetes encompasses a series of metabolic diseases characterized by abnormally high blood glucose concentrations. In the case of type 1 diabetes (T1D), this situation is caused by a total absence of endogenous insulin secretion, which impedes the use of glucose by most tissues. In these circumstances, exogenous insulin supplies are necessary to maintain patient’s life; although caution is always needed to avoid acute decays in glycaemia below safe levels. In addition to insulin administrations, meal intakes and physical activity are fundamental factors influencing glucose homoeostasis. Consequently, a successful management of T1D should incorporate these two physiological phenomena, based on an appropriate identification and modelling of these events and their corresponding effect on the glucose-insulin balance. In particular, artificial pancreas systems –designed to perform an automated control of patient’s glycaemia levels– may benefit from the integration of this type of information. The first part of this PhD thesis covers the characterization of the acute effect of physical activity on glucose profiles. With this aim, a systematic review of literature and metaanalyses are conduced to determine responses to various exercise modalities in patients with T1D, assessed via rates-of-change magnitudes to quantify temporal variations in glycaemia. On the other hand, a reliable identification of physical activity periods is an essential prerequisite to feed artificial pancreas systems with information concerning exercise in ambulatory, free-living conditions. For this reason, the second part of this thesis focuses on the proposal and evaluation of an automatic system devised to recognize physical activity, classifying its intensity level (light, moderate or vigorous) and for vigorous periods, identifying also its exercise modality (aerobic, mixed or resistance); since both aspects have a distinctive influence on the predominant metabolic pathway involved in fuelling exercise, and therefore, in the glycaemic responses in T1D. Various combinations of machine learning and pattern recognition techniques are applied on the fusion of multi-modal signal sources, namely: accelerometry and heart rate measurements, which describe both mechanical aspects of movement and the physiological response of the cardiovascular system to exercise. An additional temporal filtering module is incorporated after recognition in order to exploit the considerable temporal coherence (i.e. redundancy) present in data, which stems from the fact that in practice, physical activity trends are often maintained stable along time, instead of fluctuating rapid and repeatedly. The third block of this PhD thesis addresses meal intakes in the context of T1D. In particular, a number of compartmental models are proposed and compared in terms of their ability to describe mathematically the remote effect of exogenous plasma insulin concentrations on the disposal rates of meal-attributable glucose, an aspect which had not yet been incorporated to the prevailing T1D patient models in literature. Data were acquired in an experiment conduced at the Institute of Metabolic Science (University of Cambridge, UK) on 16 young patients. A variable-target glucose clamp replicated their individual glucose profiles, observed during a preliminary visit after ingesting either a high glycaemic-load or a low glycaemic-load evening meal. The six mechanistic models under evaluation here comprised: a) two-compartmental submodels for glucose tracer masses, b) a single-compartmental submodel for insulin’s remote effect, c) two types of activations for this remote effect (either linear or with a ‘cut-off’ point), and d) diverse forms of initial conditions.

Pattern Analysis Techniques for the Recognition of Unconstrained Handwritten Malayalam Character Images

The objective of the study is to develop a hand written character recognition system that could recognisze all the characters in the mordern script of malayalam language at a high recognition rate

Analysis of pattern recognition and dimensionality reduction techniques for odor biometrics

In this paper, we analyze the performance of several well-known pattern recognition and dimensionality reduction techniques when applied to mass-spectrometry data for odor biometric identification. Motivated by the successful results of previous works capturing the odor from other parts of the body, this work attempts to evaluate the feasibility of identifying people by the odor emanated from the hands. By formulating this task according to a machine learning scheme, the problem is identified with a small-sample-size supervised classification problem in which the input data is formed by mass spectrograms from the hand odor of 13 subjects captured in different sessions. The high dimensionality of the data makes it necessary to apply feature selection and extraction techniques together with a simple classifier in order to improve the generalization capabilities of the model. Our experimental results achieve recognition rates over 85% which reveals that there exists discriminatory information in the hand odor and points at body odor as a promising biometric identifier.

Bearing Fault Diagnostics Using the Spectral Pattern Recognition

In the field of diagnostics of rolling element bearings, the development of sophisticated techniques, such as Spectral Kurtosis and 2nd Order Cyclostationarity, extended the capability of expert users to identify not only the presence, but also the location of the damage in the bearing. Most of the signal-analysis methods, as the ones previously mentioned, result in a spectrum-like diagram that presents line frequencies or peaks in the neighbourhood of some theoretical characteristic frequencies, in case of damage. These frequencies depend only on damage position, bearing geometry and rotational speed. The major improvement in this field would be the development of algorithms with high degree of automation. This paper aims at this important objective, by discussing for the first time how these peaks can draw away from the theoretical expected frequencies as a function of different working conditions, i.e. speed, torque and lubrication. After providing a brief description of the peak-patterns associated with each type of damage, this paper shows the typical magnitudes of the deviations from the theoretical expected frequencies. The last part of the study presents some remarks about increasing the reliability of the automatic algorithm. The research is based on experimental data obtained by using artificially damaged bearings installed in a gearbox.

Human identification from video using advanced gait recognition techniques

The solutions proposed in this thesis contribute to improve gait recognition performance in practical scenarios that further enable the adoption of gait recognition into real world security and forensic applications that require identifying humans at a distance. Pioneering work has been conducted on frontal gait recognition using depth images to allow gait to be integrated with biometric walkthrough portals. The effects of gait challenging conditions including clothing, carrying goods, and viewpoint have been explored. Enhanced approaches are proposed on segmentation, feature extraction, feature optimisation and classification elements, and state-of-the-art recognition performance has been achieved. A frontal depth gait database has been developed and made available to the research community for further investigation. Solutions are explored in 2D and 3D domains using multiple images sources, and both domain-specific and independent modality gait features are proposed.

Skeleton based visual pattern recognition. Applications to tabletop interaction

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Molecular cloning and characterisation of a pattern recognition protein, lipopolysaccharide and beta-1,3-glucan binding protein (LGBP) from Chinese shrimp Fenneropenaeus chinensis

A pattern recognition protein (PRP), lipopolysaccharide and beta-1,3-glucan binding protein (LGBP) cDNA was cloned from the haemocyte of Chinese shrimp Fenneropenaeus chinensis by the techniques of homology cloning and RACE. Analysis of nucleotide sequence revealed that the full-length cDNA of 1,275 bp has an open reading frame of 1,098 bp encoding a protein of 366 amino acids including a 17 amino acid signal peptide. Sequence comparison of the deduced amino acid sequence of F. chinensis LGBP showed a high identity of 94%, 90%, 87%, 72% and 63% with Penaeus monodon BGBP, Litopenaeus stylirostris LGBP, Marsupenaeu japonicus BGBP, Homarus gammarus BGBP and Pacifastacus leniusculus LGBP, respectively. The calculated molecular mass of the mature protein is 39,857 Da with a deduced pI of 4.39. Two putative integrin binding motifs, RGD (Arg-Gly-Asp) and a potential recognition motif for beta-1,3-linkage of polysaccharides were observed in LGBP sequence. RT-PCR analysis showed that LGBP gene expresses in haemocyte and hepatopancreas only, but not in other tissues. Capillary electrophoresis RT-PCR method was used to quantify the variation of mRNA transcription level during artificial infection with heat-killed Vibrio anguillarum and Staphylococcus aureusin. A significant enhancement of LGBP transcription was appeared at 6 h post-injection in response to bacterial infection. These results have provided useful information to understand the function of LGBP in shrimp.

An indirect bridge inspection method incorporating a wavelet-based damage indicator and pattern recognition

In recent years, there has been a move towards the development of indirect structural health monitoring (SHM)techniques for bridges; the low-cost vibration-based method presented in this paper is such an approach. It consists of the use of a moving vehicle fitted with accelerometers on its axles and incorporates wavelet analysis and statistical pattern recognition. The aim of the approach is to both detect and locate damage in bridges while reducing the need for direct instrumentation of the bridge. In theoretical simulations, a simplified vehicle-bridge interaction model is used to investigate the effectiveness of the approach in detecting damage in a bridge from vehicle accelerations. For this purpose, the accelerations are processed using a continuous wavelet transform as when the axle passes over a damaged section, any discontinuity in the signal would affect the wavelet coefficients. Based on these coefficients, a damage indicator is formulated which can distinguish between different damage levels. However, it is found to be difficult to quantify damage of varying levels when the vehicle’s transverse position is varied between bridge crossings. In a real bridge field experiment, damage was applied artificially to a steel truss bridge to test the effectiveness of the indirect approach in practice; for this purpose a two-axle van was driven across the bridge at constant speed. Both bridge and vehicle acceleration measurements were recorded. The dynamic properties of the test vehicle were identified initially via free vibration tests. It was found that the resulting damage indicators for the bridge and vehicle showed similar patterns, however, it was difficult to distinguish between different artificial damage scenarios.