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.

Information processing in sleep-onset insomnia : a test of the neurocognitive model /

The present thesis study is a systematic investigation of information processing at sleep onset, using auditory event-related potentials (ERPs) as a test of the neurocognitive model of insomnia. Insomnia is an extremely prevalent disorder in society resulting in problems with daytime functioning (e.g., memory, concentration, job performance, mood, job and driving safety). Various models have been put forth in an effort to better understand the etiology and pathophysiology of this disorder. One of the newer models, the neurocognitive model of insomnia, suggests that chronic insomnia occurs through conditioned central nervous system arousal. This arousal is reflected through increased information processing which may interfere with sleep initiation or maintenance. The present thesis employed event-related potentials as a direct method to test information processing during the sleep-onset period. Thirteen poor sleepers with sleep-onset insomnia and 1 2 good sleepers participated in the present study. All poor sleepers met the diagnostic criteria for psychophysiological insomnia and had a complaint of problems with sleep initiation. All good sleepers reported no trouble sleeping and no excessive daytime sleepiness. Good and poor sleepers spent two nights at the Brock University Sleep Research Laboratory. The first night was used to screen for sleep disorders; the second night was used to investigate information processing during the sleep-onset period. Both groups underwent a repeated sleep-onsets task during which an auditory oddball paradigm was delivered. Participants signalled detection of a higher pitch target tone with a button press as they fell asleep. In addition, waking alert ERPs were recorded 1 hour before and after sleep on both Nights 1 and 2.As predicted by the neurocognitive model of insomnia, increased CNS activity was found in the poor sleepers; this was reflected by their smaller amplitude P2 component seen during wake of the sleep-onset period. Unlike the P2 component, the Nl, N350, and P300 did not vary between the groups. The smaller P2 seen in our poor sleepers indicates that they have a deficit in the sleep initiation processes. Specifically, poor sleepers do not disengage their attention from the outside environment to the same extent as good sleepers during the sleep-onset period. The lack of findings for the N350 suggest that this sleep component may be intact in those with insomnia and that it is the waking components (i.e., Nl, P2) that may be leading to the deficit in sleep initiation. Further, it may be that the mechanism responsible for the disruption of sleep initiation in the poor sleepers is most reflected by the P2 component. Future research investigating ERPs in insomnia should focus on the identification of the components most sensitive to sleep disruption. As well, methods should be developed in order to more clearly identify the various types of insomnia populations in research contexts (e.g., psychophysiological vs. sleep-state misperception) and the various individual (personality characteristics, motivation) and environmental factors (arousal-related variables) that influence particular ERP components. Insomnia has serious consequences for health, safety, and daytime functioning, thus research efforts should continue in order to help alleviate this highly prevalent condition.

Geological image processing of petrographic thin sections using the rotating polarizer stage

One of the fundamental problems with image processing of petrographic thin sections is that the appearance (colour I intensity) of a mineral grain will vary with the orientation of the crystal lattice to the preferred direction of the polarizing filters on a petrographic microscope. This makes it very difficult to determine grain boundaries, grain orientation and mineral species from a single captured image. To overcome this problem, the Rotating Polarizer Stage was used to replace the fixed polarizer and analyzer on a standard petrographic microscope. The Rotating Polarizer Stage rotates the polarizers while the thin section remains stationary, allowing for better data gathering possibilities. Instead of capturing a single image of a thin section, six composite data sets are created by rotating the polarizers through 900 (or 1800 if quartz c-axes measurements need to be taken) in both plane and cross polarized light. The composite data sets can be viewed as separate images and consist of the average intensity image, the maximum intensity image, the minimum intensity image, the maximum position image, the minimum position image and the gradient image. The overall strategy used by the image processing system is to gather the composite data sets, determine the grain boundaries using the gradient image, classify the different mineral species present using the minimum and maximum intensity images and then perform measurements of grain shape and, where possible, partial crystallographic orientation using the maximum intensity and maximum position images.

Sleep and information processing in individuals who have sustained a traumatic brain injury

Individuals who have sustained a traumatic brain injury (TBI) often complain of t roubl e sleeping and daytime fatigue but little is known about the neurophysiological underpinnings of the s e sleep difficulties. The fragile sleep of thos e with a TBI was predicted to be characterized by impairments in gating, hyperarousal and a breakdown in sleep homeostatic mechanisms. To test these hypotheses, 20 individuals with a TBI (18- 64 years old, 10 men) and 20 age-matched controls (18-61 years old, 9 men) took part in a comprehensive investigation of their sleep. While TBI participants were not recruited based on sleep complaint, the fmal sample was comprised of individuals with a variety of sleep complaints, across a range of injury severities. Rigorous screening procedures were used to reduce potential confounds (e.g., medication). Sleep and waking data were recorded with a 20-channel montage on three consecutive nights. Results showed dysregulation in sleep/wake mechanisms. The sleep of individuals with a TBI was less efficient than that of controls, as measured by sleep architecture variables. There was a clear breakdown in both spontaneous and evoked K-complexes in those with a TBI. Greater injury severities were associated with reductions in spindle density, though sleep spindles in slow wave sleep were longer for individuals with TBI than controls. Quantitative EEG revealed an impairment in sleep homeostatic mechanisms during sleep in the TBI group. As well, results showed the presence of hyper arousal based on quantitative EEG during sleep. In wakefulness, quantitative EEG showed a clear dissociation in arousal level between TBls with complaints of insomnia and TBls with daytime fatigue. In addition, ERPs indicated that the experience of hyper arousal in persons with a TBI was supported by neural evidence, particularly in wakefulness and Stage 2 sleep, and especially for those with insomnia symptoms. ERPs during sleep suggested that individuals with a TBI experienced impairments in information processing and sensory gating. Whereas neuropsychological testing and subjective data confirmed predicted deficits in the waking function of those with a TBI, particularly for those with more severe injuries, there were few group differences on laboratory computer-based tasks. Finally, the use of correlation analyses confirmed distinct sleep-wake relationships for each group. In sum, the mechanisms contributing to sleep disruption in TBI are particular to this condition, and unique neurobiological mechanisms predict the experience of insomnia versus daytime fatigue following a TBI. An understanding of how sleep becomes disrupted after a TBI is important to directing future research and neurorehabilitation.

Early adversity, brain development and emotion processing in monozygotic twins

Il existe actuellement de nombreuses preuves démontrant que des facteurs génétiques et environnementaux interagissent pendant des périodes spécifiques du développement pour rendre une personne vulnérable aux troubles psychologiques via diverses adaptations physiologiques. Cette thèse porte sur l'impact de l’adversité prénatale (représentée par le petit poids à la naissance, PPN) et de l’adversité postnatale précoce (symptômes dépressifs maternels et comportements maternels négatifs), sur le développement du cerveau, particulièrement les régions fronto-limbiques impliquées dans le traitement des émotions, pendant l'enfance et l'adolescence. Des jumeaux monozygotes (MZ) sont utilisés, lorsque possible, afin de contrôler pour les effets génétiques. Les chapitres 1 et 2 présentent les résultats de la vérification de l'hypothèse que l’adversité prénatale et postnatale précoce sont associées à une altération du fonctionnement des régions fronto-limbique tels que l’amygdale, l’hippocampe, l’insula, le cortex cingulaire antérieur et le cortex préfrontal, en réponse à des stimuli émotifs chez des enfants et des adolescents. On observe que les symptômes dépressifs maternels sont associés à une activation plus élevée des régions fronto-limbiques des enfants en réponse à la tristesse. Les résultats de l’étude avec des adolescents suggèrent que le PPN, les symptômes dépressifs et les comportements maternels négatifs sont associés à une fonction altérée des régions fronto-limbiques en réponse à des stimuli émotionnels. Chez les jumeaux MZ on observe également que la discordance intra-paire de PPN et de certains comportements maternels est associée à une discordance intra-paire du fonctionnement du cerveau et que ces altérations diffèrent selon le sexe. Le chapitre 3 présente les résultats de la vérification de l'hypothèse que l’adversité prénatale et postnatale précoce sont associées à un volume total réduit du cerveau et de l’hypothèse que les comportements maternels peuvent servir de médiateur ou de modérateur de l'association entre le PPN et le volume du cerveau. Avec des jumeaux MZ à l’adolescence on observe a) que le PPN est effectivement associé à une diminution du volume total du cerveau et b) que la discordance intra-paire de PPN est associée à une discordance du volume du cerveau. En somme, cette thèse présente un ensemble de résultats qui soutiennent deux hypothèses importantes pour comprendre les effets de l’environnement sur le développement du cerveau : que l’environnement prénatal et postnatal précoce ont un impact sur le développement du cerveau indépendamment du code génétique et que les mécanismes impliqués peuvent différer entre les garçons et les filles. Finalement, l’ensemble de ces résultats sont discutés à la lumière des autres travaux de recherche dans ce domaine et des avenues à explorer pour de la recherche ultérieure sont proposées.

Neural Network based studies on Spectroscopic Analysis and Image Processing

International School of Photonics, Cochin University of Science and Technology

“Development of lymphoid cell culture system from Penaeus monodon and molecular approaches for its transformation

Unveiling the molecular and regulatory mechanisms that prevent in vitro transformation in shrimp remains elusive in the development of continuous cell lines, with an arduous history of over 25 years (Jayesh et al., 2012). Despite presenting challenges to researchers in developing a cell line, the billion dollar aquaculture industry is under viral threat. In addition, the regulatory mechanisms that prevent in vitro transformation and carcinoma in shrimps might provide new leads for the development of anti-ageing and anti-cancer interventions in human (Vogt, 2011) and in higher vertebrates. This highlights the importance of developing shrimp cell lines, to bring out effective prophylactics against shrimp viruses and for understanding the mechanism that induce cancer and ageing in human.. Advances in molecular biology and various gene transfer technologies for immortalization of cells have resulted in the development of hundreds of cell lines from insects and mammals, but yet not a single cell line has been developed from shrimp and other marine invertebrates. With this backdrop, the research described in this thesis attempted to develop molecular tools for induced in vitro transformation in lymphoid cells from Penaeus monodon and for the development of continuous cell lines using conventional and novel technologies to address the problems at cellular and molecular level.

Face processing in humans is compatible with a simple shape-based model of vision

Understanding how the human visual system recognizes objects is one of the key challenges in neuroscience. Inspired by a large body of physiological evidence (Felleman and Van Essen, 1991; Hubel and Wiesel, 1962; Livingstone and Hubel, 1988; Tso et al., 2001; Zeki, 1993), a general class of recognition models has emerged which is based on a hierarchical organization of visual processing, with succeeding stages being sensitive to image features of increasing complexity (Hummel and Biederman, 1992; Riesenhuber and Poggio, 1999; Selfridge, 1959). However, these models appear to be incompatible with some well-known psychophysical results. Prominent among these are experiments investigating recognition impairments caused by vertical inversion of images, especially those of faces. It has been reported that faces that differ "featurally" are much easier to distinguish when inverted than those that differ "configurally" (Freire et al., 2000; Le Grand et al., 2001; Mondloch et al., 2002) ??finding that is difficult to reconcile with the aforementioned models. Here we show that after controlling for subjects' expectations, there is no difference between "featurally" and "configurally" transformed faces in terms of inversion effect. This result reinforces the plausibility of simple hierarchical models of object representation and recognition in cortex.

Colour image processing

In the context of the round table the following topics related to image colour processing will be discussed: historical point of view. Studies of Aguilonius, Gerritsen, Newton and Maxwell. CIE standard (Commission International de lpsilaEclaraige). Colour models. RGB, HIS, etc. Colour segmentation based on HSI model. Industrial applications. Summary and discussion. At the end, video images showing the robustness of colour in front of B/W images will be presented

Amphioxus molecular biology: insights into vertebrate evolution and developmental mechanisms

The cephalochordate amphioxus is the best available proxy for the last common invertebrate ancestor of the vertebrates. During the last decade, the developmental genetics of amphioxus have been extensively examined for insights into the evolutionary origin and early evolution of the vertebrates. Comparisons between expression domains of homologous genes in amphioxus and vertebrates have strengthened proposed homologies between specific body parts. Molecular genetic studies have also highlighted parallels in the developmental mechanisms of amphioxus and vertebrates. In both groups, a similar nested pattern of Hox gene expression is involved in rostrocaudal patterning of the neural tube, and homologous genes also appear to be involved in dorsoventral neural patterning. Studies of amphioxus molecular biology have also hinted that the protochordate ancestor of the vertebrates included cell populations that modified their developmental genetic pathways during early vertebrate evolution to yield definitive neural crest and neurogenic placodes. We also discuss how the application of expressed sequence tag and gene-mapping approaches to amphioxus have combined with developmental studies to advance our understanding of chordate genome evolution. We conclude by considering the potential offered by the sequencing of the amphioxus genome, which was completed in late 2004.

The challenges for molecular nutrition research 1: linking genotype to healthy nutrition

Nutrition science finds itself at a major crossroad. On the one hand we can continue the current path, which has resulted in some substantial advances, but also many conflicting messages which impair the trust of the general population, especially those who are motivated to improve their health through diet. The other road is uncharted and is being built over the many exciting new developments in life sciences. This new era of nutrition recognizes the complex relation between the health of the individual, its genome, and the life-long dietary exposure, and has lead to the realisation that nutrition is essentially a gene - environment interaction science. This review on the relation between genotype, diet and health is the first of a series dealing with the major challenges in molecular nutrition, analyzing the foundations of nutrition research. With the unravelling of the human genome and the linking of its variability to a multitude of phenotypes from " healthy'' to an enormously complex range of predispositions, the dietary modulation of these propensities has become an area of active research. Classical genetic approaches applied so far in medical genetics have steered away from incorporating dietary effects in their models and paradoxically, most genetic studies analyzing diet-associated phenotypes and diseases simply ignore diet. Yet, a modest but increasing number of studies are accounting for diet as a modulator of genetic associations. These range from observational cohorts to intervention studies with prospectively selected genotypes. New statistical and bioinformatics approaches are becoming available to aid in design and evaluation of these studies. This review discusses the various approaches used and provides concrete recommendations for future research.

Smoothed histogram modification for image processing

The technique of constructing a transformation, or regrading, of a discrete data set such that the histogram of the transformed data matches a given reference histogram is commonly known as histogram modification. The technique is widely used for image enhancement and normalization. A method which has been previously derived for producing such a regrading is shown to be “best” in the sense that it minimizes the error between the cumulative histogram of the transformed data and that of the given reference function, over all single-valued, monotone, discrete transformations of the data. Techniques for smoothed regrading, which provide a means of balancing the error in matching a given reference histogram against the information lost with respect to a linear transformation are also examined. The smoothed regradings are shown to optimize certain cost functionals. Numerical algorithms for generating the smoothed regradings, which are simple and efficient to implement, are described, and practical applications to the processing of LANDSAT image data are discussed.