Color in context and spatial color computation

The purpose of this dissertation is to contribute in the field of spatial color computation models.We begin introducing an overview about different approaches in the definitionof computational models of color in digital imaging. In particular, we present a recent accurate mathematical definition of the Retinex algorithm, that lead to the definition of a new computational model called Random Spray Retinex (RSR). We then introduce the tone mapping problem, discussing the need for color computation in the implementation of a perceptual correct computational model. At this aim we will present the HDR Retinex algorithm, that addresses tone mappingand color constancy at the same time. In the end, we present some experiments analyzing the influence of HDR Retinex spatial color computation on tristimulus colors obtained using different Color Matching Functions (CMFs) on spectral luminance distribution generated by a photometric raytracer

Studying the selectivity of neuronal subpopulations within fMRI voxels

Functional magnetic resonance imaging (fMRI) has become a ubiquitous tool in cognitive neuroscience. The technique allows the non-invasive measurements of cortical responses, but only on the millimeter scale. Recently, two methods aimed at studying the selectivity of neuronal populations on a subvoxel scale. The first technique, fMRI adaptation, relies on the observation that the fMRI response in a given voxel is reduced after prolonged presentation of a stimulus, and that this reduction is selective to the characteristics of the repeated stimuli. The second technique, multi-variate pattern analysis (MVPA), makes use of multi-variate statistics to recover small biases in individual voxels. This thesis compared the two techniques with the aim of studying early- and mid-level processing in the visual cortex. Chapter 3 investigated whether adaptation and MVPA provide consistent results about the properties of the cortical areas under study. To address this question, this thesis compared the two methods for their ability to detect the well documented orientation selectivity in early visual cortex. Using optimised experimental designs for each, this thesis found that the MVPA approach was more sensitive to small differences in stimulus orientation than the adaptation paradigm. Estimates of orientation selectivity obtained with the two methods were, however, very highly correlated across visual areas. Chapters 4 and 5 used both techniques to investigate how local orientation signals are combined and detected in intermediate levels of visual processing. In both chapters the MVPA was more efficient in detecting differences between stimulus categories. In particular, chapter 4 used plaid stimuli, made of the linear sum of two sinusoidal gratings. We obtained weak but consistent evidence, pointing to the direction that V2 might play a role in Fourier component integration. Chapter 5 used contour stimuli constructed from two luminance modulated sinusoidal gratings, with different orientations. Whereas, adaptation failed to reveal contour selectivity, MVPA accuracy was high in most areas tested. However, the experiment did not reveal a significant difference between the test and control conditions. Chapter 6 investigated the encoding of spatial phase in the cortex. Phase is a fundamental aspect of spatial vision, crucial both for the extraction of local features and overall scene perception. This thesis showed that several visual areas, including the primary visual cortex, were sensitive to relative phase combinations. However, phase coherence was optimally encoded in extrastriate areas as predicted by the physiological properties of higher regions

Measuring visual stimulation and attention signals in human superior colliculus using high-resolution fMRI

textThe superior colliculus (SC) is a laminated oculomotor structure in the midbrain. In non-human primates SC has long been known to contain a retinotopically-organized map of visual stimulation in its superficial layers, which is aligned to a map of saccadic eye movements in the deeper layers. Microstimulation and electrophysiology experiments have shown that SC also plays a key role in covert visuospatial attention and suggest that attentional modulation also occurs in a retinotopic manner. Retinotopic organization of the visual field can be non-invasively mapped in humans using functional MRI with a technique called phase-encoded retinotopy. In this technique, rotating wedges and expanding rings of visual stimuli are used to map the polar angle and eccentricity dimensions of a polar coordinates system, respectively. A similar technique can also be used to map spatial attention by keeping the visual stimulus constant and cueing subjects to attend to apertures of rotating wedges and expanding rings within the stimulus. A previous study using fMRI has shown the polar angle representation of visual stimulation in human SC but was unable to find a representation of eccentricity. This work uses high-resolution fMRI along with special surface analysis techniques developed in our lab to demonstrate maps of both polar angle and eccentricity for visual stimulation. Moreover, visual attention is also shown to be topographically organized within SC and in registration with visual stimulation. Finally, in human visual cortex, fMRI is known to show activity for sustained spatial attention even in the absence of a significant visual stimulus, an attentional "base response". In this work, SC is shown to exhibit a similar sustained attention base response using a threshold-contrast detection paradigm. This base response was compared with a response for attention with visual stimulation. The peak amplitude of the base response occurred more deeply within SC tissue than the peak for attention with stimulation. It is proposed that this reflects the specific attentional enhancement of the deeper visuomotor neurons, which are hypothesized to be a direct neuronal correlate of the oculomotor theory of attention.Psycholog

A Modular and Open-Source Framework for Virtual Reality Visualisation and Interaction in Bioimaging

Life science today involves computational analysis of a large amount and variety of data, such as volumetric data acquired by state-of-the-art microscopes, or mesh data from analysis of such data or simulations. The advent of new imaging technologies, such as lightsheet microscopy, has resulted in the users being confronted with an ever-growing amount of data, with even terabytes of imaging data created within a day. With the possibility of gentler and more high-performance imaging, the spatiotemporal complexity of the model systems or processes of interest is increasing as well. Visualisation is often the first step in making sense of this data, and a crucial part of building and debugging analysis pipelines. It is therefore important that visualisations can be quickly prototyped, as well as developed or embedded into full applications. In order to better judge spatiotemporal relationships, immersive hardware, such as Virtual or Augmented Reality (VR/AR) headsets and associated controllers are becoming invaluable tools. In this work we present scenery, a modular and extensible visualisation framework for the Java VM that can handle mesh and large volumetric data, containing multiple views, timepoints, and color channels. scenery is free and open-source software, works on all major platforms, and uses the Vulkan or OpenGL rendering APIs. We introduce scenery's main features, and discuss its use with VR/AR hardware and in distributed rendering. In addition to the visualisation framework, we present a series of case studies, where scenery can provide tangible benefit in developmental and systems biology: With Bionic Tracking, we demonstrate a new technique for tracking cells in 4D volumetric datasets via tracking eye gaze in a virtual reality headset, with the potential to speed up manual tracking tasks by an order of magnitude. We further introduce ideas to move towards virtual reality-based laser ablation and perform a user study in order to gain insight into performance, acceptance and issues when performing ablation tasks with virtual reality hardware in fast developing specimen. To tame the amount of data originating from state-of-the-art volumetric microscopes, we present ideas how to render the highly-efficient Adaptive Particle Representation, and finally, we present sciview, an ImageJ2/Fiji plugin making the features of scenery available to a wider audience.:Abstract Foreword and Acknowledgements Overview and Contributions Part 1 - Introduction 1 Fluorescence Microscopy 2 Introduction to Visual Processing 3 A Short Introduction to Cross Reality 4 Eye Tracking and Gaze-based Interaction Part 2 - VR and AR for System Biology 5 scenery — VR/AR for Systems Biology 6 Rendering 7 Input Handling and Integration of External Hardware 8 Distributed Rendering 9 Miscellaneous Subsystems 10 Future Development Directions Part III - Case Studies C A S E S T U D I E S 11 Bionic Tracking: Using Eye Tracking for Cell Tracking 12 Towards Interactive Virtual Reality Laser Ablation 13 Rendering the Adaptive Particle Representation 14 sciview — Integrating scenery into ImageJ2 & Fiji Part IV - Conclusion 15 Conclusions and Outlook Backmatter & Appendices A Questionnaire for VR Ablation User Study B Full Correlations in VR Ablation Questionnaire C Questionnaire for Bionic Tracking User Study List of Tables List of Figures Bibliography Selbstständigkeitserklärun

Studying neural selectivity for motion using high-field fMRI

Functional magnetic resonance imaging (fMRI) offers a number of opportunities to non-invasively study the properties of the human visual system. Advances in scanner technology, particularly the development of high-field scanners, allow improvements in fMRI such as higher resolution and higher signal to noise ratio (SNR). We aimed to examine what these advances in scanner technology, combined with novel analysis techniques, can tell us about the processing of motion stimuli in the human visual cortex. In Chapter 3 we investigated whether high-resolution fMRI allows us to directly study motion-selective responses in MT+. We used event-related and adaptation methods to examine selectivity for coherent motion and selectivity for direction of motion, and examined the potential limitations of these techniques. One particular analysis technique that has been developed in recent years uses multivariate methods to classify patterns of activity from visual cortex. In Chapter 4 we investigated these methods for classifying direction of motion, particularly whether successful classification responses are based on fine-scale information such as the arrangement of direction-selective columns, or a global signal at a coarser scale. In Chapter 5 we investigated multivariate classification of non-translational motion (e.g. rotation) to see how this compared to the classification of translational motion. The processing of such stimuli have been suggested to be free from the large-scale signals that may be involved in other stimuli, and therefore a more powerful tool for studying the neural architecture of visual cortex. Chapter 6 investigated the processing of plaid motion stimuli, specifically ’pattern’ motion selectivity in MT+ as opposed to ’component’ motion selectivity. These experiments highlight the usefulness of multivariate methods even if the scale of the signal is unknown

Appearance Modelling and Reconstruction for Navigation in Minimally Invasive Surgery

Minimally invasive surgery is playing an increasingly important role for patient care. Whilst its direct patient benefit in terms of reduced trauma, improved recovery and shortened hospitalisation has been well established, there is a sustained need for improved training of the existing procedures and the development of new smart instruments to tackle the issue of visualisation, ergonomic control, haptic and tactile feedback. For endoscopic intervention, the small field of view in the presence of a complex anatomy can easily introduce disorientation to the operator as the tortuous access pathway is not always easy to predict and control with standard endoscopes. Effective training through simulation devices, based on either virtual reality or mixed-reality simulators, can help to improve the spatial awareness, consistency and safety of these procedures. This thesis examines the use of endoscopic videos for both simulation and navigation purposes. More specifically, it addresses the challenging problem of how to build high-fidelity subject-specific simulation environments for improved training and skills assessment. Issues related to mesh parameterisation and texture blending are investigated. With the maturity of computer vision in terms of both 3D shape reconstruction and localisation and mapping, vision-based techniques have enjoyed significant interest in recent years for surgical navigation. The thesis also tackles the problem of how to use vision-based techniques for providing a detailed 3D map and dynamically expanded field of view to improve spatial awareness and avoid operator disorientation. The key advantage of this approach is that it does not require additional hardware, and thus introduces minimal interference to the existing surgical workflow. The derived 3D map can be effectively integrated with pre-operative data, allowing both global and local 3D navigation by taking into account tissue structural and appearance changes. Both simulation and laboratory-based experiments are conducted throughout this research to assess the practical value of the method proposed

Studying neural selectivity for motion using high-field fMRI

Functional magnetic resonance imaging (fMRI) offers a number of opportunities to non-invasively study the properties of the human visual system. Advances in scanner technology, particularly the development of high-field scanners, allow improvements in fMRI such as higher resolution and higher signal to noise ratio (SNR). We aimed to examine what these advances in scanner technology, combined with novel analysis techniques, can tell us about the processing of motion stimuli in the human visual cortex. In Chapter 3 we investigated whether high-resolution fMRI allows us to directly study motion-selective responses in MT+. We used event-related and adaptation methods to examine selectivity for coherent motion and selectivity for direction of motion, and examined the potential limitations of these techniques. One particular analysis technique that has been developed in recent years uses multivariate methods to classify patterns of activity from visual cortex. In Chapter 4 we investigated these methods for classifying direction of motion, particularly whether successful classification responses are based on fine-scale information such as the arrangement of direction-selective columns, or a global signal at a coarser scale. In Chapter 5 we investigated multivariate classification of non-translational motion (e.g. rotation) to see how this compared to the classification of translational motion. The processing of such stimuli have been suggested to be free from the large-scale signals that may be involved in other stimuli, and therefore a more powerful tool for studying the neural architecture of visual cortex. Chapter 6 investigated the processing of plaid motion stimuli, specifically ’pattern’ motion selectivity in MT+ as opposed to ’component’ motion selectivity. These experiments highlight the usefulness of multivariate methods even if the scale of the signal is unknown

Visual Cortex

The neurosciences have experienced tremendous and wonderful progress in many areas, and the spectrum encompassing the neurosciences is expansive. Suffice it to mention a few classical fields: electrophysiology, genetics, physics, computer sciences, and more recently, social and marketing neurosciences. Of course, this large growth resulted in the production of many books. Perhaps the visual system and the visual cortex were in the vanguard because most animals do not produce their own light and offer thus the invaluable advantage of allowing investigators to conduct experiments in full control of the stimulus. In addition, the fascinating evolution of scientific techniques, the immense productivity of recent research, and the ensuing literature make it virtually impossible to publish in a single volume all worthwhile work accomplished throughout the scientific world. The days when a single individual, as Diderot, could undertake the production of an encyclopedia are gone forever. Indeed most approaches to studying the nervous system are valid and neuroscientists produce an almost astronomical number of interesting data accompanied by extremely worthy hypotheses which in turn generate new ventures in search of brain functions. Yet, it is fully justified to make an encore and to publish a book dedicated to visual cortex and beyond. Many reasons validate a book assembling chapters written by active researchers. Each has the opportunity to bind together data and explore original ideas whose fate will not fall into the hands of uncompromising reviewers of traditional journals. This book focuses on the cerebral cortex with a large emphasis on vision. Yet it offers the reader diverse approaches employed to investigate the brain, for instance, computer simulation, cellular responses, or rivalry between various targets and goal directed actions. This volume thus covers a large spectrum of research even though it is impossible to include all topics in the extremely diverse field of neurosciences

High resolution anatomical and functional imaging

The signal-to-noise ratio available in Magnetic Resonance Imaging (MRI)is determined by the static magnetic field strength, causing a continued drive toward higher fields to enable faster image acquisition at finer spatial resolution. The work in this thesis is primarily concerned with the development of sequences for Ultra High Field Magnetic Resonance Imaging (7T) which allow the acquisition of images with high spatial resolution for study of the structure and function of the brain. The methods developed here for high spatial resolution structural imaging allow the identification of regions of the cortex which exhibit layers of high myelin concentration within the cortical strip. This permits the investigation of the correspondence of functional regions in the visual cortex to their underlying structure 'in vivo'. A robust methodology for high resolution functional mapping over a restricted field of view is presented and the results of fMRI studies demonstrating 1 mm isotropic resolution in the primary somatosensory cortex S1 using this methodology are shown. BOLD responses to vibrotactile digit stimulation were investigated using a travelling wave paradigm to measure the topographic representation of the digits in S1 and an event related paradigm for characterization of the haemodynamic delay. A spin-echo EPI acquisition has been optimized and tested to compare the BOLD response in GE and SE echo planar images by employing visual and motor tasks. The specificity of the BOLD responses of SE and GE data was found to be similar using a travelling wave paradigm

Activity in area V3A predicts positions of moving objects

No description supplie