Finding faint HI structure in and around galaxies: scraping the barrel

Soon to be operational HI survey instruments such as APERTIF and ASKAP will produce large datasets. These surveys will provide information about the HI in and around hundreds of galaxies with a typical signal-to-noise ratio of $\sim$ 10 in the inner regions and $\sim$ 1 in the outer regions. In addition, such surveys will make it possible to probe faint HI structures, typically located in the vicinity of galaxies, such as extra-planar-gas, tails and filaments. These structures are crucial for understanding galaxy evolution, particularly when they are studied in relation to the local environment. Our aim is to find optimized kernels for the discovery of faint and morphologically complex HI structures. Therefore, using HI data from a variety of galaxies, we explore state-of-the-art filtering algorithms. We show that the intensity-driven gradient filter, due to its adaptive characteristics, is the optimal choice. In fact, this filter requires only minimal tuning of the input parameters to enhance the signal-to-noise ratio of faint components. In addition, it does not degrade the resolution of the high signal-to-noise component of a source. The filtering process must be fast and be embedded in an interactive visualization tool in order to support fast inspection of a large number of sources. To achieve such interactive exploration, we implemented a multi-core CPU (OpenMP) and a GPU (OpenGL) version of this filter in a 3D visualization environment ($\tt{SlicerAstro}$).Comment: 17 pages, 9 figures, 4 tables. Astronomy and Computing, accepte

What we see changes how we see : analyzing the plasticity of the horizontal effect.

The relationship between the processing of orientations by the human visual system has been related to the orientation content of the natural environment; horizontal orientations, while predominant in natural environments, are perceived less well than vertical and oblique orientations are perceived best, though they are least prevalent in the natural world. This ‘horizontal effect’ has further extended the well-studied relationship between visual encoding and natural scene statistics as the differential perception of orientations in broadband scenes inversely matches their differential representation in the natural environment. However, the original hypothesis that this relationship may have evolved across millennia in order to make the visual system an efficient information-transmitting system has been called into question by research showing the modification of orientation perception by exposure to altered environments and studies showing a later development of adult-like orientation processing. Recent work into the effects of adaptation on visual encoding of the natural environment have led me to the conclusion that the relationship between the statistics of the natural world and visual encoding is, in a way, much simpler than previously posited; rather than being adapted over millennia to whiten the typical natural scene anisotropy, the visual system adjusts processing dynamically to match the current visual environment. The project presented here details how the statistics of the recently viewed environment affect the way that the visual brain processes information. To assess the effect of recent exposure on broadband orientation processing, the orientation content subjects viewed was modified via fast Fourier transform (FFT) filtering of their environment in near-real-time. Results show that experience in an altered environment modifies anisotropic processing: observers’ orientation perception changes from matching the typical environmental distribution to matching that of the recently experienced atypical environment. The results of these experiments can be predicted by assuming that observers’ biases of perception are probabilistic and rely on an internal model that matches the recently experienced environmental distribution. This change in perception indicates not only that orientation processing is plastic, but that it is related in a predictable way to an observer’s recent visual environment

Assessing Optic Neuritis in a Mouse Model of Multiple Sclerosis with Diffusion MR Imaging

Optic neuritis (ON) is an early manifestation in patients of multiple sclerosis (MS), typically resulting in visual dysfunction. The inflammatory demyelination of the optic nerve in ON closely resembles pathologies of the rest of central nervous system (CNS) white matter in MS. Since accumulated axonal degeneration in MS was considered as the potential cause leading to permanent disability, correlating optic nerve pathology and visual function in ON could be a model system to investigate the relationship between functional outcome and neuropathology. It may also present a new way to reflect the disease progression in MS. Various MR techniques have been used to assess inflammation (inflammatory cell infiltration and vasogenic edema) of ON, but rarely demonstrated the ability to image cellularity changes non-invasively. Diffusion MRI measures the Brownian motion of water molecules in the microstructure of biological tissues. Diffusion tensor imaging (DTI) holds the promise to provide a specific biomarker of axonal injury and demyelination in CNS white matter by axial diffusivity (the diffusion parallel to white matter fibers) and radial diffusivity (the diffusion perpendicular to white matter fibers), respectively. However, DTI assumes a single diffusion tensor model and thus takes an average of varied diffusion components. In contrast, our recently developed diffusion basis spectrum imaging (DBSI) resolves the complex diffusion components and provides relatively accurate directional diffusivities and diffusion component fractions, relating to the detail and accurate pathological picture of the disease or injury. In the current work, in vivo 25-direction DBSI was applied to the optic nerve of mice with experimental autoimmune encephalomyelitis (EAE), an animal model of MS, with visual impairment at onset of ON. Our results demonstrate that inflammation correlated well with visual impairment in acute ON. DBSI successfully detected inflammatory cell infiltration and optic nerve white matter pathology in EAE that was consistent with histology, supporting the capability of DBSI to quantify increased cellularity, axonal injury and myelin damage in the optic nerve of EAE mice

Neural BRDF Representation and Importance Sampling

Controlled capture of real-world material appearance yields tabulated sets of highly realistic reflectance data. In practice, however, its high memory footprint requires compressing into a representation that can be used efficiently in rendering while remaining faithful to the original. Previous works in appearance encoding often prioritized one of these requirements at the expense of the other, by either applying high-fidelity array compression strategies not suited for efficient queries during rendering, or by fitting a compact analytic model that lacks expressiveness. We present a compact neural network-based representation of BRDF data that combines high-accuracy reconstruction with efficient practical rendering via built-in interpolation of reflectance. We encode BRDFs as lightweight networks, and propose a training scheme with adaptive angular sampling, critical for the accurate reconstruction of specular highlights. Additionally, we propose a novel approach to make our representation amenable to importance sampling: rather than inverting the trained networks, we learn to encode them in a more compact embedding that can be mapped to parameters of an analytic BRDF for which importance sampling is known. We evaluate encoding results on isotropic and anisotropic BRDFs from multiple real-world datasets, and importance sampling performance for isotropic BRDFs mapped to two different analytic models

Mapping Trabecular Bone Fabric Tensor by in Vivo Magnetic Resonance Imaging

The mechanical competence of bone depends upon its quantity, structural arrangement, and chemical composition. Assessment of these factors is important for the evaluation of bone integrity, particularly as the skeleton remodels according to external (e.g. mechanical loading) and internal (e.g. hormonal changes) stimuli. Micro magnetic resonance imaging (µMRI) has emerged as a non-invasive and non-ionizing method well-suited for the repeated measurements necessary for monitoring changes in bone integrity. However, in vivo image-based directional dependence of trabecular bone (TB) has not been linked to mechanical competence or fracture risk despite the existence of convincing ex vivo evidence. The objective of this dissertation research was to develop a means of capturing the directional dependence of TB by assessing a fabric tensor on the basis of in vivo µMRI. To accomplish this objective, a novel approach for calculating the TB fabric tensor based on the spatial autocorrelation function was developed and evaluated in the presence of common limitations to in vivo µMRI. Comparisons were made to the standard technique of mean-intercept-length (MIL). Relative to MIL, ACF was identified as computationally faster by over an order of magnitude and more robust within the range of the resolutions and SNRs achievable in vivo. The potential for improved sensitivity afforded by isotropic resolution was also investigated in an improved µMR imaging protocol at 3T. Measures of reproducibility and reliability indicate the potential of images with isotropic resolution to provide enhanced sensitivity to orientation-dependent measures of TB, however overall reproducibility suffered from the sacrifice in SNR. Finally, the image-derived TB fabric tensor was validated through its relationship with TB mechanical competence in specimen and in vivo µMR images. The inclusion of trabecular bone fabric measures significantly improved the bone volume fraction-based prediction of elastic constants calculated by micro-finite element analysis. This research established a method for detecting TB fabric tensor in vivo and identified the directional dependence of TB as an important determinant of TB mechanical competence

Neurite imaging reveals microstructural variations in human cerebral cortical gray matter

We present distinct patterns of neurite distribution in the human cerebral cortex using diffusion magnetic resonance imaging (MRI). We analyzed both high-resolution structural (T1w and T2w images) and diffusion MRI data in 505 subjects from the Human Connectome Project. Neurite distributions were evaluated using the neurite orientation dispersion and density imaging (NODDI) model, optimized for gray matter, and mapped onto the cortical surface using a method weighted towards the cortical mid-thickness to reduce partial volume effects. The estimated neurite density was high in both somatosensory and motor areas, early visual and auditory areas, and middle temporal area (MT), showing a strikingly similar distribution to myelin maps estimated from the T1w/T2w ratio. The estimated neurite orientation dispersion was particularly high in early sensory areas, which are known for dense tangential fibers and are classified as granular cortex by classical anatomists. Spatial gradients of these cortical neurite properties revealed transitions that colocalize with some areal boundaries in a recent multi-modal parcellation of the human cerebral cortex, providing mutually supportive evidence. Our findings indicate that analyzing the cortical gray matter neurite morphology using diffusion MRI and NODDI provides valuable information regarding cortical microstructure that is related to but complementary to myeloarchitecture

Quantification of microscopic diffusion anisotropy disentangles effects of orientation dispersion from microstructure: Applications in healthy volunteers and in brain tumors

AbstractThe anisotropy of water diffusion in brain tissue is affected by both disease and development. This change can be detected using diffusion MRI and is often quantified by the fractional anisotropy (FA) derived from diffusion tensor imaging (DTI). Although FA is sensitive to anisotropic cell structures, such as axons, it is also sensitive to their orientation dispersion. This is a major limitation to the use of FA as a biomarker for “tissue integrity”, especially in regions of complex microarchitecture. In this work, we seek to circumvent this limitation by disentangling the effects of microscopic diffusion anisotropy from the orientation dispersion.The microscopic fractional anisotropy (μFA) and the order parameter (OP) were calculated from the contrast between signal prepared with directional and isotropic diffusion encoding, where the latter was achieved by magic angle spinning of the q-vector (qMAS). These parameters were quantified in healthy volunteers and in two patients; one patient with meningioma and one with glioblastoma. Finally, we used simulations to elucidate the relation between FA and μFA in various micro-architectures.Generally, μFA was high in the white matter and low in the gray matter. In the white matter, the largest differences between μFA and FA were found in crossing white matter and in interfaces between large white matter tracts, where μFA was high while FA was low. Both tumor types exhibited a low FA, in contrast to the μFA which was high in the meningioma and low in the glioblastoma, indicating that the meningioma contained disordered anisotropic structures, while the glioblastoma did not. This interpretation was confirmed by histological examination.We conclude that FA from DTI reflects both the amount of diffusion anisotropy and orientation dispersion. We suggest that the μFA and OP may complement FA by independently quantifying the microscopic anisotropy and the level of orientation coherence

Spatial biases and computational constraints on the encoding of complex local image structure

The decomposition of visual scenes into elements described by orientation and spatial frequency is well documented in the early cortical visual system. How such 2nd-order elements are sewn together to create perceptual objects such as corners and intersections remains relatively unexplored. The current study combines information theory with structured deterministic patterns to gain insight into how complex (higher-order) image features are encoded. To more fully probe these mechanisms, many subjects (N = 24) and stimuli were employed. The detection of complex image structure was studied under conditions of learning and attentive versus preattentive visual scrutiny. Strong correlations (R2 > 0.8, P < 0.0001) were found between a particular family of spatially biased measures of image information and human sensitivity to a large range of visual structures. The results point to computational and spatial limitations of such encoding. Of the extremely large set of complex spatial interactions that are possible, the small subset perceivable by humans were found to be dominated by those occurring along sets of one or more narrow parallel lines. Within such spatial domains, the number of pieces of visual information (pixel values) that may be simultaneously considered is limited to a maximum of 10 points. Learning and processes involved in attentive scrutiny do little if anything to increase the dimensionality of this system

Influence of Sensorimotor Noise on the Planning and Control of Reaching in 3-Dimensional Space

abstract: The ability to plan, execute, and control goal oriented reaching and grasping movements is among the most essential functions of the brain. Yet, these movements are inherently variable; a result of the noise pervading the neural signals underlying sensorimotor processing. The specific influences and interactions of these noise processes remain unclear. Thus several studies have been performed to elucidate the role and influence of sensorimotor noise on movement variability. The first study focuses on sensory integration and movement planning across the reaching workspace. An experiment was designed to examine the relative contributions of vision and proprioception to movement planning by measuring the rotation of the initial movement direction induced by a perturbation of the visual feedback prior to movement onset. The results suggest that contribution of vision was relatively consistent across the evaluated workspace depths; however, the influence of vision differed between the vertical and later axes indicate that additional factors beyond vision and proprioception influence movement planning of 3-dimensional movements. If the first study investigated the role of noise in sensorimotor integration, the second and third studies investigate relative influence of sensorimotor noise on reaching performance. Specifically, they evaluate how the characteristics of neural processing that underlie movement planning and execution manifest in movement variability during natural reaching. Subjects performed reaching movements with and without visual feedback throughout the movement and the patterns of endpoint variability were compared across movement directions. The results of these studies suggest a primary role of visual feedback noise in shaping patterns of variability and in determining the relative influence of planning and execution related noise sources. The final work considers a computational approach to characterizing how sensorimotor processes interact to shape movement variability. A model of multi-modal feedback control was developed to simulate the interaction of planning and execution noise on reaching variability. The model predictions suggest that anisotropic properties of feedback noise significantly affect the relative influence of planning and execution noise on patterns of reaching variability.Dissertation/ThesisPh.D. Bioengineering 201