Variational segmentation of vector-valued images with gradient vector flow

International audienceIn this paper, we extend the gradient vector flow field for robust variational segmentation of vector-valued images. Rather than using scalar edge information, we define a vectorial edge map derived from a weighted local structure tensor of the image that enables the diffusion of the gradient vectors in accurate directions through the 4DGVF equation. To reduce the contribution of noise in the structure tensor, image channels are weighted according to a blind estimator of contrast. The method is applied to biological volume delineation in dynamic PET imaging, and validated on realistic Monte Carlo simulations of numerical phantoms as well as on real images

Cancellous bone and theropod dinosaur locomotion. Part I—an examination of cancellous bone architecture in the hindlimb bones of theropods

This paper is the first of a three-part series that investigates the architecture of cancellous (‘spongy’) bone in the main hindlimb bones of theropod dinosaurs, and uses cancellous bone architectural patterns to infer locomotor biomechanics in extinct non-avian species. Cancellous bone is widely known to be highly sensitive to its mechanical environment, and has previously been used to infer locomotor biomechanics in extinct tetrapod vertebrates, especially primates. Despite great promise, cancellous bone architecture has remained little utilized for investigating locomotion in many other extinct vertebrate groups, such as dinosaurs. Documentation and quantification of architectural patterns across a whole bone, and across multiple bones, can provide much information on cancellous bone architectural patterns and variation across species. Additionally, this also lends itself to analysis of the musculoskeletal biomechanical factors involved in a direct, mechanistic fashion. On this premise, computed tomographic and image analysis techniques were used to describe and analyse the three-dimensional architecture of cancellous bone in the main hindlimb bones of theropod dinosaurs for the first time. A comprehensive survey across many extant and extinct species is produced, identifying several patterns of similarity and contrast between groups. For instance, more stemward non-avian theropods (e.g. ceratosaurs and tyrannosaurids) exhibit cancellous bone architectures more comparable to that present in humans, whereas species more closely related to birds (e.g. paravians) exhibit architectural patterns bearing greater similarity to those of extant birds. Many of the observed patterns may be linked to particular aspects of locomotor biomechanics, such as the degree of hip or knee flexion during stance and gait. A further important observation is the abundance of markedly oblique trabeculae in the diaphyses of the femur and tibia of birds, which in large species produces spiralling patterns along the endosteal surface. Not only do these observations provide new insight into theropod anatomy and behaviour, they also provide the foundation for mechanistic testing of locomotor hypotheses via musculoskeletal biomechanical modelling

The State of the Art in Flow Visualization: Dense and Texture-Based Techniques

Flow visualization has been a very attractive component of scientific visualization research for a long time. Usually very large multivariate datasets require processing. These datasets often consist of a large number of sample locations and several time steps. The steadily increasing performance of computers has recently become a driving factor for a reemergence in flow visualization research, especially in texture-based techniques. In this paper, dense, texture-based flow visualization techniques are discussed. This class of techniques attempts to provide a complete, dense representation of the flow field with high spatio-temporal coherency. An attempt of categorizing closely related solutions is incorporated and presented. Fundamentals are shortly addressed as well as advantages and disadvantages of the methods. Categories and Subject Descriptors (according to ACM CCS): I.3 [Computer Graphics]: visualization, flow visualization, computational flow visualizatio

Point Normal Orientation and Surface Reconstruction by Incorporating Isovalue Constraints to Poisson Equation

Oriented normals are common pre-requisites for many geometric algorithms based on point clouds, such as Poisson surface reconstruction. However, it is not trivial to obtain a consistent orientation. In this work, we bridge orientation and reconstruction in implicit space and propose a novel approach to orient point clouds by incorporating isovalue constraints to the Poisson equation. Feeding a well-oriented point cloud into a reconstruction approach, the indicator function values of the sample points should be close to the isovalue. Based on this observation and the Poisson equation, we propose an optimization formulation that combines isovalue constraints with local consistency requirements for normals. We optimize normals and implicit functions simultaneously and solve for a globally consistent orientation. Owing to the sparsity of the linear system, an average laptop can be used to run our method within reasonable time. Experiments show that our method can achieve high performance in non-uniform and noisy data and manage varying sampling densities, artifacts, multiple connected components, and nested surfaces

Characterization and surface reconstruction of objects in tomographic images of composite materials

Dissertação para obtenção do Grau de Mestre em Engenharia InformáticaIn the scope of the project Tomo-GPU supported by FCT / MCTES the aim is to build an interactive graphical environment that allows a Materials specialist to define their own programs for analysis of 3D tomographic images. This project aims to build a tool to characterize and investigate the identified objects, where the user can define search criteria such as size, orientation, bounding boxes, among others. All this processing will be done on a desktop computer equipped with a graphics card with some processing power. On the proposed solution the modules for characterizing objects, received from the identification phase, will be implemented using some existing software libraries, most notably the CGAL library. The characterization modules with bigger execution times will be implemented using OpenCL and GPUs. With this work the characterization and reconstruction of objects and their research can now be done on conventional machines, using GPUs to accelerate the most time-consuming computations. After the conclusion of this thesis, new tools that will help to improve the current development cycle of new materials will be available for Materials Science specialists

An image-based modeling framework for patient-specific computational hemodynamics

We present a modeling framework designed for patient-specific computational hemodynamics to be performed in the context of large-scale studies. The framework takes advantage of the integration of image processing, geometric analysis and mesh generation techniques, with an accent on full automation and high-level interaction. Image segmentation is performed using implicit deformable models taking advantage of a novel approach for selective initialization of vascular branches, as well as of a strategy for the segmentation of small vessels. A robust definition of centerlines provides objective geometric criteria for the automation of surface editing and mesh generation. The framework is available as part of an open-source effort, the Vascular Modeling Toolkit, a first step towards the sharing of tools and data which will be necessary for computational hemodynamics to play a role in evidence-based medicine

Thermo-fluid-dynamics of impinging swirling jets

The superimposition of a tangential motion on a conventional round jet has been demonstrated to significantly affect the large-scale topology of the flow. Swirling flows are widely employed, in the impinging configuration, in several industrial processes which involve both non-reacting and reacting applications. In the present dissertation, the simultaneously acquired thermal and three-dimensional velocity fields of an impinging hot jet emerging from a custom swirl generator in a cold ambient are presented. The velocity and temperature fields are experimentally measured using time-resolved Tomographic PIV and high-speed Infrared thermography in a combined system. A detailed description of a custom swirl generator is provided, and the time-averaged velocity profiles of a free swirling flow are discussed in order to estimate the swirl number. The instantaneous three-dimensional dynamics in proximity of the nozzle is discussed and the main features of a free swirling jet are investigated through the application of Proper Orthogonal Decomposition technique. The time-dependent features of velocity and temperature fields of an impinging swirling jet are investigated through the description of the time sequences of the temperature fluctuations and the synchronised instantaneous vortical structures. Taking advantage of the simultaneous acquisition and of the knowledge of the relative positioning of thermal and velocity frames, two different correlation techniques are applied, and their outcomes discussed

Visual analytics methods for shape analysis of biomedical images exemplified on rodent skull morphology

In morphometrics and its application fields like medicine and biology experts are interested in causal relations of variation in organismic shape to phylogenetic, ecological, geographical, epidemiological or disease factors - or put more succinctly by Fred L. Bookstein, morphometrics is "the study of covariances of biological form". In order to reveal causes for shape variability, targeted statistical analysis correlating shape features against external and internal factors is necessary but due to the complexity of the problem often not feasible in an automated way. Therefore, a visual analytics approach is proposed in this thesis that couples interactive visualizations with automated statistical analyses in order to stimulate generation and qualitative assessment of hypotheses on relevant shape features and their potentially affecting factors. To this end long established morphometric techniques are combined with recent shape modeling approaches from geometry processing and medical imaging, leading to novel visual analytics methods for shape analysis. When used in concert these methods facilitate targeted analysis of characteristic shape differences between groups, co-variation between different structures on the same anatomy and correlation of shape to extrinsic attributes. Here a special focus is put on accurate modeling and interactive rendering of image deformations at high spatial resolution, because that allows for faithful representation and communication of diminutive shape features, large shape differences and volumetric structures. The utility of the presented methods is demonstrated in case studies conducted together with a collaborating morphometrics expert. As exemplary model structure serves the rodent skull and its mandible that are assessed via computed tomography scans