Interactive Segmentation and Visualization of DTI Data Using a Hierarchical Watershed Representation

Magnetic resonance diffusion tensor imaging (DTI) measures diffusion of water molecules and is used to characterize orientation of white matter fibers and connectivity of neurological structures. Segmentation and visualization of DT images is challenging, because of low data quality and complexity of anatomical structures. In this paper, we propose an interactive segmentation approach, based on a hierarchical representation of the input DT image through a tree structure. The tree is obtained by successively merging watershed regions, based on the morphological waterfall approach, hence the name watershed tree. Region merging is done according to a combined similarity and homogeneity criterion. We introduce filters that work on the proposed tree representation, and that enable region-based attribute filtering of DTI data. Linked views between the visualizations of the simplified DT image and the tree enable a user to visually explore both data and tree at interactive rates. The coupling of filtering, semiautomatic segmentation by labeling nodes in the tree, and various interaction mechanisms support the segmentation task. Our method is robust against noise, which we demonstrate on synthetic and real DTI data

Iamxt: max-tree toolbox for image processing and analysis

The iamxt is an array-based max-tree toolbox implemented in Python using the NumPy library for array processing. It has state of the art methods for building and processing the max-tree, and a large set of visualization tools that allow to view the tree and the contents of its nodes. The array-based programming style and max-tree representation used in the toolbox make it simple to use. The intended audience of this toolbox includes mathematical morphology students and researchers that want to develop research in the field and image processing researchers that need a toolbox simple to use and easy to integrate in their applications68184CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP311228/2014-32013/23514-0; 2013/07559-

QuadStack: An Efficient Representation and Direct Rendering of Layered Datasets

We introduce QuadStack, a novel algorithm for volumetric data compression and direct rendering. Our algorithm exploits the data redundancy often found in layered datasets which are common in science and engineering fields such as geology, biology, mechanical engineering, medicine, etc. QuadStack first compresses the volumetric data into vertical stacks which are then compressed into a quadtree that identifies and represents the layered structures at the internal nodes. The associated data (color, material, density, etc.) and shape of these layer structures are decoupled and encoded independently, leading to high compression rates (4× to 54× of the original voxel model memory footprint in our experiments). We also introduce an algorithm for value retrieving from the QuadStack representation and we show that the access has logarithmic complexity. Because of the fast access, QuadStack is suitable for efficient data representation and direct rendering. We show that our GPU implementation performs comparably in speed with the state-of-the-art algorithms (18-79 MRays/s in our implementation), while maintaining a significantly smaller memory footprint

Finding and Visualizing Relevant Subspaces for Clustering High-Dimensional Astronomical Data Using Connected Morphological Operators

Data sets in many scientific areas are growing to enormous sizes. For example, modern astronomical surveys provide not only image data but also catalogues of millions of objects (stars, galaxies), each object with hundreds of associated parameters. Gene expression ex-periments produce data about the complete genome of an organism under different conditions and at a sequence of time points. Ex-ploration of such very high-dimensional data spaces poses a huge challenge. Subspace clustering is one among several approaches which have been proposed for this purpose in recent years. How-ever, many clustering algorithms require the user to set a large num-ber of parameters without any guidelines. Some methods also do not provide a concise summary of the datasets, or, if they do, they lack additional important information such as the number of clus-ters present or the significance of the clusters

Parallel Attribute Computation for Distributed Component Forests

Component trees are powerful image processing tools to analyze the connected components of an image. One attractive strategy consists in building the nested relations at first and then deriving the components' attributes afterward, such that the user can switch between different attribute functions without having to re-compute the entire tree. Only sequential algorithms allow such an approach, while no parallel algorithm is available. In this paper, we extend a recent method using distributed memory techniques to enable posterior attribute computation in a parallel or distributed manner. This novel approach significantly reduces the computational time needed for combining several attribute functions interactively in Giga and Tera-Scale data sets

A graph-based mathematical morphology reader

This survey paper aims at providing a "literary" anthology of mathematical morphology on graphs. It describes in the English language many ideas stemming from a large number of different papers, hence providing a unified view of an active and diverse field of research

Interactive inspection of complex multi-object industrial assemblies

The final publication is available at Springer via http://dx.doi.org/10.1016/j.cad.2016.06.005The use of virtual prototypes and digital models containing thousands of individual objects is commonplace in complex industrial applications like the cooperative design of huge ships. Designers are interested in selecting and editing specific sets of objects during the interactive inspection sessions. This is however not supported by standard visualization systems for huge models. In this paper we discuss in detail the concept of rendering front in multiresolution trees, their properties and the algorithms that construct the hierarchy and efficiently render it, applied to very complex CAD models, so that the model structure and the identities of objects are preserved. We also propose an algorithm for the interactive inspection of huge models which uses a rendering budget and supports selection of individual objects and sets of objects, displacement of the selected objects and real-time collision detection during these displacements. Our solution–based on the analysis of several existing view-dependent visualization schemes–uses a Hybrid Multiresolution Tree that mixes layers of exact geometry, simplified models and impostors, together with a time-critical, view-dependent algorithm and a Constrained Front. The algorithm has been successfully tested in real industrial environments; the models involved are presented and discussed in the paper.Peer ReviewedPostprint (author's final draft

Sparse Volumetric Deformation

Volume rendering is becoming increasingly popular as applications require realistic solid shape representations with seamless texture mapping and accurate filtering. However rendering sparse volumetric data is difficult because of the limited memory and processing capabilities of current hardware. To address these limitations, the volumetric information can be stored at progressive resolutions in the hierarchical branches of a tree structure, and sampled according to the region of interest. This means that only a partial region of the full dataset is processed, and therefore massive volumetric scenes can be rendered efficiently. The problem with this approach is that it currently only supports static scenes. This is because it is difficult to accurately deform massive amounts of volume elements and reconstruct the scene hierarchy in real-time. Another problem is that deformation operations distort the shape where more than one volume element tries to occupy the same location, and similarly gaps occur where deformation stretches the elements further than one discrete location. It is also challenging to efficiently support sophisticated deformations at hierarchical resolutions, such as character skinning or physically based animation. These types of deformation are expensive and require a control structure (for example a cage or skeleton) that maps to a set of features to accelerate the deformation process. The problems with this technique are that the varying volume hierarchy reflects different feature sizes, and manipulating the features at the original resolution is too expensive; therefore the control structure must also hierarchically capture features according to the varying volumetric resolution. This thesis investigates the area of deforming and rendering massive amounts of dynamic volumetric content. The proposed approach efficiently deforms hierarchical volume elements without introducing artifacts and supports both ray casting and rasterization renderers. This enables light transport to be modeled both accurately and efficiently with applications in the fields of real-time rendering and computer animation. Sophisticated volumetric deformation, including character animation, is also supported in real-time. This is achieved by automatically generating a control skeleton which is mapped to the varying feature resolution of the volume hierarchy. The output deformations are demonstrated in massive dynamic volumetric scenes

Efficient and High-Quality Rendering of Higher-Order Geometric Data Representations

Computer-Aided Design (CAD) bezeichnet den Entwurf industrieller Produkte mit Hilfe von virtuellen 3D Modellen. Ein CAD-Modell besteht aus parametrischen Kurven und Flächen, in den meisten Fällen non-uniform rational B-Splines (NURBS). Diese mathematische Beschreibung wird ebenfalls zur Analyse, Optimierung und Präsentation des Modells verwendet. In jeder dieser Entwicklungsphasen wird eine unterschiedliche visuelle Darstellung benötigt, um den entsprechenden Nutzern ein geeignetes Feedback zu geben. Designer bevorzugen beispielsweise illustrative oder realistische Darstellungen, Ingenieure benötigen eine verständliche Visualisierung der Simulationsergebnisse, während eine immersive 3D Darstellung bei einer Benutzbarkeitsanalyse oder der Designauswahl hilfreich sein kann. Die interaktive Darstellung von NURBS-Modellen und -Simulationsdaten ist jedoch aufgrund des hohen Rechenaufwandes und der eingeschränkten Hardwareunterstützung eine große Herausforderung. Diese Arbeit stellt vier neuartige Verfahren vor, welche sich mit der interaktiven Darstellung von NURBS-Modellen und Simulationensdaten befassen. Die vorgestellten Algorithmen nutzen neue Fähigkeiten aktueller Grafikkarten aus, um den Stand der Technik bezüglich Qualität, Effizienz und Darstellungsgeschwindigkeit zu verbessern. Zwei dieser Verfahren befassen sich mit der direkten Darstellung der parametrischen Beschreibung ohne Approximationen oder zeitaufwändige Vorberechnungen. Die dabei vorgestellten Datenstrukturen und Algorithmen ermöglichen die effiziente Unterteilung, Klassifizierung, Tessellierung und Darstellung getrimmter NURBS-Flächen und einen interaktiven Ray-Casting-Algorithmus für die Isoflächenvisualisierung von NURBSbasierten isogeometrischen Analysen. Die weiteren zwei Verfahren beschreiben zum einen das vielseitige Konzept der programmierbaren Transparenz für illustrative und verständliche Visualisierungen tiefenkomplexer CAD-Modelle und zum anderen eine neue hybride Methode zur Reprojektion halbtransparenter und undurchsichtiger Bildinformation für die Beschleunigung der Erzeugung von stereoskopischen Bildpaaren. Die beiden letztgenannten Ansätze basieren auf rasterisierter Geometrie und sind somit ebenfalls für normale Dreiecksmodelle anwendbar, wodurch die Arbeiten auch einen wichtigen Beitrag in den Bereichen der Computergrafik und der virtuellen Realität darstellen. Die Auswertung der Arbeit wurde mit großen, realen NURBS-Datensätzen durchgeführt. Die Resultate zeigen, dass die direkte Darstellung auf Grundlage der parametrischen Beschreibung mit interaktiven Bildwiederholraten und in subpixelgenauer Qualität möglich ist. Die Einführung programmierbarer Transparenz ermöglicht zudem die Umsetzung kollaborativer 3D Interaktionstechniken für die Exploration der Modelle in virtuellenUmgebungen sowie illustrative und verständliche Visualisierungen tiefenkomplexer CAD-Modelle. Die Erzeugung stereoskopischer Bildpaare für die interaktive Visualisierung auf 3D Displays konnte beschleunigt werden. Diese messbare Verbesserung wurde zudem im Rahmen einer Nutzerstudie als wahrnehmbar und vorteilhaft befunden.In computer-aided design (CAD), industrial products are designed using a virtual 3D model. A CAD model typically consists of curves and surfaces in a parametric representation, in most cases, non-uniform rational B-splines (NURBS). The same representation is also used for the analysis, optimization and presentation of the model. In each phase of this process, different visualizations are required to provide an appropriate user feedback. Designers work with illustrative and realistic renderings, engineers need a comprehensible visualization of the simulation results, and usability studies or product presentations benefit from using a 3D display. However, the interactive visualization of NURBS models and corresponding physical simulations is a challenging task because of the computational complexity and the limited graphics hardware support. This thesis proposes four novel rendering approaches that improve the interactive visualization of CAD models and their analysis. The presented algorithms exploit latest graphics hardware capabilities to advance the state-of-the-art in terms of quality, efficiency and performance. In particular, two approaches describe the direct rendering of the parametric representation without precomputed approximations and timeconsuming pre-processing steps. New data structures and algorithms are presented for the efficient partition, classification, tessellation, and rendering of trimmed NURBS surfaces as well as the first direct isosurface ray-casting approach for NURBS-based isogeometric analysis. The other two approaches introduce the versatile concept of programmable order-independent semi-transparency for the illustrative and comprehensible visualization of depth-complex CAD models, and a novel method for the hybrid reprojection of opaque and semi-transparent image information to accelerate stereoscopic rendering. Both approaches are also applicable to standard polygonal geometry which contributes to the computer graphics and virtual reality research communities. The evaluation is based on real-world NURBS-based models and simulation data. The results show that rendering can be performed directly on the underlying parametric representation with interactive frame rates and subpixel-precise image results. The computational costs of additional visualization effects, such as semi-transparency and stereoscopic rendering, are reduced to maintain interactive frame rates. The benefit of this performance gain was confirmed by quantitative measurements and a pilot user study