NeuroTessMesh: A Tool for the Generation and Visualization of Neuron Meshes and Adaptive On-the-Fly Refinement

Gaining a better understanding of the human brain continues to be one of the greatest challenges for science, largely because of the overwhelming complexity of the brain and the difficulty of analyzing the features and behavior of dense neural networks. Regarding analysis, 3D visualization has proven to be a useful tool for the evaluation of complex systems. However, the large number of neurons in non-trivial circuits, together with their intricate geometry, makes the visualization of a neuronal scenario an extremely challenging computational problem. Previous work in this area dealt with the generation of 3D polygonal meshes that approximated the cells’ overall anatomy but did not attempt to deal with the extremely high storage and computational cost required to manage a complex scene. This paper presents NeuroTessMesh, a tool specifically designed to cope with many of the problems associated with the visualization of neural circuits that are comprised of large numbers of cells. In addition, this method facilitates the recovery and visualization of the 3D geometry of cells included in databases, such as NeuroMorpho, and provides the tools needed to approximate missing information such as the soma’s morphology. This method takes as its only input the available compact, yet incomplete, morphological tracings of the cells as acquired by neuroscientists. It uses a multiresolution approach that combines an initial, coarse mesh generation with subsequent on-the-fly adaptive mesh refinement stages using tessellation shaders. For the coarse mesh generation, a novel approach, based on the Finite Element Method, allows approximation of the 3D shape of the soma from its incomplete description. Subsequently, the adaptive refinement process performed in the graphic card generates meshes that provide good visual quality geometries at a reasonable computational cost, both in terms of memory and rendering time. All the described techniques have been integrated into NeuroTessMesh, available to the scientific community, to generate, visualize, and save the adaptive resolution meshes

DEFORM'06 - Proceedings of the Workshop on Image Registration in Deformable Environments

Preface These are the proceedings of DEFORM'06, the Workshop on Image Registration in Deformable Environments, associated to BMVC'06, the 17th British Machine Vision Conference, held in Edinburgh, UK, in September 2006. The goal of DEFORM'06 was to bring together people from different domains having interests in deformable image registration. In response to our Call for Papers, we received 17 submissions and selected 8 for oral presentation at the workshop. In addition to the regular papers, Andrew Fitzgibbon from Microsoft Research Cambridge gave an invited talk at the workshop. The conference website including online proceedings remains open, see http://comsee.univ-bpclermont.fr/events/DEFORM06. We would like to thank the BMVC'06 co-chairs, Mike Chantler, Manuel Trucco and especially Bob Fisher for is great help in the local arrangements, Andrew Fitzgibbon, and the Programme Committee members who provided insightful reviews of the submitted papers. Special thanks go to Marc Richetin, head of the CNRS Research Federation TIMS, which sponsored the workshop. August 2006 Adrien Bartoli Nassir Navab Vincent Lepeti

Hierarchical processing, editing and rendering of acquired geometry

La représentation des surfaces du monde réel dans la mémoire d’une machine peut désormais être obtenue automatiquement via divers périphériques de capture tels que les scanners 3D. Ces nouvelles sources de données, précises et rapides, amplifient de plusieurs ordres de grandeur la résolution des surfaces 3D, apportant un niveau de précision élevé pour les applications nécessitant des modèles numériques de surfaces telles que la conception assistée par ordinateur, la simulation physique, la réalité virtuelle, l’imagerie médicale, l’architecture, l’étude archéologique, les effets spéciaux, l’animation ou bien encore les jeux video. Malheureusement, la richesse de la géométrie produite par ces méthodes induit une grande, voire gigantesque masse de données à traiter, nécessitant de nouvelles structures de données et de nouveaux algorithmes capables de passer à l’échelle d’objets pouvant atteindre le milliard d’échantillons. Dans cette thèse, je propose des solutions performantes en temps et en espace aux problèmes de la modélisation, du traitement géométrique, de l’édition intéractive et de la visualisation de ces surfaces 3D complexes. La méthodologie adoptée pendant l’élaboration transverse de ces nouveaux algorithmes est articulée autour de 4 éléments clés : une approche hiérarchique systématique, une réduction locale de la dimension des problèmes, un principe d’échantillonage-reconstruction et une indépendance à l’énumération explicite des relations topologiques aussi appelée approche basée-points. En pratique, ce manuscrit propose un certain nombre de contributions, parmi lesquelles : une nouvelle structure hiérarchique hybride de partitionnement, l’Arbre Volume-Surface (VS-Tree) ainsi que de nouveaux algorithmes de simplification et de reconstruction ; un système d’édition intéractive de grands objets ; un noyau temps-réel de synthèse géométrique par raffinement et une structure multi-résolution offrant un rendu efficace de grands objets. Ces structures, algorithmes et systèmes forment une chaîne capable de traiter les objets en provenance du pipeline d’acquisition, qu’ils soient représentés par des nuages de points ou des maillages, possiblement non 2-variétés. Les solutions obtenues ont été appliquées avec succès aux données issues des divers domaines d’application précités.Digital representations of real-world surfaces can now be obtained automatically using various acquisition devices such as 3D scanners and stereo camera systems. These new fast and accurate data sources increase 3D surface resolution by several orders of magnitude, borrowing higher precision to applications which require digital surfaces. All major computer graphics applications can take benefit of this automatic modeling process, including: computer-aided design, physical simulation, virtual reality, medical imaging, architecture, archaeological study, special effects, computer animation and video games. Unfortunately, the richness of the geometry produced by these media comes at the price of a large, possibility gigantic, amount of data which requires new efficient data structures and algorithms offering scalability for processing such objects. This thesis proposes time and space efficient solutions for modeling, editing and rendering such complex surfaces, solving these problems with new algorithms sharing 4 fundamental elements: a systematic hierarchical approach, a local dimension reduction, a sampling-reconstruction paradigm and a pointbased basis. Basically, this manuscript proposes several contributions, including: a new hierarchical space subdivision structure, the Volume-Surface Tree, for geometry processing such as simplification and reconstruction; a streaming system featuring new algorithms for interactive editing of large objects, an appearancepreserving multiresolution structure for efficient rendering of large point-based surfaces, and a generic kernel for real-time geometry synthesis by refinement. These elements form a pipeline able to process acquired geometry, either represented by point clouds or non-manifold meshes. Effective results have been successfully obtained with data coming from the various applications mentioned

Fehlerkaschierte Bildbasierte Darstellungsverfahren

Creating photo-realistic images has been one of the major goals in computer graphics since its early days. Instead of modeling the complexity of nature with standard modeling tools, image-based approaches aim at exploiting real-world footage directly,as they are photo-realistic by definition. A drawback of these approaches has always been that the composition or combination of different sources is a non-trivial task, often resulting in annoying visible artifacts. In this thesis we focus on different techniques to diminish visible artifacts when combining multiple images in a common image domain. The results are either novel images, when dealing with the composition task of multiple images, or novel video sequences rendered in real-time, when dealing with video footage from multiple cameras.Fotorealismus ist seit jeher eines der großen Ziele in der Computergrafik. Anstatt die Komplexität der Natur mit standardisierten Modellierungswerkzeugen nachzubauen, gehen bildbasierte Ansätze den umgekehrten Weg und verwenden reale Bildaufnahmen zur Modellierung, da diese bereits per Definition fotorealistisch sind. Ein Nachteil dieser Variante ist jedoch, dass die Komposition oder Kombination mehrerer Quellbilder eine nichttriviale Aufgabe darstellt und häufig unangenehm auffallende Artefakte im erzeugten Bild nach sich zieht. In dieser Dissertation werden verschiedene Ansätze verfolgt, um Artefakte zu verhindern oder abzuschwächen, welche durch die Komposition oder Kombination mehrerer Bilder in einer gemeinsamen Bilddomäne entstehen. Im Ergebnis liefern die vorgestellten Verfahren neue Bilder oder neue Ansichten einer Bildsammlung oder Videosequenz, je nachdem, ob die jeweilige Aufgabe die Komposition mehrerer Bilder ist oder die Kombination mehrerer Videos verschiedener Kameras darstellt

3D Mesh Simplification. A survey of algorithms and CAD model simplification tests

Simplification of highly detailed CAD models is an important step when CAD models are visualized or by other means utilized in augmented reality applications. Without simplification, CAD models may cause severe processing and storage is- sues especially in mobile devices. In addition, simplified models may have other advantages like better visual clarity or improved reliability when used for visual pose tracking. The geometry of CAD models is invariably presented in form of a 3D mesh. In this paper, we survey mesh simplification algorithms in general and focus especially to algorithms that can be used to simplify CAD models. We test some commonly known algorithms with real world CAD data and characterize some new CAD related simplification algorithms that have not been surveyed in previous mesh simplification reviews.Siirretty Doriast

Research on generic interactive deformable 3D models: focus on the human inguinal region

The goal of this project is to research for real-time approximate methods of physicallybased animation in conjunction with static polygonal meshes with the aim of deforming them and simulating an elastic behaviour for these meshes. Because of this, in this project it has been developed a software suite capable of doing a lot of tasks, each one from different computer graphics research fields, conforming a versatile capability project

Human Performance Modeling and Rendering via Neural Animated Mesh

We have recently seen tremendous progress in the neural advances for photo-real human modeling and rendering. However, it's still challenging to integrate them into an existing mesh-based pipeline for downstream applications. In this paper, we present a comprehensive neural approach for high-quality reconstruction, compression, and rendering of human performances from dense multi-view videos. Our core intuition is to bridge the traditional animated mesh workflow with a new class of highly efficient neural techniques. We first introduce a neural surface reconstructor for high-quality surface generation in minutes. It marries the implicit volumetric rendering of the truncated signed distance field (TSDF) with multi-resolution hash encoding. We further propose a hybrid neural tracker to generate animated meshes, which combines explicit non-rigid tracking with implicit dynamic deformation in a self-supervised framework. The former provides the coarse warping back into the canonical space, while the latter implicit one further predicts the displacements using the 4D hash encoding as in our reconstructor. Then, we discuss the rendering schemes using the obtained animated meshes, ranging from dynamic texturing to lumigraph rendering under various bandwidth settings. To strike an intricate balance between quality and bandwidth, we propose a hierarchical solution by first rendering 6 virtual views covering the performer and then conducting occlusion-aware neural texture blending. We demonstrate the efficacy of our approach in a variety of mesh-based applications and photo-realistic free-view experiences on various platforms, i.e., inserting virtual human performances into real environments through mobile AR or immersively watching talent shows with VR headsets.Comment: 18 pages, 17 figure

A framework for local terrain deformation based on diffusion theory

Terrains have a key role in making outdoor virtual scenes believable and immersive as they form the support for every other natural element in the scene. Although important, terrains are often given limited interactivity in real-time applications. However, in nature, terrains are dynamic and interact with the rest of the environment changing shape on different levels, from tracks left by a person running on a gravel soil (micro-scale), to avalanches on the side of a mountain (macro-scale). The challenge in representing dynamic terrains correctly is that the soil that forms them is vastly heterogeneous and behaves differently depending on its composition. This heterogeneity introduces difficulties at different levels in dynamic terrains simulations, from modelling the large amount of different elements that compose the oil to simulating their dynamic behaviour. This work presents a novel framework to simulate multi-material dynamic terrains by taking into account the soil composition and its heterogeneity. In the proposed framework soil information is obtained from a material description map applied to the terrain mesh. This information is used to compute deformations in the area of interaction using a novel mathematical model based on diffusion theory. The deformations are applied to the terrain mesh in different ways depending on the distance of the area of interaction from the camera and the soil material. Deformations away from the camera are simulated by dynamically displacing normals. While deformations in a neighbourhood of the camera are represented by displacing the terrain mesh, which is locally tessellated to better fit the displacement. For gravel based soils the terrain details are added near the camera by reconstructing the meshes of the small rocks from the texture image, thus simulating both micro and macro-structure of the terrain. The outcome of the framework is a realistic interactive dynamic terrain animation in real-time