Voxelbasert 3D visualisering i OpenGL

This thesis deals with volume rendering in OpenGL and looks at the different areas at which 3D modeling and visualization is used. The thesis focuses on voxel rendering, its advantages and drawbacks, and also the implementation of such a renderer. The aim of the thesis was to develop a voxel renderer in OpenGL from scratch, to a fully functional application that could visualize different 3D data sets generated from for example Diffpack. The data sets are scalar fields which are visualized by associating transparency and color to voxels from the values in the data sets. There are multiple ways to visualize voxels, I have mainly used a method that uses textures mapped to a 2D plane, which are assembled into a 3D voxel set. This is a method that is supported by common 3D hardware. To get maximum performance from the different 3D graphics cards that are available, you can use different graphics libraries. For PC’s there are two low-level graphics libraries to choose from, OpenGL and DirectX. OpenGL is developed by Silicon Graphics and are compatible with a number of different operating systems. DirectX is developed by Microsoft and is only supported in Microsoft Windows. For this thesis I chose OpenGL as the tool to use. OpenGL is a powerful software library which utilizes modern graphics hardware. Through OpenGL you get access to most of the graphic cards functions. OpenGL is however a low-level library and demands a lot of knowledge on a fundamental level to be able to visualize complex objects and scenes. I therefore take a closer look at how OpenGL works and at the theory at which it is built. I also look at the opportunities, advantages and drawbacks with voxel rendering, and looks at the requirements which is demanded by the hardware to be able to solve the tasks efficiently. I conclude this thesis by comparing my OpenGL voxel renderer with other available voxel renderers, such as The Visualization Toolkit (VTK)

VolumeEVM: A new surface/volume integrated model

Volume visualization is a very active research area in the field of scien-tific visualization. The Extreme Vertices Model (EVM) has proven to be a complete intermediate model to visualize and manipulate volume data using a surface rendering approach. However, the ability to integrate the advantages of surface rendering approach with the superiority in visual exploration of the volume rendering would actually produce a very complete visualization and edition system for volume data. Therefore, we decided to define an enhanced EVM-based model which incorporates the volumetric information required to achieved a nearly direct volume visualization technique. Thus, VolumeEVM was designed maintaining the same EVM-based data structure plus a sorted list of density values corresponding to the EVM-based VoIs interior voxels. A function which relates interior voxels of the EVM with the set of densities was mandatory to be defined. This report presents the definition of this new surface/volume integrated model based on the well known EVM encoding and propose implementations of the main software-based direct volume rendering techniques through the proposed model.Postprint (published version

Fast and robust curve skeletonization for real-world elongated objects

We consider the problem of extracting curve skeletons of three-dimensional, elongated objects given a noisy surface, which has applications in agricultural contexts such as extracting the branching structure of plants. We describe an efficient and robust method based on breadth-first search that can determine curve skeletons in these contexts. Our approach is capable of automatically detecting junction points as well as spurious segments and loops. All of that is accomplished with only one user-adjustable parameter. The run time of our method ranges from hundreds of milliseconds to less than four seconds on large, challenging datasets, which makes it appropriate for situations where real-time decision making is needed. Experiments on synthetic models as well as on data from real world objects, some of which were collected in challenging field conditions, show that our approach compares favorably to classical thinning algorithms as well as to recent contributions to the field.Comment: 47 pages; IEEE WACV 2018, main paper and supplementary materia

Weakly supervised 3D Reconstruction with Adversarial Constraint

Supervised 3D reconstruction has witnessed a significant progress through the use of deep neural networks. However, this increase in performance requires large scale annotations of 2D/3D data. In this paper, we explore inexpensive 2D supervision as an alternative for expensive 3D CAD annotation. Specifically, we use foreground masks as weak supervision through a raytrace pooling layer that enables perspective projection and backpropagation. Additionally, since the 3D reconstruction from masks is an ill posed problem, we propose to constrain the 3D reconstruction to the manifold of unlabeled realistic 3D shapes that match mask observations. We demonstrate that learning a log-barrier solution to this constrained optimization problem resembles the GAN objective, enabling the use of existing tools for training GANs. We evaluate and analyze the manifold constrained reconstruction on various datasets for single and multi-view reconstruction of both synthetic and real images

Reconstruction of hidden 3D shapes using diffuse reflections

We analyze multi-bounce propagation of light in an unknown hidden volume and demonstrate that the reflected light contains sufficient information to recover the 3D structure of the hidden scene. We formulate the forward and inverse theory of secondary and tertiary scattering reflection using ideas from energy front propagation and tomography. We show that using careful choice of approximations, such as Fresnel approximation, greatly simplifies this problem and the inversion can be achieved via a backpropagation process. We provide a theoretical analysis of the invertibility, uniqueness and choices of space-time-angle dimensions using synthetic examples. We show that a 2D streak camera can be used to discover and reconstruct hidden geometry. Using a 1D high speed time of flight camera, we show that our method can be used recover 3D shapes of objects "around the corner"

Hierarchical Surface Prediction for 3D Object Reconstruction

Recently, Convolutional Neural Networks have shown promising results for 3D geometry prediction. They can make predictions from very little input data such as a single color image. A major limitation of such approaches is that they only predict a coarse resolution voxel grid, which does not capture the surface of the objects well. We propose a general framework, called hierarchical surface prediction (HSP), which facilitates prediction of high resolution voxel grids. The main insight is that it is sufficient to predict high resolution voxels around the predicted surfaces. The exterior and interior of the objects can be represented with coarse resolution voxels. Our approach is not dependent on a specific input type. We show results for geometry prediction from color images, depth images and shape completion from partial voxel grids. Our analysis shows that our high resolution predictions are more accurate than low resolution predictions.Comment: 3DV 201

Design of a multimodal rendering system

This paper addresses the rendering of aligned regular multimodal datasets. It presents a general framework of multimodal data fusion that includes several data merging methods. We also analyze the requirements of a rendering system able to provide these different fusion methods. On the basis of these requirements, we propose a novel design for a multimodal rendering system. The design has been implemented and proved showing to be efficient and flexible.Postprint (published version

Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. Conclusions: By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. There is a pressing need for visualization and analysis tools for 5-D live cell image data. We combine accurate unsupervised processes with an intuitive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc