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

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"

An Overview of Rendering from Volume Data --- including Surface and Volume Rendering

Volume rendering is a title often ambiguously used in science. One meaning often quoted is: `to render any three volume dimensional data set'; however, within this categorisation `surface rendering'' is contained. Surface rendering is a technique for visualising a geometric representation of a surface from a three dimensional volume data set. A more correct definition of Volume Rendering would only incorporate the direct visualisation of volumes, without the use of intermediate surface geometry representations. Hence we state: `Volume Rendering is the Direct Visualisation of any three dimensional Volume data set; without the use of an intermediate geometric representation for isosurfaces'; `Surface Rendering is the Visualisation of a surface, from a geometric approximation of an isosurface, within a Volume data set'; where an isosurface is a surface formed from a cross connection of data points, within a volume, of equal value or density. This paper is an overview of both Surface Rendering and Volume Rendering techniques. Surface Rendering mainly consists of contouring lines over data points and triangulations between contours. Volume rendering methods consist of ray casting techniques that allow the ray to be cast from the viewing plane into the object and the transparency, opacity and colour calculated for each cell; the rays are often cast until an opaque object is `hit' or the ray exits the volume

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