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Rendering huge biological scenes with atomistic detail presents a significant challenge in molecular visualization due to the memory limitations inherent in traditional rendering approaches. In this paper, we propose a novel method for the interactive rendering of massive molecular scenes based on hardware-accelerated ray tracing. Our approach circumvents GPU memory constraints by introducing virtual instantiation of full-detail scene elements. Using instancing significantly reduces memory consumption while preserving the full atomistic detail of scenes comprising trillions of atoms, with interactive rendering performance and completely free user exploration. We utilize coarse meshes as proxy geometries to approximate the overall shape of biological compartments, and access all atomistic detail dynamically during ray tracing. We do this via a novel adaptive technique utilizing a volumetric shell layer of prisms extruded around proxy geometry triangles, and a virtual volume grid for the interior of each compartment. Our algorithm scales to enormous molecular scenes with minimal memory consumption and the potential to accommodate even larger scenes. Our method also supports advanced effects such as clipping planes and animations. We demonstrate the efficiency and scalability of our approach by rendering tens of instances of Red Blood Cell and SARS-CoV-2 models theoretically containing more than 20 trillion atoms.

We present a hybrid multi-volume rendering approach based on a novel Residency Octree that combines the advantages of out-of-core volume rendering using page tables with those of standard octrees. Octree approaches work by performing hierarchical tree traversal. However, in octree volume rendering, tree traversal and the selection of data resolution are intrinsically coupled. This makes fine-grained empty-space skipping costly. Page tables, on the other hand, allow access to any cached brick from any resolution. However, they do not offer a clear and efficient strategy for substituting missing high-resolution data with lower-resolution data. We enable flexible mixed-resolution out-of-core multi-volume rendering by decoupling the cache residency of multi-resolution data from a resolution-independent spatial subdivision determined by the tree. Instead of one-to-one node-to-brick correspondences, each residency octree node is mapped to a set of bricks from different resolution levels. This makes it possible to efficiently and adaptively choose and mix resolutions, adapt sampling rates, and compensate for cache misses. At the same time, residency octrees support fine-grained empty-space skipping, independent of the data subdivision used for caching. Finally, to facilitate collaboration and outreach, and to eliminate local data storage, our implementation is a web-based, pure client-side renderer using WebGPU and WebAssembly. Our method is faster than prior approaches and efficient for many data channels with a flexible and adaptive choice of data resolution., Comment: VIS 2023 - full paper

We explore the space of matrix-generated (0, m, 2)-nets and (0, 2)-sequences in base 2, also known as digital dyadic nets and sequences. In computer graphics, they are arguably leading the competition for use in rendering. We provide a complete characterization of the design space and count the possible number of constructions with and without considering possible reorderings of the point set. Based on this analysis, we then show that every digital dyadic net can be reordered into a sequence, together with a corresponding algorithm. Finally, we present a novel family of self-similar digital dyadic sequences, to be named $\xi$-sequences, that spans a subspace with fewer degrees of freedom. Those $\xi$-sequences are extremely efficient to sample and compute, and we demonstrate their advantages over the classic Sobol (0, 2)-sequence., Comment: 17 pages, 11 figures. Minor improvement of exposition; references to earlier proofs of Theorems 3.1 and 3.3 added

Reference frame optimization is a generic framework to calculate a spatially-varying observer field that views an unsteady fluid flow in a reference frame that is as-steady-as-possible. In this paper, we show that the optimized vector field is objective, i.e., it is independent of the initial Euclidean transformation of the observer. To check objectivity, the optimized velocity vectors and the coordinates in which they are defined must both be connected by an Euclidean transformation. In this paper we show that a recent publication [1] applied this definition incorrectly, falsely concluding that reference frame optimizations are not objective. Further, we prove the objectivity of the variational formulation of the reference frame optimization proposed in [1], and discuss how the variational formulation relates to recent local and global optimization approaches to unsteadiness minimization.

A connectivity graph of neurons at the resolution of single synapses provides scientists with a tool for understanding the nervous system in health and disease. Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain have made reconstructions of neurons possible at the nanometer scale. However, automatic segmentation sometimes struggles to segment large neurons correctly, requiring human effort to proofread its output. General proofreading involves inspecting large volumes to correct segmentation errors at the pixel level, a visually intensive and time-consuming process. This paper presents the design and implementation of an analytics framework that streamlines proofreading, focusing on connectivity-related errors. We accomplish this with automated likely-error detection and synapse clustering that drives the proofreading effort with highly interactive 3D visualizations. In particular, our strategy centers on proofreading the local circuit of a single cell to ensure a basic level of completeness. We demonstrate our framework's utility with a user study and report quantitative and subjective feedback from our users. Overall, users find the framework more efficient for proofreading, understanding evolving graphs, and sharing error correction strategies., Comment: This paper has been accepted for publication and presentation at the 23rd EG Conference on Visualization (EuroVis 2021)

Public health officials dealing with pandemics like COVID-19 have to evaluate and prepare response plans. This planning phase requires not only looking into the spatiotemporal dynamics and impact of the pandemic using simulation models, but they also need to plan and ensure the availability of resources under different spread scenarios. To this end, we have developed a visual analytics environment that enables public health officials to model, simulate, and explore the spread of COVID-19 by supplying county-level information such as population, demographics, and hospital beds. This environment facilitates users to explore spatiotemporal model simulation data relevant to COVID-19 through a geospatial map with linked statistical views, apply different decision measures at different points in time, and understand their potential impact. Users can drill-down to county-level details such as the number of sicknesses, deaths, needs for hospitalization, and variations in these statistics over time. We demonstrate the usefulness of this environment through a use case study and also provide feedback from domain experts. We also provide details about future extensions and potential applications of this work.

We introduce a method based on the deflectometry principle for the reconstruction of specular objects exhibiting significant size and geometric complexity. A key feature of our approach is the deployment of an Automatic Virtual Environment (CAVE) as pattern generator. To unfold the full power of this extraordinary experimental setup, an optical encoding scheme is developed which accounts for the distinctive topology of the CAVE. Furthermore, we devise an algorithm for detecting the object of interest in raw deflectometric images. The segmented foreground is used for single-view reconstruction, the background for estimation of the camera pose, necessary for calibrating the sensor system. Experiments suggest a significant gain of coverage in single measurements compared to previous methods. To facilitate research on specular surface reconstruction, we will make our data set publicly available.