Visualization

Large-scale three-dimensional (3D) microscopy acquisitions fre-quently create terabytes of image data at high resolution and magni-fication. Imaging large specimens at high magnifications requires acquiring 3D overlapping image stacks as tiles arranged on a two-dimensional (2D) grid that must subsequently be aligned and fused into a single 3D volume. Due to their sheer size, aligning many overlapping gigabyte-sized 3D tiles in parallel and at full resolution is memory intensive and often I/O bound. Current techniques trade accuracy for scalability, perform alignment on subsampled images, and require additional postprocess algorithms to refine the alignment quality, usually with high computational requirements. One common solution to the memory problem is to subdivide the overlap region into smaller chunks (sub-blocks) and align the sub-block pairs in parallel, choosing the pair with the most reliable alignment to determine the global transformation. Yet aligning all sub-block pairs at full resolution remains computationally expensive. The key to quickly developing a fast, high-quality, low-memory solution is to identify a single or a small set of sub-blocks that give good alignment at full resolution without touching all the overlapping data. In this paper, we present a new iterative approach that leverages coarse resolution alignments to progressively refine and align only the promising candidates at finer resolutions, thereby aligning only a small user-defined number of sub-blocks at full resolution to determine the lowest error transformation between pairwise overlapping tiles. Our progressive approach is 2.6x faster than the state of the art, requires less than 450MB of peak RAM (per parallel thread), and offers a higher quality alignment without the need for additional postprocessing refinement steps to correct for alignment errors.

Background:

Computational biomedical simulations frequently contain parameters that model physical features, material coefficients, and physiological effects, whose values are typically assumed known a priori. Understanding the effect of variability in those assumed values is currently a topic of great interest. A general-purpose software tool that quantifies how variation in these parameters affects model outputs is not broadly available in biomedicine. For this reason, we developed the ‘UncertainSCI’ uncertainty quantification software suite to facilitate analysis of uncertainty due to parametric variability.

Across domains massive amounts of scientific data are generated. Because of the large volume of information, data discoverability is often hard if not impossible, especially for scientists who have not generated the data or are from other domains. As part of the NSF-funded National Science Data Fabric (NSDF) initiative, we develop a testbed to demonstrate that these boundaries to data discoverability can be overcome. In support of this effort, we identify the need for indexing large-amounts of scientific data across scientific domains. We propose NSDF-Catalog, a lightweight indexing service with minimal metadata that complements existing domain-specific and rich-metadata collections. NSDF-Catalog is designed to facilitate multiple related objectives within a flexible microservice to: (i) coordinate data movements and replication of data from origin repositories within the NSDF federation; (ii) build an inventory of existing scientific data to inform the design of next-generation cyberinfrastructure; and (iii) provide a suite of tools for discovery of datasets for cross-disciplinary research. Our service indexes scientific data at a fine-granularity at the file or object level to inform data distribution strategies and to improve the experience for users from the consumer perspective, with the goal of allowing end-to-end dataflow optimizations

Computational fluid dynamics (CFD) is known for producing high-dimensional spatiotemporal data. Recent advances in machine learning (ML) have introduced a myriad of techniques for extracting physical information from CFD. Identifying an optimal set of coordinates for representing the data in a low-dimensional embedding is a crucial first step toward data-driven reduced-order modeling and other ML tasks. This is usually done via principal component analysis (PCA), which gives an optimal linear approximation. However, fluid flows are often complex and have nonlinear structures, which cannot be discovered or efficiently represented by PCA. Several unsupervised ML algorithms have been developed in other branches of science for nonlinear dimensionality reduction (NDR), but have not been extensively used for fluid flows. Here, four manifold learning and two deep learning (autoencoder)-based NDR methods are investigated and compared to PCA. These are tested on two canonical fluid flow problems (laminar and turbulent) and two biomedical flows in brain aneurysms. The data reconstruction capabilities of these methods are compared, and the challenges are discussed. The temporal vs spatial arrangement of data and its influence on NDR mode extraction is investigated. Finally, the modes are qualitatively compared. The results suggest that using NDR methods would be beneficial for building more efficient reduced-order models of fluid flows. All NDR techniques resulted in smaller reconstruction errors for spatial reduction. Temporal reduction was a harder task; nevertheless, it resulted in physically interpretable modes. Our work is one of the first comprehensive comparisons of various NDR methods in unsteady flows.

We present a new topological connection method for the local bilinear computation of Jacobi sets that improves the visual representation while preserving the topological structure and geometric configuration. To this end, the topological structure of the local bilinear method is utilized, which is given by the nerve complex of the traditional piecewise linear method. Since the nerve complex consists of higher-dimensional simplices, the local bilinear method (visually represented by the 1-skeleton of the nerve complex) leads to clutter via crossings of line segments. Therefore, we propose a homotopy-equivalent representation that uses different collapses and edge contractions to remove such artifacts. Our new connectivity method is easy to implement, comes with only little overhead, and results in a less cluttered representation.

We propose a novel method for the computation of Jacobi sets in 2D domains. The Jacobi set is a topological descriptor based on Morse theory that captures gradient alignments among multiple scalar fields, which is useful for multi-field visualization. Previous Jacobi set computations use piecewise linear approximations on triangulations that result in discretization artifacts like zig-zag patterns. In this paper, we utilize a local bilinear method to obtain a more precise approximation of Jacobi sets by preserving the topology and improving the geometry. Consequently, zig-zag patterns on edges are avoided, resulting in a smoother Jacobi set representation. Our experiments show a better convergence with increasing resolution compared to the piecewise linear method. We utilize this advantage with an efficient local subdivision scheme. Finally, our approach is evaluated qualitatively and quantitatively in comparison with previous methods for different mesh resolutions and across a number of synthetic and real-world examples.

We propose a simple, yet effective method for clustering finite elements in order to improve preprocessing times and rendering performance of unstructured volumetric grids. Rather than building bounding volume hierarchies (BVHs) over individual elements, we sort elements along a Hilbert curve and aggregate neighboring elements together, significantly improving BVH memory consumption. Then to further reduce memory consumption, we cluster the mesh on the fly into sub-meshes with smaller indices using series of efficient parallel mesh re-indexing operations. These clusters are then passed to a highly optimized ray tracing API for both point containment queries and ray-cluster intersection testing. Each cluster is assigned a maximum extinction value for adaptive sampling, which we rasterize into non-overlapping view-aligned bins allocated along the ray. These maximum extinction bins are then used to guide the placement of samples along the ray during visualization, significantly reducing the number of samples required and greatly improving overall visualization interactivity. Using our approach, we improve rendering performance over a competitive baseline on the NASA Mars Lander dataset by 6×(1FPS up to 6FPS including volumetric shadows) while simultaneously reducing memory consumption by 3×(33GB down to 11GB) and avoiding any offline preprocessing steps, enabling high quality interactive visualization on consumer graphics cards. By utilizing the full 48 GB of an RTX 8000, we improve performance of Lander by 17×(1FPS up to 17FPS), enabling new possibilities for large data exploration.

Understanding the response of an output variable to multi-dimensional inputs lies at the heart of many data exploration endeavours. Topology-based methods, in particular Morse theory and persistent homology, provide a useful framework for studying this relationship, as phenomena of interest often appear naturally as fundamental features. The Morse-Smale complex captures a wide range of features by partitioning the domain of a scalar function into piecewise monotonic regions, while persistent homology provides a means to study these features at different scales of simplification. Previous works demonstrated how to compute such a representation and its usefulness to gain insight into multi-dimensional data. However, exploration of the multi-scale nature of the data was limited to selecting a single simplification threshold from a plot of region count. In this paper, we present a novel tree visualization that provides a concise overview of the entire hierarchy of topological features. The structure of the tree provides initial insights in terms of the distribution, size, and stability of all partitions. We use regression analysis to fit linear models in each partition, and develop local and relative measures to further assess uniqueness and the importance of each partition, especially with respect parents/children in the feature hierarchy. The expressiveness of the tree visualization becomes apparent when we encode such measures using colors, and the layout allows an unprecedented level of control over feature selection during exploration. For instance, selecting features from multiple scales of the hierarchy enables a more nuanced exploration. Finally, we …

Convolutional neural networks (CNNs) have been successfully applied to chest x-ray (CXR) images. Moreover, annotated bounding boxes have been shown to improve the interpretability of a CNN in terms of localizing abnormalities. However, only a few relatively small CXR datasets containing bounding boxes are available, and collecting them is very costly. Opportunely, eye-tracking (ET) data can be collected in a non-intrusive way during the clinical workflow of a radiologist. We use ET data recorded from radiologists while dictating CXR reports to train CNNs. We extract snippets from the ET data by associating them with the dictation of keywords and use them to supervise the localization of abnormalities. We show that this method improves a model's interpretability without impacting its image-level classification.

Deep learning approaches have provided state-of-the-art performance in many applications by relying on extremely large and heavily overparameterized neural networks. However, such networks have been shown to be very brittle, not generalize well to new uses cases, and are often difficult if not impossible to deploy on resources limited platforms. Model pruning, i.e., reducing the size of the network, is a widely adopted strategy that can lead to more robust and generalizable network -- usually orders of magnitude smaller with the same or even improved performance. While there exist many heuristics for model pruning, our understanding of the pruning process remains limited. Empirical studies show that some heuristics improve performance while others can make models more brittle or have other side effects. This work aims to shed light on how different pruning methods alter the network's internal feature representation, and the corresponding impact on model performance. To provide a meaningful comparison and characterization of model feature space, we use three geometric metrics that are decomposed from the common adopted classification loss. With these metrics, we design a visualization system to highlight the impact of pruning on model prediction as well as the latent feature embedding. The proposed tool provides an environment for exploring and studying differences among pruning methods and between pruned and original model. By leveraging our visualization, the ML researchers can not only identify samples that are fragile to model pruning and data corruption but also obtain insights and explanations on how some pruned …

In situ visualization increasingly involves rendering large numbers of images for post hoc exploration. As both the number of images to be rendered and the data being rendered are large, the scalability of the rendering component is of key concern. Furthermore, the renderer must be able to support a wide range of data distributions, simulation configurations, and HPC systems to provide the flexibility required for a portable, general purpose in situ rendering package. In this chapter, we discuss recent developments in OSPRay’s support for MPI-parallel applications to provide a flexible and scalable rendering API, with a focus on how these developments can be applied to enable scalable, high-quality in situ visualization.

Importance. Medical images are essential for modern medicine and an important research subject in visualization. However, medical experts are often not aware of the many advanced three-dimensional (3D) medical image visualization techniques that could increase their capabilities in data analysis and assist the decision-making process for specific medical problems. Our paper provides a review of 3D visualization techniques for medical images, intending to bridge the gap between medical experts and visualization researchers. Highlights. Fundamental visualization techniques are revisited for various medical imaging modalities, from computational tomography to diffusion tensor imaging, featuring techniques that enhance spatial perception, which is critical for medical practices. The state-of-the-art of medical visualization is reviewed based on a procedure-oriented classification of medical problems for studies of individuals and populations. This paper summarizes free software tools for different modalities of medical images designed for various purposes, including visualization, analysis, and segmentation, and it provides respective Internet links. Conclusions. Visualization techniques are a useful tool for medical experts to tackle specific medical problems in their daily work. Our review provides a quick reference to such techniques given the medical problem and modalities of associated medical images. We summarize fundamental techniques and readily available visualization tools to help medical experts to better understand and utilize medical imaging data. This paper could contribute to the joint effort of the medical and visualization communities to advance precision medicine.

Time-varying vector fields produced by computational fluid dynamics simulations are often prohibitively large and pose challenges for accurate interactive analysis and exploration. To address these challenges, reduced Lagrangian representations have been increasingly researched as a means to improve scientific time-varying vector field exploration capabilities. This paper presents a novel deep neural network-based particle tracing method to explore time-varying vector fields represented by Lagrangian flow maps. In our workflow, in situ processing is first utilized to extract Lagrangian flow maps, and deep neural networks then use the extracted data to learn flow field behavior. Using a trained model to predict new particle trajectories offers a fixed small memory footprint and fast inference. To demonstrate and evaluate the proposed method, we perform an in-depth study of performance using a well-known analytical data set, the Double Gyre. Our study considers two flow map extraction strategies, the impact of the number of training samples and integration durations on efficacy, evaluates multiple sampling options for training and testing, and informs hyperparameter settings. Overall, we find our method requires a fixed memory footprint of 10.5 MB to encode a Lagrangian representation of a time-varying vector field while maintaining accuracy. For post hoc analysis, loading the trained model costs only two seconds, significantly reducing the burden of I/O when reading data for visualization. Moreover, our parallel implementation can infer one hundred locations for each of two thousand new pathlines in 1.3 seconds using one NVIDIA Titan RTX GPU.

Performing exploratory analysis and visualization of large-scale time-varying computational science applications is challenging due to inaccuracies that arise from under-resolved data. In recent years, Lagrangian representations of the vector field computed using in situ processing are being increasingly researched and have emerged as a potential solution to enable exploration. However, prior works have offered limited estimates of the encumbrance on the simulation code as they consider “theoretical” in situ environments. Further, the effectiveness of this approach varies based on the nature of the vector field, benefitting from an in-depth investigation for each application area. With this study, an extended version of Sane et al. (2021), we contribute an evaluation of Lagrangian analysis viability and efficacy for simulation codes executing at scale on a supercomputer. We investigated previously unexplored cosmology and seismology applications as well as conducted a performance benchmarking study by using a hydrodynamics mini-application targeting exascale computing. To inform encumbrance, we integrated in situ infrastructure with simulation codes, and evaluated Lagrangian in situ reduction in representative homogeneous and heterogeneous HPC environments. To inform post hoc accuracy, we conducted a statistical analysis across a range of spatiotemporal configurations as well as a qualitative evaluation. Additionally, our study contributes cost estimates for distributed-memory post hoc reconstruction. In all, we demonstrate viability for each application — data reduction to less than 1% of the total data via Lagrangian representations, while maintaining accurate reconstruction and requiring under 10% of total execution time in over 90% of our experiments.

Morse complexes are gradient-based topological descriptors with close connections to Morse theory. They are widely applicable in scientific visualization as they serve as important abstractions for gaining insights into the topology of scalar fields. Data uncertainty inherent to scalar fields due to randomness in their acquisition and processing, however, limits our understanding of Morse complexes as structural abstractions. We, therefore, explore uncertainty visualization of an ensemble of 2D Morse complexes that arises from scalar fields coupled with data uncertainty. We propose several statistical summary maps as new entities for quantifying structural variations and visualizing positional uncertainties of Morse complexes in ensembles. Specifically, we introduce three types of statistical summary maps – the probabilistic map , the significance map , and the survival map – to characterize the uncertain behaviors of gradient flows. We demonstrate the utility of our proposed approach using wind, flow, and ocean eddy simulation datasets.

The current generation of radio and millimeter telescopes, particularly the Atacama Large Millimeter Array (ALMA), offers enormous advances in observing capabilities. While these advances represent an unprecedented opportunity to facilitate scientific understanding, the increased complexity in the spatial and spectral structure of these ALMA data cubes lead to challenges in their interpretation. In this paper, we perform a feasibility study for applying topological data analysis and visualization techniques never before tested by the ALMA community. Using techniques based on contour trees, we seek to improve upon existing analysis and visualization workflows of ALMA data cubes, in terms of accuracy and speed in feature extraction. We review our development process in building effective analysis and visualization capabilities for the astrophysicists. We also summarize effective design practices by identifying domain-specific needs of simplicity, integrability, and reproducibility, in order to best target and service the large astrophysics community.

Adaptive representations are increasingly indispensable for reducing the in-memory and on-disk footprints of large-scale data. Usual solutions are designed broadly along two themes: reducing data precision, e.g., through compression, or adapting data resolution, e.g., using spatial hierarchies. Recent research suggests that combining the two approaches, i.e., adapting both resolution and precision simultaneously, can offer significant gains over using them individually. However, there currently exist no practical solutions to creating and evaluating such representations at scale. In this work, we present a new resolution-precision-adaptive representation to support hybrid data reduction schemes and offer an interface to existing tools and algorithms. Through novelties in spatial hierarchy, our representation, Adaptive Multilinear Meshes (AMM), provides considerable reduction in the mesh size. AMM creates a piecewise multilinear representation of uniformly sampled scalar data and can selectively relax or enforce constraints on conformity, continuity, and coverage, delivering a flexible adaptive representation. AMM also supports representing the function using mixed-precision values to further the achievable gains in data reduction. We describe a practical approach to creating AMM incrementally using arbitrary orderings of data and demonstrate AMM on six types of resolution and precision datastreams. By interfacing with state-of-the-art rendering tools through VTK, we demonstrate the practical and computational advantages of our representation for visualization techniques. With an open-source release of our tool to create AMM, we make such evaluation of data reduction accessible to the community, which we hope will foster new opportunities and future data reduction schemes

The Scientific Computing and Imaging (SCI) Institute at the University of Utah evolved from the SCI research group, started in 1994 by Professors Chris Johnson and Rob MacLeod. Over time, research centers funded by the National Institutes of Health, Department of Energy, and State of Utah significantly spurred growth, and SCI became a permanent interdisciplinary research institute in 2000. The SCI Institute is now home to more than 150 faculty, students, and staff. The history of the SCI Institute is underpinned by a culture of multidisciplinary, collaborative research, which led to its emergence as an internationally recognized leader in the development and use of visualization, scientific computing, and image analysis research to solve important problems in a broad range of domains in biomedicine, science, and engineering. A particular hallmark of SCI Institute research is the creation of open source software systems, including the SCIRun scientific problem-solving environment, Seg3D, ImageVis3D, Uintah, ViSUS, Nektar++, VisTrails, FluoRender, and FEBio. At this point, the SCI Institute has made more than 50 software packages broadly available to the scientific community under open-source licensing and supports them through web pages, documentation, and user groups. While the vast majority of academic research software is written and maintained by graduate students, the SCI Institute employs several professional software developers to help create, maintain, and document robust, tested, well-engineered open source software. The story of how and why we worked, and often struggled, to make professional software engineers an integral part of an academic research institute is crucial to the larger story of the SCI Institute’s success in translational computer science (TCS).

Predicting the effects of brain stimulation with computer models presents many challenges, including estimating the possible error from the propagation of uncertain input parameters through the model. Quantification and control of these errors through uncertainty quantification (UQ) provide statistics on the likely impact of parameter variation on solution accuracy, including total variance and sensitivity associated to each parameter. While the need and importance of UQ in clinical modeling is generally accepted, tools for implementing UQ techniques remain limited or inaccessible for many researchers.

We present a nonparametric statistical framework for the quantification, analysis, and propagation of data uncertainty in direct volume rendering (DVR). The state-of-the-art statistical DVR framework allows for preserving the transfer function (TF) of the ground truth function when visualizing uncertain data; however, the existing framework is restricted to parametric models of uncertainty. In this paper, we address the limitations of the existing DVR framework by extending the DVR framework for nonparametric distributions. We exploit the quantile interpolation technique to derive probability distributions representing uncertainty in viewing-ray sample intensities in closed form, which allows for accurate and efficient computation. We evaluate our proposed nonparametric statistical models through qualitative and quantitative comparisons with the mean-field and parametric statistical models, such as uniform and Gaussian, as well as Gaussian mixtures. In addition, we present an extension of the state-of-the-art rendering parametric framework to 2D TFs for improved DVR classifications. We show the applicability of our uncertainty quantification framework to ensemble, downsampled, and bivariate versions of scalar field datasets.