Designed especially for neurobiologists, FluoRender is an interactive tool for multi-channel fluorescence microscopy data visualization and analysis.
Deep brain stimulation
BrainStimulator is a set of networks that are used in SCIRun to perform simulations of brain stimulation such as transcranial direct current stimulation (tDCS) and magnetic transcranial stimulation (TMS).
Developing software tools for science has always been a central vision of the SCI Institute.

SCI Publications

2020


C. R. Johnson, T. Kapur, W. Schroeder,, T. Yoo. “Remembering Bill Lorensen: The Man, the Myth, and Marching Cubes,” In IEEE Computer Graphics and Applications, Vol. 40, No. 2, pp. 112-118. March, 2020.
DOI: 10.1109/MCG.2020.2971168



F. Wang, N. Marshak, W. Usher, C. Burstedde, A. Knoll, T. Heister, C. R. Johnson. “CPU Ray Tracing of Tree-Based Adaptive Mesh Refinement Data,” In Eurographics Conference on Visualization (EuroVis) 2020, Vol. 39, No. 3, 2020.

ABSTRACT

Adaptive mesh refinement (AMR) techniques allow for representing a simulation’s computation domain in an adaptive fashion. Although these techniques have found widespread adoption in high-performance computing simulations, visualizing their data output interactively and without cracks or artifacts remains challenging. In this paper, we present an efficient solution for direct volume rendering and hybrid implicit isosurface ray tracing of tree-based AMR (TB-AMR) data. We propose a novel reconstruction strategy, Generalized Trilinear Interpolation (GTI), to interpolate across AMR level boundaries without cracks or discontinuities in the surface normal. We employ a general sparse octree structure supporting a wide range of AMR data, and use it to accelerate volume rendering, hybrid implicit isosurface rendering and value queries. We demonstrate that our approach achieves artifact-free isosurface and volume rendering and provides higher quality output images compared to existing methods at interactive rendering rates.



L. Zhou, M. Rivinius, C. R. Johnson,, D. Weiskopf. “Photographic High-Dynamic-Range Scalar Visualization,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 26, No. 6, IEEE, pp. 2156-2167. 2020.

ABSTRACT

We propose a photographic method to show scalar values of high dynamic range (HDR) by color mapping for 2D visualization. We combine (1) tone-mapping operators that transform the data to the display range of the monitor while preserving perceptually important features based on a systematic evaluation and (2) simulated glares that highlight high-value regions. Simulated glares are effective for highlighting small areas (of a few pixels) that may not be visible with conventional visualizations; through a controlled perception study, we confirm that glare is preattentive. The usefulness of our overall photographic HDR visualization is validated through the feedback of expert users.


2019


T. Athawale, C. R. Johnson. “Probabilistic Asymptotic Decider for Topological Ambiguity Resolution in Level-Set Extraction for Uncertain 2D Data,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 25, No. 1, IEEE, pp. 1163-1172. Jan, 2019.
DOI: 10.1109/TVCG.2018.2864505

ABSTRACT

We present a framework for the analysis of uncertainty in isocontour extraction. The marching squares (MS) algorithm for isocontour reconstruction generates a linear topology that is consistent with hyperbolic curves of a piecewise bilinear interpolation. The saddle points of the bilinear interpolant cause topological ambiguity in isocontour extraction. The midpoint decider and the asymptotic decider are well-known mathematical techniques for resolving topological ambiguities. The latter technique investigates the data values at the cell saddle points for ambiguity resolution. The uncertainty in data, however, leads to uncertainty in underlying bilinear interpolation functions for the MS algorithm, and hence, their saddle points. In our work, we study the behavior of the asymptotic decider when data at grid vertices is uncertain. First, we derive closed-form distributions characterizing variations in the saddle point values for uncertain bilinear interpolants. The derivation assumes uniform and nonparametric noise models, and it exploits the concept of ratio distribution for analytic formulations. Next, the probabilistic asymptotic decider is devised for ambiguity resolution in uncertain data using distributions of the saddle point values derived in the first step. Finally, the confidence in probabilistic topological decisions is visualized using a colormapping technique. We demonstrate the higher accuracy and stability of the probabilistic asymptotic decider in uncertain data with regard to existing decision frameworks, such as deciders in the mean field and the probabilistic midpoint decider, through the isocontour visualization of synthetic and real datasets.



T. M. Athawale, K. A. Johnson, C. R. Butson, C. R. Johnson. “A statistical framework for quantification and visualisation of positional uncertainty in deep brain stimulation electrodes,” In Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, Vol. 7, No. 4, Taylor & Francis, pp. 438-449. 2019.
DOI: 10.1080/21681163.2018.1523750

ABSTRACT

Deep brain stimulation (DBS) is an established therapy for treating patients with movement disorders such as Parkinson’s disease. Patient-specific computational modelling and visualisation have been shown to play a key role in surgical and therapeutic decisions for DBS. The computational models use brain imaging, such as magnetic resonance (MR) and computed tomography (CT), to determine the DBS electrode positions within the patient’s head. The finite resolution of brain imaging, however, introduces uncertainty in electrode positions. The DBS stimulation settings for optimal patient response are sensitive to the relative positioning of DBS electrodes to a specific neural substrate (white/grey matter). In our contribution, we study positional uncertainty in the DBS electrodes for imaging with finite resolution. In a three-step approach, we first derive a closed-form mathematical model characterising the geometry of the DBS electrodes. Second, we devise a statistical framework for quantifying the uncertainty in the positional attributes of the DBS electrodes, namely the direction of longitudinal axis and the contact-centre positions at subvoxel levels. The statistical framework leverages the analytical model derived in step one and a Bayesian probabilistic model for uncertainty quantification. Finally, the uncertainty in contact-centre positions is interactively visualised through volume rendering and isosurfacing techniques. We demonstrate the efficacy of our contribution through experiments on synthetic and real datasets. We show that the spatial variations in true electrode positions are significant for finite resolution imaging, and interactive visualisation can be instrumental in exploring probabilistic positional variations in the DBS lead.



M. Han, I. Wald, W. Usher, Q. Wu, F. Wang, V. Pascicci, C. D. Hansen, C. R. Johnson. “Ray Tracing Generalized Tube Primitives: Method and Applications,” In Computer Graphics Forum, Vol. 38, No. 3, John Wiley & Sons Ltd., 2019.

ABSTRACT

We present a general high-performance technique for ray tracing generalized tube primitives. Our technique efficiently supports tube primitives with fixed and varying radii, general acyclic graph structures with bifurcations, and correct transparency with interior surface removal. Such tube primitives are widely used in scientific visualization to represent diffusion tensor imaging tractographies, neuron morphologies, and scalar or vector fields of 3D flow. We implement our approach within the OSPRay ray tracing framework, and evaluate it on a range of interactive visualization use cases of fixed- and varying-radius streamlines, pathlines, complex neuron morphologies, and brain tractographies. Our proposed approach provides interactive, high-quality rendering, with low memory overhead.



F. Wang, I. Wald, Q. Wu, W. Usher, C. R. Johnson. “CPU Isosurface Ray Tracing of Adaptive Mesh Refinement Data,” In IEEE Transactions on Visualization and Computer Graphics, Vol. 25, No. 1, IEEE, pp. 1142-1151. Jan, 2019.
DOI: 10.1109/TVCG.2018.2864850

ABSTRACT

Adaptive mesh refinement (AMR) is a key technology for large-scale simulations that allows for adaptively changing the simulation mesh resolution, resulting in significant computational and storage savings. However, visualizing such AMR data poses a significant challenge due to the difficulties introduced by the hierarchical representation when reconstructing continuous field values. In this paper, we detail a comprehensive solution for interactive isosurface rendering of block-structured AMR data. We contribute a novel reconstruction strategy—the octant method—which is continuous, adaptive and simple to implement. Furthermore, we present a generally applicable hybrid implicit isosurface ray-tracing method, which provides better rendering quality and performance than the built-in sampling-based approach in OSPRay. Finally, we integrate our octant method and hybrid isosurface geometry into OSPRay as a module, providing the ability to create high-quality interactive visualizations combining volume and isosurface representations of BS-AMR data. We evaluate the rendering performance, memory consumption and quality of our method on two gigascale block-structured AMR datasets.



A. Warner, J. Tate, B. Burton,, C.R. Johnson. “A High-Resolution Head and Brain Computer Model for Forward and Inverse EEG Simulation,” In bioRxiv, Cold Spring Harbor Laboratory, Feb, 2019.
DOI: 10.1101/552190

ABSTRACT

To conduct computational forward and inverse EEG studies of brain electrical activity, researchers must construct realistic head and brain computer models, which is both challenging and time consuming. The availability of realistic head models and corresponding imaging data is limited in terms of imaging modalities and patient diversity. In this paper, we describe a detailed head modeling pipeline and provide a high-resolution, multimodal, open-source, female head and brain model. The modeling pipeline specifically outlines image acquisition, preprocessing, registration, and segmentation; three-dimensional tetrahedral mesh generation; finite element EEG simulations; and visualization of the model and simulation results. The dataset includes both functional and structural images and EEG recordings from two high-resolution electrode configurations. The intermediate results and software components are also included in the dataset to facilitate modifications to the pipeline. This project will contribute to neuroscience research by providing a high-quality dataset that can be used for a variety of applications and a computational pipeline that may help researchers construct new head models more efficiently.



L. Zhou, D. Weiskopf, C. R. Johnson. “Perceptually guided contrast enhancement based on viewing distance,” In Journal of Computer Languages, Vol. 55, Elsevier, pp. 100911. 2019.
ISSN: 2590-1184
DOI: https://doi.org/10.1016/j.cola.2019.100911

ABSTRACT

We propose an image-space contrast enhancement method for color-encoded visualization. The contrast of an image is enhanced through a perceptually guided approach that interfaces with the user with a single and intuitive parameter of the virtual viewing distance. To this end, we analyze a multiscale contrast model of the input image and test the visibility of bandpass images of all scales at a virtual viewing distance. By adapting weights of bandpass images with a threshold model of spatial vision, this image-based method enhances contrast to compensate for contrast loss caused by viewing the image at a certain distance. Relevant features in the color image can be further emphasized by the user using overcompensation. The weights can be assigned with a simple band-based approach, or with an efficient pixel-based approach that reduces ringing artifacts. The method is efficient and can be integrated into any visualization tool as it is a generic image-based post-processing technique. Using highly diverse datasets, we show the usefulness of perception compensation across a wide range of typical visualizations.



L. Zhou, R. Netzel, D. Weiskopf,, C. R. Johnson. “Spectral Visualization Sharpening,” In ACM Symposium on Applied Perception 2019, No. 18, Association for Computing Machinery, pp. 1--9. 2019.
DOI: https://doi.org/10.1145/3343036.3343133

ABSTRACT

In this paper, we propose a perceptually-guided visualization sharpening technique.We analyze the spectral behavior of an established comprehensive perceptual model to arrive at our approximated model based on an adapted weighting of the bandpass images from a Gaussian pyramid. The main benefit of this approximated model is its controllability and predictability for sharpening color-mapped visualizations. Our method can be integrated into any visualization tool as it adopts generic image-based post-processing, and it is intuitive and easy to use as viewing distance is the only parameter. Using highly diverse datasets, we show the usefulness of our method across a wide range of typical visualizations.


2018


T. M. Athawale, K. A. Johnson, C. R. Butson, C. R. Johnson. “A statistical framework for quantification and visualisation of positional uncertainty in deep brain stimulation electrodes,” In Computer Methods in Biomechanics and Biomedical Engineering: Imaging & Visualization, Taylor & Francis, pp. 1-12. 2018.
DOI: doi:10.1080/21681163.2018.1523750

ABSTRACT

Deep brain stimulation (DBS) is an established therapy for treating patients with movement disorders such as Parkinson's disease. Patient-specific computational modelling and visualisation have been shown to play a key role in surgical and therapeutic decisions for DBS. The computational models use brain imaging, such as magnetic resonance (MR) and computed tomography (CT), to determine the DBS electrode positions within the patient's head. The finite resolution of brain imaging, however, introduces uncertainty in electrode positions. The DBS stimulation settings for optimal patient response are sensitive to the relative positioning of DBS electrodes to a specific neural substrate (white/grey matter). In our contribution, we study positional uncertainty in the DBS electrodes for imaging with finite resolution. In a three-step approach, we first derive a closed-form mathematical model characterising the geometry of the DBS electrodes. Second, we devise a statistical framework for quantifying the uncertainty in the positional attributes of the DBS electrodes, namely the direction of longitudinal axis and the contact-centre positions at subvoxel levels. The statistical framework leverages the analytical model derived in step one and a Bayesian probabilistic model for uncertainty quantification. Finally, the uncertainty in contact-centre positions is interactively visualised through volume rendering and isosurfacing techniques. We demonstrate the efficacy of our contribution through experiments on synthetic and real datasets. We show that the spatial variations in true electrode positions are significant for finite resolution imaging, and interactive visualisation can be instrumental in exploring probabilistic positional variations in the DBS lead.



F. Wang, W. Li, S. Wang, C.R. Johnson. “Association Rules-Based Multivariate Analysis and Visualization of Spatiotemporal Climate Data,” In ISPRS International Journal of Geo-Information, Vol. 7, No. 7, MDPI AG, pp. 266. July, 2018.
DOI: 10.3390/ijgi7070266

ABSTRACT

Understanding atmospheric phenomena involves analysis of large-scale spatiotemporal multivariate data. The complexity and heterogeneity of such data pose a significant challenge in discovering and understanding the association between multiple climate variables. To tackle this challenge, we present an interactive heuristic visualization system that supports climate scientists and the public in their exploration and analysis of atmospheric phenomena of interest. Three techniques are introduced: (1) web-based spatiotemporal climate data visualization; (2) multiview and multivariate scientific data analysis; and (3) data mining-enabled visual analytics. The Arctic System Reanalysis (ASR) data are used to demonstrate and validate the effectiveness and usefulness of our method through a case study of "The Great Arctic Cyclone of 2012". The results show that different variables have strong associations near the polar cyclone area. This work also provides techniques for identifying multivariate correlation and for better understanding the driving factors of climate phenomena.


2017


M. Chen, G. Grinstein, C. R. Johnson, J. Kennedy, M. Tory. “Pathways for Theoretical Advances in Visualization,” In IEEE Computer Graphics and Applications, IEEE, pp. 103--112. July, 2017.

ABSTRACT

More than a decade ago, Chris Johnson proposed the "Theory of Visualization" as one of the top research problems in visualization. Since then, there have been several theory-focused events, including three workshops and three panels at IEEE Visualization (VIS) Conferences. Together, these events have produced a set of convincing arguments.



M. Kern, A. Lex, N. Gehlenborg, C. R. Johnson. “Interactive Visual Exploration And Refinement Of Cluster Assignments,” In BMC Bioinformatics, Cold Spring Harbor Laboratory, April, 2017.
DOI: 10.1101/123844

ABSTRACT

Background:
With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don't properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data.

Results:
In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes.

Conclusions:
Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.


2016


B. Hollister, G. Duffley, C. Butson,, C.R. Johnson. “Visualization for Understanding Uncertainty in Activation Volumes for Deep Brain Stimulation,” In Eurographics Conference on Visualization, Edited by K.L. Ma G. Santucci, and J. van Wijk, 2016.

ABSTRACT

We have created the Neurostimulation Uncertainty Viewer (nuView or nView) tool for exploring data arising from deep brain stimulation (DBS). Simulated volume of tissue activated (VTA), using clinical electrode placements, are recorded along withpatient outcomes in the Unified Parkinson's disease rating scale (UPDRS). The data is volumetric and sparse, with multi-value patient results for each activated voxel in the simulation. nView provides a collection of visual methods to explore the activated tissue to enhance understanding of electrode usage for improved therapy with DBS.



M. Larsen, K. Moreland, C.R. Johnson,, H. Childs. “Optimizing Multi-Image Sort-Last Parallel Rendering,” In Symposium on Large Data Analysis and Visualization, IEEE, 2016.

ABSTRACT

Sort-last parallel rendering can be improved by considering the rendering of multiple images at a time. Most parallel rendering algorithms consider the generation of only a single image. This makes sense when performing interactive rendering where the parameters of each rendering are not known until the previous rendering completes. However, in situ visualization often generates multiple images that do not need to be created sequentially. In this paper we present a simple and effective approach to improving parallel image generation throughput by amortizing the load and overhead among multiple image renders. Additionally, we validate our approach by conducting a performance study exploring the achievable speed-ups in a variety of image-based in situ use cases and rendering workloads. On average, our approach shows a 1.5 to 3.7 fold improvement in performance, and in some cases, shows a 10 fold improvement.



P. Rosen, B. Burton, K. Potter, C.R. Johnson. “muView: A Visual Analysis System for Exploring Uncertainty in Myocardial Ischemia Simulations,” In Visualization in Medicine and Life Sciences III, Springer Nature, pp. 49--69. 2016.
DOI: 10.1007/978-3-319-24523-2_3

ABSTRACT

In this paper we describe the Myocardial Uncertainty Viewer (muView or µView) system for exploring data stemming from the simulation of cardiac ischemia. The simulation uses a collection of conductivity values to understand how ischemic regions effect the undamaged anisotropic heart tissue. The data resulting from the simulation is multi-valued and volumetric, and thus, for every data point, we have a collection of samples describing cardiac electrical properties. µView combines a suite of visual analysis methods to explore the area surrounding the ischemic zone and identify how perturbations of variables change the propagation of their effects. In addition to presenting a collection of visualization techniques, which individually highlight different aspects of the data, the coordinated view system forms a cohesive environment for exploring the simulations.We also discuss the findings of our study, which are helping to steer further development of the simulation and strengthening our collaboration with the biomedical engineers attempting to understand the phenomenon.



X. Tong, J. Edwards, C. Chen, H. Shen, C. R. Johnson, P. Wong. “View-Dependent Streamline Deformation and Exploration,” In Transactions on Visualization and Computer Graphics, Vol. 22, No. 7, IEEE, pp. 1788--1801. July, 2016.
ISSN: 1077-2626
DOI: 10.1109/tvcg.2015.2502583

ABSTRACT

Occlusion presents a major challenge in visualizing 3D flow and tensor fields using streamlines. Displaying too many streamlines creates a dense visualization filled with occluded structures, but displaying too few streams risks losing important features. We propose a new streamline exploration approach by visually manipulating the cluttered streamlines by pulling visible layers apart and revealing the hidden structures underneath. This paper presents a customized view-dependent deformation algorithm and an interactive visualization tool to minimize visual clutter in 3D vector and tensor fields. The algorithm is able to maintain the overall integrity of the fields and expose previously hidden structures. Our system supports both mouse and direct-touch interactions to manipulate the viewing perspectives and visualize the streamlines in depth. By using a lens metaphor of different shapes to select the transition zone of the targeted area interactively, the users can move their focus and examine the vector or tensor field freely.

Keywords: Context;Deformable models;Lenses;Shape;Streaming media;Three-dimensional displays;Visualization;Flow visualization;deformation;focus+context;occlusion;streamline;white matter tracts


2015


C.R. Johnson, K. Potter. “Visualization,” In The Princeton Companion to Applied Mathematics, Edited by Nicholas J. Higham, Princeton University Press, pp. 843-846. September, 2015.
ISBN: 9780691150390



H. De Sterck, C.R. Johnson. “Data Science: What Is It and How Is It Taught?,” In SIAM News, SIAM, July, 2015.