The Research Computing Center maintains data visualization resources that are available to all RCC users. These resources include high-end 3D graphics processing and display hardware, commercial and open-source data visualization software, and custom remote visualization tools for in-situ visualization of data stored on RCC's compute cluster. Additionally, RCC computational scientists are available to consult with users to develop effective data visualizations and customized data visualization tools.

Data Visualization Lab

The RCC Data Visualization Laboratory is located in the Kathleen A. Zar Room in the John Crerar Library and is available for use by all RCC users. The Data Visualization Lab is outfitted with a high-performance visualization workstation equipped with an Nvidia Quadro 5000 GPU and a high-performance 6 TB locally attached disk array. The visualization workstation is coupled with a ProjectionDesign F35 AS3D active stereoscopic projector which provides a 2.3 MPixel active-3D display.

In addition to the visualization hardware and local storage in the lab, the workstation is connected to the RCC compute cluster and storage system, providing straightforward access to research data and introducing the possibility of interactive supercomputing.

For more information or to reserve the Data Visualization Lab, please contact RCC.

Remote Visualization

RCC has developed a remote visualization tool called Sviz that allows users to run graphics-intensive applications remotely. Visualization software can be run on the Midway compute cluster with all graphical output sent to a the user’s local machine. Through Sviz, a user can directly visualize data stored on Midway without having to transfer the data to a local visualization workstation. The Sviz server runs on Midway’s high-performance GPU-equipped compute nodes, making it possible to run high-end visualization software regardless of local hardware capabilities.

Sviz can be used by all users with an RCC account. For more information on how to use Sviz, see the Remote Visualization section of the user guide.

Visualization Consulting Services

RCC computational scientists are available to consult with users to develop data visualizations, provide training on visualization software, and develop customized data-visualization tools. To inquire about visualization consulting services, please contact RCC.

The RCC use of the Zar Room in the Crerar Science Library

1. Situational Summary

Since its creation in 2012, The Research Computing Center (RCC) has used the Kathleen A. Zar room in the Crerar Science Library as its data visualization laboratory and for all its hands-on workshops and trainings. The lab serves not only as a data analysis and visualization resource, but also as a forum for educational activities. This document provides a summary of RCC services and programs currently supported in the Zar Room that are available to all UChicago faculty, researchers, and students. The RCC currently supports 422 faculty with a total of 3,179 active users – numbers that grow daily.

2. The Zar Room Data Visualization Laboratory

The Zar room data visualization lab currently has the following hardware:

  • Two ceiling-mounted stereo projectors with a 10-foot silver screen specially formulated for high-quality polarized 3-D projections.


     
  • A High-performance Visualization Workstation connected to an active stereoscopic projector: This workstation is equipped with an NVidia Quadro 5000 GPU and a high-performance 6 TB locally attached disk array. It is connected to a ProjectionDesign F35 AS3D active stereoscopic projector which provides a 2.3 MPixel active-3D display. About 30 pairs of 3D glasses are available for use with the 3D projector during a class. The workstation is also connected to the RCC compute cluster and storage system, providing straightforward access to research data and enabling interactive supercomputing. Example application: 
    • 3D visualization of MRI and CT segmented atlases of brain and liver. 3D reconstructions of segmented MRI and CT scans of brain and liver, together with their labelmaps are displayed using a 3D Slicer software tool with active stereo option.
  • Multi-Touch Virtual Reality Workbench: a visualization system that combines touch screen technology with 3D projection and motion tracking used for exploratory visualization. Example application: 
    • Interactive Exploratory Visualization of 4D heart blood flow data in VR. simulations of blood flow in the right ventricle of the heart using Bento Box, a software application for visualizing 4D simulation assembles of data.
    • Investigating Tooth Enamel Fractures with Interactive Volume Visualization.


       
  • SensAble Phantom Omni Haptic Device: a device that applies force feedback on the user’s hand, allowing a realistic feel of the virtual objects and producing touch sensations as the user is exploring the 3D model.
    • The demanding nature of haptic rendering, requiring 1kHz rates to deliver simulation of realistic forces, allows researchers to explore different approaches to alleviate computational load. RCC is developing tools for distributing haptic and graphical rendering over a network. Thus, the force is applied to the haptic device and the feedback is transmitted to RCC Midway High Performance Computing cluster.


       
  • VR Systems for mobile phone: 20 Google Cardboards and 2 Google Daydream View VR headsets are available for teaching and training or VR application development purposes. 
  • Kinect for Windows: Microsoft XBOX 360 Kinect technology provides full-body 3D motion capture, facial and voice recognition. RCC is using Kinect technology to interface with visualization displays (e.g., visualization wall).
  • HTC Vive with motion tracking: A comprehensive virtual reality station. Example projects:
    • Visualization of genes mirroring geography within Europe: A 3D representation of genetic variation acrossEurope produced by principal component analysis (PCA). The project was developed by John Novembre (Department of Human Genetics) and RCC computational scientists and presented during the Mind Bytes 2017 Symposium.
    • ATLSrift: an immersive visit to the ATLAS experiment: A 3D reproduction of the Large Hadron Collider to view the ATLAS experiment using ATLASrift (https://atlasrift.web.cern.ch/). The users are able to learn about the ATLAS experiment and view real-time data from the ATLAS detectors. ATLASrift was developed by Ilija Vukotic (Computation Institute) and provides an example of how research can utilize virtual interfaces to produce immersive tools for making experimental data accessible and interactive. This projet was presented during the Mind Bytes 2017 Symposium.
    • Presenting stimuli in VR environments: A VR environment designed to present ‘creepy’ stimuli to participants while measurements of biological (heart rate, cortisol, eye-movements etc.) and psychological responses are taken. The project is developed in collaboration with Mikaela Armenta and Coltan Scrivner from Department of Psychology.


       
  • Visualization Tile Wall: an 18 screen (6x3) tile display wall has been designed and will be installed in the Zar room to allow faculty and students to visualize and interact with data through multiple screens in a collaborative environment. Its purpose is to visualize large and complex datasets with ultra-high resolution, and enhance remote collaboration. The faculty serving on the Data Visualization Advisory Committee after a year of planning recommended this project. It will be compatible with the visualization wall at Argonne and faculty will not need to travel to Argonne to visualize data coming from the Advance Photon Source (APS).

     
  • Control Station: A system that controls all audio, video and computer hardware in the Zar room.
  • Visualization consulting, hackathons, and tutorials.
     

3. RCC Programs, Applications and Services in the K.A. Zar room–Data Visualization Lab

  • ​3.1 Interactive Supercomputing -
    This is a mode of computational research where real-time analysis and visualization are automatically performed on results from high resolution and realistic calculations carried out on the RCC Midway HPC cluster. Computational simulations can generate thousands of files and terabytes of data that need to be moved, stored, post-processed, and then visualized. The fact that the visual representations of such large and complex calculations can be obtained while the calculation is running, when previously scientists had to wait for days or even weeks to view them, makes it possible to quickly evaluate a calculation running on the Midway HPC cluster as it is underway and revise and adjust it without waiting for it to run to completion. The Zar room also provides the only collaborative environment where researchers can congregate to analyze a large-scale calculation as it progresses from the Midway HPC cluster or any other national HPC center. 
  • 3.2 Education and Teaching support - The RCC has supported more than 45 courses by providing Midway computer accounts for the duration of the courses which trained many students. RCC Computational Scientists have also facilitated more than 103 specialized computational and data visualization workshops.
    • Training and hands-on workshops: The RCC offers approximately 50 educational and training workshops annually (~300 since its creation), which are attended by 25-50 students and faculty. Most of these trainings need to take place in the Zar room because they are hands-on and need to use RCC computational and data visualization resources. Many workshops have waiting lists or given twice.
    • Non-credit courses: RCC is in the final planning stages to offer discipline specific non-credit courses in partnership with a faculty advisory committee and divisional Deans. As part of this offering, the RCC plans to pilot an active learning classroom set up in the Zar room. 
    • Corporate partnerships: The RCC invites and hosts 5-7 workshops facilitated by hardware and software companies such as IBM, NVidia, Intel, Mathworks and ESRI. These workshops are to introduce and allow hands-on opportunities with the latest technology platforms relevant to HPC and GIS.
    • Hackhathons: RCC organized data visualization Hackhathons that enabled faculty to work on their own projects.  

The hardware available in the Zar room allowed RCC to conduct education and training that would not be otherwise possible. For example, the Zar room was used to teach an immersive virtual anatomy course to University students (http://www.ncbi.nlm.nih.gov/pubmed/17377320). People can learn more efficiently in a stereoscopic environment with a focused curriculum.  Another good example is of an effective engagement and collaboration globally: a 3D course was given to college students at UChicago in the K. A. Zar room while 3,831 miles away, another group in Cardiff, Wales, saw the same presentations simultaneously via the AccessGrid.

  • 3.3.  3D MRI reconstruction - Current advances in computer and imaging technologies have made it possible to generate precise 3D reconstructed images in several hours using routine clinical radiological data. These 3D reconstructed images are becoming very useful for scientific exploratory visualization and planning medical procedures.  For example, they can help a surgeon choose the best method of intervention, evaluate surgical risks, select a surgical approach, and localize lesions.  The stereoscopic projectors in the Zar room provide capability to view 3D MRI images in an immersive environment that provide a greater understanding of the data.

  • 3.4.  VR systems - In recent years, VR has introduced a large number of new technologies and new concepts and research topics are constantly being introduced. VR applications are also growing exponentially: from gaming to healthcare and data analysis. The user has the ability to explore data from new perspectives and interact with images in 3D environments.

  • 3.5. High-resolution data visualization - Today’s processors can quickly calculate large 3D grid simulations which produce very high-resolution data output.  Advanced scanning technologies can create high-resolution images from a wide variety of subjects.  These datasets can be impractical or impossible to properly analyze and visualize using a desktop computer.  Outfitted with GPU hardware, the Zar room provides the compute resources to visualize the data and uses the high-resolution projectors to display the results.  

  • 3.6. Remote visualization - RCC has developed a remote visualization tool called Sviz that allows users to run graphics-intensive applications remotely. Visualization software can be run on the Midway compute cluster with all graphical output sent to the user’s local machine. Through Sviz, a user can directly visualize data stored on Midway without having to transfer the data to a local computer. With the use of software developed at RCC, users can run visualizations remotely to display on their desktops while using the high end graphic card of the machine in the Zar room.

  • 3.7. Outreach - Visualization of data is one of the most effective methods for conveying results to an otherwise un-initiated audience.  Data visualizations are also effective for outreach to future students, faculty, alumni and visitors from granting agencies.   The outreach activities in the Zar room have also been used to help faculty fulfill their federal grant agencies’ broader impact requirements or when submitting a grant proposal.  Below are few examples:

    • Annual Brain Awareness week: Students from Chicago Public Schools spend half a day learning about how computation enables groundbreaking research in neuroscience (2013, 2014, 2015, 2016 and 2017). https://rcc.uchicago.edu/support-and-services/outreach
    • Imaging/Imagining the Human Body in Anatomical Representation - March 25 - June 20, 2014
      • Session was hosted in the Zar Room and curated by Brian Callender, MD, Assistant Professor of Medicine. 3D models of MRI and CT scans were displayed using the 3D projector. RCC helped in creating the models.
    • Visualization Hackathon - Saturday, April 22nd, 2017
    • Virtual Reality Workshop - Tuesday, August 15th, 2017
    • Virtual Reality Internship for High School Students - Summer 2017
    • Hosted the Virtual School of Computational Science and Engineering (http://www.vscse.org/)
    • Petascale Institute - June 26 - 30, 2017
    • Software Carpentry - July 11-12, 2017
       
  • 3.8 Current commitments and projects
     
    • Building a virtual world to study the physical and social environment of cognitive and affective processes (5 faculty in the Department of Psychology).
    • Connectivity of Argonne APS and ALCF to UChicago for data visualization
    • Visualization Hackathons for 2018 (at least two)
    • Brain Awareness week – March 2018
    • Virtual Reality Workshop - for the UChicago Simulation Center
    • Imaging/Imagining the Human Body in Anatomical Representation - 2018/2019 - in collaboration with Brian Callender, MD, Assistant Professor of Medicine.
    • Institute for Molecular Engineering summer 2018 workshop

​The RCC receives many requests to support data visualization related projects, however, the number of projects and initiatives it can support is limited by the available limited resources. 

  • 4 Conclusion

The Kathleen A. Zar 3-D environment is a great resource for the University and has supported many projects and training activities. The ability to interactively analyze large datasets in real time, explore and fly through 3D visualization datasets can accelerate new discoveries compared to analyzing large numerical data or looking at 2D visualizations. Hosting a large number of custom training activities annually and various programs that rely on the RCC advanced computational resources will be very difficult without a dedicated space.