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Examples of the CAVE working for Scientists

Examples of the CAVE working for Scientists. Rachael Brady Beckman Institute, UIUC August 15, 2000. Outline. Crumbs Overview Motivation Rendering Toolset Audio Formative Evaluation Uses by Scientists. Writing a VR Application for Scientists (Biologists). Navigation

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Examples of the CAVE working for Scientists

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  1. Examples of the CAVE working for Scientists Rachael Brady Beckman Institute, UIUC August 15, 2000 CAVERNUS - Advanced CAVE Workshop Series

  2. Outline • Crumbs Overview • Motivation • Rendering • Toolset • Audio • Formative Evaluation • Uses by Scientists CAVERNUS - Advanced CAVE Workshop Series

  3. Writing a VR Application for Scientists (Biologists) • Navigation • Driving/Flying paradigms only work with landmarks and horizon • Interaction • Object control • Parameter setting • Measuring • Hardcopy CAVERNUS - Advanced CAVE Workshop Series

  4. Illustration or Exploration • Illustration • High rendering quality • Annotation • Accurate measurements • Exploration • Fast, interactive rendering • Multiple viewpoints • Multiple viewing tools • Measurement/Analytic tools CAVERNUS - Advanced CAVE Workshop Series

  5. 48 Hour Old Chicken Embryo Jo Ann Eurell, Janet Sinn-Hanlon Veterinary Biosciences, UIUC Exploration Illustration CAVERNUS - Advanced CAVE Workshop Series

  6. Crumbs General viewing tool for regularly gridded 3D scalar data in the CAVE. Developed to trace and measure 1D fibers CAVERNUS - Advanced CAVE Workshop Series

  7. Outline • Crumbs Overview • Motivation • Rendering • Toolset • Audio • Formative Evaluation • Uses by Scientists CAVERNUS - Advanced CAVE Workshop Series

  8. Motivation of Crumbs (Feb ’94) • Problem • Trace and model fibrous structures in dense, volumetric datasets from imaging modalities such as MRI, TEM and Optical Microscopy • Will a virtual environment help? CAVERNUS - Advanced CAVE Workshop Series

  9. Ray Traced Texture Mapped Volume Rendering CAVERNUS - Advanced CAVE Workshop Series

  10. First Attempts • Navigation • Flying • Outside/Inside + Map • Windshield • Physical Object you pick up & resize • Rendering • Show entire data set at once • Viewing window • Several viewing windows • Slices CAVERNUS - Advanced CAVE Workshop Series

  11. Current Features • Parameter Settings • Menus • Colormap & Opacity Control • Voice Command • Crumbs Placement • Intelligent use of space • Spline Plane • Sonification CAVERNUS - Advanced CAVE Workshop Series

  12. What Crumbs Looks Like in Use Data volume is a horse fetlock (ankle). Source: Mark Martinelli CAVERNUS - Advanced CAVE Workshop Series

  13. Outline • Crumbs Overview • Motivation • Rendering • Toolset • Audio • Formative Evaluation • Uses by Scientists CAVERNUS - Advanced CAVE Workshop Series

  14. Crumbs Environment CAVERNUS - Advanced CAVE Workshop Series

  15. Color Map Adjustment CAVERNUS - Advanced CAVE Workshop Series

  16. Opacity Adjustment CAVERNUS - Advanced CAVE Workshop Series

  17. Voice Command Necessary for Instrument Control CAVERNUS - Advanced CAVE Workshop Series

  18. crumbs Manipulation CAVERNUS - Advanced CAVE Workshop Series

  19. Spline Plane CAVERNUS - Advanced CAVE Workshop Series

  20. Outline • Crumbs Overview • Motivation • Rendering • Toolset • Audio • Formative Evaluation • Uses by Scientists CAVERNUS - Advanced CAVE Workshop Series

  21. Audio • Ambient Sounds (mood music) • Event Feedback • Localization • Sonification • Can sound help in Crumbs placement? • Must be fatigue resistant • Must convey data value • Must synchronize with graphical rendering & task Music CAVERNUS - Advanced CAVE Workshop Series

  22. First Attempt • Four Melodies • Orchestration mapped to data value • Implemented by Robin Bargar & Insook Choi CAVERNUS - Advanced CAVE Workshop Series

  23. Current Implementation • No MIDI device needed • Implementation by Carlos Ricci CAVERNUS - Advanced CAVE Workshop Series

  24. Current Implementation CAVERNUS - Advanced CAVE Workshop Series

  25. Outline • Crumbs Overview • Motivation • Rendering • Toolset • Audio • Formative Evaluation • Uses by Scientists CAVERNUS - Advanced CAVE Workshop Series

  26. Formative Evaluation • Kent Swartz & Deborah Hix • Virginia Tech, Dept. of Computer Science • Umesh Thakkar • University of IL, NCSA CAVERNUS - Advanced CAVE Workshop Series

  27. Formative Evaluation - Tasks • Crumbs has “feature-itis”. Decided to focus on core task of placing crumbs along a 1D feature of interest. • Two data sets chosen. • Fertilized fruit fly embryo, place crumbs along sperm tail within egg nucleus • Human Spine, place crumbs on 3D centroid of each vertebrae CAVERNUS - Advanced CAVE Workshop Series

  28. Formative Evaluation - Users • User #1, pilot study • Wide VR experience, demos Crumbs, not user • User #2 • Wide VR experience, runs Crumbs for demos, used once for own data • User #3 • User, no VR experience • User #4 • Developer, no VR experience • User #5 • User, no VR experience CAVERNUS - Advanced CAVE Workshop Series

  29. Formative Evaluation - Survey Results CAVERNUS - Advanced CAVE Workshop Series

  30. Formative Evaluation - Results • Removal of objects from the environment • Delete vs. Hide, not a problem in general. One person had trouble with this. • Some aural feedback choices “bad” • “Ouch” caused people to release button and cringe • “Good Luck” made people pause and wonder why • “Grab and Drag” button changes for thumbslider on Opacity, Colormap & Contrast tools • True problem. Lots of confusion from this • Suggestion: Grey out unavailable options on the menu CAVERNUS - Advanced CAVE Workshop Series

  31. Outline • Crumbs Overview • Motivation • Rendering • Toolset • Audio • Formative Evaluation • Uses by Scientists CAVERNUS - Advanced CAVE Workshop Series

  32. Uses by Scientists • Fruit Fly Fertilization • Protozoa • Spinal Stenosis • Human Pharynx • Egyptian Mummy • Chicken Development • Oil Exploration • Plasma Physics • Optical Tomography • Architecture CAVERNUS - Advanced CAVE Workshop Series

  33. Drosophila Sperm Tails Tim Karr University of Chicago Beckman Institute UIUC CAVERNUS - Advanced CAVE Workshop Series

  34. Structure of fertilized Drosophilla Egg CAVERNUS - Advanced CAVE Workshop Series

  35. Evolution of sperm study • What is length of tail? 1994 - 1995 • Initially used CAVE to trace twisting, knotty tail in order to determine length. Topological accuracy was not important. CAVERNUS - Advanced CAVE Workshop Series

  36. Evolution of sperm study • What is shape of tail? 1996-1998 • Why do different species have different shapes? • What is statistical variation of shape within a species? CAVERNUS - Advanced CAVE Workshop Series

  37. Evolution of sperm study • How does sample preparation effect measurements (1999-present) • Results so far: • Same prep, same gestation, same species yield measurement repeatability within 5% • Compression of sample from confocal imaging results in longer tail measurements CAVERNUS - Advanced CAVE Workshop Series

  38. Sperm’s effect on Crumbs • Added capability to view many tracings simultaneously • Added seim-automatic tracing capability • Branching capability out of knots Published in Nature (1995) and Science (1996) CAVERNUS - Advanced CAVE Workshop Series

  39. Oral Region Infundibulum Peristome Trochal Band Aboral Region Howard E. Buhse Jr. Biological Sciences University of Illinois at Chicago Protozoa: Vorticella convallaria CAVERNUS - Advanced CAVE Workshop Series

  40. Structure of Vorticella convallaria CAVERNUS - Advanced CAVE Workshop Series

  41. Discovering the OF-1 Antibody in the Myonemes • Use of the confocal microscope forced the scientist to prepare his organism with a different stain • The proteins carrying the stain appeared in an unexpected location in the organism CAVERNUS - Advanced CAVE Workshop Series

  42. Spinal Stenosis Budinger, Schoenem, Maltz, LBL CAVERNUS - Advanced CAVE Workshop Series

  43. Spinal Stenosis • Want to find point of tightest constriction along vertebrae of spine • Added capability to select locations for 2D slices, and save images to disk • Results: no significant differences discovered from classical methods CAVERNUS - Advanced CAVE Workshop Series

  44. Human Pharynx David Kuehn & Sandy Ettema Speech and Hearing Science, UIUC CAVERNUS - Advanced CAVE Workshop Series

  45. Mummy Sarah Wisseman Ancient Technologies UIUC CAVERNUS - Advanced CAVE Workshop Series

  46. Mummy • CAT scan performed at CARLE clinic • Mummy is boy, around 9 years old • Teeth • Pelvis • Body is on wood (pine?) board • Organs not removed prior to mummification CAVERNUS - Advanced CAVE Workshop Series

  47. 48 Hour Old Chicken Embryo Jo Ann Eurell Janet Sinn-Hanlon Veterinary Biosciences, UIUC CAVERNUS - Advanced CAVE Workshop Series

  48. Chicken Embryo • Optical serial sections • 24-hour and 48-hour embryos available • Used as field trip for developmental biology course • Heart development • Nervous system development • Now illustration available (video) CAVERNUS - Advanced CAVE Workshop Series

  49. Oil Exploration • Seismic data is very dense and difficult to see structures • Slice planes most popular rendering method • Incorporated ability to render predefined meshes so that land marks could be seen in seismic volume • Jan 99: oil drill hit calcium deposit • decided to stop drilling in that location • used Crumbs to explore area around well • data showed oil deposit behind deposit • continued drilling: found deposit worth $15M CAVERNUS - Advanced CAVE Workshop Series

  50. Militzer/Ceperly version of Crumbs Path-integral Monte Carlo simulations of hydrogen. The calculation is used to study hydrogen transition from the plasma state with free protons and electrons to a molecular gas, and finally to molecular metallic liquid. CAVERNUS - Advanced CAVE Workshop Series

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