Comp/Phys/Mtsc 715 Visualization System Design Examples In-Class - PDF document

3/15/2012 Comp/Phys/Mtsc 715 Visualization System Design Examples In-Class Design 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 1 Example Videos • cad-glyph.avi: Meyer Vis 2008 – Glyphs for multivariate surface visualization • vis-1006_mpeg4.avi: Termeer Vis 2008 – Blood supply to heart surface multivariate • Airfoil.avi: Von Funk Vis 2008 – Fading stream surface and ribbon flow display 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 2 Administrative • Be talking with your client – Questions/Goals – Getting final data set 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 3 1

3/15/2012 Example Final Projects++ • ImageSurfer - confocal microscopy data • GyVe - supercluster of galaxies • CDView - 3D molecule charge densities • InnerSpace - virtual arthroscopy 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 4 ImageSurfer (2002) • Clients: – Alain Burette, Cell Bio Postdoc – Richard Weinberg, Cell and Developmental Bio • Team: – Dennis Jen, CS student – Peter Parente, CS student • Problem: – How to correlate membrane and calcium? 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 5 How is the concentration of PMCA distributed along a dendrite? DiO PMCA 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 6 2

3/15/2012 Looking through the stacks… 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 7 End of Course • Two views, 3D volume and 2D slice 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 8 Going Beyond the Course 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 9 3

3/15/2012 Failed Attempts 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 10 CISMM-sponsored additions 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 11 … easing the pain 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 12 4

3/15/2012 … adding analysis 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 13 Measures of Success • http://www.imagesurfer.org – Maintained by scientist collaborators! – ~3 downloads per day • Dennis Jen, Peter Parente, Jonathan Robbins, Christopher Weigle, Alain Burette, Richard Weinberg, and Russell M. Taylor II, “ImageSurfer: A Tool for Visualizing Correlations between Two Volume Scalar Fields,” IEEE Visualization 2004 Proceedings , October 10-15, Austin Texas, pp. 529-536. • David Feng, David Marshburn, Dennis Jen, Richard Weinberg, Russell M. Taylor II, Alain Burette, “ToolBox: Stepping into the third dimension,” Journal of Neuroscience , 27(47), Nov. 21, 2007, pp. 12757-12760. 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 14 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 15 5

3/15/2012 Galaxy Viewer (2005) • Clients – Matthew Fleenor, Astronomy graduate student – James Rose, Astronomer • Team – Jameson Miller, CS student – Cory Quammen, CS student • Problem: – Seeing structure in Horologium Reticulum data 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 16 Gyve Advertisement Link 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 17 Gyve Display 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 18 6

3/15/2012 Gyve Results • Revealed Spherical Voids 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor Gyve Results • Disproved incorrect filament structures 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 20 Gyve: What Helped? • Stereo • Torsional Rocking • Curved drop shadows – Tied to previous technique’s views – Showed appropriate space warping 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 21 7

3/15/2012 Measures of Success • Scientists trooped over to CS repeatedly to use the stereo display! • Linux version to run on scientists’ computers • http://sourceforge.net/projects/gyve • Jameson Miller, Cory W. Quammen, and Matthew C. Fleenor, Interactive Visualization of Intercluster Galaxy Structures in the Horologium-Reticulum Supercluster, IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2006), vol. 12, no. 5, pp. 1149–1155, Sept.–Oct. 2006. 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 22 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 23 CDView: Problem Description • Client – Luci Teague from UNC Chemistry • Team – Chad Hantak (CS), David Borland (CS) • Problem domain – 3D molecular charge densities, generated by simulating molecular interactions of a 1-3 Cyclohexadine molecule bonding to a tetrahedral Silicon surface scanned by a Tungsten STM tip. • Data Collection – Data is collected through CASTEP (CAmbridge Serial Total Energy Package) charge density simulations in the Cerius2 software package. Output is various ASCII files. http://surface.iphy.ac.cn/schinese/SF4/stm.ht1.gif 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 24 8

3/15/2012 CDView: Goals and Data • Goals – Understand how the charge density varies throughout the volume, and how it relates to the molecular models. Specifically, the charge density values and the shape of the volume where the tip is interacting with the molecule. – Correlate the STM image data with the simulated data. • Data – Regular 3D grid of ratio scalar data from simulation (no noise, no missing data, no appreciable quantization) – Irregular 3D grid of atom coordinates and bonds (no noise, no missing data, no appreciable quantization) 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 25 CDView: Design • 3D Scalar Field – Volume Render vs. Isosurface • Interested in shape • Specific charge density values • (Russ had an idea for displaying several isosurfaces…) • 3D Model – For context, simple ball and stick model • Other Techniques – Bounding box – Axis glyph – Clipping planes – Slices with colormaps 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 26 CDView: Implementation • VTK + Java – Java wrappers for VTK – Wrote most of the code in Java—platform independent – Wrote new VTK class for translucent isosurfaces in C++ (had to reimplement in Java due to wrapping problems…) – Used Java Swing for the GUI 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 27 9

3/15/2012 CDView: Interface 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 28 CDView: Images Tungsten • Bounding Box STM tip • 3 Nominally Colored 1-3 Cyclohexadine Isosurfaces • Axes Silicone 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 29 CDView: Images • Clipping Plane Tungsten – To remove data of STM tip little interest 1-3 Cyclohexadine 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 30 10

3/15/2012 CDView: Images • Clipping Plane – To display interior surfaces 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 31 CDView: Images • Run reaction-diffusion on isosurfaces, use to modulate opacity • Show inner and outer structure 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 32 CDView: Images 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 33 11

3/15/2012 CDView: Images • Slice with black-body radiation colormap applied (goes to blue) • Enables showing of ratio data. • Used a lot to compare different data sets. 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 34 Lessons Learned • What Went Right – Application for prototyping (AVS express) • Great for making sure you can load the data correctly • You guys have ParaView and VisTrails – Extensible toolkit (VTK) • Don’t need to reinvent the wheel for most things, but flexible enough to do so Good communication with scientist – • Very important! You are designing a tool to answer their questions. • What Went Wrong – Undocumented data file formats *Never enough: • Spent a large portion of our time figuring this out – VTK documentation isn’t always the greatest David Borland continued – VTK wrapper problems working with Lucie for the – VTK opacity bug semester after the course • Need to depth sort for half of the views! project on fine-tuning, • Ideal Implementation adding various generated – Head-tracked stereo data sets, etc. – More interactive (Volume Render Isosurfaces?) 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 35 Measures of Success • Students worked with collaborator after end of semester • Collaborator used visualization in preparation of paper 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 36 12

3/15/2012 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 37 Innerspace • David Borland’s dissertation work 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 38 Arthroscopy • Use fiber-optic camera and surgical tools to investigate joint for pathology • Problems – Invasive – Costs time and money – Very cramped area to maneuver in 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 39 13

3/15/2012 MRI Slice Viewing Contrast agent in the joint-space • Current standard for joint pathology diagnosis Humeral Humeral Head Socket Head • Features – Less invasive – Contrast agent routinely injected to aid imaging • Problems Shoulder MRI – Requires tedious selection of slices – Requires non-intuitive Socket Humeral mental reconstruction Head of 3D features 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 40 Virtual Arthroscopy • Work by John Clarke from UNC Radiology • Features – Also less invasive – More intuitive visualization • Problems – Viewpoints limited to the joint-space – Must maneuver the virtual Humeral camera across the entire joint Head surface for evaluation – “Like looking at the palm of your hand with it touching your nose.” 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 41 Visualization Course Project • Sean Hanlon, Karl Strohmaier, Kelly Van Busum • DVR for context • Extracted isosurface for detail – Slow… • Adjustable clipping planes – Problem… 3/15/2012 Designs Comp/Phys/Mtsc 715 Taylor 42 14