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Scientific Visualization with VisIt Mathematica and ImageJ

Title Date Times Venue
Scientific Visualization with VisIt Mathematica and ImageJ June 14 - 15 2013 830 AM - 500 PM 307 Frey CSC

The objective is an understanding of the procedure for converting a series of 2D images into 3D images, movies, and fly-throughs. This is the basis of the medical CT scan, industrial non-destructive testing, and much of scientific visualization. The second objective is introduction to two software packages---ImageJ and VisIt---that are both extremely powerful, will run on your laptop, and are free. When finished with this course, you should be able to perform visualizations of 3D data sets when provided with data in open access formats such as raw binary, stacked TIFF, and HDF5. You will run Mathematica notebooks in class as we discuss: (a) 2D image sequences into 3D volumes, (b) histograms and binarization, (c) image transformations such as Gaussian filtering, distance transform, and watershed transform, (d) connected component analysis, and (e) simple movie making.

Using the VisIt visualization software, we’ll teach students visualize large scale datasets in distributed mode so that the expensive computation runs on high performance computing clusters. Students will have take-away visit-python scripts to do: pseudo-color, histogram, volume rendering, isosurface, orthoslices, volume re-sample, sub-volume selection, and movie making. These visit-python scripts can be submitted to HPC resources for batch processing and the result images will be saved and retrieved back for user inspection.


  • Prof. Les Butler, LSU Chemistry
  • Dr. Jinghua Ge, LSU CCT
  • Prof. Juana Moreno, LSU Physics


  • June 14
    Time Topic
    8:00 - 8:30 Registration and Setup
    8:30 - 10:00 Washington Post Puzzle: Mathematica: binarization, histograms, morphological component analysis; repeat with ImageJ. ImageJ: binary data sets, HDF5 data sets
    10:00 - 10:15 Break
    10:15 - 12:00 Transforms: distance, watershed, affine, Gaussian filtering. Connected component analysis
    12:00 - 1:00 Lunch
    1:00 - 2:45 2D image sequences into 3D volumes, demonstrate HPC.
    2:45 - 3:00 Break
    3:00 - 5:00 Mathematica: Fly-around movie making. Individual projects with Teapot, Stanford Bunny, or other 3D object
  • June 15
    Time Topic
    8:30 - 10:00 Visit: setup, connect to HPC, prepare datasets
    10:00 - 10:15 Break
    10:15 - 12:00 Plots and Operators
    12:00 - 1:00 Lunch
    1:00 - 3:00 Write Python Script, submit batch job
    3:00 - 3:15 Break
    3:15 - 5:00 present your visualization
  • Downloads and Instructions
    1. Software List
    2. Exercise Material


Special thanks to the following for their generous support of the Scientific Visualization with VisIt, Mathematica, and ImageJ Workshop

  • Board of Regents, State of Louisiana.
  • Louisiana Alliance for Simulation-Guided Materials Applications (LA-SiGMA).
  • Center for Computation & Technology, Louisiana State University.
  • Information Technology Services, Louisiana State University.
  • Louisiana Optical Network Initiative (LONI).


There are limited travel funds available for attending the Symposium and Workshops. All participants traveling to Baton Rouge for attending the Symposium and Workshops will be considered for travel awards provided:

  • Register for the Symposium and Workshop,
  • To be considered for a travel award, please upload a one or two paragraph proposal (in pdf/doc format) describing why a travel award is beneficial to your research for attending the workshop and
  • submit an abstract for poster or oral presentation (if attending Symposium) by May 27th, 2013.

If you are attending both the LONI Programming and Scientific Visualization Workshops, you can upload one combined proposal. Make a note in the proposal that you are requesting travel support for both workshops.

Priority will be given first to participants who are presenting (poster or oral) at the Symposium and then to participants who are attending the workshops held preceeding and following the symposium.

Requesting Travel Award

Please upload an one or two paragraph proposal in the field provided by Noon on May 27, 2013,
Accepted formats are .pdf, .doc, .docx and .odt.
Files should have the naming convention travel_lastname_firstname.extension.
Your proposal should contain a title (could be as simple as Travel Proposal for LONI Workshop), your name and institution. Use the Symposium abstract template if you need. All proposals without a name, institution and travel in filename will be rejected.
Maximum file size is 2MB.
Click here to upload travel proposal

Registration & Costs

$50.00. All registration and payments must be received by May 27th, 2013.