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keckcaves:visualizer_quick_guide

Visualizer Quick Guide

These (evolving) instructions come from Dawn's research group, members of which are using Visualizer to analyze microbial structures in image stacks and x-ray computed tomography scans.

1. Log on and open a terminal window. (Terminal is a program you can find under “Accessories” on a Linux machine or in “Applications → Accessories” on a Mac.)

2. Change directories to the place you want your results stored. (For Dawn's students, please use /share/Projects/SumnerLabProjects/<your folder name> By storing your results in one of these directories, you make them available to other lab members. This allows us to share color palettes, etc.)

cd /share/Projects/SumnerLabProjects/

You may also drag your folder onto the terminal window after typing in “cd ” (with the space afterwards) to change directories. You can find your folder if you go by going to places→computer→file system→share→projects→sumner lab proj

3. Start 3dvisualizer with your data. There are two ways to do this. One is to put all the commands on the command line in the terminal window.

3dvisualizer -class ImageStack <path/header_file>

Another way to start 3dvisualizer is to type in “3<tab button> <drag in text file> -vislet sceneGraphViewer <drag in axes folder>” then press enter. Be sure to include the spaces when typing and dragging folders onto the terminal window.

The other way to start visualizer is to make an input file that contains all this information.

4. Once the 3dvisualizer is turned on, turn on the 3d glasses by pressing onto the button on the tracker until the light starts to flash. You can start manipulating your sample by using different tools on the main menu button.

  To use the revolver tool:
      -press on the trigger button, then go to main menu-> transformer -> revolver, then click on a second unassigned button
      -a window will pop up, have the laser pointing at the menu, then click on the trigger button
      -to check if the revolver tool is working, press down on the trigger button and numbers should appear in a circle formation
  To use the clipping plane (similar to cutting plane, but also cuts away isosurfaces as well) tool:
      -main menu->pointer->clipping plane
keckcaves/visualizer_quick_guide.txt · Last modified: 2012/06/28 10:50 by aphan28