Table of Contents:

• Creating a PVO File
• Opening a PVO File
• Navigating the View
• Selecting Model Resolution
• Changing Scene Colors
• Changing the Grid Step
• Additional Settings
• License Terms

PView uses as input a file in pvo format. To create a new pvo file select Create New from the File Menu. This will bring up the Create New PVO File dialog shown below.

Start by selecting the location of the stack you would like to visualize. Images in the the stack must be named according to their Z order using a [prefix]n[postfix].tif notation. Where prefix and postfix are optional and n is the integer indicating the position of the individual stack. For example m37.tif is a valid name.

Then select the location where you want the output to be saved. This must be a empty location. You can always create a new folder by typing its path in the destination box.

You should also set the voxel dimensions. By default these are set to 1.0,1.0,1.0 but you should use the actual sampling dimensions of your data to preserve the aspect ratio of the object. Also the grid sizing is done according to voxel size so using the correct values will allow you to estimate distances when viewing your data.

Finally the surface threshold must be set before you can continue. The threshold must be selected to be the lowest gray scale value that is considered to be part of the object. This applies to Fluorescent CLSM data, where the object is brighter than the background. You can estimate the correct threshold value by looking at maximal projections in an image editing program that has a contour tracing filter.

Once you are finished select OK to start the pvo assembly process.

To open a pvo file select Open from the File menu. Using the Open File dialog navigate to the location where you have created your pvo file and select the file with the pvo extension. This file is named out.pvo by default. Depending on the size of the file opening the pvo file may take a few seconds.

To close a pvo file just select Close from the File menu.

Once the pvo file is opened, the location of the view will be initialized to the polygon closest to the front. To move the position of the camera you use the following keys as navigation commands:

• Press W to move forward
• Press S to move backwards
• Press D to move right
• Press A to move left
• Press the Left Arrow to rotate left
• Press the Right Arrow to rotate left
• Press the Up Arrow to increase the pitch
• Press the Down Arrow to decrease the pitch
• Press the Space Bar to stop movement
• Press R to reset the view to the original position

By default pview will attemp to dynamically adjust the distance function used to select the correct Level of Detail (LOD). In order to force pview to display a specific LOD for the entire model you may use the number keys in your keyboard. You may use numbers from 1 to 9 to select from highest resolution to lowest respectively. To revert back to dynamic selection use the 0 key.

Note that you must use the number keys above the letters on your keyboard, not the numeric keypad.

To change the colors used for rendering the scene select Colors from the Settings menu. This will bring up the Scene Colors dialog (shown below). From here you can click on the change buttons to set any of the colors using the standard Windows color dialog.

To change the spacing between cells in the grid displayed in the view select Grid Step from the Settings menu. This will bring the Grid Step dialog (shown below). Here just type the desired distance using the same units provided to the pmake utility for the voxel dimensions and click OK.

From the Settings menu you can make the following changes to the view:

1. Check or uncheck the Show Grid menu item to show or hide the grid from the view.
2. Check or uncheck the Use Antialiasing menu to instruct the program to use smooth lines for grid and wireframe of object.
3. Check or uncheck Use Wireframe to draw the model as wireframe or as a solid.

The author of this software grants to any individual or organization the right to use and to make an unlimited number of copies of this software. You may not decompile, disassemble, reverse engineer, or modify the software. This software cannot be sold, redistributed or incorporated into commercial software.

The author of this software accepts no responsibility for damages resulting from the use of this software and makes no representation, either express or implied, including but not limited to, any implied warranty of merchantability or fitness for a particular purpose. This software is provided as is, and the user assumes all risks when using it.