Adding Orthogonal Planes to Jim's 3-D Display

To add a set of orthogonal planes to the 3-D display, select Load Orthogonal Planes ... from the File menu of the 3-D Viewer:

A dialog will now appear, from which you can select the image from which the orthogonal planes will be extracted and displayed.

First, select the image you want to work with by clicking on the

icon, by typing in the folder (directory) and file name of the image, or by pressing the right mouse button and selecting from the menu of recently-used images.

This will automatically generate and display a set of three orthogonal planes You can now make the following adjustments to change how the orthogonal planes are displayed.

Contrast settings. Set the brightness and contrast for the orthogonal planes using the slider just as you would for an image in Jim's main display.
Click the button to set the brightness/contrast automatically.

Background transparency. You can make the "background" of low-intensity pixels completely transparent, regardless of the transparency of the planes as a whole by selecting the

check-box. All pixels with an intensity below that of the the background threshold will be considered to be "background" and set completely transparent. Change the level of what is considered to be "background" using the background threshold slider:

In the case above, all pixels with intensity of 143 or lower will be counted as background, and invisible in the 3-D Viewer.

The effect of having a transparent background is illustrated in the figure below.
Orthogonal planes with opaque and transparent backgrounds. All pixels with an intensity below the background threshold are completely transparent.

Opaque background Transparent background

Plane opacity. The plane opacity has a value between 0 (completely transparent) and 1 (completely opaque). Change the opacity using the opacity slider.
Colour mapping. Set the colour mapping just as you would for an image in Jim's main display by selecting the colour mapping from the View menu.

Orthogonal planes with opaque and transparent backgrounds. All pixels with an intensity below the background threshold are completely transparent.

Opaque background	Transparent background

You can change the position of the orthogonal planes as described in the section about general controls.

If you click the button, the orthogonal planes will be removed from the 3-D viewer.

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