General Controls for Jim's 3-D Display

At the top of the Jim's 3-D display are the general controls that affect the objects that are loaded into the display.

The effect of each of these is described below.

Lighting. The 3-D display has two light sources: a uniform ambient light and a directional light. You can change the brightness of each of these light sources independently using the lighting level spinners:
Light levels can be set between 0 (light off) and 1 (brightest).
The directional light source is situated behind you (the viewer), but you can set the position of the light source (left-right, top-bottom) using the light direction gadget:
The white spot represents the light source. To change its position, click within the black square to set the light source to that position. You can also drag the light source with the mouse.
Cut plane and cut out. These are used to change the position of the orthogonal planes, and also the position and the cut-out in rendered surfaces. Cutouts are used to reveal the interior contents of the rendered surfaces.
Move the sliders to change the position of the orthogonal planes:
Move the:
- X slider to change the plane position in the image column direction.
- Y slider to change the plane position in the image row direction.
- Z slider to change the plane position in the image slice direction.
Click the cut out buttons to change which segment of the image is cutout when you are displaying a surface, and the check-box is selected:
Click the:
- X+ cut out the segment of the image for columns greater than the plane position.
- X- cut out the segment of the image for columns less than the plane position.
- Y+ cut out the segment of the image for rows greater than the plane position.
- Y- cut out the segment of the image for rows less than the plane position.
- Z+ cut out the segment of the image for slices greater than the plane position.
- Z- cut out the segment of the image for slices less than the plane position.
The effect of changing the cutout is shown below.
3-D display showing orthogonal planes and an iso-surface with cutouts.

Cutout X+ Y+ Z+ Cutout X+ Y- Z+
Flip. Jim's 3-D display assumes that the 3-dimensional images that you display have a standard radiological orientation that forms a right-handed coordinate system. If you try to load an image that has a left-handed coordinate system, then you will see a warning message pop up:
Click on the button to flip the z-coordinate so that the image is displayed with the correct orientation in space. You can suppress this message for the rest of your session using Jim by selecting the check-box.
Note: you cannot rely on Jim displaying images with the correct spatial orientation. Xinapse Systems makes no guarantees about the correctness of the orientation, and the view you see cannot be relied upon to be true to the patient left-right/anterior-posterior or superior/inferior orientations.
If you independently verify that the displayed orientation is incorrect, you can make a manual correction by flipping any of the axes by selecting the appropriate check-box:
Bounding box. You can show the outline of a box that just encloses the displayed image data by selecting the check-box.
Note: if you have more than one 3-D object displayed, with different fields of view for each, the displayed bounding box will be large enough to contain the all of the displayed objects.
Show axes. You can show the show the axis system that the 3-D display uses by selecting the check-box.
The origin of the coordinate system is at the centre of the 3-D image pixel matrix. The x-coordinate increases with increasing column number; the y-coordinate increases with increasing row number; and the z-coordinate increases with increasing slice number.

3-D display showing orthogonal planes and an iso-surface with cutouts.

Cutout X+ Y+ Z+	Cutout X+ Y- Z+

Creating Screen Shots

You can create screen shot pictures for inclusion into presentations, reports and Web pages. The screen shot image shows exactly what is shown in the 3-D image display window.

Compose the image in the display to appear as you want it, then select "Screen shot ..." from the File menu:

A dialog will pop up, allowing you to choose the format for the screen shot picture.

You will then be asked to select a folder and file name for the screen capture image.

Changing the View Position

You can rotate, zoom and scroll the view of the data using the computer mouse.

Click and hold down the left mouse button, and move the mouse to rotate the image.
Click and hold down the middle mouse button, and move the mouse (or use the mouse scroll wheel) to zoom in and out on the image. Pulling the scroll wheel towards you zooms in, pushing it away zooms out. (You can reverse the scroll wheel behaviour in the user Preferences).
Click and hold down the right mouse button, and move the mouse to pan the image.

To reset the view of the data to a standard view, click the

button.

Using the left mouse button allows you to freely rotate the image to any orientation. However, it is easy to become disorientation and hard to get exactly the view you want. To make life easier, you can constrain the rotation by selecting the check-box. Then select the axis about which you want to constrain the rotation (x- y- or z-axis). Then, when you rotate the image, only certain types of rotation will be allowed, keeping the selected axis constrained to a fixed plane in space.

If you want a particular, reproducible view position, you can set an exact view location using by selecting Set view ... from the View menu. This brings up the dialog below:

Using this, you can set:

The distance from the viewer's eye to the origin.
The longitude and latitude of the viewer's eye location.

By stepping through various angles, it is possible to create a series of screen shots, that when played in sequence, give an impression of motion around the 3-D displayed objects. The animated GIF movie below was created by making a series of GIF screen shots, before putting them together as an animated GIF. However, this process is rather tedious.

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