3D Viewer: User FAQs

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(Return to the main 3D Viewer page)


1. Basic Usage

How to display a stack

After you have started the 3D viewer, click on '->File->Add content'. A dialog window opens, asking for some information:

  • Image: The image which should be displayed in the viewer. The user can select from a list of all open images.
  • Name: A name for the 3D object. The default is the image title.
  • Display as: Stacks can be displayed as volume renderings, orthoslices, surfaces or surface plots.
  • Color: The color of the 3D object.
  • Threshold: For surfaces, this is the isovalue of the surface. For all other display modes, this value is the lower threshold of displayed values.
  • Resampling factor: Large images require downsampling before displaying, to be rendered interactively. A value of 2 means here that the image is downsampled by a factor of 2 in x-, y- and z-direction.
  • Channels: If displaying color images, this specifies the color channels which are to be displayed.

After clicking OK, the 3D object appears in the viewer window.


How to interact with the viewer (rotate, shift, zoom)

The user can rotate, translate and zoom in the 3D space: Two sorts of trans- formations are distinguished:

1. Transformation of the view:

Rotation:

Select the 'Hand' tool in ImageJ's tool bar. If no 3D object is selected, dragging with the left mouse button rotates the view around the universe center.

Translation:

Dragging while pressing the 'Shift' key shifts the view.

Zooming:

Zooming is done by selecting the 'Glas' tool in ImageJ's tool bar and drag with the left mouse button. On many platforms, it is alternatively possible to scroll (while the 'Hand' tool is selected) for zooming.

2. Transformation of objects:

Individual objects can be transformed with the same key/mouse combinations. To transform a specific object, that object needs to be selected. An object is selected by a single left mouse click. Selection is indicated by a red bounding box.


How to change the color, transparency... of a 3D object

Color, transparency, threshold and displayed channels of color images are so-called attributes of 3D objects. These attributes have the following meaning:

  • Color: The color of the 3D object. If 'None' is selected, the color is taken from the stack image.
  • Transparency: The transparency of the 3D object: A value of 0 means fully transparent, a value of 1 means fully opaque.
  • Threshold: In case of surfaces, the threshold specifies the isovalue of the surface. Otherwise, it specifies the lower threshold of displayed pixels.
  • Channels: In color images, the channels attribute specifies the channels to be displayed. In greyscale images, this attribute has no effect.

The attributes can be changed by

  1. Select the corresponding object by clicking on it
  2. Click on -> Edit -> Attributes and select the attribute you want to
  change.


How to make animations and movie recordings

To animate the view, click on ->View->Start animation. The view begins immediately to rotate around the y-axis. If you now want to record such an animation, click on ->View->Start recording. The animation is now recorded for one full 360° rotation. The result is displayed in a stack.

If you want to include the recording in a presentation, save it via ImageJ's Save as AVI function. You can incorporate the resulting movie file in powerpoint presentations.

To stop an animation, click on ->View->Stop animation.


How to reset the view

You can reset the 3D universe to its initial view by clicking on ->View->Reset View. This resets the view.

Note however, that this does not change the transformation of individual 3D objects. To reset them, too, select each object and click on ->Transformation->Reset transformation.


How to hide the coordinate system

There are two types of coordinate systems: One global coordinate system, which indicates the origin of the universe, and one local coordinate system for each object.

For hiding the global coordinate system, have a look at "How to general view settings"

For hiding the local coordinate system, select the object and click on ->Edit->Hide/Show and disable 'Show coordinate system'.

See "How to general view settings" for how you can avoid to show local coordinate systems in general.


How to change the background color

To change the background color of the 3D world, click on ->View->Change background color. A dialog opens, which lets you interactively adjust the background color.

To use the current background color by default, see "How to change general view settings".


2. Surfaces