3D Viewer: User FAQs

Revision as of 01:35, 22 October 2019 by Bene (talk | contribs)

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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. Top

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:


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.


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


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. Top

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. Top

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. Top

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. Top

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. Top


What is the idea of a surface

Intuitively, the surface of an object is understood as the border between the object and the background. One common way to find a surface is to choose a threshold which divides object and background: Values above the threshold are assumed to belong to the object, values below are assumed to belong to the background. To construct a surface, an algorithm like the marching cubes algorithm can be utilized. Top

How to change the color, transparency... of a surface

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

How to change the isovalue of a surface

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

How to smooth a surface

In order to smooth the surface of a 3D object, select the object and click on ->Edit->Smooth surface.

You can also smooth all displayed surfaces by clicking on ->Edit->Smooth all surfaces Top

How to export surfaces

The displayed surfaces can be exported to files in different surface file formats. Currently supported is Wavefront (.obj) and Drawing Interchange Format (.dxf). Top


What are volumes/volume renderings?

A volume rendering generates the 3D effect by putting the slices of a stack one behind another, separated by a certain distance. To each pixel in each slice a transparency value is assigned, which depends on the pixel's brightness. Top

How to change the color, transparency, ... of a volume

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

How to edit volumes?

The 3D viewer offers the possibility to edit volumes. To crop volumes,

  1. Select an object by clicking on it.
  2. Use one of ImageJ's selection tools to draw a region of interest (ROI).
  3. Click on ->Edit->Fill selection to erase the volume which is covered

by the ROI. (Erasing means actually filling it with black). Top


What are orthoslices?

Orthoslices are three orthogonal slices through the volume. The three slices show one xy-plane, one xz-plane and one yz-plane. Top

How to change the color, transparency, ... of orthoslices

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

How to change the displayed slice

The position of the three slices can be changed. To do so, click on -> Edit -> Adjust slices. A dialog opens, which lets you adjust interactively the position of each of the three slices.

There exist also keyboard shortcuts to adjust the slices: hold one of the x, y, and z key pressed and use either the arrow keys or mouse scrolling to adjust the slices.

To hide a slice, hold one of the x, y or z key pressed and hit the 'space' bar. Top

How to hide a slice

See #How to change the displayed slice