3D Viewer

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3D Viewer (ImageJ)
Author Benjamin Schmid, Albert Cardona, Mark Longair, Johannes Schindelin
Maintainer
File [1]
Source on GitHub
Initial release April 2007
Latest version January 2013
Development status beta
Category Visualization
Website http://3dviewer.neurofly.de

Purpose

This plugin offers hardware-accelerated visualization possibilities for image stacks. Stacks can be displayed as texture-based volume renderings, surfaces or orthoslices.

3D Viewer overview.png


Screencasts

There is a demo screencast (~15 min, 8 MB, FLV format) available, showing many of the features of the 3D viewer. It has been transcoded for this wiki to meet the size and codec constraints, the original file is available on the old 3D Viewer website as an AVI (60 MB)

Beyond this, the original homepage provides a lot more screencasts, covering the following topics:

  • Display stacks
  • Rendering modes and attributes
  • Adjusting the transfer functions
  • Editing volumes
  • Point lists
  • Landmark-based registration
  • Transformations
  • 3D Content in PDFs

For developers

A lot of functions of the 3D Viewer are macro-recordable. However, if that is not enough (or if the function is not recorded properly), it is better to write a plugin. In the latter case no macros should be called from Java, as that would limit the code to work with the currently active 3D Viewer (even if the user clicked somewhere else).

This code snippet should get you started:

Image3DUniverse univ = new Image3DUniverse();
univ.show();
univ.addMesh(yourImagePlus, null, "somename", 50, new boolean[] {true, true, true}, 2);
...

Until everything is migrated to this wiki, the original website provides the full 3D Viewer developer documentation.

Javadocs

The Fiji Javadocs povide detailed information about the 3D Viewer API

FAQ

The 3D Viewer opens a window saying An unexpected exception occurred.

If in the same window, it also says:

java.lang.NullPointerException:Canvas3D: null GraphicsConfiguration

the reason is most likely that your graphics setup does not have any hardware 3D acceleration. This can happen e.g. when you run ImageJ via a remote X11 connection (3D acceleration works only when the graphics are displayed on the same machine as the program runs).

Unfortunately, there is not workaround/fix for this situation yet, except to use ImageJ locally when you want to use the 3D Viewer.

Problem with Intel graphics cards

There is a known problem with older Windows drivers for some Intel graphics cards. Usually, this is fixed by installing new drivers. If you would like to help make ImageJ nicer by detecting faulty driver versions, please contact us.

The 3D Viewer simply crashes

Unfortunately, there are quite a large number of possible reasons. Please help us by debugging the issues and contacting us with the information. You can also report a bug, which will provide a lot of additional, potentially useful information.

Only a gray rectangle is shown by the 3D Viewer

As with 3D Viewer crashes, there are quite a large number of possible reasons. Please help us by debugging the issues and contacting us with the information. You can also report a bug, which will provide a lot of addidtional, potentially useful information.