2016-05-10 - ImageJ HOWTO - Java 8, Java 6, Java 3D

Revision as of 17:48, 11 May 2016 by Rueden (talk | contribs)

ImageJ2 (and hence also Fiji) is currently in the midst of a transition to Java 8.

However, at the moment, it is still possible to run a (slightly outdated now) version of Fiji with Java 6.

Current recommendations and possibilities

Flavor Java
version
Platforms Installation Updates Java 3D
Fiji Java 8

Windows
OS X
Linux

Recommended.

Download the newest Fiji for your platform. It comes bundled with Java 8, with the Java-8 update site enabled.

Run Help › Update... to update to the latest version of ImageJ core and Fiji components. This version of Fiji comes bundled with Java 3D 1.6. The 3D Viewer works out of the box, though there are still some bugs.
Java 6

Windows
Linux

Download the 2015-Dec-22 Life-Line version of Fiji for your platform. It comes bundled with Java 6, with the Java-8 update site disabled. Run Help › Update... to update to the latest Java-6-compatible version. Your Fiji will become outdated over time, stuck on the final Java-6-compatible plugin versions. Run Plugins › 3D Viewer to trigger installation of Java 3D 1.5 if you need 3D viz.
OS X Download the 2015-Dec-22 Life-Line version of Fiji for OS X. It is distributed without Java, so you must install Apple Java 6 on your system.
  • If you have Java 7 and/or Java 8 installed, uninstall them—or else ImageJ will not use your Java 6 installation.
  • Afterwards, verify that Fiji is using Java 6.
ImageJ2 Java 8

Windows
OS X
Linux

Download the newest ImageJ for your platform. It comes bundled with Java 8, but without the Java-8 update site enabled.

Run Help › Update... to update to the latest Java-6-compatible version. Your ImageJ will become outdated over time, stuck on the final Java-6-compatible plugin versions. The 3D Viewer is not bundled with "plain" ImageJ2 (yet). It is (for now) part of the Fiji update site.
Java 6

Windows
OS X
Linux

It is possible to set up a "plain" ImageJ2 with Java 6, but not recommended:
  • Set up Fiji + Java 6 as described above.
  • Disable the Fiji update site.
  • Restart ImageJ.
  • Delete all Fiji-specific files using the updater's Advanced mode, View "Local only files" and deleting them all.
ImageJ1 See the ImageJ 1.x downloads page for instructions.

About the Java-8 update site

Right now, the Java-8 update site includes the latest Java-8 versions of all core ImageJ and Fiji components. Later, we will migrate these components to the core ImageJ and Fiji update sites, respectively, so that users can choose between "plain" ImageJ2 (lighter weight without "plugin bloat") and Fiji (with "more parts on the table").

About Java 3D

  • Java 3D 1.6 requires Java 7 or newer. Hence, we ship it on the Java-8 update site only.
  • Java 3D 1.5 works with Java 6, but:
    • It has a restrictive license.
    • It does not work Java 7 or 8 on OS X.
    • It does not work with Java 8 (or 7?) on some Windows systems.

Please be aware that Java 3D is essentially a dead technology. The future of 3D visualization in ImageJ is the ClearVolume plugin. But we still need to do some work to rebuild the 3D Viewer on top of ClearVolume.