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

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However, at the moment, it is still possible to run a (slightly outdated now) version of Fiji with Java 6.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
macOS
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 Your Fiji will become outdated over time, stuck on the final Java-6-compatible plugin versions.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.
macOS Download the 2015-Dec-22 Life-Line version of Fiji for macOS. 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
macOS
Linux

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

  • If you have not already done so: install Java 8 from java.com.
  • Do not enable the Java-8 update site, because (at the moment) it contains a mixture of core ImageJ and Fiji components.
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 Your ImageJ will become outdated over time, stuck on the final Java-6-compatible plugin versions.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
macOS
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.

Upgrading an old installation

If you have downloaded Fiji or ImageJ2 quite some time ago (before 2016), you probably have the Java 6 version (how do I find out?). So when you update, you will not receive the latest plugin releases anymore, as described above.



Alternately, you can simply download a new Fiji as described above.

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. So unfortunately, at the moment, there is no way to get a "latest and greatest plain ImageJ2" built on Java 8, but without Fiji components.

But later this year, we will migrate the latest Java-8 components back 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"). We only want to proceed with this migration once there is a mechanism in place to notify users that Java 8 is now required, without breaking existing installations.

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 with Java 7 or 8 on macOS.
    • 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 and ThreeDViewer plugins. But it will be a lot of work to rewrite all 3D Viewer functionality, so the ImageJ and Fiji teams are still exploring the best ways to proceed here.