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

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However, at the moment, it is still possible to run a (slightly outdated now) version of Fiji with Java 6.

Here is breakdown of the 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.

This version 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 Your Fiji will become outdated over time, stuck on the final Java-6-compatible plugin versions.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.

This version 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 (descriptions coming soon)
ImageJ1 (descriptions coming soon)