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Installation

Fiji

One easy way to use SciJava Ops is within Fiji, using SciJava's Script Editor. Note that to use Fiji, you must use Java 11+. Please follow the instructions below carefully to ensure you receive the needed Java update.

Installing SciJava Ops

You can install SciJava Ops into Fiji by enabling the SciJava Ops update site, as described in the Update site tutorial.

  1. With Fiji open, navigate to Help → Update...
  2. Click Manage Update Sites
  3. In the Search bar at the top of the popup, search SciJava Ops
  4. Find the SciJava Ops row, and check the checkbox in the Active column.
  5. Click Apply and Close. You should see many items appear in the ImageJ Updater table.
  6. Click Apply Changes
  7. Note: launcher change Close and restart Fiji using the new launcher: fiji-[platform]. For example, if you were on 64-bit Windows your old (deprecated) launcher was ImageJ-win64.exe, and you would instead now use fiji-windows-x64.exe.
  8. Run Help → Update... a second time. Historically Fiji has shipped with Java 8, but a newer Java is required for SciJava Ops. You should get a dialog saying a new Java version is recommended, and asking if you'd like to update. Click OK to start the update. This download and extraction may take longer than a usual update.
  9. After receiving a notification that the Java update is complete you can close Fiji and restart one more time to take advantage of the new Java. Note: always use the new fiji- launcher going forward.
  10. After Fiji restarts, you can double-check the Java version - it should be 21 or newer.

At this point you can proceed with using SciJava Ops!

Troubleshooting

SciJava Ops uses a branch new launcher and updating logic to get access to new Java programming language features. These have not reached the main Fiji release yet and thus have not gone through community hardening yet, so errors may pop up.

If the following steps do not help resolve your situation, please report the issue on the ImageJ forum or Zulip.

The new fiji- launcher doesn't start

Double-check the Fiji.app/config/jaunch directory [Windows/Linux] or Fiji.app/Contents/MacOS. There should be a number of files including jvm.toml, fiji.toml, common.toml. If they aren't there, they may be stuck in the same path under the Fiji.app/update directory: you can manually copy them out to the base Fiji.app diretory, following the same subdirectory structure they had under /update/.

I did the new Java update but after restarting Fiji is not using Java 21

In your Fiji.app/config/jaunch directory you should have a file named fiji.cfg. If this file is not present but you instead have an ImageJ.cfg, first try renaming ImageJ.cfg → fiji.cfg and launch Fiji again. This is a potential bug that can arise due to the switching of the launchers.

If Java 21 is still not being used, look at the actual contents of the fiji.cfg file. This is a plain text file and can be edited in any text editor. It should be along the lines of:

jvm.app-configured=/path/to/downloaded/java

The right-hand side of this assignment should be a path to the location where Java 21 was downloaded. It will be in the form of Fiji.app/java/[platform/zulu21[...]jdk21[...]. Ensure that this path is valid and correct.

Other failures

We have tested these steps using freshly downloaded Fiji installations for each platform. Given the number of update sites and plugins available for Fiji, it is possible there are unforseen interactions. Thus, falling back to one of these fresh installs is a recommended starting point.