Simplifying Fiji and plugin options

As a new Fiji user, I’m sometimes overwhelmed by the sheer number of choices, options and commands (there are over 900 of them in my system!), and would like to eliminate possibly unnecessary for me Plugin Menu options.

How does one go safely about customizing Fiji by eliminating certain (mostly Plugin menu) options while minimizing the risk of breaking the entire installation? Is there a way to move recently added plugins to the top of the Plugin dropdown menu, instead of having to hunt for them three screen heights down at the bottom of the menu?

Previously, there was a discussion on that topic here on the forum. I don’t know exactly what the outcome was, but you can read up on it here:

I guess, however, one remedy to your problem would be to use the Command Finder instead of going through the menu structure.


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Thanks, Stefan; I found that post, but the issue does not seem to have been resolved to anybody’s satisfaction. This may be a nonissue for power users, but is an unnecessary barrier for those like me, Fiji freshmen with more limited and focused needs.

Would some Plugin menu items vanish if I re(moved) their jars? I’m trying to be careful not to kill my installation.

That would be the way to go, @TG3. You can crawl through the plugins/ directory and look for unused plugins. To guide that process, you can use the Updater to check for dependencies between the plugin you want to remove and others. For an example take a look at this screenshot on the wiki page of the Updater:

You can see the dependencies of this library in the right panel at the bottom. Those should be fairly accurate for the plugins bundled with Fiji. Other update sites might ship jars for which some dependencies were (unintentionally) removed? Although this should rarely be the case…

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To add to @stelfrich’s answer: I would advise to always use the updater’s Uninstall functionality (and not remove jar files manually by just deleting them). This way you can be sure that Fiji remembers your decisions and doesn’t try to re-install the missing plugins upon the next update.


@TG3 I certainly agree. My personal long-term vision is to make ImageJ2 more modular, with the Updater allowing you to browse and install plugins as needed. We can still offer Fiji as the “batteries included” version of ImageJ, but quite a few people do not want all the batteries—they only want some of them. There have been numerous discussions in the past about this. It’s just that no one has time to work on improving the situation right now. I currently have several more urgent priorities, but as ImageJ2 continues to develop and stabilize, and as more and more update sites continue to be created, I expect that we will invest more effort into the tools for managing these extensions.

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I appreciate all the responses and advice I received so far. The Updater seems to be the way to prune my installation; however, many plugins have zero documentation on what they are supposed to do. I’m not complaining, just stating the fact hoping that future contributors will keep other users in mind when submitting. For now I’ll play it safe and make a copy of the entire list to be able to reinstall any removed plugin if it turns out to be something I should have. I should also add that I found Shortcuts to be very useful for my particular purpose.

Thanks again for your help!

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Simply get used to hitting L then typing name of the thing you want. Drop the mouse. Use the command launcher!
You will find your problem disappears at that point. It did for me!


Thanks, I will, although using Shortcuts has already helped. So many options, so little time…