Missing plugins menu item



I have an ImageJ update site called quantixed which puts a folder in Fiji.app/plugins. It contains a few macros that normally appear under a menu item in Plugins called quantixed (the name of the folder in plugins). This has been working fine until a recent FIJI update (I think) which has removed the menu item. The folder and files are all still there in Fiji.app/plugins and are updating correctly from the update site but are not showing in the menu.

Steps to reproduce

  • A user told me the menu item has disappeared for them and I can reproduce this on a clean FIJI install.
  • An old FIJI install freshly subscribed to quantixed has the item showing correctly in Plugins.
    I subscribed to FiloQuant which has a similar structure to quantixed and this is also missing so I don’t think the problem is specific to my update site.

Is this a known issue since a recent update?
Please feel free to tell me a better way to structure files on my update site.

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Hi @quantixed,

thanks for reporting, I can reproduce the issue with an up-to-date Fiji.

I’d consider this a bug, but don’t know (yet) what’s causing it.

As a workaround, you can put all your scripts in a subfolder of ./Fiji.app/scripts/. For example, your folder quantixed should be in:


to appear in the menu as Plugins > quantixed (mind the exact spelling and capitalization).


Hi @quantixed and @imagejan,

I tried to reproduce the issue with a fresh fiji and activated the quantixed update site. I found the quantixed sub-menu at the very bottom:

Is it possible that the sub-menu is still there and just moved to the end of the menu? Could you please check?



Hi @haesleinhuepf

That’s the normal location for the sub-menu, but it is definitely missing in my FIJI install. I have only tested on mac though, looks as though it is still working on your OS.


I see. So I can confirm it works on Windows 10 and Fedora linux…

@imagejan: do you by chance know which module/class builds up the ImageJ menu?


There’s some code in imagej-legacy that builds the menu, but I don’t remember which class exactly :frowning:

And scripts in ./plugins/ should actually be recognized by ImageJ 1.x itself. What puzzles me is that scripts in ./scripts/ work just fine, because that’s some code in imagej-legacy.
We’ll have to investigate…

UPDATE: It’s possible that the issue is in LegacyService, as this Groovy script doesn’t list scripts from the ./plugins/ directory (again, tested only on Mac):

#@ LegacyService legacy

scriptlist = legacy.getScriptsAndNonLegacyCommands()

println scriptlist.size() 

scriptlist.each {
	println it.getKey()


UPDATE2: I don’t think it’s in the imagej-legacy component, and it’s actually not a problem of populating the menus (as script from ./scripts/ work just fine), but rather a problem that scripts are not discovered at startup. Calling scriptService.getScripts() shows that they’re not registered:

#@ ScriptService scripts

println scripts.getScripts().size()

scripts.getScripts().each {
	println it



Try to rename your plugin to quantixed_.jar


Dear all,
this is a VERY big issue.
After some updates (I don’t know exactly which one) on MacOS users plugins disappear.
I am now facing some users (and myself too) of the campus with this problems:
in few words the plugins (python and ijm all with “_” in the name) plugins are disappeared.
By now I am keeping an old version where plugins are visible.

I have really no idea what is causing that and how to fix it.
Are someone of the community/developers/head of Fiji taking care of it?

THanks a lot,


@ctrueden is currently working on it, see e.g. this commit.

As I mentioned above, you can move all script files from ./plugins into ./scripts/Plugins and they will be discovered just fine.


It gets weirder and weirder.

Indeed, the above linked commit in imagej-legacy avoids the issue. However, I also found that the issue is avoided in SciJava Common as follows:

So the fix is likely to be on the scijava-common side. Still digging, until I understand more fully what is going on. (As an aside: I also tried writing a regression test in imagej-legacy to replicate the issue, but was unable to do so. The test I tried to write would always successfully discover all the scripts, whether executed from imagej-legacy or imagej.)

Edit: All right, I believe I have a better fix now:

A regression test is still needed before the branch can be merged.

Would interested parties please test the fix-script-discovery branch of scijava-common and let us know if the issue is resolved?


Indeed, this fixes the issue for me on MacOSX. Thanks a lot for that thorough investigation, @ctrueden!

Note that I had to change the order of services in ContextCreationTest to make the test pass (when building on Windows):

From e25dabf15f9ce1c80ce23e394c17a6850015bd7e Mon Sep 17 00:00:00 2001
From: Jan Eglinger <jan.eglinger@fmi.ch>
Date: Wed, 25 Jul 2018 09:32:06 +0200
Subject: [PATCH] Fix service order

 src/test/java/org/scijava/ContextCreationTest.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/test/java/org/scijava/ContextCreationTest.java b/src/test/java/org/scijava/ContextCreationTest.java
index 9c6e15c8..0be58b78 100644
--- a/src/test/java/org/scijava/ContextCreationTest.java
+++ b/src/test/java/org/scijava/ContextCreationTest.java
@@ -87,7 +87,6 @@ public class ContextCreationTest {
 	public void testFull() {
 		final Class<?>[] expected =
 			{ org.scijava.event.DefaultEventService.class,
-				org.scijava.script.DefaultScriptService.class,
@@ -113,6 +112,7 @@ public class ContextCreationTest {
+				org.scijava.script.DefaultScriptService.class,

Unrelatedly, I had noticed earlier that on Windows (Git Bash), I would have to change assertTrue to assertFalse in FileHandleTest to make all tests pass:

I guess that’s a platform-specific problem, but I never got around to file an issue or PR for that.


Great, I merged it.

Thanks for the heads up; I fixed that oversight before merging.

Thanks for the report. I committed a workaround:

I will cut a new scijava-common and upload to the Java-8 update site before week’s end.

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