Saved macro not appearing in Plugins menu


I’ve seen several posts regarding this topic, but not have resolved my issue.

the latest discussion I found was here: Intalling a working macro in Fiji

Instructions in the wiki aren’t helping either. . .

“Simply save your macro in a “Plugins” subfolder of ./ (e.g. ./, and it will appear in the respective menu (e.g. Plugins > MyScripts > My Macro) upon restart of Fiji.”

I’m able to load a macro into the menu and call on it during a session, but upon restarting Fiji it disappears.

Any help would be appreciated!

Hi @TomJ

If your macro is in the ImageJ macro language, can you paste your macro into the bottom of the macros/StartupMacros.fiji.ijm file?

If you take a look at the other macros in the file, you will see you need to add to the start and end:

macro "My Macro" {


Best wishes

Hi Cameron,

YES! This worked - thank you!!

While it works. . .it certainly feels like an awkward work-around. At the moment though, I’m happy for it!

Dear @TomJ,

How exactly are you “loading the macro into the menu”?

They are working for me (I have just done a quick check). Which version of ImageJ/Fiji are you running (i.e. what does the status bar say right after the start)?


For anyone who finds this topic:

While this approach is certainly possible, I would advise to be very careful with it: StartupMacros.fiji.ijm is served from the Fiji update site and might change in future. If this happens, your edited StartupMacros.fiji.ijm will be marked as locally modified without a straightforward way to merge your changes into the new version. So you will either have to merge your changes into the new versions manually or overwrite your changes with the next update (which will not happen automatically).

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Hi Stefan,

I’m using 2.0.0 - rc64. . .and just did an update today. Still no success.

One method of loading I’ve tried is to select “Install” from the Plugins menu: image

This works during the session, and allows me to select my macro from the Macro menu. After restarting, my macro disappears from the menu.

I’ve also tried following the wiki instructions; “Simply save your macro in a “Plugins” subfolder of ./ (e.g. ./, and it will appear in the respective menu (e.g. Plugins > MyScripts > My Macro) upon restart of Fiji.” and this does nothing at all.

Hi Stefan, thank you for the wise warning! This makes sense.

Hi @TomJ,

One other requirement: the filename has to have an underscore in it.

See [emphasis added]:

The macro will be automatically installed … in the Plugins menu when you restart ImageJ, assuming the file name has an underscore in it and the macro was saved in the plugins folder or a subfolder.

Hope this helps.


Thank you Theresa. The underscore was the solution!

The instructions at the link you provided may be out of date though - using the “.txt” extension did NOT work. I saved with an “.ijm” extension.