ImageJ plugin help please!

Hi All. First time posting and desperate. I recently updated to macOS Catalina (Version 10.15.2) and am having issues with ImageJ and FIJI.

  1. While I can see plugins when I open ImageJ, many plugins I previous downloaded and have used for years are no longer there despite still being within the plugin folder. One example is StackReg. It seems they are _.jar and and not _.class? No idea what this means or how to remedy. But I really need to recovery StackReg within either ImageJ or FIJI to finalize a few quants for a publication I am wrapping up.

  2. I also downloaded and was attempting to move towards FIJI, as I thought it may have my plugins already preloaded. But when I open it, it states my ImageJ is read only and can not be loaded. ImageJ is not a ReadOnly.

Is anyone able to help? I live in NJ and work at Rutgers. Would love to recover my beloved ImageJ plugin’s ASAP.

Thank you to anyone with time and help to offer.


Hi @dibonavl

if you download a fresh new Fiji and unpack it to a folder where you have write access, it should be possible to install plugins. Start it, go to the menu “Help > Update” and click on the “Manage Update sites” button. In the list of update sites, activate BIG-EPFL. Restart Fiji and Stackreg should be there! If it doesn’t work, please send us screenshots so that we can have a look at error messages and the folder where your Fiji is :wink:

Which other plugins are missing?


Hi @haesleinhuepf. Thank you most kindly for replying!!!
I followed your instructions exactly and the error messages are on the right. I don’t understand why not states ImageJ is a read only. Here is the ImageJ folder from my applications. I can not find a FIJI folder. When I was reading online it stated there is no FIJI folder or something to that extent since it runs off of ImageJ.
I am computer literate, but basic. So these issues and troubleshooting in codes are a tad over my head. I sincerely appreciate your time and help!

When I select ok (from the first screenshot of running the updater, this is the resulting error message. I have seriously angered the ImageJ/FIJI computer lords.

Hey @dibonavl,

ok, two things: If you right-click on, an select “Show Package Contents”, the folder will open (it is in fact a folder). In there are subfolders such as jars and plugins. This is the place where the plugins should be - not next to; inside

Furthermore, have you tried my instructions I posted above? In your screenshot it says, Fiji is in /private/var/… put it on your Desktop instead :wink:

It’s worth a try! :wink:


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Good news first. I got StackReg back into ImageJ and FIJI by adding inside the apps. Thank you for that help. So, my quants can resume!

Now, I did move both ImageJ and FIJI to my desktop. And I did go through the steps you suggested and activated BIG-EPFL. But I still am getting error messages. I don’t know if it really matters now that the plugins I need are available through ImageJ. But it is annoying that FIJI states it ImageJ is a read only and can not update ImageJ. Some screen shots to show what I’m seeing.

This is what shows after I activate BIG-EPFL.

And clicking apply changes shows this.

Are any of these messages overly troubling? Should I just be happy with my StackReg back in action and go on my quantifying ways :smile:

Thank you again for the expertise and help. I sincerely appreciate your time.

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Could you please download a fresh Fiji and put it on your desktop directly? I suspect something access-related happened to your Fiji, while it was in the other location…

Or related question: When you download Fiji, it comes as zip file, right? I assume you unpacked this file? I’m asking because on of the screenshots above shows a ImageJ.exe which is not in the archive I just downloaded for macos. I’m wondering where this file comes from…

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