RunImageJ module in Mac BUG

Hi guys!

First of all thank you very much for this wonderful piece of software. It’s been giving me many new insights.

I have been trying to use the Tubeness plugin without success, because I always get the message Unrecognized command: Tubeness in the Imagej call.

I’ve setup in cell profiler preferences the ImageJ pluginfolder to my fiji plugin folder

I’ve setup the ImageJ pluginfolder in Preferences to
where I have downloaded and copied the Tubeness 2.0 cited elsewhere in this forum

I am using the runimagej module with macro option, where I wrote the space after Tubeness
run("Tubeness ",“sigma=1.5000 use”);

Cant find it if I select Command and search for it.

Using Mac OS X 10.7.2 and everything else freshly downloaded from the internet.

What am I doing wrong?

Thanks in advance,


Hi Roberto,

Sadly, RunImageJ is not working on Mac, compiled or not. From what I understand, we can’t run Java AWT in same process as WX on Mac. Windows and Linux it runs fine. We are working on this, but it will likely have to wait until the next, major version of ImageJ is released.

So for now, the only thing I can suggest is to use Windows or Linux, sorry.


Hi David,

Thank you very much for your quick reply, and well, this is a tremendous relief to me. At least I’m not doing anything wrong, and there is a quick and dirty solution to it - switching the OS. It’s the downside of having a software run every OS, you can’t have everything. =)

Kind Regards,


Thanks for understanding! Indeed, an inordinate amount of our programming woes are interoperability issues. Glad the OS switch is feasible for you.

P.S. I added a bug on Github to alert others:

Hi all,
We’ve recently made changes to our Java / Python bridge to fix the problems that prevented us from running ImageJ on OS/X / Mac. If you need this functionality, you can try our trunk build ( for the Mac. There are a couple known problems in the trunk build, but it should be serviceable if you need the run_imagej functionality on that platform.