ImageJ module problem on MacBook Pro


Hello, I found CellProfiler a few days ago and am working through the tutorials on your website. I have reached the ‘Sequencing RNA molecules in situ combining CellProfiler with ImageJ plugins’ and am getting the following error when I try to run the imageJ modules in test mode:-

Traceback (most recent call last):
File “/Applications/”, line 2826, in do_step
File “/Applications/”, line 2067, in run_module
File “/Applications/”, line 697, in run
File “/Applications/”, line 802, in do_imagej
File “/Applications/”, line 104, in run_batch_macro
File “/Applications/”, line 62, in
File “/Applications/”, line 148, in __call
File “/Applications/”, line 885, in call
File “/Applications/”, line 852, in fn
JavaException: Macro canceled

I am using a MacBook Pro running El Capitan (10.11.5). I have been into the CellProfiler preferences to make sure the path to the imagej plugin folder is correct. I’m now a bit stuck, I have had a good look through this forum, but I can’t find an answer that helps me. Would you be able to point me in the right direction? Thank you.

Background removal and rolling ball algorithm

RunImageJ unfortunately doesn’t work in CP 2.2 and support for it is being removed in future releases. If you need to run that pipeline you can download a legacy version of CP (2.1.1) but if you’re just trying to test things out you can just bypass that tutorial.


Thanks for getting back to me so quickly. It’s a shame that ImageJ is no longer supported, that seemed a really good feature. It hasn’t put me off though! I really like what I have seen so far of CellProfiler.


Glad to hear you like it!



I wonder if the same problem still occurs in the current version due to the same reason?


Yes, RunImageJ does not work in anything after 2.1.1. We hope to restore the functionality some day (see link herein) but if you want to use that module 2.1.1 is currently your most up-to-date option.