Error with runilastic plugin on CellProfiler

[DrAwesome32]

Hoping for a little help here. This is a bit outside my expertise. I'm trying to run the Ilastic plugin in CellProfiler to assist with IHC quantitation. I have set up a profile in Ilastic and saved it. I have tried running runilastic in Docker and downloaded both the current version and v4.49 and I keep getting this error. When I try running ilastic as a local program, it says it can't find the app.
I'm running all this on MacOS 26.3.1 and CellProfiler 4.2.6
Can anyone help me fix this error.

[bethac07]

Can you try both renaming your ilastik project to not have spaces in the file name and setting your CellProfiler output directory to folders not containing spaces? I'm not certain that's the issue, but both are things that can often cause problems.

[DrAwesome32]

Can you try both renaming your ilastik project to not have spaces in the file name and setting your CellProfiler output directory to folders not containing spaces? I'm not certain that's the issue, but both are things that can often cause problems.

Thank you. I did try both of those options and I still get the same error.

[bethac07]

Thanks! Since you're on Windows, if you can show the terminal output for the run after you'd adjusted both things, that would help with the debugging process. Sorry for the issues!

[DrAwesome32]

Here is the error after naming the folder containing the Project file "test" and the project file "pTau.ilp"
Error while processing Runilastik:
(Worker) CalledProcessError: Command '['/usr/local/bin/docker', 'run', '--rm', '-v', '/Users/brianspencer/.cellprofiler_temp/23b02e06-0ba4-4c36-8703-6f649d3c5167:/data', '-v', '/Users/brianspencer/Documents/Test:/model', 'biocontainers/ilastik:1.4.0_cv2', '/opt/ilastik-1.4.0-Linux/run_ilastik.sh', '--headless', '--project', '/model/pTau.ilp', '--output_format', 'hdf5', '--export_source', 'Probabilities', '--output_filename_format', '/data/tmpg5u0x87e.h5', '/data/tmpkfkq18rd.h5']' returned non-zero exit status 1.

Do you want to stop processing?

[bethac07]

Would you be able to copy in more of the trace error (more preferred) or show a screenshot (less preferred but still helpful) of the terminal window?

For example, when I induce an error in my RunIlastik (in my case, by not turning Docker on while using Docker mode), my terminal shows the below (and then a bunch more, I've truncated it for the example here).

failed to connect to the docker API at unix:///Users/bcimini/.docker/run/docker.sock; check if the path is correct and if the daemon is running: dial unix /Users/bcimini/.docker/run/docker.sock: connect: no such file or directory
--- Logging error ---
Traceback (most recent call last):
  File "/Users/bcimini/Documents/GitHub/CellProfiler/CellProfiler-plugins/active_plugins/runilastik.py", line 284, in run
    subprocess.check_call(cmd)
  File "/opt/homebrew/Caskroom/mambaforge/base/envs/cellprofiler_426/lib/python3.8/subprocess.py", line 364, in check_call
    raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/usr/local/bin/docker', 'run', '--rm', '-v', '/Users/bcimini/Desktop/test/PotC/output/testing/20260505/.cellprofiler_temp/19352d20-a9f6-4cbd-b6e2-cee3e25060dd:/data', '-v', '/Users/bcimini/Desktop:/model', 'biocontainers/ilastik:1.4.0_cv2', '/opt/ilastik-1.4.0-Linux/run_ilastik.sh', '--headless', '--project', '/model/PCOC.ilp', '--output_format', 'hdf5', '--export_source', 'Probabilities', '--output_filename_format', '/data/tmpfr1knvzy.h5', '/data/tmp096mv9pb.h5']' returned non-zero exit status 1.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):