Errors executing CellProfiler

Hello everyone,

I'm trying to use CellProfiler within Knime. After some difficulties I downloaded the example workflow 'cellprofiler_human' and tried to execute it. The latest version of CellProfiler is installed but Knime still shows some error messages in its console and doesn't seem to run the pipeline.

Here the messages:

Usage: CellProfiler.exe [options] [<output-file>])
                where <output-file> is the optional filename for the output file of
                            measurements when running headless.
                
CellProfiler.exe: error: no such option: --knime-bridge-address

 

Thanks for any help,

Rufus

Hi Rufus,

thanks for letting us know. I will look into this today and give you detailed instructions how to use it.

Sorry for the trouble,

Christian

Hi Rufus,

can you ellaborate a bit more on your setup? Which KNIME and KNIME Image Processing version? Which CellProfiler version? Did you set the path to CellProfiler in the KNIME propreties?

 

Thanks and happy Easter,

Christian

Hello Christian,

I'm using CellProfiler 2.1.1, KNIME 3.1.1 and Image Processing 1.4.2.201603260602. The version of CellProfiler Integration is 0.2.1.v201510261651.

I checked the path to my CellProfiler installation again. It should be correct, since the execution fails immediately giving out the message of not finding CellProfiler.exe when I change the path.

 

Thanks and happy Easter, too

Rufus

 

 

Hi Rufus,

it seems that you are not using the bleeding edge version of CellProfiler. See the remark on https://tech.knime.org/community/cellprofiler. Does this help?

Christian

Hi Christian,

unfortunately the link in the remark to the bleeding edge version isn't working. But I downloaded the stable bleeding edge version from cellprofiler.org directly using the link on the download page at the very bottom. I reinstalled CellProfiler but the error still occurs.

 

Rufus

 

PS: I tried the nightly version now and this one works.

Thank you Christian!

Hi Rufus,

Perfect. Sorry for the trouble. I updated the link! Thanks!

Anyway, I will get in touch with Lee from CellProfiler and try to provide more information about when we don't have to rely on the nightly version anymore.

Best,

Christian