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
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?
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.
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?
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.
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.