I am trying to execute Cellprofiler in command line on Windows. I successfully ran it using a Batch file and the command
Cellprofiler.exe -p Batch_file.h5 -c -r
however, I would be able to run in command line, specifying the pipeline without input images and set them thanks to the -i (–image-directory) option.
i have tried the following command
Cellprofiler.exe --pipeline=my_pipeline.cppipe -c -r --image-directory=my_image_folder --output-directory=my_output_dir
This command output the following result:
CP-JAVA WARN 0.c.imageset.ChannelFilter - Empty image set list: no images passed the filtering criteria.
However, I know that my images are able to pass the filter since it works in the UI and I have double-check the path of the folders
Does somebody have an idea on the issue I am encoutering?
Thanks in advance