Trouble getting started



I just downloaded CP and Java, everything seems to be running. I am trying to use CellProfiler to detect aphids(small insects) from leaves they reside on using the Cell/particle counting, and scoring the percentage of stained objects pipeline. When I load images into the drag and drop images folder, I get this message “the pipeline cannot be started because of a configuration problem. The pipeline did not detect any image sets. Please correct any problems in your input module settings and try again.” I’m stuck here and need some help.



You may want to take a look at this blog post about that error and/or search the forum for that error to look at what other situations people have had that error in and how they’ve solved the issue.

If after all that you’re still having trouble, feel free to post a pipeline and image set(s) that reproduce the error.


Thanks Beth, I made some additional progress, but I’m still having issues with the image naming. I’m not quite sure how I’m supposed to name the images to get the program to run them.



I think then you should spend some time with the help for the NamesAndTypes module- it’ll explain in detail how to configure that module.


Hi Beth, I figured it out mostly. Thanks for your help on that. I am trying to run images that are of leaves with aphids on them. I need the CellProfiler to ID the aphids and count them. Any way you can help me setup CellProfiler to do that? I need to run around 6400 images using this.
Also, is there a way to use CellProfiler Analyst to teach (machine learning) the program to identify what is an aphid. That would be extremely useful for me. Please help!


While we’re always happy to help users troubleshoot specific issues on the forum, we unfortunately don’t have the bandwidth or resources to do de-novo pipeline creation on the forum for everyone who would like it while still keeping CellProfiler free!

If your lab is interested in setting up a more formal collaboration with ours you can reach out via email to imagingadmin [at] broadinstitute [dot] org ; we can then discuss various forms those collaborations can take.