The pipeline did not identify any image sets


Complete newbie to Cell Profiling and I have followed all instructions online for downloading the software and pipelines. I get the following message when I try to analyse the images I dragged in:

The pipeline cannot be started because of a configuration problem: The pipeline did not identify any image sets, Please correct any problems in your input module setting and try again.

But I have dragged the images in and can see them there…
Any ideas on how to troubleshoot are greatly appreciated.

Hi LC93K,
This usually happens when you extract metadata from your images (from the filename or foldername or both) and when either your regex is problematic for some pictures or if one picture is missing…
First check the Metadata module: click on update and check that all the metadata you want are indeed extracted from each file. Then check NamesAndTypes module: click on update and check if there is a “problematic” image set…
It’ll help if you give more information, i.e. the pipeline, a few example picts…
Good luck,


Thanks Fabienk. I will try now.

You may also find this blog post helpful- good luck!