Pipeline doesn't produce any valid image sets

Hi all,

I’m running a pipeline on an .nd2 file produced by Nikon Elements. I’m using CP 2.1.1. This is my CP project.

syn_scorer.cpproj (108.9 KB)

It was running fine yesterday and this morning. However, suddenly, it is failing at the NamesAndTypes module. I have tried to retrace my footsteps but I can’t find the error. I can’t upload the file but you can see in the attached screenshot that ImageJ lists ChannelName meta data that matches the names I’m trying to find in NamesAndTypes.

Totally stumped. Any advice much appreciated.

Regards,

John

When you say it was “running fine yesterday and this morning”, was that with the exact same ND2 file, pipeline, etc?

That error comes up usually when any combination of Metadata, NamesAndTypes, or Groups are set incorrectly. Check all 3 modules carefully- if for example, one of your images in your nd2 file only acquired in DAPI but not in FITC or Cy5, you might have different numbers of each and therefore not configured correctly. Or if your Metadata extraction for something you use in Groups (like Well) went wrong, you still won’t have valid image sets.

Hi Bcimini,

Thanks for the quick response. I figured it out. I hit the Update button at the bottom of the Metadata module but I didn’t hit the Update button higher up in the green part of the screen that is specific to the image header meta data. When I hit that, everything went back to normal.

John

Glad to hear it all worked out!