Analyzing Multiple Images

Hi, I wanted to analyze multiple images at once through CellProfiler but I’m not sure how to do that. I have my pipeline set up (a basic one where it turns color to gray, inverts image, and reads at certain threshold value) but I can only get it to run for one image. Thanks!

It’s probably an issue in the Images module, or NamesAndTypes. I’m guessing you dragged and dropped multiple images into the Images module but they are not being recognized by the pipeline?

If you can upload your pipeline we can take a quick look and I’m sure figure it out.

Hi Anne,

Thanks for getting back to me. I’ve uploaded my pipeline, it only has two images at the moment but I aim to add over 100, if possible. I’m only enabling three modules right now. I essentially want to analyze the images and identify the marker (stained red).

Also, it recently started giving me error “None” in names and types when I run test mode…this wasn’t happening up until a few runs ago. Not sure what happened there.

Thank you!
CPOwnTest.cpproj (106.2 KB)

Ah, lucky you: this is an easy one, even the PI of the lab (me) can fix it :slight_smile:

In NamesAndTypes you have made your rules too specific: you told it to only analyze images with the filename containing “Foxp3-1-2.tif” which of course matches only one image. If you change that to “Fox” you will capture both images that I see in the file list in the Images module.

Or to keep it super simple, in NamesAndTypes, you can just change “Images matching rules” to “All images”, so long as you don’t have any images you don’t want to process in the Images module.

Hope that helps!


Thank you, that cleared it up!

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