Need help with input module setting


Hi, I just started to learn CellProfiler and met a problem with image input module setting. Any suggestion from you will be very appreciated. I did RNA in situ hybridization on tissue microarray through padlock probe based RCA. The fluorescence stained section was scanned using Aperio ScanScope. Then the selected image which containing DAB stained nuclear and Cy5 or Cy3 stained dots (Rolling cycle amplification product of target molecular) was took and saved as TIF file. I want count the number of dot and cell within each image for now. But the program showed “no images passed the filtering criteria” after I load images. And, when I click the “analyze Images”, it is show up that “the pipeline cannot be started because of the configuration problem: the pipeline did not identify any image set. Please correct any problems in your input module settings and try again”. I adopted the speckle counting pipeline. What should I do next? Sincerely, Wusheng


If “Images” is telling you that nothing is passing the filtering criteria, the place to start your troubleshooting would be the filter settings- they’re directly below the drag-and-drop window in Images. Make sure that all of your images are being loaded and that when you look at NamesAndTypes you’re creating the correct image sets your pipeline is going to be looking for- for example if your object identification is supposed to be done on an image named “DAPI”, make sure you’re actually designating an image as “DAPI”. Seeing which downstream modules are showing check marks and which are showing red triangles (and what the error messages are when you hover your cursor over the red triangles) will give you a sense of where the problems are and when you’ve fixed them.

See if you can work it from there, and if not you can try uploading your pipeline and images ala the directions below. Good luck!


Thanks for your quick response. How to design an image?


Hi Beth,
It is really help. I can now move one more step further. It is showing that “Image must be grayscale, but it was color”. How can I change them to grayscale using ColorToGray?



Check out this recent thread for instructions and discussions of how to handle multi-channel images- the short version is that if your image metadata is configured correctly then yes, set them as “Color Image” under names and types and then use a ColorToGrey module but there are a few different ways to handle it.


Hi Beth,

Thanks for your help. Finally I could set up the pipeline matched to my images and performed the “Analyze images” successfully at my first run. But since then I have met another problem. My PC (Window 7) always crashed down after a few circles of run, no matter how many images I input and how many modules the pipeline contains. Based on some old discussions from the Forum, I re-signed a individual temporary folder for this program to avoid the anti-virus software issue. But it does not help. Someone mentioned that this program may has some issue with Window 7 which might cause this issue? Is it true? What should I do next?



I’m sorry to hear that!

I don’t have a ton of experience with Windows 7, but it’s definitely possible that it could be an antivirus issue- it could also be due to having insufficient memory. Take a look at this thread.

You can try playing with the number of workers permitted and check your antivirus settings; if neither of those work, my suggestions would be to a) upgrade CP to a newer version in hopes that this is a bug that’s been fixed or b) try it on a different computer.

Good luck!