Importing a cif file from IDEAS into cellprofiler fails

Hi all

New to CP. From the information found here cif files from IDEAS software can be dragged and dropped into CP and images analyzed without having to create a montage using a python or matlab script.

But when I drag and drop eeither the example cif file provided on the imaging flow cytometry webpage of cell profiler or my own cif files, the program complains that no images could be found in these files when it tries to analyze images.

I am a windows user and have downloaded and installed the latest executable from the CP website.

Can someone help me out? Thanks.

Hello! Hopefully the community can help with this. I’ll not very familiar with the feature myself, but my best guess is that the issue is in the settings for the first four modules. Have you set those up as described? Or downloaded an example pipeline and then used the example data?

Once we get a “positive control” working in your hands, we can see how it goes for your own data.

Hi there. Thanks for the reply. I found a solution here.

After I used Amnis IDEAS software to export a new cif file which had a population gated for focus and single cells, I was able to get CP image modification modules to work. So it looks like CP is actually recognizing the images.

I still have a few other problems with learning CP and using it in my workflow, but I will continue to look for answers here and in the program help features.


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So, while I am able to import a cif file and sort of analyze a few features such as co-localization of different channel fluorescences, I still have several questions. The workflow in the Hennig article from 2017 suggests that when the cif file is imported, image montages will be automatically generated. However, that does not seem to happen. While CP is able to retrieve the images, I really don’t see any way I can view the montages.

I also don’t really know who I need to talk to about using CP for imaging flow cytometry data as I have several questions. While I love the software for the little that I am able to do, I am eager to find out what more it can do for IFC data.


Glad you got things starting to move along!

Have you checked out this resource?
It might help accelerate your learning curve.

As for whom to talk to, this forum is definitely the right place! Those who have worked on this have dispersed across the globe but this is a good place to connect to them.