Importing cif file to cell profiler

Hi, I’ve been trying to load .cif files in cellprofiler.

Originally I couldn’t get the program to recognise the .cif file but I used the solution here Analyzing ImageStream cytometry data with CellProfiler

Now I can load, and even apply processing to the .cif file, however, it seems to treat the .cif file as just a single image (the first cell image on the first channel). I can’t find any way of processing or seeing the other cell/channel images.

I was wondering if there is an example pipeline which uses .cif files as input?

The pipeline provided here uses the old version of cellprofiler and requires pre-stitching of images with python (which I currently can’t get to work). It would be great if I could just load .cif files directly into cellprofiler.

Thanks for your help!

Hi @lelliottp,

Within the 'metadata' module, did you try adding an 'extract from image file headers' option and pressing the 'Update' button that appears below it? This might be necessary to extract the individual images.

Hi, thanks for getting back to me, I tried the ‘extract from image file headers’ option but it doesn’t seem to recognise any metadata from the file…

This is what it gives me after ‘update’


Thanks for trying that. Just to check - you pressed the ‘Update Metadata’ button that appears in the extraction method panel, rather than just the ‘Update’ button on the preview table?

If you have a small .cif file you could upload I might be able to look into this further.

Actually I only pressed ‘update’, not ‘update metadata’ and that seems to fix the problem

It looks very promising now, it seems to identify all the images. Although I seem to get duplicates as previously reported here When importing a cif file, duplicates seem to be generated. The duplicates give a zero value on the measurement I did (granularity)

In any case I managed to output a csv file with measurements so its a good start! I’m still new to cellprofiler but I think I should be able to work out the rest.

Thanks for your help!

Sorry I tried to upload the cif file but the forum doesn’t allow that file type…

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Hi @lelliottp,
I had worked with .cif files with CP. I always ensure the metadata using FIJI though I have never faced the problem you had mentioned. If you couldn’t resolve the problem, you can try uploading your image in the drive.
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