Cell Counter ##

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I am having issues with this workflow. More specifically, the module debug tells me that the czifile module cannot be found for my czi file. Any ideas why this is happening? Thanks,

Here is the debug tread below:
/root/cziconverter/czifile.py:147: UserWarning: ImportError: No module named ‘_czifile’. Decoding of JXR and JPEG encoded images will not be available. Czifile.pyx can be obtained at http://www.lfd.uci.edu/~gohlke/
"ImportError: No module named ‘_czifile’. "
convert start
Traceback (most recent call last):
File “./main.py”, line 78, in
File “./main.py”, line 38, in main
ccd = cziconverter.convert(filename, outdir, outputformat=output_format)
File “/root/cziconverter/cziconverter.py”, line 12, in convert
czi = czifile.CziFile(inputfile, detectmosaic = False)
File “/root/cziconverter/czifile.py”, line 216, in init
raise ValueError(“not a CZI file”)
ValueError: not a CZI file

Dear Serge,

Thank you for posting your question in our forum.

We already discussed this via mail but other users might also run into this issue…so it might make sense to post the solution here too:

This specific “Cell Counter” module seems to have issues with CZI files.

Instead, I used the “Count Cells (Fiji Modules)” Workflow by Sebastian Rhode:

  • I used the Count Cells (Fiji Modules) workflow
  • I modified it by adding the APEER OME Tiff Converter as first Module
  • I only modified the parameters in the Advanced Threshold Module for testing (still some finetuning is needed for best results):
    • Channel extraction active, Ch1
    • Background correction inactive
    • Filter method NONE
    • Threshold OTSU, use stack histogram active, corr factor 1
    • Fill holes inactive
    • Watershed inactive
    • Convert inactive

The workflow looks like this:

Generally, users just need to set/finetune the parameters to their needs (for example filtering or background correction). Also the Particle Analyzer Module will surely need some finetuning.