Error in generating the histocat folder with masks

[cassandraman]

Dear Votti,

I'm having trouble with the step generating histocat folder with masks using the example data. The following error is returned.

NotADirectoryError Traceback (most recent call last)

in /anaconda3/envs/imctools/lib/python3.6/site-packages/imctools/scripts/ome2micat.py in omefolder2micatfolder(fol_ome, outfolder, fol_masks, mask_suffix, dtype) 58 mask_suffix = '_mask.tiff' 59 ---> 60 ome_files = [fn for fn in os.listdir(fol_ome) if fn.endswith('.ome.tiff')] 61 if fol_masks is not None: 62 fn_masks = [fn for fn in os.listdir(fol_masks) if fn.endswith(mask_suffix)] NotADirectoryError: [Errno 20] Not a directory: '../output/ometiff/.DS_Store' ------------------------- While files are created within the histocat folder in output, they all appear to be empty black images. I really appreciate your help!

[votti]

Hi cassandraman, The NotADirectoryError is a problem with temporary files that MacOS is generating sometimes - it can be temporary fixed by removing the '../output/ometiff/.DS_Store' file (e.g. doing it from within the Python script using: os.remove("../output/ometiff/.DS_Store") and then rerunning everything.

I will also do a bug report in the imctools library to make the script more robust towards these random temporary files.

@Black images: are they truely black or do they just look black in a standard image editor? Could you open them in ImageJ and try to adjust the contrast: https://imagej.net/Image_Intensity_Processing

Let me know if this helps! Cheers!

[cassandraman]

Thank you Votti!

I was able to rerun the script and avoid the error. As you suggested, making some adjustments on ImageJ helped with viewing the images, and I was able to visualize them in histocat as well. Really appreciate your help.

[votti]

Cool! In this case I will consider this issue solved. Cheers!