Error in generating the histocat folder with masks about imcsegmentationpipeline

[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!