Generate the histocat folder with masks

[chinoeke]

Hi,
I have attempted to generate "the histocat folder with masks" portion of the imc_preporcessing script on JupyterNotebooks multiple times but to no avail. Whenever I run the chunk, all the .tiff files contained within each subfolder of the general histocat folder update but the masks files are not. I have tried to tried manually moving the mask files into the corresponding folders and re-running the chunk but the same thing happens. Only the .tiff files update and the mask files remain the same. As a result, histocat has been unable to load the histocat subfolders when they contain the mask files and only load the subfolders when I manually remove the mask files. I see that the chunk is calling the final_masks_dir which contains the mask files when it runs but they do not update. If you could let me know, what format the files are converted to when imcsegpipe.export_to_histocat is applied so I can manually change each mask or help me understand why this is happening, I would greatly appreciate it.
Best,
Chino