BiofilmQ Opens but when I Browse and select a folder with lif. stacks from microscope nothing opens.
I think we were already able to solve this problem via mail, but I am going to post the answer here anyway so that others can benefit from it.
When a directory is loaded into BiofilmQ, the program tries to identify valid files for import. In principle, any file type supported by the Bio-Formats toolbox can be imported, meaning that files are converted into the BiofilmQ-specific format, which is a a pair of tif-file and metadata .mat file. If a directory already contains files in this format, they do not need to be imported, BiofilmQ will automatically detect them. If you have a series of tif-files representing different channels, slices or timepoints of your image, you can convert them into the BiofilmQ format via the custom tif-file import.
In order to have everything running smoothly, there should not be a mixture of different file types, specifically not tif-files mixed with for example .nd2 or .lif files present in the same folder. The reason for this is that in those cases BiofilmQ does not “know” which file type you want to import and therefore which import type (“normal” or “custom tif”) to use. In your case, the presence of a .tif file was sort of blocking the import of your .lif files, and moving those files to a separate folder resolved the issue.