I am assuming that the .lif format is being used for containing image stacks? If so, the most straightforward alternative is to convert the .lif image stack into individual files (preferably TIF or PNG), one for each slice/channel combination.
Organizationally, you can place the individual into folders for each stack, set the Default Output Folder to the parent folder containing the rest, and set LoadImages with the following settings:
- Analyze all subfolders within the selected folder: “All” or “Some”.
- For each channel you specify, for “Extract metadata from where?” select “Path” and enter the following regular expression:
- Check the “Group image sby metadata?” setting and select “Subfolder” from the list that appears.
This will enable each folder (i.e, each image stack) to be processed independently from the others in CP.