Attached below is a diagram that describes the organisation of image folders that I am using at the moment with Run_initialize and Run_acquire scripts.
Once the uppermost folder 'image' is set up, other folders in it will be created by the matlab codes if not present. Still it may be of less hassle to create the folders beforehand.
Images that are used during State 1 are saved inside 'probe' and 'secondary' folders (but not inside 'cbt' folders) with prefixes, e.g., 'dark' (for background count estimation) 'expadj' (for exposure adjustments), 'test' etc.
Hope this helps to understand image saving/reading procedures used throuout the two Run scripts.