In my experience, the 'common' or 'standard' convention is to store FITS data such that images have their (0,0) origin at the 'bottom-left' of the image - however, this is more of a 'convention' than a rigidly enforced requirement.
That said, it does annoy me that some software - including 'expensive' or 'high-end' software packages do not follow the convention, or do not provide a means of allowing the user to decide. Fortunately, PI does not fall into that category, which at least allows users to make up for the shortfalls of the other packages!!
Cheers,
