When you encode a .MOV file in QuickTime using the PhotoJPEG codec you get a slider that gives you a "percentage" of compression.
Typically when delivering clips to clients who require PhotoJPEG I use "80%" as my base (I increase it if it causes issues).
In attempts and using FFmpeg to encode to PhotoJPEG I have not yet found an equivalent formula/method for obtaining the same results. I spent a solid day one weekend comparing encoded files with different commands line settings and various files encoded using QuickTime Pro and couldn't come up with anything consistent across different types of clips (animation, DV footage, hi res HD footage, etc..).
Has anyone else experimented with this or do you know of a way to encode a file at "80% PhotoJPEG" using FFmpeg that gets similar results to QuickTime Pro?