2001.06.12 18:03 "Re: Is there a TIFF "cut" utility for a poor-man's telecine?", by Peter Montgomery
Yikes! I'm sure there's some reason you're not just doing telecine of the 16mm film. Bear in mind that a 16mm frame is rather small, and your resolution using a desktop scanner will probably be quite low. Remember that even if your scanner interpolates up to some ridiculous figure, it's only interpolated data and thus will not provide any more information (i.e. it will still be fuzzy).
Assuming you still feel compelled to pursue this, I would recommend downloading a copy of the GIMP. It comes in both Linux and Windows flavors. It's a freeware PhotoShop style paint program, but it also has a scripting language called Script-Fu. I have read on some of the GIMP mailing lists that you can create scripts for cutting sub-images out of larger images, although I have never tried it myself.
I think you're still looking at a tremendous amount of work. Don't forget that there are 24 frames per second in standard sound film, which means a lot of works to even get a couple of seconds of footage. In addition, all the handling of the film will add to the amount of dirt and scratches you'll probably want to get rid of later. Good luck!