If you could upload your sheets in JPEG format, the whole process would run much more efficiently. This task is basically a matter of graphic data processing, and that can be done much better over a graphic format like JPEG. Then we could easily locate and read the QR code, capture the answer boxes and store them again as JPEG files in a folder on your server. This is not difficult in itself, but it's very computational intensive because graphic processing involves checking hundreds of tausends of pixels and that is yet for a standard processor a heavy load, that's why we should try to avoid performing additional format conversions. PHP adds besides that an overhead due to the interpretation, but is indeed at the server the most practical solution nowadays, so we would try to optimize the code as much as possible letting it anyway clear enough to allow for easy maintenance in the future. The whole could be ready to test in no more that two weeks.
Regards
The Bramfeld Team