Others have pointed out that once you determine the slide's skew, you may be better off having the spot grabber compensate, rather than trying to rotate the entire image.

One option for accessing the pixels which no-one has mentioned is simply to use substr and unpack. Convert the jpg to ppm, which is just a row-major sequence of pixels, 3 bytes (rgb) per pixel. Just slurp it in as a string. The arithmetic for converting from pixel coordinates to string offset is trivial. Substr 3 bytes and unpack. Two lines of code. It is quite "fast" (in perl, rather than C terms). I wouldn't suggest touching every pixel with it, but it's great for sampling. And to grab the hypothetical 16x16 pixel spot, one can just concatenate 16 substr's, slap "P6 16 16 255 " on the front, and you have the spot ppm image. And with Inline::C, it is not difficult to convert parts of this to C, should the need perhaps someday arise.

Perl is quite good at doing _simple_ things with images. It is only when you get slightly more complex that you can get bogged down in the zoo of partial solutions.