Usually there is no need for pixel perfect collision. It does not map well on different resolutions and perform pretty badly. Also collision results are rubbish because of lack of collision on normal.
Using some approximated collision shape is much more robust, faster and give higher quality collision results. Using box2d and tool like this
http://code.google.com/p/box2d-editor/ would make sens.
If you still want do pixel perfect collision use libgdx pixmap class to grab pixels and make bitmask from those and then combine bits to bit vectors(shot/int/long) so you can test many pixels at once by using AND operation.
