you can't replace the particles in pixel polly....
you can create custom animated particles in other particle systems, but most of them won't let you use a layer as an emitter/producer so it would be difficult to break apart a layer into those particles.
but you can do both in trapcode's particular (you can download the trial version if you want to try it). you'll find many tutorials (and posts) for particular that will give you the basis for what you need to create this effect.
here's one that shows how to use a layer as an emitter: