This is a straightforward technique but is arguably a veterinary only one.
It requires implantation in the pipping muscle of 1 day old birds. The pipping muscle is thick and chunky at the back of the head, this develops whilst the chick is in the egg and provides the strength to the beak to smash through at pipping.
The muscle atrophies after hatching and is not identifiable by 3 wks old. This leaves the microchip embedded in a fibrous band from where it can't migrate, but where it can be easily read.
Video of microchipping emu
Courtesy of Park Farm Emus