The emitter and absorber need a high relative velocity. It is not useful to put them both on a fast track, because then they have both the same velocity. However, it is possible to make 2 tracks in opposite directions. Then each track needs only half the speed.
I would realize this speed by conveyor belts. If the two samples are not too large/heavy, then it could be possible to use a continuous operation. This would give the conveyor belts the time to accelerate till they reach the desired speed.