In this work, a magnetic visual control system for automated protein crystal harvesting is proposed. The system consists of a rod-shaped microrobot, a magnetic actuation system and a visual control system. A rotating magnetic field induces the microrobot to roll on the supporting surface, thereby creating a vortex in a liquid environment. This vortex enables the robot to trap and transport even delicate objects in a non-contact manner to a pre-defined position. We present the micro-agent, the actuation system and the visual control system to achieve this automated procedure.