A gripping element may be commanded to move to pre-determined robot-frame locations, and markings may be punched into a calibration sample capture substrate at each location. A calibration image may be obtained, and fiducial markings on the gripping element may be detected. A set of calibration regions of interest may be predicted, and the previously punched markings may be detected. A sampling system may then create a mapping transfer function between detected image locations and real-world locations resulting from the commanded locations of the gripping element when the markings were punched. An indication may subsequently be received that a biological sample capture substrate is ready to be processed. An image of the sample capture substrate may be obtained, and the fiducial markings may be detected. Based on those image locations and the mapping transfer function, biological sample portions may be automatically taken from the sample capture substrate.