1. A method associated with an automated biological sample processing system having a gripping element to hold biological sample capture substrates, the method comprising: receiving an indication that a biological sample capture substrate is ready to be processed; obtaining an image of the sample capture substrate; automatically detecting, within the image, a plurality of fiducial markings on the gripping element; and based on image locations of the detected fiducial markings in the image and a mapping transfer function between detected image locations and real-world locations, arranging for biological sample portions to be automatically taken from the sample capture substrate by the sample processing system, further comprising, prior to said receiving commanding the gripping element to move to a set of re-determined robot-frame locations, wherein a marking is punched into a calibration sample capture substrate at each location; obtaining a calibration image of the calibration sample capture substrate; automatically detecting, within the calibration image, the plurality of fiducial markings on the gripping element; based on image locations of the detected fiducial markings in the calibration image, predicting a set of calibration regions of interest within the calibration image; detecting the previously punched marking within each calibration region of interest; and automatically creating, by the sampling system, the mapping transfer function between detected image locations and real-world locations resulting front the commanded locations of the gripping element when the markings were punched.