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.