An automated method for analyzing seeds generally includes collecting image data from individual seeds using a seed sampling system, determining at least one characteristic of each of the individual seeds based on the collected image data, and removing tissue from each of the individual seeds using the seed sampling system. The method also includes, prior to removing the tissue sample from each of the individual seeds, adjusting at least one operational parameter of the seed sampling system based on the at least one characteristic of the seed from which the tissue is to be removed to thereby allow for generally consistent removal of tissue from each of the individual seeds. In some aspects, the method further includes analyzing the tissue removed from the seeds for presence or absence of at least one characteristic, and selecting seeds based on presence or absence of the at least one characteristic.