A seed sorter system is operable to sort seeds based on one or more characteristics of the seeds. The system includes a seed loading station operable to isolate individual seeds from a plurality of seeds and load the isolated seeds into a seed tray, an imaging and analysis subsystem operable to collect image data of at least a top portion and a bottom portion of each of the seeds in the seed tray and determine one or more characteristics of each of the seeds, a seed off-load and sort station operable to remove the seeds from the seed tray and sort the seeds to desired receptacles based on the determined one or more characteristics of the seeds, and a seed transport operable to move the seed tray between the seed loading station, the imaging and analysis subsystem, and the seed off-load and sort station.