A sub stream auto sampling system includes an inspection unit and a sorter unit. The inspection unit includes a camera configured to capture an image of a sample, a light configured to illuminate a sample, a processor configured to process the captured image, and a memory configured to store the captured image. The sorter unit is configured to divert a sub stream of samples, from a main stream of samples, toward the inspection unit. The output of the inspection unit may be directed to the main stream of samples, or the output of the inspection unit may be directed to a collection unit. In addition to the inspection performed by the inspection unit, weighing of the sub stream of samples may also be performed by a weighing unit before the sub stream of samples are routed to the main stream of samples or the collection unit.