A seed imaging system for imaging seeds includes a seed transfer station configured to move seeds through the system. An imaging assembly includes a first camera mounted relative to the seed transfer station and configured to acquire images of the seeds as the seeds move through the system. A second camera is mounted relative to the seed transfer station and is configured to acquire images of the seeds as the seeds move through the system. The second camera has an imaging modality different from an imaging modality of the first camera. First and second cameras may be disposed above and below the seed transfer stations, such as a transparent belt.