A system for analyzing intact cotton, wherein the system comprises an X-ray scanner system and a plurality of sample containers, wherein at least one seed cotton sample container is structured and operable to retain a respective one of a plurality of intact cotton samples. The system additionally comprises a sample support platform that is structured and operable to move the plurality of sample containers past an image data generation assembly of the X-ray scanner system. The system further comprises a computer based system that is structured and operable to execute image analysis software to determine at least one metric of at least one of the intact cotton samples.