1. A method in a computer system for classifying a seed by determining which of any of a group of seed structures the seed is detected to have, the computer system including a processor and a memory coupled to the processor, the method comprising: producing a set of modeling parameters that identify the seed structure from the rest of a model image data, based on a selected region of interest identified in the model image data; generating scripts based on the set of modeling parameters; subjecting the seed to a first spectral signal; recording a first reflection of the spectral signal; causing the processor to produce a first image data of the recording; storing the first image data in the memory; causing the processor to identify, using the set of modeling parameters, one or more morphological seed structures for the seed based on the first image data stored in the memory; wherein the morphological seed structures include a seed coat, a root, a stem, and a leaf, or a morphological seed structure occurring between the development of any two seed structures of the seed; or a sub-structure occurring in the development of any one or more of the morphological seed structures; wherein the seed sub-structure includes one or more from the following group: hilium, micropyle, testa, embryonic root, radicle, root tip, root meristem, embryonic shoot, shoot meristem, epicotyl, plummule, coleoptiles, shoot, stem, hypocotyls, hook, round cotyledon, true leaf, and cotyledon leaf; and causing the processor to classify, using the generated scripts, the seed based on the one or more identified morphological seed structures and sub-structures.