Methods and systems for three-dimensionally imaging an apical dome located at the cotyledon end of a plant embryo are provided. Three-dimensional information of an apical dome can be obtained by scanning the apical dome at varying focal planes along an axis of the embryo, or by using multiple cameras arranged in a confocal manner to image the apical dome. It can also be obtained by irradiating the apical dome with polychromatic light, wherein light beams of multiple wavelengths are focused at multiple focal planes along the axis of the embryo so that the dome's height information can be obtained based on the wavelength of the light precisely focused and reflected at each surface point of the dome. The three-dimensional information is used to ascertain various morphological features (e.g., size, shape, texture, etc.) of the apical dome, which are in turn used to assess the embryo's germinant vigor.