An apparatus and method for nondestructively acquiring images of a plant root system is described. The apparatus includes a substrate for supporting the plant root system, a container for holding the substrate, an x-ray radiation source for generating x-ray radiation and directing the radiation to pass through the plant root system, and an x-ray image capture system for receiving the x-ray radiation having passed through the plant root system and for generating an image of the plant root system based on the radiation. The x-ray radiation source generates x-ray radiation having an energy level in the range of about 8 keV to about 20 keV. In this energy range, the attenuation of the x-ray radiation due to air is minimized and the contrast between the root system and the container and substrate is sufficiently high to provide a resolvable image. The substrate and container are preferably formed of materials having a low mass density, such as less than about 3 pounds per cubic foot, and a low x-ray mass attenuation coefficient. The low density materials of the substrate and the container introduce comparatively low attenuation of the x-ray radiation when compared to the attenuation introduced by the roots, thereby enhancing the visibility of the root system in the image.