Roots and their biota interact from the smallest spatiotemporal scale at the level of bacteria, to intermediate fungal-invertebrate spatiotemporal scales, and ultimately to the large, scale of structural roots. The micron-second bacterial scale is best known because it is amenable to standard microbial techniques. Intermediate and large spatiotemporal scales of interaction need comparable study because events at each scale affect the others. Borescopes, minirhizotrons and soil biotrons are well suited to studying events at the intermediate, millimeter-minute spatiotemporal scale of fine roots, fungi and invertebrates. Soil biotrons are particularly well-suited for study of the intermediate spatiotemporal scale because microscopes, cameras and video can be used within them, and in situ experimental manipulations can be performed. The large amounts of observational data that can be collected with video recording can be analyzed using computer image analysis. Image analysis is especially valuable in visualizing the spatial relationships of roots and their biota, and in quantifying growth, feeding and turnover rates.