A new tool for analysis of root growth in the spatio-temporal continuum.

• Quantification of overall growth and local growth zones in root system development is key to understanding the biology of plant growth, and thus to exploring the effects of environmental, genotypic and mutational variations on plant development and productivity. • We introduce a methodology for analyzing growth patterns of plant roots from two-dimensional time series images, treating them as a spatio-temporal three-dimensional (3D) image volume. The roots are segmented from the images and then two types of analysis are performed: 3D spatio-temporal reconstruction analysis for simultaneous assessment of initiation and growth of multiple roots; and spatio-temporal pixel intensity analysis along root midlines for quantification of the growth zones. • The test measurements show simultaneous emergence of basal roots but sequential emergence of lateral roots in Phaseolus vulgaris, while lateral roots of Cicer arietinum emerge in a rhythmic pattern. Local growth analysis reveals multimodal transient growth zone in basal roots. At the initial stages after emergence, the roots oscillate rapidly, which slows down with time. • The methodology presented here allows detailed characterization of the phenomenology of roots, providing valuable information of spatio-temporal development, with applications in a wide range of growing plant organs.