To study the plasticity of root traits related to exploration and exploitation of soil environments, a range of methods need to be applied simultaneously. Trade-offs between sample size and resolution for visualisation as well as sample size for metabolome and transcriptome analysis and potential compromise of the quantification of root system size and diameters, need to be considered. An ‘in-depth traits assessment and understanding of plasticity’ combines (1) X-ray computed tomography (CT) for the visualisation and characterisation of root system architecture (RSA) in 3D during growth (figure 1); (2) WinRHIZO-analysis for quantification of root system size and diameters; (3) root gene expression analysis (Transcriptomics) for adaption of the plants to actual growth conditions, and (4) root metabolome analysis (Metabolomics) for information on the history of growth conditions. This is examplined in more detail in this practice abstract.