In this paper we propose a motion-aware variational approach to reconstruct moving objects from sparse dynamic data. The motivation of this work stems from x-ray imaging of plants perfused with a liquid contrast agent, aimed at increasing the contrast of the images and studying the phloem transport in plants over time. The key idea of our approach is to deploy 3D shearlets as a space-temporal prior, treating time as the third dimension. The rationale behind this model is that a continuous evolution of a cartoon-like object is well suited for the use of 3D shearlets. We provide a basic mathematical analysis of the variational model for the image reconstruction. The numerical minimization is carried out with primal-dual scheme coupled with an automated choice of the regularization parameter. We test our model on different measurement setups: a simulated phantom especially designed to resemble a plant stem, with spreading points to simulate a spreading contrast agent; a measured agarose gel phantom to demonstrate iodide diffusion and geometry prior to imaging living sample; a measured living tree grown in vitro and perfused with a liquid sugar–iodine-mix. The results, compared against a 2D static model, show that our approach provides reconstructions that capture well the time dynamic of the contrast agent onset and are encouraging to develop microCT as a tool to study phloem transport using iodine tracer.