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This article describes the state-of-the-art in 2D and 3D tomographic mid-IR imaging and its current and potential applications in the imaging of material and biological systems with a focus on cells and tissues. 2D FTIR microscopy is first presented in terms of the basic experimental configurations of the technique, optics, data and image acquisition. This first section provides a basis for the ensuing discussion on 3D FTIR spectro-microtomography. In the second part, examples of 2D and 3D chemical imaging are given with a focus on the use of molecular chemical probes and probe-free applications, respectively.