Recent improvements in a SEM-based X-ray tomography system are described. In this type of equipment, X-rays are generated through the interaction between a highly focused electron-beam and a geometrically confined anode target. Unwanted long-term drifts of the e-beam can lead to loss of X-ray flux or decrease of spatial resolution in images. To circumvent this issue, a closed-loop control using FFT-based image correlation is integrated to the acquisition routine, in order to provide an in-line drift correction. The X-ray detection system consists of a state-of-the-art scientific CMOS camera (indirect detection), featuring high quantum efficiency (?60%) and low read-out noise (?1.2 electrons). The system performance is evaluated in terms of resolution, detectability, and scanning times for applications covering three different scientific fields: microelectronics, technical textile, and material science. © 2017 Author(s).