The lab-based X-ray microscope with in situ mechanical testing, Xradia 810 Ultra, referred to as nanoCT, is a resourceful tool for the 3D characterization of samples down to 50 nm of resolution. In the mechanical in situ mode, a maximum force of 0.8 N can be exerted on the specimen in compression or indentation experiments. A centric diatom from the species Actinoptychus senarius was characterized using the in situ nanoCT at different levels of loading. At no load and for each of the loading steps, it is possible to observe the 3D structure and to extract the mechanical responses in each region of the sample.