The image data (in .mrc format) were collected with the Helmholtz-Zentrum Berlin transmission soft X-ray microscope (TXM) and used for comparison to predictions of a 3D imaging model for such a microscope. The detailed analysis is presented in the publication “Towards a quantitative theory for transmission X-ray microscopy” by McNally et al. in the Beilstein Journal of Nanotechnology (2025). The files beginning with “Dataset 1,2 or 3” correspond to the data presented in Fig. 2 of the publication. These data reflect a set of through-focus 2D images of ~60 nm gold nanoparticles acquired from the microscope at 510 eV with a pixel size of 5.47 nm and a z spacing of 40 nm. The remaining files, all beginning with “GoldNP”, correspond to the data presented in Fig. 5 of the publication. Each filename includes a number (directly after “GoldNP”) corresponding to the diameter of the gold nanoparticle (in nm) as measured by scanning electron microscopy. The energy is again 510 eV and the pixel size is again 5.47 nm. These images were all collected in the same focal plane of the nanoparticle, namely its best focus. That best-focal-plane image is then acquired ten times, leading to the ten images in the stack.