Transmission x-ray microimages of 3D cultured EMT cells. EMT cells were grown on an OPLA scaffold. A) Cells from an untreated (without nanoparticles) specimen stained with uranium acetate. The nuclei (one of them marked by an arrow) are clearly visible. Bar: 20 μm. B) EMT cells co-cultured with 500 μM naked AuNPs for 6h. The nucleus would not be visible without staining whereas the AuNPs could be observed for unstained specimens due to their strong contrast. Bar: 5 μm. (C) Patchwork of projection micrograph for an EMT cell co-cultured with 500 μM naked AuNPs. Bar: 5 μm. (D) Single projection images like this were collected for tomographic reconstruction at 1 degree intervals with respect to the incoming x-rays (Additional file 2). Bar: 5 μm. The cell was stained with uranium acetate, targeting the lipid membrane. E) Picture of the 3D tomographic reconstruction of an EMT cell. The nanoparticle cluster distribution can be reliably extracted from the corresponding movie (Additional file 3).