bioimagesUnknownDavide Bottonehttps://www.ebi.ac.uk/biostudies/studies/S-BIAD3263bioimagesSpecimenImage analysisFundingStudy ComponentBiosampleorganisationAssociationsAnnotationImage acquisitionMiriam S LucasSebastian HabermannInge K HerrmannJosé María MateosMelanie FachetDavide BottoneUte Resch-GengerLukas RH GerkenVera M KisslingAlexander GogosMatthias RössleinJohannes Riemannfalse3D Volume Electron Microscopy Dataset of Gold Nanoparticle-Loaded FaDu Tumor Spheroids with Segmentation AnnotationsThis dataset contains a serial block-face scanning electron microscopy (SBF-SEM) volume of a FaDu head-and-neck carcinoma tumor spheroid loaded with 50 nm citrate-capped gold nanoparticles (AuNPs), acquired at 10×10×50 nm voxel size, covering an approximate 102×102×35 µm field of view close to the spheroid core. The dataset includes instance segmentation masks for cells, nuclei, and AuNPs, produced by a fine-tuned Cellpose-SAM model and an empirical Bayes approach respectively, together with manually annotated ground truth masks for cells and nuclei across 20 image slices at two isotropic resolutions. All data are provided as a single zarr archive with OME-NGFF compliant image groups, alongside TIFF ground truth slices. The dataset is intended as a benchmark resource for segmentation model2026-04-16T00:00:00Z2026-07-31T10:14:42.251Z2026-04-16T17:40:18.816ZS-BIAD3263