cryoPANDA: A 37-million-particle dataset from over 250 experiments to accelerate data-driven cryo-EM analysis

This dataset was produced within the ERA Chair / Hot4Cryo project by the Institute of Chemical Biology of the National Hellenic Research Foundation (NHRF), in collaboration with the laboratory of Professor Panagiotis Kastritis at Martin Luther University Halle-Wittenberg. Cryo-EM images (micrographs) contain background noise and 2D protein projections (particles), which are used to reconstruct 3D protein structures. Existing cryo-EM datasets primarily provide micrographs, with limited particle-level collections, which restrict coverage of particle-level variability across EMPIAR experiments. To address this gap, the cryo-EM Particles ANnotated DAtaset (cryoPANDA) provides a large-scale cryo-EM particle dataset that is more than 10-fold larger than prior particle collections. cryoPANDA comprises over 37 million particles from 252 cryo-EM experiments spanning a wide range of protein types, totaling more than 13 TB of data. For each experiment, the dataset includes particle images, per-particle annotations, the corresponding 3D electrostatic potential map, the published Electron Microscopy Data Bank map, and the corresponding Protein Data Bank model, where available. The data are arranged in separate directories, one per cryo-EM experiment. The cryoPANDA dataset is also provided in HDF5 format, chunked by experiment into 252 separate .h5 files.