Deciphering the three-dimensional atomic structure of solid-solid interfaces in core-shell nanomaterials is the key to understand their remarkable catalytical, optical and electronic properties. Here, we probe the three-dimensional atomic structures of palladium-platinum core-shell nanoparticles at the single-atom level using atomic resolution electron tomography. We successfully quantify the rich structural variety of core-shell nanoparticles with heteroepitaxy in 3D at atomic resolution. Instead of forming an atomically-sharp boundary, the core-shell interface is atomically diffuse with an average thickness of 4.2 Å, irrespective of the particle's morphology or crystallographic texture. We observed dissolved free Pd and Pt single atoms and sub-nanometer clusters using cryogenic electron microscopy. The high concentration of Pd in the diffusive interface is highly related to the free Pd atoms dissolved from the Pd seeds. These results advance our understanding of core-shell structures at the fundamental level, providing potential strategies into precise nanomaterial manipulation and chemical property regulation. The data and source codes for the paper "Probing the atomically diffuse interfaces in core-shell nanoparticles in three dimensions" are posted below. # Repositary Contents ### 1. Experiment Data Folder: [Measured_data](./1_Measured_data) This folder contains denoised and aligned ADF-STEM projections and corresponding finalized tilt angles for three Pd@Pt core-shell nanoparticles. Three particles are named PB (pentagonal bipyramid shaped), EPB (elongated pentagonal bipyramid shaped) and TO (truncated octahedron shaped), respectively. ### 2. Reconstructed 3D Volume Folder: [Final_reconstruction_volume](./2_Final_reconstruction_volume) This folder contains 3D tomographic reconstruction volumes of three particles. For the source code of RESIRE algorithm used in these reconstructions, please see the [source code](https://github.com/AET-MetallicGlass/Supplementary-Data-Codes/tree/master/2_RESIRE_package) of Yao Yang's paper on github. ### 3. Atom Tracing and Classification Folder: [Tracing_and_classification](./3_Tracing_and_classification) This folder contains the source code to trace and classify atoms in the 3D volume. ### 4. Experimental Atomic Models Folder: [Final_coordinates](./4_Final_coordinates) This folder contains the final coordinates of three nanoparticles. ### 5. Analysis of core-shell interface and others Folder: [Analysis_of_interface](./5_Analysis_of_interface) This folder contains the codes to analyse the pair distribution function (PDF), the core-shell interface, the local coordination structure (PTM), the displacement and strain map of three nanoparticles.