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The structures, as building-blocks for designing functional nanomaterials,have fueled the development of versatile nanoprobes to understand localstructures of noncrystalline specimens. Progresses in analyzing structures ofindividual specimens with atomic scale accuracy have been notable recently. Inmost cases, however, only a limited number of specimens are inspected lackingstatistics to represent the systems with structural inhomogeneity. Here, byemploying single-particle imaging with X-ray free electron lasers and newalgorithm for multiple-model 3D imaging, we succeeded in investigating severalthousand specimens in a couple of hours, and identified intrinsicheterogeneities with 3D structures. Quantitative analysis has unveiled 3Dmorphology, facet indices and elastic strains. The 3D elastic energydistribution is further corroborated by molecular dynamics simulations to gainmechanical insight at atomic level. This work establishes a new route tohigh-throughput characterization of individual specimens in large ensembles,hence overcoming statistical deficiency while providing quantitativeinformation at the nanoscale.

High-throughput ensemble characterization of individual core-shell nanoparticles with quantitative 3D density from XFEL single-particle imaging