AET-Bench: Pixel-Accurate Atomic Tomography Is Not Atom-Accurate

Atomic electron tomography (AET) aims to recover the three-dimensional arrangement, chemical identity, and temporal evolution of individual atoms. Yet most reconstruction methods are still evaluated primarily by voxel-level image similarity, such as PSNR, SSIM, or Fourier shell correlation. In this work, we show that this evaluation practice can select scientifically incorrect reconstructions: a volume that looks accurate can contain atoms that are shifted, merged, missed, hallucinated, chemically mislabeled, or assigned inconsistent identities through time. We introduce AET-Bench, a dataset and benchmark for atom-first evaluation of atomic electron tomography. AET-Bench contains 755 samples across a six-tier realism ladder, spanning clean analytical simulations, binary alloys, 4D atomic dynamics, multislice scattering, real experimental tilt series, and Brownian Pt nanocrystal trajectories. It defines four complementary tasks and evaluates 14 core method families with 21 logged method entries under a unified protocol. AET-Bench reveals a central failure mode hidden by voxel-only evaluation. On the AET-Sim-Mono tier, high-SSIM neural and Gaussian reconstructions can recover substantially fewer atoms than classical or sparsity-regularized methods: for example, 4D-GS achieves strong voxel similarity but only 43.9\% atom recall, while FISTA-TV reaches 95.1\% atom recall despite much lower SSIM. This inversion persists across atom-matching thresholds, showing that it is not an artifact of a single cutoff. On more realistic multislice and real tiers, atom recovery further degrades, exposing a physics gap between visually plausible volumes and reference atomic models. For 4D reconstruction, we find that smooth temporal density fields do not guarantee persistent atom identities. AET-Bench establishes atom-level fidelity as a necessary evaluation axis for AET. Our results suggest that future AET methods should not be judged only by how reconstructions look, but by whether they recover the atoms, species, and trajectories that scientists actually use.