Reliable determination of sub-nanometer gaps in plasmonic gold dimers for correlation to their optical properties

Accurately characterizing sub-nanometer gaps in plasmonic nanoparticle dimers is essential for understanding their optical properties, particularly in the transition from classical to quantum plasmonic behavior. While two-dimensional (scanning) transmission electron microscopy imaging provides high spatial resolution, it lacks the three-dimensional (3D) morphological information needed to reliably extract gap sizes. In this work, we combine electron tomography with a robust data analysis workflow to quantify interparticle gaps in gold nanosphere dimers with sub-nanometer precision. We show that gap size estimates are highly sensitive to reconstruction algorithms, segmentation thresholds, and meshing parameters. To overcome this, we introduce a model-fitting approach based on convolving a step function with a Gaussian, enabling consistent and accurate gap measurements even in the absence of a known ground truth. Validation on simulated datasets confirms pixel-level accuracy, and application to experimental data demonstrates the robustness and general applicability of the method. The resulting 3D reconstructions are directly integrated into electromagnetic simulations, allowing reliable interpretation of the optical response of the dimer. This workflow offers a broadly applicable strategy for correlating morphology and optical function in plasmonic systems and provides a crucial step toward resolving quantum effects in nanoscale light-matter interactions.