Abstract: 3D characterization of assemblies of nanoparticles is of great importance to determine their structure-property connection. Such investigations become increasingly more challenging when the assemblies become larger and more compact. In this paper, we propose an optimized approach for electron tomography to minimize artefacts related to beam broadening in High Angle Annular Dark-Field Scanning Transmission Electron Microscopy mode. These artefacts are typically present at one side of the reconstructed 3D data set for thick nanoparticle assemblies. To overcome this problem, we propose a procedure in which two tomographic tilt series of the same sample are acquired. After acquiring the first series, the sample is flipped over 180o, and a second tilt series is acquired. By merging the two reconstructions, blurring in the reconstructed volume is minimized. Next, this approach is combined with an advanced three-dimensional reconstruction algorithm yielding quantitative structural information. Here, the approach is applied to a thick and compact assembly of spherical Au nanoparticles, but the methodology can we used to investigate a broad range of samples.