An analytical tool to monitor the arrangement of pebbles in a pebble bed as well as the morphology of gas bubbles in as fabricated and neutron irradiated beryllium pebbles is presented. The context of this study is the Helium Cooled Pebble Bed (HPCB) blanket design for the forthcoming generation of fusion reactors. The thermal-mechanical behavior of pebble beds is a basic issue for the HPCB. It depends strongly on the configuration of the pebbles in the bed, and in particular on the number of contacts between pebbles, and between pebbles and the blanket walls. The related contact surfaces play also a major role. The knowledge on the inner structure of the pebbles is required since during the life cycle of a power reactor helium and tritium bubbles are produced inside the beryllium pebbles and the tritium build-up can be in excess of several kilograms, being thereby a key safety issue. All the non-destructive analyses are based on 3D computer aided microtomography using a very powerful synchrotron radiation x-ray source with high spatial resolution. The data analysis relies on a topological operator called filtered medial line applied to the entire data volumes and the related graph representation. By this technique the number of contacts between the pebbles in pebble packs and their angular distribution are obtained, as well as the corresponding contact surfaces. The evaluation of bubble sizes and densities in single pebbles, the assessment of the pore channel network topology, the 3D reconstruction of the fraction of interconnected bubble porosity, and the open-to-closed-porosity ratio are among the most interesting findings.