To date, very little is known about the distribution of gas hydrates in sedimentary matrices and the resulting matrix-pore network affecting the seismic properties at low hydrate concentration. Digital rock physics offers a unique solution to this issue yet requires good quality, high resolution 3D representations for the accurate modelling of petrophysical and transport properties. Although such models are readily available via in-situ synchrotron radiation X-ray tomography the analysis of such data asks for complex workflows and high computational power to maintain valuable results. Here, we present a best-practise procedure complementing data from Chaouachi et al. (Geochemistry, Geophysics, Geosystems 2015, 16 (6), 1711–1722) with data post-processing, including image enhancement and segmentation as well as numerical simulations in 3D using the derived results as a direct model input. The method presented opens a path to a model-free deduction of the properties of gas hydrate bearing sediments when aiming for in-situ experiments linked to synchrotron-based tomography and 3D modelling.