Modern estimation of rock properties combines imaging with advanced numerical simulations. This approach is known as digital rock physics. In this paper we suggest a specific segmentation procedure which is applied to a set of carbonate rocks. Starting point are CT-scans with three different resolutions. The first step applied to the raw image data is a non-local mean filter. We then apply different thresholds to identify pores and solid phases. Because we are aware of a non-neglectable amount of unresolved micro-porosity ("mikritic phase") we also define intermediate phases. Based on this segmentation we determine porosity-dependent values for the p- and s-wave velocity and for the permeability. The porosity measured in the laboratory is then used to predict finally the effective rock properties to compare with experimental data.