While cell analysis is conventionally performed on 2D slices, novel micro and nano-CT system opens new perspectives in this area. Here, we show that synchrotron radiation (SR) micro-CT is well suited to analyze the 3D distribution of osteocyte lacunae in bone tissue. Osteocytes are receiving increasing interest in the comprehension of bone diseases. Here, we propose a fast automated method to extract 3D quantitative morphological descriptors on these cells. To this aim, after a fast connected component analysis applied on the segmented image, a moment-based approach and intrinsic volumes are calculated to derive 3D descriptors on each object. The segmentation is refined by eliminating artifacts according to some descriptors. Validation of segmentation and experimental results on twelve bone samples are presented. This method is efficient and is believed to open new perspectives to quantify physiopathologic changes at the cell level.