3D X-ray tomography was used to unravel the inner and outer morphology of a centric diatom namely the Coscinodiscus sp. We show how holotomography carried out with a 40 nm voxel size can provide detailed information about the sizes of the different parts of the diatom frustule. We have in particular analyzed quantitatively the pore size in the cribrum and cribellum parts of the diatom together with an estimation of the wall size. We evidence that in center of the diatom, walls are forming a hexagonal arrangement that is containing some pentagons to promote paving the space in 3D.