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A new method is developed for three-dimensional (3D) reconstruction of multi-material objects using propagation-based X-ray phase-contrast tomography (PB-CT) with phase retrieval via the contrast transfer function (CTF) formalism. The approach differs from conventional PB-CT algorithms that apply phase retrieval on individual two-dimensional (2D) projections. Instead, this method involves performing phase retrieval to the CT-reconstructed volume in 3D. The CTF formalism is further extended to the cases of partially-coherent illumination and strongly absorbing samples. Simulated results demonstrate that the proposed post-reconstruction CTF method provides fast and stable phase retrieval, producing results equivalent to conventional pre-reconstruction 2D CTF phase retrieval. Moreover, it is shown that application can be highly localised to isolated objects of interest, without a significant loss of quality, thus leading to increased computational efficiency. Combined with the extended validity of the CTF to greater propagation distances, this method provides additional advantages over approaches based on the transport-of-intensity equation., Comment: 11 pages, 5 figures