A method comprising performing the following steps on a programmed data-processing apparatus: a) obtaining (2-02) a sequence of images captured (1-500) from a three-dimensional (1-400) object by a penetrating radiation imaging apparatus (1-100) over a scanning period, wherein each captured image is associated with a specific imaging angle (φ), and wherein the three-dimensional object is transformed relative to the imaging apparatus in an unknown manner during the scanning period; b) applying an initial reconstruction (2-04) on the sequence of the captured images, thereby creating an initial reconstructed volumetric image (3-510); for each of several imaging angles (φ): c) generating a set of simulated images (3-530) corresponding to the imaging angle (φ), by repeatedly applying simulated projections (2-14) on the initial reconstructed volumetric image under a set of varied spatial transformation parameters (3-520) of at least a portion of the initial reconstructed volumetric image relative to the imaging apparatus; d) within the set of the simulated images (3-530) corresponding to the imaging angle (φ), determining (2-16) an optimized set of spatial transformation parameters (3-540), wherein the optimized set of spatial transformation parameters, when used for the simulated projection in the preceding step, results in an improved fit with the captured image associated with the imaging angle (φ) compared with the simulated projection without spatial transformation parameters; and e) applying a second reconstruction (2-24) on the sequence of captured images, wherein the second reconstruction is corrected by the optimized set of spatial transformation parameters, thereby creating a transformation-corrected reconstructed volumetric image (3-560). a) obtaining (2-02) a sequence of images captured (1-500) from a three-dimensional (1-400) object by a penetrating radiation imaging apparatus (1-100) over a scanning period, wherein each captured image is associated with a specific imaging angle (φ), and wherein the three-dimensional object is transformed relative to the imaging apparatus in an unknown manner during the scanning period; b) applying an initial reconstruction (2-04) on the sequence of the captured images, thereby creating an initial reconstructed volumetric image (3-510); c) generating a set of simulated images (3-530) corresponding to the imaging angle (φ), by repeatedly applying simulated projections (2-14) on the initial reconstructed volumetric image under a set of varied spatial transformation parameters (3-520) of at least a portion of the initial reconstructed volumetric image relative to the imaging apparatus; d) within the set of the simulated images (3-530) corresponding to the imaging angle (φ), determining (2-16) an optimized set of spatial transformation parameters (3-540), wherein the optimized set of spatial transformation parameters, when used for the simulated projection in the preceding step, results in an improved fit with the captured image associated with the imaging angle (φ) compared with the simulated projection without spatial transformation parameters; and e) applying a second reconstruction (2-24) on the sequence of captured images, wherein the second reconstruction is corrected by the optimized set of spatial transformation parameters, thereby creating a transformation-corrected reconstructed volumetric image (3-560). <EOS>