1. A method for producing an image of a region of interest while correcting artifacts caused by sub-objects within the region of interest, the method comprising: (a) receiving three-dimensional image data of the region of interest; (b) receiving a library of shape information and imaging characteristics of the sub-objects; (c) using the three-dimensional image data and the library to produce images of the sub-objects in the region of interest; (d) using an optimization process to produce segmented images of the sub-objects in the region of interest; (e) using the segmented images to produce error projections; and (f) using the error projections to produce the projection images of the region of interest such that the artifacts are corrected in the image; (g) performing a tomographically reconstructed image of the region of interest from the corrected projection images.