A payload recovery system includes a reference halftone image of a data-bearing halftone image and a reference map of the data-bearing halftone image. The system further includes a cell alignment system for receiving a scanned image of a hard copy of the data-bearing halftone image and for generating an aligned scan of the scanned image using the reference halftone image and the reference map. A raw payload recovery system determines possible shift positions of each carrier cell of the aligned scan using a shift rule and the reference map; and a reconstructed data-bearing halftone image is generated by the raw payload recovery system using the possible shift positions and the reference halftone. The system also includes a recovered raw payload generated by the raw payload recovery system using the shift rule and the reference map.