Methods for energy-sensitive computed tomography systems that use checkerboard filtering. A method of enhancing image analysis of projection data acquired using a detector configured with a checkerboard filter includes disposing in a system a detector to receive a transmitted beam of X-rays traversing through an object, where the system is configured so the detector receives both high- and one of total- and low-energy projection data; receiving the high- and one of total- and low-energy projection data at the detector; and then estimating an effective atomic number of the object and/or processing the projection data so as to mitigate reconstruction artifacts. The present invention has been described in terms of specific embodiment(s), and it is recognized that equivalents, alternatives, and modifications, aside from those expressly stated, are possible and within the scope of the appended claims.