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The incorporation of anatomical reference images into limited view transmission tomography has been attempted previously by using the joint entropy prior. However, this prior has been found to be sensitive to local optima. Here, we propose to increase robustness to local optima by using a multiresolution optimisation scheme. To our knowledge, this is the first work to apply multiresolution optimisation to the joint entropy prior in limited view transmission tomography. The results show a substantial mitigation of the sensitivity to local optima, as well as a robustness to missing as well as extra regions in the anatomical reference image. In addition, we demonstrate the method's robustness to misalignment between the reconstruction and the anatomical reference image.