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This paper addresses the reconstruction of high-resolution omnidirectional images from multiple low-resolution images with inexact registration. When omnidirectional images from low-resolution vision sensors can be uniquely mapped on the 2-sphere, such a reconstruction can be described as a transform-domain super-resolution problem in a spherical imaging framework. We describe how several spherical images with arbitrary rotations in the SO(3) rotation group contribute to the reconstruction of a high-resolution image with help of the spherical Fourier transform (SFT). As low-resolution images might not be perfectly registered in practice, the impact of inaccurate alignment on the transform coefficients is analyzed. We then cast the joint registration and super-resolution problem as a total least-squares norm minimization problem in the SFT domain. A l1-regularized total least-squares problem is considered and solved efficiently by interior point methods. Experiments with synthetic and natural images show that the proposed methods lead to effective reconstruction of high-resolution images even when large registration errors exist in the low-resolution images. The quality of the reconstructed images also increases rapidly with the number of low-resolution images, which demonstrates the benefits of the proposed solution in super-resolution schemes. Finally, we highlight the benefit of the additional regularization constraint that clearly leads to reduced noise and improved reconstruction quality.