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This paper presents the first demonstration of real time 3D tracking of organ deformation based on one-sided, limited view needlescopic optical imaging and a single pre-operative MRI/CT scan. The reconstruction is based on the empirical observation that the spherical harmonic coefficients corresponding to distorted surfaces of any given organ lie in lower dimensional spaces that can be learned during training. The paper discusses the details of the selection of the limited optical views and the registration of the real time partial optical images with the single pre-operative MRI/CT scan. Finally, it demonstrates the first experimental 3D reconstruction of ex-vivo kidneys based on a single MRI scan with 1 mm resolution and real time single side optical imagery achieving spatial resolution of better than 2 mm, even on the hidden organ surface, or less than 1.85% relative error.