We present a novel method to acquire whole-heart 3D image-based navigators (iNAVs) for tracking and correction of localized motion in free-breathing coronary angiography. More specifically, a variable-density, phyllotaxis-based trajectory is utilized for homogeneous sampling of the desired k-space extent. To reconstruct the 3D iNAVs, a locally low rank regularized iterative scheme is implemented. Across all volunteer studies, compared to 3D iNAVs generated with prior design and reconstruction strategies, the proposed 3D iNAVs provide superior delineation of the structures of interest. Application of the proposed 3D iNAVs for motion correction in volunteer studies yields improved depiction of the coronary arteries.