Background Cardiac structure and function results from complex interactions between genes, molecular regulators and environmental factors. Until recently, imaging-genetics studies had limited power as standard methods of cardiac phenotyping rely on global indices of mass and function, providing only macroscopic descriptors. Manual analysis of large cohorts is time consuming and subject to interobserver variability. Current cardiac magnetic resonance (CMR) cine imaging techniques are limited by poor through-plane resolution. Here we present a high resolution 3D left ventricular atlas with automated segmentation.