This study involves the reconstruction of a distortion-free ultrahigh-resolution 3D model of a whole murine heart. This is achieved by multimodal registration of serial images generated by confocal laser scanning microscopy (CLSM) with the aid of a micro-CT 3D image as a template. High-resolution information from CLSM is utilized for study of fine soft tissue structures in 3D, including fiber orientation and gap junctions. CLSM requires physical sectioning of the sample resulting in missing tissue and in various degrees of tissue distortion depending on thickness. The micro-CT data are distortion free and provide complete information on whole-object interfaces both external and internal. However, they do not provide information on the soft-tissue fine structure. In this project, we used a micro-CT image as template to spatially co-register all the individual CLSM images and to correct the resulting volume for distortion.