Congenital heart disease, the most common birth defect, occurs up to 5% of live births in humans. Understanding the relationship between morphology and function during development in the embryonic heart has important medical implications. Our studies focus on developing non-invasive heart imaging tools to observe the dynamics of morphogenesis while the heart is growing and functioning. Our approach consists in setting up a computer-driven automated microscope equipped with high-speed and sensitive cameras, implementing sample mounting protocols, and developing image reconstruction and analysis software. In order to improve the specificity with which structures can be imaged in the beating heart, we developed multi-modal microscopy by combining high-speed and multi-color sequences taken in brightfield and fluorescence microscopy, respectively. In an effort to improve axial resolution in conventional widefield microscopy, we implemented dynamic optical projection tomography. To quantify variability when characterizing heart function, we developed in vivo high-throughput microscopy. Finally, we carried out joint and quantitative studies of heart morphogenesis and functiogenesis by use of a novel imaging technique, burst time-lapse microscopy (BTLM). This allowed building time-lapses revealing the morphogenesis of the highly dynamic cardiac valve leaflets as they progressively prevent retrograde flow between cardiac chambers. This work provides new insights into cardiogenesis and should allow better understanding of normal and diseased development. We anticipate that the developed tools will be applicable for imaging a wide range of dynamic biological samples.