An integrated instrument is being developed to study live cardiac trabeculae, which is capable of stimulating the muscle under controlled conditions while measuring the heat production, force, and sarcomere length distribution. To improve the accuracy of estimation of stress, strain, and volumetric heat production, the geometry of the muscle must be known. A spectral domain optical coherence tomography system (SD-OCT) has been constructed and calibrated to image the trabecula mounted inside the instrument. This system was mounted above the muscle chamber and a series of equally-spaced cross-sectional images were obtained. These were processed using a workflow developed to extract cross-sectional area and volume. The initial results have demonstrated the feasibility of using OCT to capture the overall geometry of cardiac trabecula mounted in the instrument. Further work will be directed to improve the image quality for larger samples and apply meshing algorithms to the acquired data.