The heart is a crucial organ that drives the circulatory system. However, it is vulnerable to cardiovascular diseases like atrial fibrillation (AF). To understand the mechanisms of AF and develop effective treatments, it is necessary to accurately reconstruct the geometry of the heart. This study validates a customized 3D mapping technique against 3D Slicer segmentation using hearts of New Zealand rabbits. For the in-house method, the heart was Langendorff-perfused, stained, and imaged using a custom setup that captured electric and fluorescence electrophysiological signals. The geometry reconstruction of the heart involved image acquisition, calibration, silhouette identification, volume carving, and mesh refinement. For the 3D Slicer segmentation, it was necessary to acquire MRI images of the heart. The images were segmented using seed points to grow the segmentation region, which was used to generate the 3D volume of the heart. To compare the resulting segmentations, the Dice coefficient analysis was performed, demonstrating a good overlap (0.74) between the in-house and Slicer segmentations, despite visual differences attributed to MRI-induced distortions. While the study validates the in-house method, improving MRI techniques could enhance segmentation accuracy. This research highlights the importance of precise heart geometry reconstruction in understanding and treating AF, thus providing valuable insights for the electroanatomical study of complex arrhythmias, which can positively interfere with clinical practice.