The above protocol outlines key steps to generate a novel finite element geometric model of cardiomyocyte ultrastructure. The method enables computational fusion of different microscopy (or, in principle, other data) modalities to develop a more comprehensive computational model of cardiomyocyte dynamics that includes details of spatial cell architecture. There is currently no other protocol available to create such a model of a cardiomyocyte. Step 1 outlines a protocol for perfusion fixation.