One of the main problems of the decellularization technique is the subjectivity of the final evaluation of its efficacy in individual organs. This problem can result in restricted cell repopulation reproducibility and worse responses to transplant tissues. Our proposal is to analyze the optical profiles produced by hearts during perfusion decellularization, as an additional method for evaluating the decellularization process of each individual organ. An apparatus comprised of a structured LED source and photo detector on an adjustable base was developed to capture the relationship between transmitted light during the perfusion of murine hearts, and residual DNA content. Voltage-time graphic records were used to identify a nonlinear mathematical model to discriminate between decellularizations with remaining DNA above (Incomplete Decellularization) and below (Complete Decellularization) the standardized limits. The results indicate that temporal optical evaluation of the process enables inefficient cell removal to be predicted in the initial stages, regardless of the apparent transparency of the organ. Our open system also creates new possibilities to add distinct photo detectors, such as for specific wavelengths, image acquisition, and physical-chemical evaluation of the scaffold, in order to collect different kinds of information, from dozens of studies. These data, when compiled and submitted to machine learning techniques, have the potential to initiate an exponential advance in tissue bioengineering research.