Photodynamic therapy (PDT) is an alternative treatment for cancer that involves the administration of a photosensitizing agent, which is activated by light at a specific wavelength. In this project, we aim at developing a model-based approach to compare the in vivo photodynamic efficiencies of different photosentizers. Unfortunately, constraints of in vivo experiments are such that it is impossible to estimate all the photophysical parameters. However in this paper, a feasibility study is performed to (i) select the most relevant model parameters and (ii) estimate their value and their confidence interval. Despite the previously mentioned difficulties, the results obtained in practice from in vivo experiments have shown promising results.