Head and neck squamous cell carcinomas (HNSCC) are a type of cancer which are now becoming a serious health issue in Taiwan, due to prevalent alcohol and tobacco use. Patients usually need to take biopsy in order to examine the tumor’s condition. Since there are many evidences showing that the production of collagen fibrils are found related with tumor clones. The collagen’s birefringent patterns, which are distinctive to other tissues, can be applied to investigate in HNSCC studies. Here we implemented the theoretical model of collagen birefringence under the basis of Jones Calculus by scientific programming to research the collagens optical properties in tumors. The slides of beef tendons and HNSCCs are tested in our experiment. We also constructed the polarized microscopy system with Whole Slide Imaging (WSI) to map the distribution of retardance and orientation of birefringence in HNSCC slides for 19 patients. Results of our program tests showed the good quality of the fitting for the orientation and retardance.