System calibration is a crucial step for improving the accuracy of the Mueller matrix microscope, many calibration methods have been proposed and widely used in practice. Most existing calibration methods adopt modeled or un-modeled strategy for the entire system. In this paper, we propose a hybrid calibration method to reduce systematic errors of the Mueller matrix microscope. By considering the characteristics of polarization state generator (PSG) and polarization state analyzer (PSA), we adopt modeled strategy for PSG and un-modeled strategy for PSA, therefore combines the advantages of both modeled and un-modeled calibration methods. By measuring only two reference samples to solve the error model of the PSG and then reconstructing the instrument matrix of PSA. Hybrid calibration method is validated on different Mueller matrix microscopes established in our previous studies, the results show that this method can perform satisfactorily on Mueller matrix microscope with different PSG & PSA schemes, numerical apertures, wavelengths, and optical geometries.
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