Optical system polarizer calibration

A method to calibrate a polarizer in a polarized optical system at any angle of incidence, by decoupling a polarization effect of the system from a polarization effect of a sample, the method comprising the steps of:

• providing a calibration apparatus comprising a substrate with a polarizer, with an indicator on the substrate for indicating a polarization orientation of the polarizer,
• loading the calibration apparatus in the polarized optical system with the indicator in a desired position,
• determining an initial angle between the polarization orientation of the calibration apparatus and a reference of the polarized optical system,
• acquiring signals based on optical readings of the calibration apparatus using the polarized optical system at a plurality of known angles between the polarization orientation of the calibration apparatus and the reference of the polarized optical system,
• using the signals to plot a curve indicating an angle of a polarizer in the polarized optical system, and
• when the angle of the polarizer in the polarized optical system is outside of a desired range, adjusting the angle of the polarizer in the polarized optical system, and repeating the steps of acquiring the signals, and plotting a curve indicating the angle of the polarizer in the polarized optical system.