A method is provided for characterizing color separation misregistration of a printer device using color separations of a color space for marking substrate. The method includes providing an input image including a pattern of patches including at least one measurement patch, each measurement patch having at least a first and second color separation of the color space, and marking a substrate in accordance with the input image for generating an output image having a marked pattern of patches which corresponds to the pattern of patches. Spectral reflectance of at least one respective patch of the marked patch pattern of the output image is measured and respective spectral reflectance values corresponding to the measuring are generated. Misregistration is characterized between the at least first and second color separations of each measurement patch of the at least one measurement patch based on the spectral reflectance values.