Method and system for spectral imaging of density, anisotropy, and orientation

A system comprising:

• an illumination source;
• a specimen stage operable to support a specimen;
• imaging optics;
• a polarization state analyzer optically coupled to the imaging optics;
• and
• one or more processors in communication with the illumination source and the polarization state analyzer, the one or more processors configured to perform operations comprising:
• generating a plurality of illumination wavelengths;
• positioning the specimen at a plurality of specimen positions and orientations;
• receiving an array of multiple sets of polarization channels from the polarization state analyzer;
• receiving a calibration tensor associated with the imaging optics;
• converting the array of multiple sets of polarization channels into Stokes parameter maps;
• deconvolving the Stokes parameter maps to provide 3D density, 3D anisotropy, and 3D orientation measurements of the specimen at multiple wavelengths;
• denoising the Stokes parameter maps to sensitively detect changes in density, anisotropy, and orientation using data correlation across spatial and temporal dimensions;
• and
• segmenting specific structures from dispersion of density, anisotropy, and orientation from above measurements.