Abstract: Described herein are techniques for denoising images of samples produced using polarization microscopy. Polarization images captured by polarization microscopy contain not only signals produced from polarization, but also signals produced from scattering by artifacts (e.g., crystals and/or hemosiderin). These off-target signals reduce the signal-to-noise ratio (SNR) of the birefringent substance of interest, and reduce the utility and accuracy of polarization microscopy for substance quantification. The techniques developed by the inventors and described herein reduce noise resulting from scattering, thus enabling much cleaner, noise-reduced images. The images so produced can be either directly visualized by a medical practitioner or used for downstream machine-learning models. Noise reduction involves i) dividing an image in segments (e.g., pixels or groups of pixels), ii) performing spectral analysis of each segment, and iii) separating each segment on the basis of its spectral profiles.