Mueller transmission microscopy has been used for both theoretical and experimental studies of anisotropic scattering biological tissue. In our prior study, the linear dependence of retardance and quadratic dependence of depolarization on thickness was demonstrated for a dermal layer of skin model. During the primary analysis of polarimetric images of histological cuts both epidermal and dermal layers were delineated manually in order to calculate the spatially averaged values of retardance and depolarization parameters. Consequently, these average values contained the contribution of outliers (noise, not correctly identified pixels, etc.) which produces large standard deviation and biased mean values of the parameters mentioned above. For preventing the errors, the normalized maps of optical properties were calculated pixel-wise taking into account local optical density (e. i. logarithm of M11 element of Mueller matrix at each image pixel) to compensate varying tissue thickness across the cut area. Furthermore, the DBSCAN (Density-based spatial clustering of applications with noise) algorithm was applied for segmentation of microscopic images using the normalized values of retardance, depolarization, and intensity. From the results of image segmentation, we could discriminate the regions of dermal and epidermal layers in Muller microscopic images of skin cuts more accurately and obtain more reliable values of tissue’s optical properties.