The present disclosure includes methods of assessing a histologically stained specimen based on a determined color signature of a region of interest of the specimen. Such assessments may be performed for a variety of purposes including but not limited to assessing the quality of the histological stain, as part of identifying one or more biologically relevant features of the image, as part of differentiating one feature of the image from other features of the image, identifying an anomalous area of the stained specimen, classifying cells of the specimen, etc. Also provided are systems configured for performing the disclosed methods and computer readable medium storing instructions for performing steps of the disclosed methods.