Method and system of determining the stain quality of slides using scatter plot distribution

Methods, systems, and computer software for determining the stain quality of a plurality of biological specimens. A number of objects of interest are identified in a biological specimen. A first feature of each object of interest (e.g., nuclear area) and a second feature of each object of interest (e.g., nuclear integrated optical density) are measured, and a scatter plot of the first and second features is generated. The stain quality of the specimens are determined based on the distribution of points within the scatter plot.