Systems and methods for automatically excluding artifacts from an analysis of a biological specimen image are disclosed. An exemplary method includes obtaining an immunohistochemistry (IHC) image and a control image, determining whether the control image includes one or more artifacts, upon a determination that the control image includes one or more artifacts, identifying one or more artifact regions within the IHC image by mapping the one or more artifacts from the control image to the IHC image, and performing image analysis of the IHC image where any identified artifact regions are excluded from the image analysis.