An image analysis system for analyzing biological specimen images, the image analysis system comprising: an image registration engine configured to: obtain an immunohistochemistry image and a control image; perform a registration operation to align the IHC image and the control image; compute a distance value between two point sets p1 and p2, whereby p1 comprises positions of objects in the aligned IHC image and p2 comprises positions of corresponding objects in the aligned control image; determine that the IHC image and the control image are structurally similar if and only if the computed distance value is below a predefined threshold; an artifact detection engine configured to: upon a determination by the image registration engine that the IHC image and the control image are structurally similar; determine that the control image includes one or more artifacts, and upon a determination that the control image includes the one or more artifacts, identify one or more artifact regions within the IHC image by mapping a region of the control image that includes the one or more artifacts to a corresponding region of the IHC image; and an image analysis engine configured to perform an image analysis of the IHC image, wherein the one or more artifact regions are excluded from the image analysis based on a determination that the IHC image and the control image are structurally similar. an image registration engine configured to: obtain an immunohistochemistry image and a control image; perform a registration operation to align the IHC image and the control image; compute a distance value between two point sets p1 and p2, whereby p1 comprises positions of objects in the aligned IHC image and p2 comprises positions of corresponding objects in the aligned control image; determine that the IHC image and the control image are structurally similar if and only if the computed distance value is below a predefined threshold; obtain an immunohistochemistry image and a control image; perform a registration operation to align the IHC image and the control image; compute a distance value between two point sets p1 and p2, whereby p1 comprises positions of objects in the aligned IHC image and p2 comprises positions of corresponding objects in the aligned control image; determine that the IHC image and the control image are structurally similar if and only if the computed distance value is below a predefined threshold; an artifact detection engine configured to: upon a determination by the image registration engine that the IHC image and the control image are structurally similar; determine that the control image includes one or more artifacts, and upon a determination that the control image includes the one or more artifacts, identify one or more artifact regions within the IHC image by mapping a region of the control image that includes the one or more artifacts to a corresponding region of the IHC image; and upon a determination by the image registration engine that the IHC image and the control image are structurally similar; determine that the control image includes one or more artifacts, and upon a determination that the control image includes the one or more artifacts, identify one or more artifact regions within the IHC image by mapping a region of the control image that includes the one or more artifacts to a corresponding region of the IHC image; and an image analysis engine configured to perform an image analysis of the IHC image, wherein the one or more artifact regions are excluded from the image analysis based on a determination that the IHC image and the control image are structurally similar.