A system for providing fully automated image segmentation and quality control of a protein array with no human interaction is presented. The system includes a memory and a processor configured by the memory. The processor is configured to receive an image file of the protein array, to geometrically distinguish a first block within the image, register a nominal location of the first block to the image by assigning a geometric code identifying the first block, draw a plurality of grid line on the array to delineate the first block from a second block, iteratively cluster a sub image for each feature in the delineated blocks to define a foreground area and a background area, identify pixels containing an artifact for each feature, and extract and return the signal intensity, variance, and quality of background and foreground pixels in each feature.