1. A method of automatically identifying microarray chip corners and probes in a high density and high resolution microarray scanned image having an image space comprising the steps of: (a) applying a Radon transform to an input microarray image to project the image into an angle and distance space where it is possible to find the orientation of the straight lines; (b) applying a fast Fourier transform to the projected image of (a) and applying a heuristic to find the optimal tilting angle of the projected image; (c) applying a heuristic for determining the optimal first and last local maxima for the optimal tilting angle; (d) back projecting the determined first and last local maxima to the image space to find the first approximation of the first and last column lines of the image; (e) rotating the image and repeating steps (a) through (d) to find the first approximation of the top and bottom row lines of the image; (f) determining the first approximation of the four corners of the image from the intersection of the column and row lines; (g) applying a heuristic for determining if the first approximation of step (f) is accurate; and (h) if the approximation is not accurate, trimming the scanned image around the first approximation of the four corners and repeating steps (a) through (f).