1. A computer implemented method of determining feature locations in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array, the method comprising: (a) presenting on a display a complete image of the array or a sub-array; (b) presenting on the display magnified images of corner regions of the displayed complete image simultaneously with the complete image; (c) receiving a user selection of corners for the array or sub-array and generating an array or sub-array actual outline by linearly connecting the user selected corners; (d) presenting the generated actual outline simultaneously on the displayed complete and magnified images; (e) determining feature locations in the array or sub-array image based on the actual outline.