1. A method for estimating the probe cell locations in a hybridized microarray, comprising: obtaining an image of the intensity of a microarray having a plurality of individual probe cells; estimating the center of individual probe cell locations in the image to provide the first estimated locations of the centers of estimated probe cell locations; and for respective probe cell locations undergoing analysis: generating a first fitting region that has a center that coincides with the location of the first estimated center and that has a boundary that can include partial pixel volumes; obtaining pixel intensity data of the first fitting region; generating a second fitting region that has a center that is spaced apart from the center of the first fitting region by less than about one pixel, the second fitting region having a boundary that can include partial pixel volumes; obtaining pixel intensity data of the second fitting region; comparing the variance of pixel intensity from the first and second fitting regions; and determining the likely estimated probe cell location in the image based on the step of comparing the pixel intensity data in the first and second fitting regions.