Gene expression levels are obtained from microarray experiments through the extraction of pixel intensities from a scanned image of the slide. It is widely acknowledged that variabilities can occur in expression levels extracted from the same images by different users with the same software packages. These inconsistencies arise due to differences in the refinement of the placement of the microarray grids. We introduce a novel automated approach to the refinement of grid placements that is based upon the use of Bayesian inference for determining the size, shape and positioning of the microarray spots, capturing uncertainty that can be passed to downstream analysis.