In this paper we present an image stitching method based on dynamic programming and describe its application to automated slide acquisition for Virtual Microscopy (VM). Given a large number of fields of view (FOVs) acquired from a single microscope slide, we composite these images into a single large ?virtual slide? image. The location of each FOV is determined using a new algorithm based on dynamic programming. We compare the performance of the proposed algorithm to an existing greedy algorithm. In a visual trial it is shown that the new algorithm provides a significant improvement in perceived image quality at image boundaries compared to the existing algorithm.