Abstract: An imaging system generates an image of a specimen by acquiring images of individual portions of the specimen and combining the images to form a composite image. The system moves the specimen to a set of predetermined locations such that all portions of the specimen are captured into images. At each location, images are heuristically acquired at a different distance from an acquisition lens, and the image with the sharpest focus is selected. The selected images are combined to form a composite image by computing and removing overlapping regions of the adjacent images with sub-pixel spatial accuracy. And, the system is capable of imaging thick specimens with high topological variations.