1. A method of registering images captured by a computer controlled microscope, comprising: partitioning a microscopic image into a series of segments, wherein each segment comprises a discrete portion of the microscopic image; capturing image data for each of the segments, wherein the image data for each segment includes at least one duplicate region of image data that overlaps with the image data of an adjacent segment; determining an anchor-segment by which all adjacent segments will be compared; aligning the segments with one another to create a single macroscopic image comprised of the aligned segments.