1. A computer implemented method of registering images captured by a computer controlled microscope, comprising: partitioning a microscope image of a microscope slide having a biological sample into a series of segments, wherein each segment comprises a discrete portion of the microscopic image; classifying each segment as either an interesting segment that contains at least a portion of the sample or a non-interesting segment that contains none of the sample; 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, wherein the anchor segment is determined based on which segment has the highest number of adjacent interesting segments; and aligning the segments with one another to create a single macroscopic image comprised of the aligned segments.