1. A computer implemented method for creating three dimensional virtual microscope slides, comprising: orienting a microscope slide on a stage of an image acquisition device configured to scan the microscope slide and create a digital image of a specimen on the microscope slide; receiving three dimensional scan parameters, the three dimensional scan parameters comprising at least one Z-stack set, wherein a Z-stack set includes a length parameter, a width parameter, and a depth parameter; scanning a two dimensional image of the specimen on the microscope slide; scanning a three dimensional Z-stack in accordance with each of the at least one Z-stack sets, wherein each scanned Z-stack includes a plurality of Z-plane images, each Z-plane image corresponding to the length and width parameters of its respective Z-stack set at a focus depth level within the depth parameter of its respective Z-stack set; combining the two dimensional image of the specimen on the microscope slide with the at least one three dimensional Z-stack; and storing the combined two dimensional image of the specimen on the microscope slide and the at least one three dimensional Z-stack a three dimensional virtual microscope slide.