1. A system for creating and viewing three dimensional virtual microscope slides, comprising: an image acquisition device configured to scan a microscope slide and create a digital image of a specimen on the microscope slide; an image data server communicatively coupled with the image acquisition device, the image data server configured to receive virtual microscope slide images from the image acquisition device, store the virtual microscope slide images, and provide the virtual microscope slide images upon request; an image viewing workstation communicatively coupled with the image acquisition device and the image data server, the image viewing workstation configured to display a two dimensional image of a specimen on a microscope slide in the image acquisition device, receive commands from an operator, and in response to said commands, instruct the image acquisition device to capture a Z-stack of images from the specimen on the microscope slide; wherein the image data server is further configured to store said Z-stack of images with said two dimensional image to create a three dimensional virtual microscope slide.