Systems and methods for creating and viewing three dimensional virtual slides

A computer readable medium having stored thereon one or more sequences of instructions for causing one or more microprocessors to perform the steps for creating three dimensional virtual microscope slides, the steps 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.