A microscope slide scanner for creating a contiguous digital image of a portion of a microscope sample, comprising: a motorized stage configured to support a microscope sample and move the microscope sample in a first manner and a second manner, the first manner being movement of the microscope sample in a sample plane at a substantially constant velocity along a primary axis of travel, and the second manner being movement of the microscope sample along a secondary axis that is orthogonal to the primary axis of travel and in the sample plane; an illumination system configured to illuminate the portion of the microscope sample; at least one objective lens positioned along an optical axis centered about the portion of the microscope sample illuminated by the illumination system and orthogonal to the sample plane; at least one line scan camera having a linear field of view of the portion of the microscope sample illuminated by the illumination system and orthogonal to the primary axis of travel; at least one focusing optics whereby an optical signal from the objective lens is focused onto an image plane that is orthogonal to the optical axis; a data processor configured to synchronize motion of the microscope sample with the at least one line scan camera to digitize, process, and store image data to create a digital image strip of the portion of the microscope sample, the motion being movement of the microscope sample in the first manner to acquire a first digital image strip of the microscope sample, followed by movement of the microscope sample in the second manner to position the at least one line scan camera for acquiring a second digital image strip, and repeating this motion as necessary for generating a complete image of the portion of the microscope sample, wherein the data processor is further configured to pre-scan and map the best focus as a function of x/y position of the motorized stage to provide a pre-scanned focus map and to move the z position of the microscope objective lens in accordance with the pre-scanned focus map during the scanning process. a motorized stage configured to support a microscope sample and move the microscope sample in a first manner and a second manner, the first manner being movement of the microscope sample in a sample plane at a substantially constant velocity along a primary axis of travel, and the second manner being movement of the microscope sample along a secondary axis that is orthogonal to the primary axis of travel and in the sample plane; an illumination system configured to illuminate the portion of the microscope sample; at least one objective lens positioned along an optical axis centered about the portion of the microscope sample illuminated by the illumination system and orthogonal to the sample plane; at least one line scan camera having a linear field of view of the portion of the microscope sample illuminated by the illumination system and orthogonal to the primary axis of travel; at least one focusing optics whereby an optical signal from the objective lens is focused onto an image plane that is orthogonal to the optical axis; a data processor configured to synchronize motion of the microscope sample with the at least one line scan camera to digitize, process, and store image data to create a digital image strip of the portion of the microscope sample, the motion being movement of the microscope sample in the first manner to acquire a first digital image strip of the microscope sample, followed by movement of the microscope sample in the second manner to position the at least one line scan camera for acquiring a second digital image strip, and repeating this motion as necessary for generating a complete image of the portion of the microscope sample, wherein the data processor is further configured to pre-scan and map the best focus as a function of x/y position of the motorized stage to provide a pre-scanned focus map and to move the z position of the microscope objective lens in accordance with the pre-scanned focus map during the scanning process.