1. A system for capturing imagery data using a line scan camera, comprising: a motorized stage configured to move a slide in an X axis direction and a Y axis direction; a line scan camera configured to capture imagery data from the slide, wherein the imagery data is organized as a plurality of image stripes, each image stripe comprising a plurality of scan lines; an objective lens in the optical path of the line scan camera; a positioning element configured to adjust a position of the objective lens in a Z axis direction; at least one memory for storing a first stripe of imagery data from the line scan camera and a second stripe of imagery data from the line scan camera; a processor configured to instruct the positioning element to adjust the position of the objective lens in the Z axis during the capture of the first stripe of imagery data and the second stripe of imagery data, the processor further configured to copy a first plurality of image portions from the first stripe and a second plurality of image portions from the second stripe and store the first plurality of image portions and second plurality of image portions as a contiguous digital image in said at least one memory.