1. A computer implemented method for managing imagery data produced by a microscope slide scanner, the method comprising: receiving a first stripe of imagery data from the microscope slide scanner and storing the first stripe in a buffer memory; receiving a second stripe of imagery data from the microscope slide scanner and storing the second stripe in a buffer memory, wherein an edge of the second stripe overlaps an edge of the first stripe to define a first overlap area; aligning the second stripe with the first stripe; copying a first plurality of image portions from the first stripe; storing each of the first plurality of image portions as an image tile of a baseline image in a virtual slide image file; copying a second plurality of image portions; and storing each of the second plurality of image portions as an image tile of the baseline image in the virtual slide image file, wherein each of said second plurality of image portions comprises a portion of imagery data from the first overlap area.