1. A method for creating an image of at least a portion of a three-dimensional semi-transparent biological specimen, said method comprising the steps of: a) positioning a microscope slide under a microscope, said microscope slide comprising a three-dimensional biological specimen, said three-dimensional biological specimen comprising cells, said cells being located on different z-axis planes; b) obtaining a stack of images, said stack comprising a plurality of slices of said portion of said specimen, each of said plurality of slices comprising an image of said specimen obtained from a different focal distance, each of said slices comprising a plurality of pixels, said stack of images comprising images of at least two cells each of said at least two cells located on different z-axis planes; c) performing at least one of a closing and a dilation on said plurality of slices; d) calculating the sharpness values of said plurality of pixels in said plurality of slices in said stack and storing max-sharpness values for said plurality of pixels; and e) comparing the sharpness values for pixels in specific locations on a slice to stored max-sharpness values for pixels corresponding to said specific locations on previous slices in a stack.