A system for generating a composite digital image of a biological sample comprising: a computer apparatus configured to generate a composite image of the biological sample from a plurality of images of the biological sample, each of the plurality of images taken along a single axis, wherein the computer: (a) identifies a first focal plane, wherein the first focal plane comprises a first z distance, for a first collection of image objects at a first x-y location of the biological sample, and (b) identifies a second focal plane, wherein the second focal plane comprises a second z distance, for a second collection of image objects at a second x-y location of the biological sample, and (c) identifies a first optimal focal plane and a second optimal focal plane based on (a) and (b) respectively, and (d) combines image objects from the first optimal focal plane and image objects from the second optimal focal plane and generates the composite digital image, wherein the computer apparatus calculates a sharpness value for the image objects in the first focal plane and calculates a sharpness value for the image objects in the second focal plane and generates a two-dimensional map of a z-index of the objects having the highest sharpness values, and wherein the computer apparatus identifies a first optimal focal plane and second optimal focal plane for the first and second collection of image objects by performing a number of dilations followed by an equal number of erosions on the two-dimensional map of the z-index of the image objects having highest sharpness values in the first and second focal planes wherein the number of dilations and erosions is proportional to a distance between cell objects of interest in healthy tissue, so as to thereby identify a first and a second optimal focal plane, and wherein image objects located on the first optimal focal plane are presented in-focus and image objects below the first optimal focal plane are deemphasized, and wherein image objects located on the second optimal focal plane are presented in-focus and image objects below the second optimal focal plane are deemphasized. a computer apparatus configured to generate a composite image of the biological sample from a plurality of images of the biological sample, each of the plurality of images taken along a single axis, wherein the computer: (a) identifies a first focal plane, wherein the first focal plane comprises a first z distance, for a first collection of image objects at a first x-y location of the biological sample, and (b) identifies a second focal plane, wherein the second focal plane comprises a second z distance, for a second collection of image objects at a second x-y location of the biological sample, and (c) identifies a first optimal focal plane and a second optimal focal plane based on (a) and (b) respectively, and (d) combines image objects from the first optimal focal plane and image objects from the second optimal focal plane and generates the composite digital image, wherein the computer apparatus calculates a sharpness value for the image objects in the first focal plane and calculates a sharpness value for the image objects in the second focal plane and generates a two-dimensional map of a z-index of the objects having the highest sharpness values, and (a) identifies a first focal plane, wherein the first focal plane comprises a first z distance, for a first collection of image objects at a first x-y location of the biological sample, and (b) identifies a second focal plane, wherein the second focal plane comprises a second z distance, for a second collection of image objects at a second x-y location of the biological sample, and (c) identifies a first optimal focal plane and a second optimal focal plane based on (a) and (b) respectively, and (d) combines image objects from the first optimal focal plane and image objects from the second optimal focal plane and generates the composite digital image, wherein the computer apparatus calculates a sharpness value for the image objects in the first focal plane and calculates a sharpness value for the image objects in the second focal plane and generates a two-dimensional map of a z-index of the objects having the highest sharpness values, and wherein the computer apparatus identifies a first optimal focal plane and second optimal focal plane for the first and second collection of image objects by performing a number of dilations followed by an equal number of erosions on the two-dimensional map of the z-index of the image objects having highest sharpness values in the first and second focal planes wherein the number of dilations and erosions is proportional to a distance between cell objects of interest in healthy tissue, so as to thereby identify a first and a second optimal focal plane, and wherein image objects located on the first optimal focal plane are presented in-focus and image objects below the first optimal focal plane are deemphasized, and wherein image objects located on the second optimal focal plane are presented in-focus and image objects below the second optimal focal plane are deemphasized.