System and method for scanning a specimen into a focus-stacked scan

A specimen scanner comprising

• a camera;
• a stage capable of supporting a specimen;
• a light source capable of illuminating said specimen;
• a scanner processor;
• and
• a scanner memory comprising a scanner application, wherein said scanner application directs said scanner processor to
• direct said light source to illuminate said specimen with a light, said
• specimen comprising a topography, the depths of said topography variable along a z-axis;
• divide said specimen into a plurality of regions, each of said regions comprising a regional peak in said topography;
• determine within each of said regions a regional peak position along said z-axis of each of said regional peaks;
• calculate a maximum sampling distance (Δzmax based at least in cart on a characteristic of said light;
• sample each of said regions at a plurality of focal planes orthogonal to said z-axis by capturing with said camera, at each focal plane, an image of said region, said image focused on said focal plane, wherein said plurality of focal planes extends substantially from said regional peak position to a maximum depth, further wherein each of said focal planes is separated from each adjacent focal plane by a sampling distance (Δz) less than or equal to said maximum sampling distance (Δmax);
• focus-stacks, for each said region said images within said region, into a focus-stacked image;
• and
• stitch together said focus-stacked images.

A method for scanning a specimen comprising the steps aiming a camera at a plurality of regions of a specimen, one region at a time;

• illuminating said specimen with one or more lights;
• determining within each of said regions a regional peak position along said z-axis of each of said regional peaks;
• calculating maximum sampling distances (Δzmax) for each of said one or more lights, each said maximum sampling distances (Δzmax) based at least in part on a characteristic of said one or more lights;
• capturing at each of said regions for each of said one or more lights, at a plurality of focal planes for each focal plane, an image of said region, said image focused on said focal plane, wherein said plurality of focal planes extends substantially from said regional peak position to a maximum depth, further wherein for each of said one or more lights each of said focal planes is separated from each adjacent focal plane by a sampling distance (Δz) less than or equal to said maximum sampling distance (Δzmax) associate with a light of said one or more lights presently illuminating said specimen;
• focus-stacking, for each said region said images captured with a common light of said one or more lights, within said region, into a focus-stacked image;
• and
• stitching together said focus-stacked images captured with said common light.