Method for pre-focus of digital slides

1. A computer implemented method for performing pre-scanning calibration in a digital microscopy system having an objective lens coupled to a line scan camera and a stage for supporting a microscope slide, where one or more processors of the digital microscopy system are programmed to perform steps comprising:

determining a plurality of focus points in a scan area of the microscope slide;

determining an optimal focal height for each of the plurality of focus points, wherein each focus point comprises a planar location on the microscope slide and a height of the objective lens;

identifying at least three focus points to define a first polygonal planar surface;

identifying at least three focus points to define a second polygonal planar surface; and

combining the first polygonal planar surface and the second polygonal planar surface to create a non-planar focal surface.

2. The method of claim 1 , further comprising adjusting the height of the objective lens relative to the stage according to the non-planar focal surface during subsequent scanning of the microscope slide.

3. The method of claim 1 , wherein determining an optimal focal height for each of the plurality of focus points comprises moving the objective lens through a predefined set of height values and acquiring imagery data at each height.

4. The method of claim 3 , further comprising calculating a contrast value for each height.

5. The method of claim 1 , wherein determining an optimal focal height for each of the plurality of focus points comprises moving the objective lens according to a prescribed motion profile.

6. The method of claim 5 , wherein the prescribed motion profile is an oscillatory profile.

7. The method of claim 6 , wherein the oscillatory profile is selected from the group consisting of sinusoidal, triangular, and saw-tooth profiles.

8. The method of claim 1 , wherein the scan area of the microscope slide comprises a linear strip, further comprising scanning an image of the linear strip in accordance with the non-planar focal surface.

9. The method of claim 8 , further comprising performing slide illumination correction on the scanned image.

10. The method of claim 9 , wherein performing slide illumination correction comprises determining image data from the scanned image and adjusting the image data with a pixel gain value.

11. The method of claim 10 , wherein the image data comprises a recorded pixel value and the adjusting comprises multiplying the recorded pixel value by the pixel gain value.

12. The method of claim 1 , wherein the first polygonal planar surface is triangular.

13. The method of claim 12 , wherein a triangular planar surface is defined using Delaunay triangulation methods.

14. The method of claim 12 , wherein the second polygonal planar surface is triangular.

15. A computer implemented method for creating a digital image of a specimen on a microscope slide using a digital microscopy system having an objective lens coupled to a line scan camera and a stage for supporting a microscope slide, where one or more processors of the digital microscopy system are programmed to perform steps comprising:

determining a scan area of the microscope slide according to a specimen finder procedure, wherein the scan area includes at least a portion of the specimen;

determining a plurality of focus points in the scan area, wherein a focus point comprises a planar location on the microscope slide and an objective lens height;

creating a plurality of polygonal planar surfaces, wherein each polygonal planar surface comprises a planar surface connecting at least three of the plurality of focus points;

combining the plurality of polygonal planar surfaces to create a non-planar focal surface;

scanning an image of the scan area, wherein the height of the objective lens relative to the microscope slide during said scanning follows the non-planar focal surface; and

displaying the image of the scan area as an image of the specimen.

16. The method of claim 15 , wherein the scan area of the microscope slide is divided into a plurality of linear strips, further comprising creating a non-planar focal surface for each linear strip.

17. The method of claim 16 , further comprising displaying an image of the first linear strip and an image of the second linear strip as a contiguous image of the specimen.

18. The method of claim 15 , wherein the scan area of the microscope slide includes the entire specimen, further comprising combining the plurality of polygonal planar surfaces to create a non-planar focal surface of the entire specimen.

19. A system for creating a digital image of a specimen on a microscope slide, comprising:

a stage configured to support a microscope slide having a specimen;

an objective lens;

a motion control system configured to move the stage and continuously adjust the height of the objective lens relative to the stage while the stage is in motion;

a line scan camera coupled with the objective lens, wherein the line scan camera is configured to scan an image of an area of the specimen while the stage is moving;

a processor configured to determine a plurality of focus points in a scan area of the microscope slide, determine an optimal focal height for each of the plurality of focus points, wherein each focus point comprises a planar location on the microscope slide and a height of the objective lens, identify at least three focus points to define a first polygonal planar surface, identify at least three focus points to define a second polygonal planar surface, and combine the first polygonal planar surface and the second polygonal planar surface to create a non-planar focal surface.

20. The system of claim 19 , wherein the non-planar focal surface covers a portion of the specimen on the microscope slide.

21. The system of claim 20 , wherein the portion of the specimen substantially corresponds to an image stripe.