received by the International Bureau on 25 June 2015 (25.06.2015)

1. A method of determining at least one thickness parameter of a specimen from a stack of images of the specimen obtained from a microscope at a series of depths , said method comprising:

determining, within a region of interest, sets of patches at a plurality of corresponding transverse locations in each image within the stack of images;

selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the set of patches at the transverse location; and

determining at least one thickness parameter for the specimen at the region of interest from at least a distribution of the selected depth values across the plurality of transverse locations of the region of interest.

2. A method according to claim 1, further comprising forming the distribution from depth values determined at different transverse locations across the specimen.

3. A method according to claim 2, wherein the forming of the distribution comprises determining outlier depth values that exceed a predetermined corresponding thickness parameter and removing the outlier depth values from the distribution before the determining of the at least one revised thickness parameter.

4. A method according to claim 3, wherein the predetermined corresponding thickness parameter is determined at an image level larger than the patches.

5. A method of determining at least one thickness parameter of a specimen from a stack of images of the specimen captured at a series of depths, said method comprising:

determining, within a region of interest, a patch at a corresponding location in each image within the stack of images to form a set of patches;

determining at least one initial thickness parameter of the specimen at the selected region of interest based on a set of contrast metrics computed for the set of patches;

determining sets of sub-patches at a plurality of corresponding transverse locations within each patch in the set of patches;

selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the sub-patches at the transverse location; and

determining at least one revised thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest and the initial thickness parameter.

6. A method according to claim 5 wherein the thickness parameter is selected from the group consisting of a thickness of the specimen, a location of a top surface of the specimen, and a location of a bottom surface of the specimen.

7. A method according to claim 5, further comprising determining outlier depth values that exceed a corresponding thickness parameter and removing the outlier depth values from the distribution before the determining of the at least one revised thickness parameter.

8. A method according to claim 7, wherein the corresponding thickness parameter comprises the initial thickness parameter.

9. A method according to claim 7, wherein the corresponding thickness parameter comprises a value of an upper or lower percentile of determined depth values.

10. A method according to claim 5, further comprising selecting the patch within the region of interest for each image from an aligned stack of patches within the region.

11. A method according to claim 5, wherein the determining of the at least one initial thickness parameter comprises forming estimates of a first and second thickness parameters at the current region of interest based on the set of contrast metrics computed for the set of patches.

12. A method according to claim 5, wherein the determining of the at least one revised thickness parameter comprises analysing the distribution of depth values for the region to 32

obtain current estimates for a top surface location and a bottom surface location of the specimen, the analysing comprising at least one of:

(i) selecting a top surface location from a smallest one of the depth values;

(ii) selecting a bottom surface location from a largest one of the depth values; and

(iii) evaluating a percentile depth value of the distribution as one of the top or bottom surface locations.

13. A method according to claim 12, wherein the determining of the at least one revised thickness parameter comprises forming a correction factor using at least the initial thickness parameter and the current estimates and modifying the current estimates using the correction factor.

14. A method according to claim 13 wherein the initial thickness parameter comprises an initial thickness estimate, and a current thickness estimate comprises a difference of the top surface location and the bottom surface location, and the correction factor is an average of the difference between the initial thickness estimate and the current thickness estimate across the regions of the specimen, and the revised thickness parameter is a revised thickness formed by subtracting the correction factor from the initial thickness estimate.

15. A method according to claim 5, further comprising setting a size of the sub-patches according to a feature size within the specimen.

16. A method according to claim 5, wherein the specimen comprises a stained histology slide.

17. A computer readable storage medium having a program recorded thereon, the program being executable by computerised apparatus to determine at least one thickness parameter of a specimen from a stack of images of the specimen obtained from a microscope at a series of depths, said program comprising:

code for determining, within a region of interest, sets of patches at a plurality of corresponding transverse locations in each image within the stack of images;

code for selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being 33

selected with respect to a best focus defined peak region in a set of contrast metrics computed for the set of patches at the transverse location; and

code for determining at least one thickness parameter for the specimen at the region of interest from at least a distribution of the selected depth values across the plurality of transverse locations of the region of interest.

18. A computer readable storage medium having a program recorded thereon, the program being executable by computerised apparatus to determine at least one thickness parameter of a specimen from a stack of images of the specimen captured at a series of depths, said program comprising:

code for determining, within a region of interest, a patch at a corresponding location in each image within the stack of images to form a set of patches;

code for determining at least one initial thickness parameter of the specimen at the selected region of interest based on a set of contrast metrics computed for the set of patches; code for determining sets of sub-patches at a plurality of corresponding transverse locations within each patch in the set of patches;

code for selecting a depth value associated with a specimen feature located between top and bottom surfaces at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the sub- patches at the transverse location; and

code for determining at least one revised thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest and the initial thickness parameter.

19. A microscope system comprising:

a microscope having a controllable stage upon which a specimen is positionable; a camera for capturing images of the specimen via the microscope; and

a processor system coupled to the camera for receiving and storing the images and for controlling movement of the stage during image capture, the processor system having a memory with a program recorded thereon, the program being executable by a processor to determine at least one thickness parameter of the specimen from a stack of the images of the specimen captured at a series of depths, said program comprising:

code for determining, within a region of interest, sets of patches at a 34

corresponding transverse locations in each image within the stack of images;

code for selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the set of patches at the transverse location; and

code for determining at least one thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest.

20. A microscope system comprising:

a microscope having a controllable stage upon which a specimen is positionable; a camera for capturing images of the specimen via the microscope; and

a processor system coupled to the camera for receiving and storing the images and for controlling movement of the stage during image capture, the processor system having a memory with a program recorded thereon, the program being executable by a processor to determine at least one thickness parameter of a specimen from a stack of images of the specimen captured at a series of depths, said program comprising:

code for determining, within a region of interest, a patch at a corresponding location in each image within the stack of images to form a set of patches;

code for determining at least one initial thickness parameter of the specimen at the selected region of interest based on a set of contrast metrics computed for the set of patches;

code for determining sets of sub-patches at a plurality of corresponding transverse locations within each patch in the set of patches;

code for selecting a depth value associated with a specimen feature located between top and bottom surfaces of the specimen at each transverse location, said depth value being selected with respect to a best focus defined peak region in a set of contrast metrics computed for the sub-patches at the transverse location; and

code for determining at least one revised thickness parameter for the specimen at the region of interest from a distribution of the selected depth values across the plurality of transverse locations of the region of interest and the initial thickness parameter. 35

21. A method according to claim 1, wherein the at least one thickness parameter is determined independently of a determination of a specimen thickness at any of the transverse locations.

22. A method according to claim 1, wherein the at least one thickness parameter is determined based on a comparison of the selected depth values at at least two of the transverse locations.