Fast auto-focus in imaging

1. A method for automatically focusing multiple images of one or more objects on a substrate, the method comprising:

a) obtaining, by a processor, a representative focal distance for a first location on the substrate based on a set of focal distances at known locations on the substrate, wherein the representative focal distance is estimated as a weighted average of at least two focal distances from the set of focal distances at known locations, wherein a weight for a given focal distance is calculated based on a distance of the corresponding location from the first location;

b) acquiring, by an image acquisition device, a set of at least two images of the first location, wherein the images are each acquired using a different focal distance at an offset from the representative focal distance;

c) estimating, by a processor, an ideal focal distance corresponding to the first location based on comparing a quality of focus for each of the images; and

d) storing the estimated ideal focal distance and the first location in the set of focal distances at known locations.

2. The method of claim 1 , further comprising:

retrieving, by a processor, the set of focal distances at known locations;

acquiring, by the image acquisition device, an additional set of at least two images of a second location, wherein the images in the additional set are each acquired using a different focal distance at an offset from a second representative focal distance calculated for the second location based on the set of known focal distances at known locations; and

estimating, by a processor, an ideal focal distance corresponding to the second location based on comparing a quality of focus for each of the images in the additional set.

3. The method of claim 1 , wherein comparing the quality of focus further comprises calculating, for each image, a focus score by quantifying differences between neighboring pixels.

4. The method of claim 3 , wherein the focus score is a Brenner focus score.

5. The method of claim 3 , wherein estimating the ideal focal distance further comprises:

calculating a difference between logarithms of the focus scores of the images;

estimating an offset from the calculated difference; and

estimating the ideal focal distance based on the offset.

6. The method of claim 1 , wherein at least two of the images are acquired under illumination by a substantially same color of light, wherein the color of light is at least one of green, yellow, blue and red.

7. The method of claim 1 , wherein the set of images is acquired under illumination by at least two different colors and at least two images are acquired under illumination by each color.

8. The method of claim 7 , wherein estimating the ideal focal distance corresponding to the first location further comprises:

calculating a focal distance offset for each of the different colors;

determining an average focal distance offset based on the focal distance offsets calculated for the different colors; and

estimating the ideal focal distance corresponding to the first location based on the average focal distance offset.

9. An imaging system comprising:

an image acquisition device configured to acquire a set of at least two images of a first location on a substrate using a different focal distance for each image at an offset from a representative focal distance; and

a processor, connected to the image acquisition device, the processor configured to:

compute the representative focal distance for the first location based on a set of focal distances at known locations on the substrate, wherein the representative focal distance is estimated as a weighted average of at least two focal distances from the set of focal distances at known locations, wherein a weight for a given focal distance is calculated based on a distance of the corresponding location from the first location,

estimate an ideal focal distance corresponding to the first location based on comparing a quality of focus for each of the images,

store the estimated ideal focal distance and the first location in the set of focal distances at known locations, and

provide the computed representative focal distance to the image acquisition device.

10. The system of claim 9 , wherein

the processor is further configured to retrieve the set of focal distances at known locations; and

the image acquisition device is further configured to acquire an additional set of at least two images of a second location, wherein the images in the additional set are each acquired using a different focal distance at an offset from a second representative focal distance calculated for the second location based on the set of known focal distances at known locations.

11. The system of claim 10 wherein the processor is further configured to estimate an ideal focal distance corresponding to the second location based on comparing a quality of focus for each of the images in the additional set.

12. The system of claim 9 , wherein comparing the quality of focus further comprises calculating, for each image, a focus score by quantifying differences between neighboring pixels.

13. The system of claim 12 , wherein the focus score is a Brenner focus score.

14. The system of claim 12 , wherein the processor is further configured to:

calculate a difference between logarithms of the focus scores of the images;

estimate an offset from the calculated difference; and

estimate the ideal focal distance based on the offset.

15. The system of claim 9 , wherein at least two of the images are acquired under illumination by a substantially same color of light, wherein the color of light is at least one of green, yellow, blue and red.

16. The system of claim 9 , wherein the set of images is acquired under illumination by at least two different colors and at least two images are acquired under illumination by each color.

17. The system of claim 9 , wherein the processor is further configured to:

calculate a focal distance offset for each of the different colors;

determine an average focal distance offset based on the focal distance offsets calculated for the different colors; and

estimate the ideal focal distance corresponding to the first location based on the average focal distance offset.

18. A non-transitory computer readable storage device, having encoded thereon computer readable instructions that, when executed by a processor, cause the processor to:

compute a representative focal distance for a first location on a substrate based on a set of focal distances at known locations on the substrate, wherein the representative focal distance is estimated as a weighted average of at least two focal distances from the set of focal distances at known locations, wherein a weight for a given focal distance is calculated based on a distance of the corresponding location from the first location

estimate an ideal focal distance corresponding to the first location based on comparing a quality of focus for each of the images,

store the estimated ideal focal distance and the first location in the set of focal distances at known locations, and

provide the computed representative focal distance to an image acquisition device for the image acquisition device to acquire a set of at least two images of the first location using a different focal distance for each image at an offset from the representative focal distance.

19. The computer readable storage device of claim 18 , further comprising instructions that cause a processor to:

compare the quality of focus by calculating, for each image, a focus score by quantifying differences between neighboring pixels.

20. The computer readable storage device of claim 19 , further comprising instructions that cause a processor to:

calculate a difference between logarithms of the focus scores of the images;

estimate an offset from the calculated difference; and

estimate the ideal focal distance based on the offset.