Autofocus system and method

1. A microscopy system comprising:

an objective;

an imaging device configured to capture images of a specimen positioned on a stage of the microscopy system;

an illumination source configured to illuminate the specimen positioned on the stage;

an epi-illumination module comprising a focusing mechanism in a first primary optical path of a light generated by the illumination source, wherein the focusing mechanism is tilted in relation to a plane perpendicular to the first primary optical path, the focusing mechanism configured to produce a pattern on the specimen; and

a controller in communication with the imaging device, wherein the controller comprises one or more programming instructions that, when executed, cause the controller to receive a single image of the specimen from the imaging device, the single image comprising the pattern produced by the focusing mechanism and focus the microscopy system based on only the single image captured by the imaging device, the single image comprising the pattern produced by the focusing mechanism.

2. The microscopy system of claim 1 , wherein the one or more programming instructions that, when executed, cause the controller to focus the microscopy system further comprises one or more programming instructions that, when executed, cause the controller to determine an optimal distance of the objective to the specimen based on the pattern produced by the focusing mechanism.

3. The microscopy system of claim 2 , wherein the one or more programming instructions that, when executed, cause the controller to determine an optimal distance of the objective to the specimen further comprises one or more programming instructions that, when executed, cause the controller to determine a pixel position of a sharpest region in the single image.

4. The microscopy system of claim 3 , wherein the one or more programming instructions that, when executed, cause the controller to determine a pixel position of a sharpest region in the single image further comprises one or more programming instructions that, when executed, cause the controller to:

perform feature enhancement on the single image;

determine a sharp region of the single image based on the feature enhancement;

determine an average projection along an axis for the sharp region; and

determine a peak value of the average projection.

5. The microscopy system of claim 4 , wherein the one or more programming instructions that, when executed, cause the controller to perform feature enhancement on the single image further comprises one or more programming instructions that, when executed, cause the controller to apply an edge detection algorithm to the single image.

6. The microscopy system of claim 5 , wherein the one or more programming instructions that, when executed, cause the controller to apply the edge detection algorithm to the single image further comprises one or more programming instructions that, when executed, cause the controller to calculate a difference of Gaussians.

7. The microscopy system of claim 4 , wherein the one or more programming instructions that, when executed, cause the controller to determine the peak value of the average projection further comprises one or more programming instructions that, when executed, cause the controller to:

determine a best fit Gaussian to the average projection; and

determine a peak value for the best fit Gaussian.

8. The microscopy system of claim 1 , wherein the focusing mechanism is configured to be moved in and out of the first primary optical path.

9. The microscopy system of claim 5 , wherein the epi-illumination module further comprises a motor to move the focusing mechanism in and out of the first primary optical path.

10. The microscopy system of claim 1 , further comprising:

a second illumination source with a second primary optical path; and

a beam splitter configured to merge the first primary optical path and the second primary optical path.

11. The microscopy system of claim 10 , wherein the second illumination source generates white light.

12. The microscopy system of claim 10 , wherein the illumination source generates a unique light wavelength.

13. The microscopy system of claim 1 , wherein the focusing mechanism is a mesh screen.

14. The microscopy system of claim 1 , wherein the focusing mechanism is a glass slide comprising the pattern etched therein.

15. A method for focusing a microscopy system, comprising:

causing, by a controller, an illumination source of the microscopy system to illuminate a specimen positioned on a stage of the microscopy system, wherein a focusing mechanism positioned in a light path between the illumination source and the stage forms a pattern on the specimen;

receiving, by the controller, only a single image of the specimen, wherein the single image comprises the pattern produced by the focusing mechanism; and

focusing, by the controller, the microscopy system based on only the single image by:

determining that the single image is not in focus by analyzing the pattern produced by the focusing mechanism, and

determining adjustments to the microscopy system based on the analyzed pattern produced by the focusing mechanism in the single image the determining, focusing, by the controller, the microscopy system.

16. The method of claim 15 , wherein analyzing the pattern produced by the focusing mechanism comprises:

analyzing, by the controller, the pattern produced by the focusing mechanism to determine an optimal distance of an objective of the microscopy system to the specimen; and

focusing, by the controller, the microscopy system based on the optimal distance.

17. The method of claim 16 , wherein determining, by the controller, the optimal distance of the objective to the specimen comprises:

determining a pixel position of a sharpest region in the single image by:

performing feature enhancement on the single image;

determining a sharp region of the single image based on the feature enhancement;

determining an average projection along an axis for the sharp region; and

determining a peak value of the average projection.

18. A focusing system for automatically focusing a microscopy system, comprising:

an illumination source; and

a focusing mechanism configured to be positioned within a light path produced by the illumination source, the focusing mechanism configured to project a pattern on a specimen to be imaged by the microscopy system, wherein the focusing mechanism allows for focusing of the microscopy system using only a single image, wherein the single image comprises the pattern on the specimen.

19. The focusing system of claim 18 , wherein the focusing mechanism is a mesh screen or a glass slide comprising the pattern etched therein.