Autofocus system for a computational microscope

1. An autofocus microscope, comprising:

at least one image capture device configured to capture images of a sample located on a stage, wherein the at least one image capture device includes a lens;

a focus actuator configured to adjust a distance between the sample and a focal plane of the at least one image capture device;

an illumination assembly including a plurality of light sources to illuminate the sample from any of a plurality of illumination angles; and

at least one controller programmed to:

cause the illumination assembly to illuminate the sample from a first illumination angle;

acquire, from the at least one image capture device, a first image of the sample illuminated from the first illumination angle;

cause the illumination assembly to illuminate the sample from a second illumination angle different from the first illumination angle;

acquire, from the at least one image capture device, a second image of the sample illuminated from the second illumination angle;

determine an amount of shift between one or more image features present in the first image of the sample and a corresponding one or more image features present in the second image of the sample; and

where the amount of determined shift is non-zero, cause the focus actuator to change the distance between the sample and the focal plane.

2. The microscope of claim 1 , wherein the at least one controller is further programmed to cause the focus actuator to reduce the distance between the sample and the focal plane to substantially zero.

3. The microscope of claim 1 , wherein the at least one controller is further programmed to:

cause the illumination assembly to illuminate the sample from at least one more illumination angle different from the first and second illumination angle;

acquire, from the at least one image capture device, at least one more image of the sample illuminated from the at least one more illumination angle;

determine a plurality of shift values between one or more image features present in the first image of the sample, the second image of the sample, and the at least one more image of the sample.

4. The microscope of claim 1 , wherein the at least one controller is further programmed to determine a plurality of shift values based on multiple image features and to calculate an overall shift.

5. The microscope of claim 1 , wherein the focus actuator is configured to move the at least one image capture device to adjust the distance between the sample and the focal plane.

6. The microscope of claim 1 , wherein the focus actuator is configured to move the stage to adjust the distance between the sample and the focal plane.

7. The microscope of claim 1 , wherein the stage includes at least a portion that enables passage of light.

8. The microscope of claim 1 , wherein the first illumination angle and the second illumination angle are symmetrically located with respect to an optical axis of the at least one image capture device.

9. The microscope of claim 1 , wherein the first illumination angle and the second illumination angle are not symmetrically located with respect to an optical axis of the at least one image capture device.

10. The microscope of claim 1 , wherein the at least one controller is further programmed to cause the illumination assembly to illuminate the sample from the first and second illumination angles using a single light source located within a numerical aperture of the at least one image capture device.

11. The microscope of claim 1 , wherein the at least one controller is further programmed to cause the illumination assembly to illuminate the sample from the first and second illumination angles using a plurality of light sources located within a numerical aperture of the at least one image capture device.

12. The microscope of claim 1 , wherein the at least one controller is further programmed to determine a size of the distance change based on a magnitude of the shift.

13. The microscope of claim 1 , wherein the at least one controller is further programmed to determine a direction of the distance change based on a direction of the shift.

14. The microscope of claim 1 , wherein the at least one controller is further programmed to determine a direction of the distance change by purposely introducing a known separation between the sample and the focal plane.

15. The microscope of claim 1 , wherein the focus actuator changes the distance between the sample and the focal plane in a first direction, and the at least one controller is further programmed to determine that the amount of shift has increased after the change in the first direction, and to cause the focus actuator to change the distance in a second direction.

16. An autofocus microscope, comprising:

at least one image capture device configured to capture images of a sample located on a stage, wherein the at least one image capture device includes a lens;

a focus actuator configured to adjust a distance between the sample and a focal plane of the at least one image capture device;

an illumination assembly including a plurality of light sources to illuminate the sample from any of a plurality of illumination angles; and

at least one controller programmed to:

cause the illumination assembly to concurrently illuminate the sample from a first illumination angle and from a second illumination angle different from the first illumination angle;

acquire, from the at least one image capture device, a single image of the sample illuminated from the first illumination angle and the second illumination angle;

determine an amount of shift in the image of the sample between one or more image features associated with the first illumination angle and a corresponding one or more image features associated with the second illumination angle; and

where the amount of determined shift is non-zero, cause the focus actuator to change the distance between the sample and the focal plane.

17. A method for focusing an image using image information acquired under a plurality of different illumination conditions, the method comprising:

illuminating a sample at a first illumination condition;

acquiring, from at least one image capture device, a first image of the sample illuminated from the first illumination condition;

illuminating a sample at a second illumination condition;

acquiring, from the at least one image capture device, a second image of the sample illuminated from the second illumination condition; and

determining an amount of shift between one or more image features present in the first image of the sample and a corresponding one or more image features present in the second image of the sample.

18. The method of claim 17 further comprising:

where the amount of determined shift is above a predetermined threshold, changing the distance between the sample and a focal plane of the at least one image capture device; and

where the amount of determined shift is below the predetermined threshold, storing the amount of determined shift for future focus compensation calculations.

19. The method of claim 17 , wherein illuminating the sample at the first illumination condition and at the second illumination condition includes transmitting light from an illumination assembly through the sample and towards the at least one image capture device.

20. The method of claim 17 further comprising:

determining a plurality of shift values that correspond with a plurality of portions of a field of view of the at least one image capture device; and

using the plurality of shift values to determine three-dimensional information.