Patent Number: 
Section: claims

1. A method of Fourier ptychographic imaging with embedded pupil function recovery, the method comprising:(a) receiving image data for a plurality of intensity images of a sample, the intensity images acquired sequentially by a light detector while the sample is being illuminated at different oblique incidence angles and the light detector is receiving light issuing from the illuminated sample through an optical system having a lens;(b) Fourier transforming the image data;(c) simultaneously updating a pupil function of the optical system and a sample spectrum, wherein the sample spectrum is updated in overlapping regions with the Fourier-transformed intensity image data, and the overlapping regions correspond to the different oblique illumination angles; and(d) inverse Fourier transforming the updated sample spectrum to determine an image of the sample having a higher resolution than the plurality of intensity images. 2. The method of claim 1, wherein each of the overlapping regions has an area corresponding to the numerical aperture of the lens. 3. The method of claim 2, wherein the lens is an objective lens, wherein the overlapping regions are in the form of circular pupil apertures. 4. The method of claim 3, wherein the numerical aperture of the lens is in a range between about 0.02 and about 0.13. 5. The method of claim 3, wherein the numerical aperture of the lens is about 0.08. 6. The method of claim 2, further comprising calculating an aberration in the optical system using the updated pupil function. 7. The method of claim 6, further comprising adaptively correcting an incident wavefront based on the calculated aberration. 8. The method of claim 6, further comprising determining a substantially aberration-free image of the sample using the calculated aberration. 9. The method of claim 6, further comprising re-focusing the sample using the calculated aberration. 10. The method of claim 2, wherein adjacent overlapping regions overlap in area by between 20% and 90%. 11. The method of claim 1, repeating (c) until the updated sample spectrum is self-consistent. 12. A method of Fourier ptychographic imaging with embedded pupil function recovery, the method comprising:receiving image data for a plurality of intensity images of a sample, the intensity images acquired sequentially by a light detector while the sample is being illuminated at different oblique incidence angles and the light detector is receiving light issuing from the illuminated sample through an optical system having a lens;Fourier transforming the image data;simultaneously updating a pupil function of the optical system and a sample spectrum, wherein the sample spectrum is updated in overlapping regions with the Fourier-transformed intensity image data, and the overlapping regions correspond to the different oblique illumination angles; andcalculating an aberration in the optical system using the updated pupil function. 13. The method of claim 12, further comprising decomposing a phase component of the updated pupil function into coefficients of Zernike polynomials. 14. The method of claim 13, further comprising determining wavefront aberration based on coefficients of lower order modes of Zernike polynomials. 15. The method of claim 13, further comprising determining wavefront aberration based on coefficients of or one or more of a mode associated with defocus aberration, a mode associated with a stigmatism in the x-direction, and a mode associated with a stigmatism in one or two directions. 16. The method of claim 13, further comprising determining coma aberration based on coefficients of one or more modes of Zernike polynomials. 17. The method of claim 12, further comprising adaptively correcting an incident wavefront based on the calculated aberration. 18. The method of claim 12, further comprising inverse Fourier transforming the updated sample spectrum to determine an image of the sample having a higher resolution than the plurality of intensity images. 19. The method of claim 18, further comprising determining a substantially aberration-free image of the sample using the calculated aberration. 20. The method of claim 18, further comprising: decomposing a phase component of the updated pupil function to determine a coefficient of a mode associated with defocus aberration; calculating defocus aberration from the coefficient; and re-focusing the higher resolution image of the sample using the calculated defocus aberration. 21. A Fourier ptychographic imaging system employing embedded pupil function recovery, comprising: a variable illuminator configured to illuminate a sample being imaged at a plurality of oblique illumination angles; an optical system having an objective lens configured to collect light issuing from the illuminated sample; a radiation detector configured to receive light issuing from the illuminated sample and transmitted by the optical system, and configured to acquire a plurality of intensity images based on the light received; a processor configured to: simultaneously update a pupil function and a separate sample spectrum, wherein the sample spectrum is updated in overlapping regions with the Fourier-transformed intensity image data, and the overlapping regions correspond to the different oblique illumination angles; and calculate an aberration in the optical system using the updated pupil function. 22. The Fourier ptychographic imaging system of claim 20, further comprising a wavefront modulator configured to adaptively correct an incident wavefront based on the calculated aberration. 23. The Fourier ptychographic imaging system of claim 20, wherein the objective lens has a numerical aperture between about 0.02 and 0.13. 24. The Fourier ptychographic imaging system of claim 20, wherein the objective lens has a numerical aperture numerical aperture of about 0.08. 25. The Fourier ptychographic imaging system of claim 20, wherein the variable illuminator comprises a circular array of discrete light elements. 26. The Fourier ptychographic imaging system of claim 20, wherein the processor is further configured to decompose a phase component of the updated pupil function into coefficients of Zernike polynomials. 27. The Fourier ptychographic imaging system of claim 25, wherein the processor is further configured to determine wavefront aberration based on coefficients of or one or more of a mode associated with defocus aberration, a mode associated with a stigmatism in the x- direction, and a mode associated with a stigmatism in one or two directions. 28. The Fourier ptychographic imaging system of claim 25, wherein the processor is further configured to determine coma aberration based on coefficients of one or more modes of Zernike polynomials. 29. The Fourier ptychographic imaging system of claim 27, wherein the processor is further configured to determine coma aberration based on coefficients of one or more modes of Zernike polynomials. 30. The Fourier ptychographic imaging system of claim 20, wherein the processor is further configured to inverse transform the updated sample spectrum to determine an image of the sample, wherein the image has a higher resolution than the captured intensity images. 31. The Fourier ptychographic imaging system of claim 27, wherein the processor is further configured to determine a substantially aberration-free image of the sample using the calculated aberration. 32. The Fourier ptychographic imaging system of claim 27, wherein the processor is further configured to:decompose a phase component of the updated pupil function to determine a coefficient of a mode associated with defocus aberration;calculate defocus aberration from the coefficient; andre-focus the higher resolution image of the sample using the calculated defocus aberration. 33. A method of Fourier ptychographic imaging with embedded pupil function recovery, the method comprising:providing plane wave illumination at a plurality of oblique incidence angles to a sample being imaged;collecting light issuing from the sample using an optical system having a lens;acquiring a plurality of intensity images of the sample using a radiation detector;simultaneously updating a pupil function of the optical system and a separate sample spectrum, wherein the sample spectrum is updated in overlapping regions with Fourier transformed intensity image data, wherein the overlapping regions corresponds to the plurality of oblique incidence angles; andinverse Fourier transforming the recovered sample spectrum to recover an image with a higher resolution than the acquired intensity images. 34. The method of claim 33, further comprising determining an aberration from the updated pupil function. 35. The method of claim 34, further comprising adaptively correcting for the determined aberration using a wavefront modulator. 36. The method of claim 34, wherein the overlapping regions overlap by between 20% and 90% in area.