Methods for high-performance electron microscopy
Methods for correcting one or more image aberrations in an electron microscopy image, including cryo-EM images, are provided. The method includes obtaining a plurality of electron microscope (EM) images of an internal reference grid sample having one or more known properties, the plurality of electron microscope images obtained for a plurality of optical conditions and for a plurality of coordinated beam-image shifts. The method may also include, among other features, determining an aberration correction function that predicts aberrations for every point in the imaged area using kernel canonical correlation analysis (KCCA).
1. A method to correct one or more image aberrations in an electron microscopy image, the method comprising:
obtaining a plurality of electron microscope (EM) images of an internal reference grid sample, the plurality of EM images captured using an electron microscope in connection with a plurality of optical conditions including a plurality of coordinated beam-image shifts;
generating an EM micrograph by correcting the plurality of EM images for sample drift;
generating a deconvolved image by deconvolving a transformed image using one or more deconvolution coefficients, the transformed image generated by applying a transform to the EM micrograph;
generating a filtered deconvolved image by applying a filter to the deconvolved image;
generating an aberration-corrected EM micrograph by calculating an inverse transform of the filtered deconvolved image;
determining an intensity distribution for the aberration-corrected EM micrograph;
calculating a moment for the intensity distribution; and
performing an iterative optimization process using one or more deconvolution coefficients until an optimal one or more of the one or more deconvolution coefficients is determined based on maximization of the moment.
2. The method of claim 1 , further comprising:
determining an aberration correction function operable to predict aberrations using a kernel canonical correlation analysis of the optimal one or more of the one or more deconvolution coefficients and the plurality of optical conditions.
3. The method of claim 2 , further comprising:
obtaining one or more EM images of a calibration check grid sample having one or more known properties that is different than at least one known property of the internal reference grid sample; and
generating an aberration corrected EM image by applying the aberration correction function to the one or more EM images.
4. The method of claim 3 , further comprising:
comparing one or more features in the aberration corrected EM image to one or more known properties of the calibration check grid sample to determine whether the aberration correction function is suitable.
5. The method of claim 4 ,
wherein,
the aberration correction function is determined to be suitable when the aberration correction function is within a range, and
the aberration correction function is determined to not be suitable when the aberration correction function is outside the range.
6. The method of claim 1 ,
wherein,
the iterative optimization process includes selecting the one or more deconvolution coefficients from a range of deconvolution coefficients values that is different than a previous iteration of the iterative optimization process.
7. The method of claim 1 ,
wherein,
the iterative optimization process includes repeating at least the calculating of the inverse transform until the optimal one or more of the one or more deconvolution coefficients is determined based on maximization of the moment.
8. The method of claim 1 ,
wherein,
the generating of the EM micrograph includes aligning and motion-correcting the plurality of EM images.
9. The method of claim 1 ,
wherein,
the filter is a high-pass filter, and
the filtered deconvolved image is generated by applying the high-pass filter to the deconvolved image.
10. The method of claim 1 ,
wherein,
the plurality of optical conditions is selected from a plurality of defocuses, a plurality of z-heights, a plurality of beam tilts, a plurality of beam parallelizations, and any combination thereof.
11. The method of claim 1 ,
wherein,
the transform is a Fourier transform, and
the transformed image is generated by applying the Fourier transform to the EM micrograph.
12. The method of claim 1 ,
wherein,
the internal reference grid sample includes an amorphous material distributed over a support, and
the amorphous material has an atomic mass heavier than a material comprising the support.
13. The method of claim 1 , wherein the calculating of the moment includes quantifying a shape of the intensity distribution based on a function suitable for optimization with independent component analysis.
14. The method of claim 13 ,
wherein,
the function is selected from a group, and
the group includes negative entropy, skewness, and kurtosis.
15. The method of claim 1 , wherein the calculating of the moment includes quantifying a shape of the intensity distribution based on optimizing negative entropy.