Methods, systems, and computer readable media for measuring and correcting drift distortion in images obtained using a scanning microscope

Patent metadata

Field	Value
Publication number	US-9831061-B2
Application number	US-201415103154-A
Country	US
Kind code	B2
Filing date	Dec 9, 2014
Priority date	Dec 9, 2013
Publication date	Nov 28, 2017
Grant date	Nov 28, 2017

Abstract

The subject matter described herein includes methods, systems, and computer readable media for measuring and correcting drift distortion in images obtained using the scanning microscope. One method includes obtaining an image series of a sample acquired using scanning-microscope by rotating scan coordinates of the microscope between successive image frames. The method further includes determining at least one measurement of an angle or a distance associated with an image feature as a function of rotation angle from the series of rotated images. The method further includes using the at least one measurement to determine a model for drift distortion in the series of images. The method further includes using the drift distortion model to generate a drift corrected image from the series of images.

First claim

What is claimed is:

1. A method for measuring and correcting sample drift distortion in a scanning microscopy system, the method comprising:
obtaining an image series of a sample acquired using a scanning microscope by rotating scan coordinates of the microscope between successive image frames;
determining at least one measurement of an angle or distance associated with an image feature as a function of rotation angle from the series of rotated images;
using the at least one measurement to determine a model for drift distortion in the series of images, wherein the sample comprises a crystal, the image feature comprises a lattice vector, and the measurements comprise distorted lattice vector angles; and
using the drift distortion model to generate a drift corrected image from the series of images.

2. The method of claim 1 wherein determining at least one measurement includes determining the distorted lattice vector angles from real image space pixel intensities.

3. The method of claim 2 wherein determining the distorted lattice vector angles from real image space pixel intensities includes projecting pixel intensities from an image plane onto a line having a slope related to a projection angle of the line and determining a projected average pixel intensity for each point on the line.

4. The method of claim 3 wherein determining the distorted lattice vector angles from real image space pixel intensities includes determining a projective standard deviation comprising a standard deviation of the average pixel intensities projected onto the line.

5. The method of claim 4 wherein determining the distorted lattice vector angles includes determining projective standard deviations for a plurality of different projection angles to identify periodic features in the images and measuring the angles of the periodic features with respect to a fixed position.

6. The method of claim 1 wherein using the at least one measurement to determine a model for drift distortion in the series of images includes selecting a model for the drift distortion and fitting the model to the at least one measurement.

7. A method for measuring and correcting sample drift distortion in a scanning microscopy system, the method comprising:
obtaining an image series of a sample acquired using a scanning microscope by rotating scan coordinates of the microscope between successive image frames;
determining at least one measurement of an angle or distance associated with an image feature as a function of rotation angle from the series of rotated images;
using the at least one measurement to determine a model for drift distortion in the series of images; and
using the drift distortion model to generate a drift corrected image from the series of images, wherein using the drift distortion model to generate a drift corrected image includes applying an inverse distortion transformation based on the drift distortion model to each image in the series, rotating each image in the series to a common coordinate system, aligning the rotated images, and averaging the images.

8. The method of claim 1 comprising using the drift corrected image to quantify scan coil distortion.

9. The method of claim 1 wherein obtaining the series of images includes obtaining the series of images while drifting.

10. The method of claim 1 wherein the generation of the drift corrected image occurs without prior knowledge of structure of the sample.

11. A system for measuring and correcting a sample drift distortion and a scanning microscopy system, the system comprising:
a processor;
an image acquisition module executable by the processor for obtaining an image series of a sample acquired using a scanning microscope by rotating scan coordinates of the microscope between successive image frames; and
a drift distortion quantification and correction module executable by the processor for determining at least one measurement of an angle or distance associated with an image feature as a function of rotation angle from the series of images and for using the measurements to determine drift distortion in the series of images, and for using the drift distortion model to generate a drift corrected image from the series of images, wherein the sample comprises a crystal, the image feature comprises a lattice vector, and the measurements comprise distorted lattice vector angles.

12. The system of claim 11 wherein determining at least one measurement includes determining the distorted lattice vector angles from real image space pixel intensities.

13. The system of claim 12 wherein determining the distorted lattice vector angles from real image space pixel intensities includes projecting pixel intensities from an image plane onto a line having a slope related to a projection angle of the line and determining a projected average pixel intensity for each point on the line.

14. The system of claim 13 wherein determining the distorted lattice vector angles from real image space pixel intensities includes determining a projective standard deviation comprising a standard deviation of the average pixel intensities projected onto the line.

15. The system of claim 14 wherein determining the distorted lattice vector angles includes determining projective standard deviations for a plurality of different projection angles to identify periodic features in the images and measuring the angles of the periodic features with respect to a fixed position.

16. The system of claim 11 wherein using the at least one measurement to determine a model for drift distortion in the series of images includes selecting a model for the drift distortion and fitting the model to the at least one measurement.

17. A system for measuring and correcting a sample drift distortion and a scanning microscopy system, the system comprising:
a processor; and
an image acquisition module executable by the processor for obtaining an image series of a sample acquired using a scanning microscope by rotating scan coordinates of the microscope between successive image frames; and a drift distortion quantification and correction module executable by the processor for determining at least one measurement of an angle or distance associated with an image feature as a function of rotation angle from the series of images and for using the measurements to determine drift distortion in the series of images, and for using the drift distortion model to generate a drift corrected image from the series of images, wherein using the drift distortion model to generate a drift corrected image includes applying an inverse distortion transformation based on the drift distortion model to each image in the series, rotating each image in the series to a common coordinate system, aligning the rotated images, and averaging the images.

18. The system of claim 11 comprising using the drift corrected image to quantify scan coil distortion.

19. The system of claim 11 wherein obtaining the series of images includes obtaining the series of images while drifting.

20. The system of claim 11 wherein the generation of the drift corrected image occurs without prior knowledge of structure of the sample.

21. A non-transitory computer readable medium comprising executable instructions that when executed by the processor of a computer control the computer to perform steps comprising:
obtaining an image series of a sample acquired using a scanning microscope by rotating scan coordinates of the microscope between successive image frames;
determining at least one m

Assignees

• Univ North Carolina State

Inventors

• Sang Xiahan
• Lebeau James Michael

Classifications

• H01J2237/2802

  Transmission microscopes · CPC title

• G01N2223/418

  electron microscope · CPC title

• H01J37/28

  with scanning beams {(H01J37/268, H01J37/292, H01J37/2955 take precedence)} · CPC title

• G01N2223/401

  image processing · CPC title

• G01N23/04

  and forming images of the material · CPC title