Camera and specimen alignment to facilitate large area imaging in microscopy

Patent metadata

Field	Value
Publication number	US-10698191-B2
Application number	US-201816023219-A
Country	US
Kind code	B2
Filing date	Jun 29, 2018
Priority date	Feb 10, 2017
Publication date	Jun 30, 2020
Grant date	Jun 30, 2020

Abstract

A microscope system and method allow for a desired x′-direction scanning along a specimen to be angularly offset from an x-direction of the XY translation stage, and rotates an image sensor associated with the microscope to place the pixel rows of the image sensor substantially parallel to the desired x′-direction. The angle of offset of the x′-direction relative to the x-direction is determined and the XY translation stage is employed to move the specimen relative to the image sensor to different positions along the desired x′-direction without a substantial shift of the image sensor relative to the specimen in a y′-direction, the y′-direction being orthogonal to the x′ direction of the specimen. The movement is based on the angle of offset.

First claim

What is claimed is:

1. A method for imaging a specimen along a desired x′-direction of the specimen, the method comprising:
rotating an image sensor such that pixel rows of the image sensor are substantially parallel with the desired x′-direction of the specimen, the desired x′-direction of the specimen being angularly offset from an x direction of an XY translation stage on which the specimen is positioned, wherein the XY translation stage is movable in an x direction and a y direction relative to the image sensor;
determining the angle of offset of the desired x′-direction as compared to the x-direction of the XY translation stage; and
moving the specimen, using the XY translation stage, to one or more positions, along the desired x′ direction.

2. The method of claim 1 , wherein the determining the angle of offset comprises:
measuring, relative to the x-direction and y-direction of the XY translation stage, an x distance and y distance between a first focal feature and a second focal feature on the specimen aligned along and defining the desired x′-direction.

3. The method of claim 2 , wherein the measuring the x distance and y distance comprises:
placing the first focal feature so as to overlap with one or more target pixels of the image sensor,
moving the specimen to place the second focal feature so as to overlap with the same one or more target pixels, and
determining the x distance and y distance by measuring the magnitude of x and y movement of the translation stage (ΔX, ΔY) necessary to achieve the moving the specimen to place the second focal feature so as to overlap with the same one or more target pixels.

4. The method of claim 3 , wherein the target pixels encompass the center of the image sensor.

5. The method of claim 3 , wherein the rotating the image sensor comprises identifying an axis-defining feature on the specimen running in the x′-direction, and using computer vision to align the pixel rows substantially parallel to the axis-defining feature.

6. The method of claim 5 , wherein the rotating the image sensor is performed before measuring the x distance and y distance.

7. The method of claim 1 , wherein the rotating the image sensor comprises
taking a mosaic of images suitable for calculating a reference line between a first focal feature and a second focal feature on the specimen aligned along and defining the desired x′-direction; and
using computer vision to align the pixel rows of the image sensor with the reference line.

8. The method of claim 7 , wherein the determining the angle of offset comprises:
measuring, relative to the x-direction and y-directions of the XY translation stage, an x distance and y distance between the first focal feature and the second focal feature, and taking the mosaic of images while measuring the x distance and y distance.

9. The method of claim 1 , further comprising aligning the pixel rows of the image sensor substantially parallel to the x-direction of the XY translation stage, before rotating the image sensor.

10. The method of claim 9 , wherein the rotating the image sensor comprises:
identifying an axis-defining feature on the specimen, the axis-defining feature having a detectable shape running in the desired x′-direction; and
using computer vision to align the pixel rows substantially parallel to the detectable shape, and wherein the determining the angle of offset includes:
measuring the degrees of rotation of the pixel rows of the image sensor from a position substantially parallel to the x-direction of the XY translation stage to a position substantially parallel to the detectable shape of the axis-defining feature.

11. A microscope system comprising:
a microscope;
an image sensor comprising pixel rows and pixel columns that is configured to record image data;
an XY translation stage that is movable in an X direction and a Y direction;
a processor configured to:
rotate the image sensor relative to a specimen such that the pixel rows are substantially parallel with an x′-direction of the specimen placed on the XY translation stage, wherein the x′ direction is angularly offset from the X direction of the XY translation stage,
move the XY translation stage;
determine the angle of offset of the x′-direction as compared to the x-direction of the XY translation stage; and
scan across the specimen in the x′ direction.

12. The microscope system of claim 11 , wherein the processor is further configured to
determine, relative to the x-direction and y-direction of the translation stage, the angle of offset by measuring an x distance and y distance between a first focal feature and a second focal feature on the specimen aligned along and thus defining the desired x′-direction.

13. The microscope system of claim 12 , wherein measuring the x distance and y distance comprises:
placing the first focal feature so as to overlap with one or more target pixels of the image sensor;
moving the specimen to place the second focal feature so as to overlap with the same one or more target pixels; and
determining the x distance and y distance by measuring the magnitude of x and y movement of the translation stage (ΔX, ΔY) necessary to achieve the moving the specimen to place the second focal feature so as to overlap with the one or more target pixels.

14. The microscope system of claim 13 , wherein the target pixels encompass the center of the image sensor.

15. The microscope system of claim 13 , wherein the rotating the image sensor comprises: identifying an axis-defining feature on the specimen running in the x′-direction; and using computer vision to align the pixel rows substantially parallel to the axis-defining feature.

16. The microscope system of claim 15 , wherein rotating the image sensor is performed before measuring the x distance and y distance.

17. The microscope system of claim 11 , wherein the rotating the image sensor comprises:
taking a mosaic of images suitable for calculating a reference line between a first focal feature and a second focal feature on the specimen aligned along and defining the desired x′-direction; and
using computer vision to align the pixel rows of the image sensor with the reference line.

18. The microscope system of claim 17 , wherein the taking a mosaic of images is performed while measuring the x distance and y distance.

19. The microscope system of claim 11 , wherein, before the rotating the image sensor, the processor is configured to align the pixel rows of the image sensor substantially parallel to the x-direction of the XY translation stage.

20. The microscope system of claim 19 , wherein the rotating the image sensor includes:
identifying an axis-defining feature on the specimen, the axis-defining feature having a detectable shape running in the desired x′-direction; and
using computer vision to align the pixel rows substantially parallel to the detectable shape, and
wherein the determining the angle of offset includes:
measuring the degrees of rotation of the pixel rows of the image sensor from a position substantially parallel to the x-direction of the XY translation stage to a position substantially parallel to the detectable shape of the axis defining feature.

Assignees

• Nanotronics Imaging Inc

Inventors

• Putman Matthew C
• Putman John B
• Scott Brandon
• Fashbaugh Dylan

Classifications

• G02B21/26 Primary

  Stages; Adjusting means therefor · CPC title

• G02B21/002 Primary

  Scanning microscopes (scanning near field optical microscopes G01Q60/18) · CPC title

• G06V20/693

  Acquisition · CPC title

• H04N1/3876

  Recombination of partial images to recreate the original image · CPC title

• G02B21/367

  providing an output produced by processing a plurality of individual source images, e.g. image tiling, montage, composite images, depth sectioning, image comparison · CPC title