Camera and specimen alignment to facilitate large area imaging in microscopy

Patent metadata

Field	Value
Publication number	US-10048477-B1
Application number	US-201715596352-A
Country	US
Kind code	B1
Filing date	May 16, 2017
Priority date	Feb 10, 2017
Publication date	Aug 14, 2018
Grant date	Aug 14, 2018

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 microscopy method for imaging a specimen along a desired x′-direction of the specimen, the specimen being placed on an XY translation stage and movable by the XY translation stage so as to have portion thereof placed within the field of view of an image sensor, wherein the XY translation stage is movable in an x-direction and a y-direction to move the specimen relative to the image sensor, the image sensor having a multitude of pixels arranged to define pixel rows and pixel columns, the desired x′-direction of the specimen being angularly offset from the x-direction of the XY translation stage so as to define a slope and angle of offset relative thereto, the image sensor viewing only a discrete segment of the specimen at a time, the method comprising the steps of:
rotating the image sensor such that the pixel rows are substantially parallel with the desired x′-direction of the specimen;
determining the angle of offset of the desired x′-direction as compared to the x-direction of the XY translation stage;
establishing a first position for the specimen relative to the image sensor as rotated in said step of rotating, said first position placing at least a portion of the specimen within the field of view of the image sensor; and,
after said step of determining and said step of establishing, moving the specimen with the XY translation stage to a second position along the desired x′-direction, wherein the second position places at least a second portion of the specimen within the field of view of the image sensor, and the second position is not substantially shifted in a y′-direction of the specimen, the y′-direction being orthogonal to the x′-direction of the specimen, wherein said step of moving is based upon the angle of offset determined in said step of determining.

2. The method of claim 1 , wherein said step of determining an angle of offset includes:
measuring the x distance and y distance between a first focal feature and a second focal feature aligned along and thus defining the desired x′-direction, the x distance and y distance being measured relative to the x-direction and y-directions of the translation stage.

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

5. The method of claim 3 , wherein said step of rotating the image sensor includes 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 detectable direction of the specimen.

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

7. The method of claim 3 , wherein said step of rotating the image sensor includes taking a mosaic of images suitable for calculating a reference line between the first focal feature and the second focal feature and using computer vision to align the pixel rows of the image sensor with the reference line.

8. The method of claim 7 , wherein said step of taking a mosaic of images is carried out while carrying out said step of measuring the x distance and y distance.

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

10. The method of claim 9 , wherein said step of 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

said step of determining the angle of offset includes:
measuring the degrees of rotation of the image sensor from its position after said step of aligning the pixel rows substantially parallel to the x-direction of the XY translation stage to its position after said step of rotating the image sensor.

11. The method of claim 9 , wherein said XY translation stage provides a specimen chuck to hold the specimen, wherein either the specimen chuck or a specimen placed thereon includes a reference mark, and said step of aligning the pixel rows substantially parallel with the x-direction of the XY translation stage includes:
placing the reference mark at a first position within in the field of view of the image sensor and taking image data to determine a first pixel row number for the position of the reference mark relative to the pixel rows,
moving the specimen chuck along only the x-direction of the XY translation stage to place the reference mark at a second position within the field of view of the image sensor and taking image data to determine a second pixel row number for the position of the reference mark relative to the pixel rows, and,
after said steps of placing and moving, rotating the image sensor to place the reference mark at a third position having a third pixel row number that is between said first pixel row number and said second pixel row number.

12. The method of claim 11 , wherein, after said step of rotating the image sensor to place the reference mark at a third position, said steps of (i) placing the reference mark at a first position, (ii) moving the specimen chuck along only the x-direction, and (iii) rotating the image sensor to place the mark at a third position are repeated until the pixel rows are substantially parallel with the x-direction of the XY translation stage.

13. The method of claim 12 , wherein said step of determining is carried out after said step of aligning the pixel rows substantially parallel with the x-direction of the XY translation stage.

14. The method of claim 13 , wherein said step of 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

said step of determining the angle of offset includes:
measuring the degrees of rotation of the image sensor from its position after said step of aligning the pixel rows substantially parallel to the x-direction of the XY translation stage to its position after said step of rotating the image sensor.

15. The method of claim 14 , wherein said step of measuring the degrees of rotation of the image sensor includes obtaining a signal output from an instrument rotating the image sensor.

16. A microscope system comprising:
a microscope;
an image sensor recording image data, said image sensor including pixel rows and pixel columns;
an XY translation stage;
a specimen on said XY translation stage and viewed by said image sensor, wherein the XY translation stage is movable in an x-direction and a y-direction to move the specimen relative to the image sensor, the image sensor having a multitude of pixels arranged to define pixel rows and pixel

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

• G02B21/362

  Mechanical details, e.g. mountings for the camera or image sensor, housings (G02B21/364 takes precedence) · 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

• H04N1/3876

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