Apparatus and method of obtaining an image of a sample in motion

Patent metadata

Field	Value
Publication number	US-12348874-B2
Application number	US-202117513042-A
Country	US
Kind code	B2
Filing date	Oct 28, 2021
Priority date	Nov 6, 2020
Publication date	Jul 1, 2025
Grant date	Jul 1, 2025

Abstract

A method is used to generate an analysis image of a moving sample based on one or more exposures. An illumination source illuminates a field of view of a camera for one or more pulses while the sample moves through the field of view. The distance moved by the sample during each of these one or more pulses may be less than the size of one pixel in an image captured by the camera.

First claim

What is claimed is:

1. A machine comprising:
a camera to capture images comprising pixels, each of which has a pixel size corresponding to a distance on a stage in a direction of movement of a sample container;
the stage to move the sample container relative to a field of view of the camera which overlaps the stage, wherein the sample container comprises an array of features having a pitch length in a direction of movement of the sample container;
an illumination source to illuminate the field of view of the camera; and
a controller to obtain an analysis image by performing acts comprising, while a feature from the array of features is in, and is in motion relative to, the field of view of the camera, obtaining one or more exposures of the feature by, for each of the one or more exposures, performing acts comprising:
exposing a sensor of the camera to illumination for a first duration; and
during a period having a second duration and which takes place while the sensor of the camera is exposed to illumination, illuminating the field of view of the camera with the illumination source;
wherein the feature's displacement in the field of view of the camera from beginning to end of the period having the second duration is less than or equal to the pitch length in the direction of movement of the sample container;

wherein:
the analysis image is one of a plurality of analysis images;
the controller is to perform a plurality of sequencing cycles, wherein each analysis image from the plurality of analysis images corresponds to a single sequencing cycle; and
the controller is to determine a cluster polynucleotide for each feature in the sample container based on the plurality of analysis images; and
the controller is to determine a complete polynucleotide for a sample associated with the sample container based on the cluster polynucleotides determined for the features from the sample container.

2. The machine of claim 1 , wherein the feature's displacement in the direction of movement of the sample container in the field of view of the camera from beginning to end of the period having the second duration is less than or equal to the pixel size.

3. The machine of claim 1 , wherein:
obtaining one or more exposures of the feature comprises obtaining a plurality of exposures of the feature;
the acts the controller is to perform comprise overlaying the plurality of exposures of the feature based on translating one or more of the plurality of exposures of the feature.

4. The machine of claim 3 , wherein:
the analysis image comprises a plurality of pixels, each having a first bit depth; and
each of the plurality of exposures comprises a plurality of pixels, each of which has a second bit depth, wherein the second bit depth is less than the first bit depth.

5. The machine of claim 4 , wherein:
each pixel comprised by each image captured by the camera has third bit depth, wherein the third bit depth is greater than the second bit depth;
obtaining the plurality of exposures of the feature comprises, for each exposure:
capturing an image with the camera while the field of view of the camera is illuminated by the illumination source; and
truncating a number of most significant bits of the pixels from the image captured by the camera, wherein the truncated number of most significant bits is equal to the difference between the third bit depth and the second bit depth.

6. The machine of claim 1 , wherein:
a threshold illumination energy dose is required for imaging the feature;
for each of the one or more exposures of the feature, illuminating the field of view of the camera with the illumination source comprises activating the illumination source at a power which:
when multiplied by the second duration, provides an individual exposure energy dose less than the threshold illumination energy dose for imaging the feature; and
when multiplied by the second duration and multiplied by the number of exposures in the plurality of exposures of the feature, provides a collective exposure energy dose greater than the threshold illumination energy dose for imaging the feature.

7. The machine of claim 1 , wherein:
the stage is mounted on a frame of the machine using ball bearings;
the camera is to capture images using complementary metal-oxide-semiconductor sensors; and
the illumination source is a diode laser.

8. The machine of claim 1 , wherein the machine comprises a motor to counteract movement of the stage by translating the field of view of the camera in the direction of movement of the sample container during the period having the second duration.

9. A method comprising:
translating, in a direction of movement, a feature on a stage relative to a field of view of a camera, wherein the camera has a pixel size corresponding to a distance in the direction of movement on the stage, wherein the feature is comprised by an array of features in a sample container, the array of features having a pitch length in the direction of movement;
generating an analysis image by performing acts comprising, while the feature is in, and is in motion relative to, the field of view of the camera, obtaining one or more exposures of the feature by, for each of the one or more exposures, performing acts comprising:
exposing a sensor of the camera to illumination for a first duration;
during a period having a second duration and which takes place while the sensor of the camera is exposed to illumination, illuminating the field of view of the camera with an illumination source;
wherein the feature's displacement of the field of view of the camera from beginning to end of the period having the second duration is less than or equal to the pitch length in the direction of movement;

wherein:
the analysis image is one of a plurality of analysis images;
the method comprises:
performing a plurality of sequencing cycles, wherein each analysis image from the plurality of analysis images corresponds to a single sequencing cycle;
determining a cluster polynucleotide for each feature in the sample container based on the plurality of analysis images; and
determining a complete polynucleotide for a sample associated with the sample container based on the cluster polynucleotides determined for the features from the sample container.

10. The method of claim 9 , wherein the feature's displacement in the direction of movement from beginning to end of the period having the second duration is less than or equal to the pixel size.

11. The method of claim 9 , wherein:
obtaining one or more exposures of the feature comprises obtaining a plurality of exposures of the feature;
the method comprises overlaying the plurality of exposures of the feature to create the analysis image of the feature by performing acts comprising translating one or more of the plurality of exposures of the feature.

12. The method of claim 11 , wherein:
the analysis image comprises a plurality of pixels, each having a first bit depth; and
each of the plurality of exposures comprises a plurality of pixels, each of which has a second bit depth, wherein the second bit depth is less than the first bit depth.

13. The method of claim 12 , wherein:
each pixel comprised by each image captured by the camera has third bit depth, wherein the third bit depth is greater than the second bit depth;
obtaining the plurality of exposures of the feature comprises, for each exposure:
capturing an image with the camera while the field of view of the camera is illuminated by the illumination source; and
truncating a number of most significant bits of the pixels from the image captured by the camera, wherein the tru

Assignees

• Illumina Inc
• Illumina Cambridge Ltd

Inventors

• Evans Geraint
• Hong Stanley
• Siu Merek
• Lu Shaoping
• Moon John

Classifications

• G01N21/6458

  Fluorescence microscopy (fluorescence microscopes per se G02B21/0076 and G02B21/16) · CPC title

• H04N23/56

  provided with illuminating means · CPC title

• G06V20/693

  Acquisition · CPC title

• G02B21/0032

  Optical details of illumination, e.g. light-sources, pinholes, beam splitters, slits, fibers (G02B21/0036 - G02B21/008; means for illumination of specimens in general G02B21/06) · CPC title

• G02B21/008

  Details of detection or image processing, including general computer control · CPC title