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EP-4737588-A2 - DYNAMIC OPTICAL SYSTEM CALIBRATION

EP4737588A2EP 4737588 A2EP4737588 A2EP 4737588A2EP-4737588-A2

Abstract

An apparatus includes a flow cell, an imaging assembly, and a processor. The flow cell includes a channel and a plurality of reaction sites. The imaging assembly is operable to receive light emitted from the reaction sites in response to an excitation light. The processor is configured to drive relative movement between at least a portion of the imaging assembly and the flow cell along a continuous range of motion to thereby enable the imaging assembly to capture images along the length of the channel. The processor is also configured to activate the imaging assembly to capture one or more calibration images of one or more calibration regions of the channel, during a first portion of the continuous range of motion. The processor is also configured to activate the imaging assembly to capture images of the reaction sites during a second portion of the continuous range of motion.

Inventors

  • BLAIR, DUSTIN
  • SIM, Daeyong
  • ABASKHARON, Rachel
  • WEN, Patrick
  • EARNEY, John
  • PRABHU, Anmiv
  • HOLST, Gregory
  • LIU, Chia-Hsi
  • THAKUR, Ravi Bhushan Singhchawhan
  • WATSON, Dakota
  • BARTIG, Kevin

Assignees

  • Illumina, Inc.

Dates

Publication Date
20260506
Application Date
20230928

Claims (16)

  1. An apparatus, comprising: a flow cell including: a channel, the channel having a first end region, a second end region, and an intermediate region extending between the first end region and the second end region, the channel defining a length that includes the first end region, intermediate region, and the second end region, the channel being configured to receive a fluid, and the channel including one or more calibration regions in the first end region, the second end region, or the intermediate region, a plurality of reaction sites positioned along the intermediate region, each reaction site being configured to contain a biological sample carried by the fluid, each reaction site being further configured to receive an excitation light; an imaging assembly operable to receive light emitted from a reactant positioned at the reaction sites in response to the excitation light; and a processor, the processor being configured to: drive relative movement between at least a portion of the imaging assembly and the flow cell along a continuous range of motion to thereby enable the imaging assembly to capture images along the length of the channel, activate the imaging assembly to capture one or more calibration images for the one or more calibration regions, during a first portion of the continuous range of motion, and activate the imaging assembly to capture images of the reaction sites during a second portion of the continuous range of motion.
  2. The apparatus of Claim 1, wherein the one or more calibration regions is positioned in the first end region.
  3. The apparatus of Claim 1 or 2, wherein the one or more calibration regions is positioned in the second end region.
  4. apparatus of any one of Claims 1-3, wherein the one or more calibration regions is positioned in the intermediate region.
  5. The apparatus of any of Claims 1-4, the one or more calibration regions include nucleotides.
  6. The apparatus of any of Claims 1-5, the processor being further configured to adjust a feature of the imaging assembly based at least in part on data from the one or more calibration images.
  7. A method comprising: communicating fluid through a channel of a flow cell; moving at least a portion of an imaging assembly relative to the flow cell through a range of motion; and while moving the at least a portion of the imaging assembly relative to the flow cell through the range of motion: capturing one or more calibration images of a first calibration region via the imaging assembly, the first calibration region being positioned in a first end region of the channel, and capturing one or more images of reaction sites via the imaging assembly, the reaction sites being positioned at an intermediate region of the channel.
  8. The method of Claim 7, further comprising, while moving the at least a portion of the imaging assembly relative to the flow cell through the range of motion, capturing one or more calibration images of a second calibration region via the imaging assembly, the second calibration region being positioned at a second end region of the channel.
  9. The method of Claim 7 or 8, further comprising adjusting a feature of the imaging assembly based at least in part on data from the one or more calibration images.
  10. The method of any one of Claims 7-9, further comprising, performing sequencing-by-synthesis analysis based on the one or more images of the reaction sites.
  11. The method of Claim 10, the sequencing-by-synthesis analysis being performed while moving the at least a portion of the imaging assembly relative to the flow cell through the range of motion.
  12. A method comprising: communicating fluid through a channel of a flow cell; performing sequencing-by-synthesis via the flow cell; and while performing sequencing-by-synthesis via the flow cell: capturing one or more calibration images of a first calibration region via an imaging assembly, the first calibration target being positioned at a first end region of the channel, and capturing one or more images of reaction sites via the imaging assembly, the reaction sites being positioned at an intermediate region of the channel.
  13. The method of Claim 12, performing sequencing-by-synthesis via the flow cell including moving at least a portion of the imaging assembly relative to the flow cell through a range of motion.
  14. The method of Claim 13, capturing one or more images of reaction sites via the imaging assembly being performed while moving the at least a portion of the imaging assembly relative to the flow cell through the range of motion.
  15. The method of Claim 14, capturing one or more calibration images of the first calibration region via the imaging assembly being performed while moving the at least a portion of the imaging assembly relative to the flow cell through the range of motion.
  16. A processor-readable medium including contents that are configured to cause a processor to process data by performing the method of Claim 12.

Description

BACKGROUND The subject matter discussed in this section should not be assumed to be prior art merely as a result of its mention in this section. Similarly, a problem mentioned in this section or associated with the subject matter provided as background should not be assumed to have been previously recognized in the prior art. The subject matter in this section merely represents different approaches, which in and of themselves may also correspond to implementations of the claimed technology. Aspects of the present disclosure relate generally to biological or chemical analysis and more particularly to systems and methods using image sensors for biological or chemical analysis. Various protocols in biological or chemical research involve performing a large number of controlled reactions on local support surfaces or within predefined reaction chambers. The designated reactions may then be observed or detected, and subsequent analysis may help identify or reveal properties of chemicals involved in the reaction. For example, in some multiplex assays, an unknown analyte having an identifiable label (e.g., fluorescent label) may be exposed to thousands of known probes under controlled conditions. Each known probe may be deposited into a corresponding well of a flow cell channel. Observing any chemical reactions that occur between the known probes and the unknown analyte within the wells may help identify or reveal properties of the analyte. Other examples of such protocols include known DNA sequencing processes, such as sequencing-by-synthesis (SBS) or cyclic-array sequencing. In some conventional fluorescent-detection protocols, an optical system is used to direct an excitation light onto fluorescently-labeled analytes and to also detect the fluorescent signals that may be emitted from the analytes. Such optical systems may include an arrangement of lenses, filters, and light sources. It may be desirable to provide calibration of such optical systems without substantially affecting overall processing times. BRIEF DESCRIPTION OF THE DRAWINGS FIG. 1 depicts a schematic diagram of an example of an imaging assembly that may be implemented in a system for biological or chemical analysis.FIG. 2 depicts a perspective view of an example of a flow cell that may be utilized with the system of FIG. 1.FIG. 3 depicts an enlarged perspective view of a channel of the flow cell of FIG. 3.FIG. 4 depicts a top plan view of another example of a flow cell that may be utilized with the system of FIG. 1FIG. 5 depicts an enlarged top plan view of a channel of the flow cell of FIG. 4.FIG. 6 depicts a graph depicting an example of image capture positions during a focus model generation process.FIG. 7 depicts a motion profile depicting an example of an integrated through focus path for moving an objective lens of an imaging assembly for focus model generation and/or updating.FIG. 8 depicts a graph detecting focus tracking spots reflected by a first surface and a second surface.FIG. 9 depicts a pair of graphs showing a substantially linear relationship between the position of a detected focus tracking spot relative to a z position height of an objective of an imaging assembly.FIG. 10 depicts a graph showing average spot separation values through a calibration region of a flow cell.FIG. 11 depicts a graph showing image quality score values through a calibration region of a flow cell.FIG. 12 depicts a graph showing image quality score values relative to average spot separation values.FIG. 13 depicts a flow chart representing an example of a method of dynamically calibrating optical system components.FIG. 14 depicts a flow chart representing an example of a method of dynamically calibrating optical system components.FIG. 15 depicts an exemplary set of regions of interest.FIG. 16 depicts a particular approach which may be taken when performing calibration acts. DETAILED DESCRIPTION I. Overview of System for Biological or Chemical Analysis Described herein are devices, systems, and methods for dynamically optically calibrating an imaging assembly for a biological or chemical analysis system. Dynamic optical calibration may improve performance of the biological or chemical analysis system by improving image quality at one or more points of a substrate of interest during a scanning process. Examples described herein may be used in various biological or chemical processes and systems for academic analysis, commercial analysis, or other analysis. More specifically, examples described herein may be used in various processes and systems where it is desired to detect an event, property, quality, or characteristic that is indicative of a designated reaction. Bioassay systems such as those described herein may be configured to perform a plurality of designated reactions that may be detected individually or collectively. The biosensors and bioassay systems may be configured to perform numerous cycles in which a plurality of designated reactions occurs in