SG10201801648VA - Optical distortion correction for imaged samples - Google Patents

Optical distortion correction for imaged samples

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Publication number
SG10201801648VA
SG10201801648VA SG10201801648VA SG10201801648VA SG10201801648VA SG 10201801648V A SG10201801648V A SG 10201801648VA SG 10201801648V A SG10201801648V A SG 10201801648VA SG 10201801648V A SG10201801648V A SG 10201801648VA SG 10201801648V A SG10201801648V A SG 10201801648VA
Authority
SG
Singapore
Prior art keywords
image
distortion correction
correction coefficients
imaging
during
Prior art date
Application number
SG10201801648VA
Inventor
Robert Langlois
Paul Belitz
Original Assignee
Illumina Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of SG10201801648VA publication Critical patent/SG10201801648VA/en

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    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
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    • G06T5/00Image enhancement or restoration
    • G06T5/80Geometric correction
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T3/00Geometric image transformations in the plane of the image
    • G06T3/04Context-preserving transformations, e.g. by using an importance map
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L3/00Containers or dishes for laboratory use, e.g. laboratory glassware; Droppers
    • B01L3/50Containers for the purpose of retaining a material to be analysed, e.g. test tubes
    • B01L3/502Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
    • B01L3/5027Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
    • B01L3/502715Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01BMEASURING LENGTH, THICKNESS OR SIMILAR LINEAR DIMENSIONS; MEASURING ANGLES; MEASURING AREAS; MEASURING IRREGULARITIES OF SURFACES OR CONTOURS
    • G01B11/00Measuring arrangements characterised by the use of optical techniques
    • G01B11/16Measuring arrangements characterised by the use of optical techniques for measuring the deformation in a solid, e.g. optical strain gauge
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N21/00Investigating or analysing materials by the use of optical means, i.e. using sub-millimetre waves, infrared, visible or ultraviolet light
    • G01N21/62Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light
    • G01N21/63Systems in which the material investigated is excited whereby it emits light or causes a change in wavelength of the incident light optically excited
    • G01N21/64Fluorescence; Phosphorescence
    • G01N21/645Specially adapted constructive features of fluorimeters
    • G01N21/6456Spatial resolved fluorescence measurements; Imaging
    • GPHYSICS
    • G02OPTICS
    • G02BOPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00Microscopes
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
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    • G06T3/02Affine transformations
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T3/00Geometric image transformations in the plane of the image
    • G06T3/14Transformations for image registration, e.g. adjusting or mapping for alignment of images
    • G06T3/147Transformations for image registration, e.g. adjusting or mapping for alignment of images using affine transformations
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T5/00Image enhancement or restoration
    • G06T5/73Deblurring; Sharpening
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06VIMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00Arrangements for image or video recognition or understanding
    • G06V10/20Image preprocessing
    • G06V10/24Aligning, centring, orientation detection or correction of the image
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06VIMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V20/00Scenes; Scene-specific elements
    • G06V20/60Type of objects
    • G06V20/69Microscopic objects, e.g. biological cells or cellular parts
    • G06V20/695Preprocessing, e.g. image segmentation
    • HELECTRICITY
    • H04ELECTRIC COMMUNICATION TECHNIQUE
    • H04NPICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N1/00Scanning, transmission or reproduction of documents or the like, e.g. facsimile transmission; Details thereof
    • H04N1/387Composing, repositioning or otherwise geometrically modifying originals
    • HELECTRICITY
    • H04ELECTRIC COMMUNICATION TECHNIQUE
    • H04NPICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N1/00Scanning, transmission or reproduction of documents or the like, e.g. facsimile transmission; Details thereof
    • H04N1/40Picture signal circuits
    • H04N1/401Compensating positionally unequal response of the pick-up or reproducing head
    • HELECTRICITY
    • H04ELECTRIC COMMUNICATION TECHNIQUE
    • H04NPICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N1/00Scanning, transmission or reproduction of documents or the like, e.g. facsimile transmission; Details thereof
    • H04N1/40Picture signal circuits
    • H04N1/409Edge or detail enhancement; Noise or error suppression
    • HELECTRICITY
    • H04ELECTRIC COMMUNICATION TECHNIQUE
    • H04NPICTORIAL COMMUNICATION, e.g. TELEVISION
    • H04N25/00Circuitry of solid-state image sensors [SSIS]; Control thereof
    • H04N25/60Noise processing, e.g. detecting, correcting, reducing or removing noise
    • H04N25/61Noise processing, e.g. detecting, correcting, reducing or removing noise the noise originating only from the lens unit, e.g. flare, shading, vignetting or "cos4"
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2200/00Solutions for specific problems relating to chemical or physical laboratory apparatus
    • B01L2200/02Adapting objects or devices to another
    • B01L2200/025Align devices or objects to ensure defined positions relative to each other
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/08Geometry, shape and general structure
    • B01L2300/0809Geometry, shape and general structure rectangular shaped
    • B01L2300/0829Multi-well plates; Microtitration plates
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/08Geometry, shape and general structure
    • B01L2300/0861Configuration of multiple channels and/or chambers in a single devices
    • B01L2300/0877Flow chambers
    • BPERFORMING OPERATIONS; TRANSPORTING
    • B01PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
    • B01LCHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
    • B01L2300/00Additional constructional details
    • B01L2300/08Geometry, shape and general structure
    • B01L2300/0896Nanoscaled
    • GPHYSICS
    • G02OPTICS
    • G02BOPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B21/00Microscopes
    • G02B21/36Microscopes arranged for photographic purposes or projection purposes or digital imaging or video purposes including associated control and data processing arrangements
    • G02B21/365Control or image processing arrangements for digital or video microscopes
    • G02B21/367Control or image processing arrangements for digital or video microscopes providing an output produced by processing a plurality of individual source images, e.g. image tiling, montage, composite images, depth sectioning, image comparison
    • GPHYSICS
    • G02OPTICS
    • G02BOPTICAL ELEMENTS, SYSTEMS OR APPARATUS
    • G02B27/00Optical systems or apparatus not provided for by any of the groups G02B1/00 - G02B26/00, G02B30/00
    • G02B27/0025Optical systems or apparatus not provided for by any of the groups G02B1/00 - G02B26/00, G02B30/00 for optical correction, e.g. distorsion, aberration
    • G02B27/0031Optical systems or apparatus not provided for by any of the groups G02B1/00 - G02B26/00, G02B30/00 for optical correction, e.g. distorsion, aberration for scanning purposes
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00Indexing scheme for image analysis or image enhancement
    • G06T2207/20Special algorithmic details
    • G06T2207/20021Dividing image into blocks, subimages or windows
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00Indexing scheme for image analysis or image enhancement
    • G06T2207/30Subject of image; Context of image processing
    • G06T2207/30004Biomedical image processing
    • G06T2207/30072Microarray; Biochip, DNA array; Well plate
    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06VIMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00Arrangements for image or video recognition or understanding
    • G06V10/20Image preprocessing
    • G06V10/24Aligning, centring, orientation detection or correction of the image
    • G06V10/247Aligning, centring, orientation detection or correction of the image by affine transforms, e.g. correction due to perspective effects; Quadrilaterals, e.g. trapezoids
    • HELECTRICITY
    • H01ELECTRIC ELEMENTS
    • H01JELECTRIC DISCHARGE TUBES OR DISCHARGE LAMPS
    • H01J2237/00Discharge tubes exposing object to beam, e.g. for analysis treatment, etching, imaging
    • H01J2237/26Electron or ion microscopes
    • H01J2237/28Scanning microscopes
    • H01J2237/2813Scanning microscopes characterised by the application
    • H01J2237/2817Pattern inspection

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • General Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Multimedia (AREA)
  • Health & Medical Sciences (AREA)
  • Signal Processing (AREA)
  • Chemical & Material Sciences (AREA)
  • General Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Biomedical Technology (AREA)
  • Pathology (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Optics & Photonics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hematology (AREA)
  • Clinical Laboratory Science (AREA)
  • Dispersion Chemistry (AREA)
  • Investigating, Analyzing Materials By Fluorescence Or Luminescence (AREA)
  • Geometry (AREA)
  • Microscoopes, Condenser (AREA)
  • Image Processing (AREA)
  • Studio Devices (AREA)
  • Optical Communication System (AREA)

Abstract

OPTICAL DISTORTION CORRECTION FOR IMAGED SAMPLES Techniques are described for dynamically correcting image distortion during imaging of a patterned sample having repeating spots. Different sets of image distortion correction coefficients may be calculated for different regions of a sample during a first imaging cycle of a multicycle imaging run and subsequently applied in real time to image data generated during subsequent cycles. In one implementation, image distortion correction coefficients may be calculated for an image of a patterned sample having repeated spots by: estimating an affine transform of the image; sharpening the image; and iteratively searching for an optimal set of distortion correction coefficients for the sharpened image, where iteratively searching for the optimal set of distortion correction coefficients for the sharpened image includes calculating a mean chastity for spot locations in the image, and where the estimated affine transform is applied during each iteration of the search. [Figure 2A]
SG10201801648VA 2017-03-07 2018-02-28 Optical distortion correction for imaged samples SG10201801648VA (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201762468347P 2017-03-07 2017-03-07
NL2018852A NL2018852B1 (en) 2017-05-05 2017-05-05 Optical distortion correction for imaged samples

Publications (1)

Publication Number Publication Date
SG10201801648VA true SG10201801648VA (en) 2018-10-30

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US (5) US10152776B2 (en)
EP (2) EP4187234A1 (en)
JP (2) JP6563539B2 (en)
KR (2) KR102072232B1 (en)
CN (2) CN111652797A (en)
AU (1) AU2018201352B2 (en)
BR (1) BR102018004557A2 (en)
CA (2) CA3139142C (en)
ES (1) ES2948760T3 (en)
IL (1) IL257826B (en)
NL (1) NL2018852B1 (en)
NZ (1) NZ740201A (en)
SA (1) SA118390405B1 (en)
SG (2) SG10201801648VA (en)
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EP4187234A1 (en) 2023-05-31
CA3139142A1 (en) 2018-09-07
ES2948760T3 (en) 2023-09-18
NZ752391A (en) 2020-09-25
IL257826B (en) 2020-02-27
KR102455926B1 (en) 2022-10-17
SG10202002144PA (en) 2020-05-28
IL257826A (en) 2018-04-30
KR20200012006A (en) 2020-02-04
BR102018004557A2 (en) 2018-12-04
TW201842322A (en) 2018-12-01
SA118390405B1 (en) 2021-04-14
KR20180102509A (en) 2018-09-17
TW202014696A (en) 2020-04-16
US10909666B2 (en) 2021-02-02
US20240029217A1 (en) 2024-01-25
US20190087948A1 (en) 2019-03-21
JP6563539B2 (en) 2019-08-21
CN111652797A (en) 2020-09-11
US10152776B2 (en) 2018-12-11
JP2019169176A (en) 2019-10-03
CN108573468B (en) 2020-06-09
US20230131965A1 (en) 2023-04-27
NZ740201A (en) 2019-09-27
TWI685653B (en) 2020-02-21
EP3373238B1 (en) 2023-04-05
CN108573468A (en) 2018-09-25
JP6871970B2 (en) 2021-05-19
AU2018201352A1 (en) 2018-09-27
US20210224961A1 (en) 2021-07-22
CA3139142C (en) 2023-01-10
US11568522B2 (en) 2023-01-31
EP3373238A1 (en) 2018-09-12
JP2018173943A (en) 2018-11-08
KR102072232B1 (en) 2020-01-31
CA2996541A1 (en) 2018-09-07
US20180260940A1 (en) 2018-09-13
AU2018201352B2 (en) 2019-05-02
NL2018852B1 (en) 2018-11-14
CA2996541C (en) 2022-01-04
US11816816B2 (en) 2023-11-14
TWI728645B (en) 2021-05-21

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