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    REGISTRATION TECHNIQUES FOR MULTIPLEXED FLUORESCENCE IN-SITU HYBRIDIZATION IMAGES
    1.
    发明申请
    REGISTRATION TECHNIQUES FOR MULTIPLEXED FLUORESCENCE IN-SITU HYBRIDIZATION IMAGES 有权

    公开(公告)号：US20210182531A1

    公开(公告)日：2021-06-17

    申请号：US17124333

    申请日：2020-12-16

    Applicant: Applied Materials, Inc.

    Inventor： Yun-Ching Chang ,  Dan Xie ,  Chloe Kim

    IPC: G06K9/00 ,  G06K9/40 ,  G06K9/62 ,  G16B50/40

    Abstract: For acquisition of spatial transcriptomic information, one or more filters are applied to deconvolution is performed on each image of a plurality of images to generate a plurality of filtered images, and registration of the plurality of filtered images is performed to generate a plurality of registered and filtered images. For each pixel of at least two pixels of the plurality of registered and filtered images, the pixel is decoded by identifying a code word from a plurality of code words in a code book that provides a best match to data values in the plurality of registered and filtered images for the pixel. For each pixel of at least two pixels, a gene is associated with the code word is determined and an indication that the gene is expressed at the pixel is stored.

    UTILIZATION OF SPARCE CODEBOOK IN MULTIPLEXED FLUORESCENT IN-SITU HYBRIDIZATION IMAGING
    4.
    发明申请
    UTILIZATION OF SPARCE CODEBOOK IN MULTIPLEXED FLUORESCENT IN-SITU HYBRIDIZATION IMAGING 有权

    公开(公告)号：US20220310202A1

    公开(公告)日：2022-09-29

    申请号：US17698769

    申请日：2022-03-18

    Applicant: Applied Materials, Inc.

    Inventor： Bongjun Son ,  Chloe Kim ,  Yun-Ching Chang ,  Debjit Ray

    IPC: G16B25/10 ,  G06V10/75 ,  G06V10/98 ,  G06V20/69

    Abstract: A method of method of spatial transcriptomics includes receiving a plurality of images of a sample from an mFISH imaging system and generating a pixel word represented by a sequence of N intensity values. For each pixel, the pixel word is compared to a codebook and a closest matching code word of a plurality of code words is identified. Each code word is represented by a sequence of N bits. The plurality of code words include a plurality of gene-identifying code words and a plurality of negative control code words, the plurality of negative control code words have an equal number of on-values, and on-values of the plurality of negative control code words are evenly distributed across the N bits such that each ordinal position in the sequence of N bits has a same total number of on-bits from the plurality of negative control code words.

    SYSTEM AND METHOD FOR ACQUISITION AND PROCESSING OF MULTIPLEXED FLUORESCENCE IN-SITU HYBRIDIZATION IMAGES
    5.
    发明申请
    SYSTEM AND METHOD FOR ACQUISITION AND PROCESSING OF MULTIPLEXED FLUORESCENCE IN-SITU HYBRIDIZATION IMAGES 有权

    公开(公告)号：US20210199584A1

    公开(公告)日：2021-07-01

    申请号：US17124353

    申请日：2020-12-16

    Applicant: Applied Materials, Inc.

    Inventor： Yun-Ching Chang ,  Dan Xie ,  Chloe Kim

    IPC: G01N21/64

    Abstract: In acquisition of spatial transcriptomic information, a plurality of images representing a common field of view of a sample are obtained and registered. Each pixel of the registered images is decoded by identifying a code word from a plurality of code words in a code book that provides a best match to data values in the plurality of registered images for the pixel. For each code word identified as a best match and each pixel, whether a bit ratio for an image word for the pixel meets a threshold for the code word is determined. The image word is formed from the data values in the plurality of registered images for the pixel. For at least one pixel that is determined to meet the threshold, a gene associated with the code word is determined. Pixels for which the bit ratio does not meet the threshold are screened.

    SYSTEM FOR ACQUISITION AND PROCESSING OF MULTIPLEXED FLUORESCENCE IN-SITU HYBRIDIZATION IMAGES
    6.
    发明申请
    SYSTEM FOR ACQUISITION AND PROCESSING OF MULTIPLEXED FLUORESCENCE IN-SITU HYBRIDIZATION IMAGES 有权

    公开(公告)号：US20210181111A1

    公开(公告)日：2021-06-17

    申请号：US17124285

    申请日：2020-12-16

    Applicant: Applied Materials, Inc.

    Inventor： Yun-Ching Chang ,  Dan Xie ,  Chloe Kim

    IPC: G01N21/64 ,  G02B21/00

    Abstract: In a fluorescent in-situ hybridization imaging system performs, as nested loops, the following: (1) a valve sequentially couples a flow cell to a plurality of different reagent sources to expose the sample to a plurality of different reagents, (2) for each reagent of the plurality of different reagents, a motor sequentially positions the fluorescence microscope relative to sample at a plurality of different fields of view, (3) for each field of view of the plurality of different fields of view, a variable frequency excitation light source sequentially emits a plurality of different wavelengths, (4) for each wavelength of the plurality of different wavelengths, an actuator sequentially positions the fluorescence microscope relative to sample at a plurality of different vertical heights, and (5) for each vertical height of the plurality of different vertical heights, an image is obtained.

    METHODS AND SYSTEMS TO REDUCE AUTO-FLUORESCENCE IN FLUORESCING SAMPLES
    7.
    发明申请
    METHODS AND SYSTEMS TO REDUCE AUTO-FLUORESCENCE IN FLUORESCING SAMPLES 有权

    公开(公告)号：US20230112114A1

    公开(公告)日：2023-04-13

    申请号：US17953575

    申请日：2022-09-27

    Applicant: Applied Materials, Inc.

    Inventor： Joseph R. Johnson ,  Yang Ming Lee ,  Hsiao-Ying Cheng ,  Christabelle Si Mei Goh ,  Ustun Serdar Tulu ,  Chang H. Choi ,  Chloe Kim

    IPC: G01N1/34 ,  G01N1/44 ,  G01N21/64

    Abstract: Exemplary sample processing methods are described that include providing an initial sample to a sample processing system. The sample processing system includes a light-emitting-diode, a temperature control unit, and a fluid supply unit. The methods also include irradiating the initial sample with light emitted from the light-emitting-diode to produce an irradiated sample. The methods may still further include adjusting a temperature of the irradiated sample with the temperature control unit to between 0° C. and 60° C., and contacting the irradiated sample with a fluid from the fluid supply unit. The irradiated sample has a reduction in auto-fluorescence of greater than or about 50% compared to the initial sample. Exemplary sample processing systems are also described that include a light-emitting-diode, a temperature control unit, and a fluid supply unit.

    GENERATION OF SPARCE CODEBOOK FOR MULTIPLEXED FLUORESCENT IN-SITU HYBRIDIZATION IMAGING
    8.
    发明申请
    GENERATION OF SPARCE CODEBOOK FOR MULTIPLEXED FLUORESCENT IN-SITU HYBRIDIZATION IMAGING 有权

    公开(公告)号：US20220310209A1

    公开(公告)日：2022-09-29

    申请号：US17698799

    申请日：2022-03-18

    Applicant: Applied Materials, Inc.

    Inventor： Bongjun Son ,  Chloe Kim ,  Yun-Ching Chang ,  Debjit Ray

    IPC: G16B50/20 ,  G06V20/69 ,  G16B25/00

    Abstract: A method of generating a codebook includes obtaining a plurality of gene-identifying code words for the codebook. Each gene-identifying code word is represented by a sequence of N bits that correspond to a best match to a pixel data value identifying a gene. A plurality of negative control code words is generated, and each negative control code word is represented by a sequence of N bits. The negative control code words have an equal number of on-values. On-values of the plurality of negative control code words are evenly distributed across the N bits such that each ordinal position in the sequence of N bits has a same total number of on-bits from the plurality of negative control code words, and a Hamming distance between each negative control code word and each gene-identify code word is at least a distance threshold.

    METHOD OF CALIBRATION OF MFISH USING SLIDES
    9.
    发明申请
    METHOD OF CALIBRATION OF MFISH USING SLIDES 有权

    公开(公告)号：US20220064719A1

    公开(公告)日：2022-03-03

    申请号：US17461816

    申请日：2021-08-30

    Applicant: Applied Materials, Inc.

    Inventor： Chloe Kim ,  Lu Yan

    IPC: C12Q1/6841 ,  G01N21/64 ,  G06T7/80

    Abstract: A method of calibrating a fluorescence in-situ hybridization (FISH) system includes contacting a calibration slide with a plurality of probes, obtaining one or more images of the calibration slide; and calibrating the FISH system based on the one or more images. The calibration slide has a surface with a first plurality of beads. Each bead of the first plurality of beads has one or more binding domains. Each probe has a tag and a targeting domain, and the targeting domain binds a binding domain from the at least one binding domain.

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