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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
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.
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公开(公告)号：US20220090182A1
公开(公告)日：2022-03-24
申请号：US17481161
申请日：2021-09-21
Applicant: Applied Materials, Inc.
Inventor： Zhen Li , Marc Glazer , Yun-Ching Chang
IPC: C12Q1/6841 , C12Q1/6876 , C12Q1/6825 , G01N21/64
Abstract: A method of fluorescent in-situ hybridization imaging includes exposing a sample to a first plurality of first readout probes and a second plurality of second readout probes, obtaining a first image of the sample with first readout probes and the second readout probes bound to a first analyte and a second analyte, respectively, so as to emit light at a first wavelength range, treating the sample so as to modify the second readout probes, and obtaining a second image of the sample with the first readout probes bound to the first analyte so as to emit light at the first wavelength range and the second analyte substantially not emitting light at the first wavelength range.
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公开(公告)号：US11255785B2
公开(公告)日：2022-02-22
申请号：US16817326
申请日：2020-03-12
Applicant: Applied Materials, Inc.
Inventor： Yun-Ching Chang
Abstract: Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for obtaining a fluorescence microscope image that depicts a sample and a plurality of fiducial markers, identifying the plurality of fiducial markers in the image, and using the plurality of fiducial markers to register the image. The sample and the plurality of fiducial markers have a common fluorescence color, and identifying the plurality of fiducial markers in the image includes comparing a spatial intensity distribution of a plurality of fluorescent regions of the image to a reference distribution function.
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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
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.
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公开(公告)号：US20240045191A1
公开(公告)日：2024-02-08
申请号：US18365853
申请日：2023-08-04
Applicant: Applied Materials, Inc.
Inventor： Ang Li , Joseph R. Johnson , Jean Marc Fan Chung Tsang Min Ching , Dan Xie , Stephen Hsiang , Yun-Ching Chang
CPC classification number: G02B21/0076 , G06T7/0012 , G02B21/06
Abstract: An imaging system for capturing spatial images of biological tissue samples may include an imaging chamber configured to hold a biological tissue sample placed in the imaging system; a light source configured to illuminate the biological tissue sample to activate a plurality of fluorophores in the biological tissue sample; and a plurality of Time Delay and Integration (TDI) imagers configured to simultaneously scan the biological tissue sample, where the plurality of TDI imagers may be configured to separately receive light from different ones of the plurality of fluorophores.
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Patent Agency Ranking
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
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.
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7.发明申请公开(公告)号：US20220092288A1
公开(公告)日：2022-03-24
申请号：US17481197
申请日：2021-09-21
Applicant: Applied Materials, Inc.
Inventor： Zhen Li , Marc Glazer , Yun-Ching Chang
Abstract: A computer program product includes instructions to cause one or more computers to obtain first and second images in the same color channel in the same hybridization step from a fluorescent in-situ hybridization imaging system, and to register the first image and the second image. One or more pixels having a first intensity exceeding a first threshold in the first image and having a second intensity exceeding a second threshold in the second image are identified and classified as activated in a first readout call, and one or more pixels having the first intensity exceeding the first threshold in the first image and the second intensity below the second threshold in the second image are identified and classified as activated in a second readout call.
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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.
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9.发明申请公开(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
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.
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10.发明公开公开(公告)号：US20230253073A1
公开(公告)日：2023-08-10
申请号：US18301875
申请日：2023-04-17
Applicant: Applied Materials, Inc.
Inventor： Yun-Ching Chang , Dan Xie , Chloe Kim
IPC: G16B40/10 , G02B21/00 , G01N21/64 , C12Q1/6841 , G02B21/16 , G02B21/36 , G06T5/00 , G06T5/20 , G06T5/50 , G06T7/00 , G16B50/40 , G06V10/30 , G06V20/69 , G06V10/50 , G06V10/75
CPC classification number: G16B40/10 , C12Q1/6841 , G01N21/6428 , G01N21/6456 , G01N21/6458 , G02B21/16 , G02B21/0076 , G02B21/365 , G02B21/367 , G06T5/003 , G06T5/006 , G06T5/20 , G06T5/50 , G06T7/0012 , G06V10/30 , G06V10/507 , G06V10/758 , G06V20/69 , G06V20/698 , G16B50/40 , G01N2021/755 , G01N2021/6419 , G01N2021/6421 , G06T2207/10056 , G06T2207/10064 , G06T2207/30004 , G06T2207/30168
Abstract: A fluorescent in-situ hybridization imaging system includes a flow cell to contain a sample, a fluorescence microscope, and a control system. The fluorescence microscope includes a variable frequency excitation light source to illuminate the sample, a plurality of emission bandpass filters on a filter wheel, an actuator to rotate the filter wheel, and a camera positioned to receive fluorescently emitted light from the sample. The control system is configured to cause the variable frequency excitation light source to emit a light beam having a selected wavelength, cause the actuator to rotate the filter wheel to position a selected filter in a light path between the sample and the camera, obtain an image from the camera, and coordinate the variable frequency excitation light source and filter wheel such that the selected filter has an emission bandpass associated with emission by the fluorescent probes when excited by the selected wavelength.
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