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.

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.

公开(公告)号：US20230230234A1

公开(公告)日：2023-07-20

申请号：US18096835

申请日：2023-01-13

Applicant: APPLIED MATERIALS, INC.

Inventor： Sumit Kumar Jha ,  Dan Xie ,  Arina Nikitina ,  Debjit Ray ,  Yun-Ching Chang ,  Suraj Rengarajan

IPC: G06T7/00 ,  G06T5/00 ,  G06T7/11 ,  G06V10/82 ,  G06V20/70

CPC classification number: G06T7/0012 ,  G06T5/002 ,  G06T7/11 ,  G06V10/82 ,  G06V20/70 ,  G06T2207/30024

Abstract: A system and method of performing deep cell body segmentation on a biological sample is provided. The method includes receiving a first and a second stained image. The first image is processed using a trained machine learned model that outputs locations of a plurality of cell nuclei in the first stained image. Seed points are then determined based on the locations of the plurality of cell nuclei. The second image is then processed using the seed points to determine a plurality of cell membranes using a watershed segmentation. The second image is then post-processed and an output image is produced. The output image is then analyzed and gene sequencing is performed.

公开(公告)号：US11630067B2

公开(公告)日：2023-04-18

申请号：US17124285

申请日：2020-12-16

Applicant: Applied Materials, Inc.

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

IPC: C12Q1/6841 ,  G01N21/64 ,  G02B21/00 ,  G02B21/16 ,  G02B21/36 ,  G06T5/00 ,  G06T5/20 ,  G06T5/50 ,  G06T7/00 ,  G16B50/40 ,  G06V10/30 ,  G06V10/75 ,  G06V20/69 ,  G01N21/75

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.

公开(公告)号：US20220375546A1

公开(公告)日：2022-11-24

申请号：US17328638

申请日：2021-05-24

Applicant: Applied Materials, Inc.

Inventor： Mike Jin-An Huang ,  Yun-Ching Chang ,  Dan Xie ,  Kok Hao Chen ,  Shijie Nigel Chou

IPC: G16B40/20 ,  G16B45/00 ,  C12Q1/6841 ,  G06T7/00

Abstract: Exemplary embodiments provide methods, mediums, and systems for processing multiplexed image data from a fluorescence in-situ hybridization (FISH) experiment. According to exemplary embodiments, a convolutional neural network (CNN) may be applied to the image data to localize and identify hybridization spots in images corresponding to different sets of targeting probes. The CNN is configured in such a way that it is able to discriminate hybridization spots in situations that are difficult for conventional techniques. The CNN may be trained on a relatively small amount of data by exploiting the nature of the FISH codebook.

公开(公告)号：US20210183034A1

公开(公告)日：2021-06-17

申请号：US17124305

申请日：2020-12-16

Applicant: Applied Materials, Inc.

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

IPC: G06T5/50 ,  G06T5/00 ,  G06T7/00 ,  G06T5/20 ,  G02B21/16 ,  G02B21/36 ,  G01N21/64 ,  C12Q1/6841

Abstract: A fluorescent in-situ hybridization imaging and analysis system includes a flow cell to contain a sample to be exposed to fluorescent probes in a reagent, a fluorescence microscope to obtain sequentially collect a plurality of images of the sample at a plurality of different combinations of imaging parameters, and a data processing system. The data processing system includes an online pre-processing system configured to sequentially receive the images from the fluorescence microscope as the images are collected and perform on-the-fly image pre-processing to remove experimental artifacts of the image and to provide RNA image spot sharpening, and an offline processing system configured to, after the plurality of images are collected, perform registration of images having a same field of view and to decode intensity values in the plurality of images to identify expressed genes.

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

IPC: G02B21/00 ,  G06T7/00 ,  G02B21/06

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.

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.

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.

公开(公告)号：US11783916B2

公开(公告)日：2023-10-10

申请号：US17124353

申请日：2020-12-16

Applicant: Applied Materials, Inc.

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

IPC: G06K9/00 ,  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 ,  G16B50/00 ,  G01N21/75

CPC classification number: G16B40/10 ,  C12Q1/6841 ,  G01N21/6428 ,  G01N21/6456 ,  G01N21/6458 ,  G02B21/0076 ,  G02B21/16 ,  G02B21/365 ,  G02B21/367 ,  G06T5/003 ,  G06T5/006 ,  G06T5/20 ,  G06T5/50 ,  G06T7/0012 ,  G06V10/30 ,  G06V10/507 ,  G06V10/758 ,  G06V20/69 ,  G06V20/698 ,  G16B50/00 ,  G16B50/40 ,  G01N2021/6419 ,  G01N2021/6421 ,  G01N2021/6441 ,  G01N2021/755 ,  G01N2201/12761 ,  G06T2207/10056 ,  G06T2207/10064 ,  G06T2207/30004 ,  G06T2207/30168

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.