Patents by Inventor Srinivas Chukka
Srinivas Chukka has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11972859Abstract: Automated systems and methods are presented for retrospectively analyzing clinical trial data. A plurality of image derived from biological samples of patients in a cohort population are accessed. Image features are computed based on the plurality of images. A diagnostic feature metric is derived based on the computed image features. A cut point value is determined by applying a statistical minimization method using the derived diagnostic feature metric and patient outcome data from the cohort population, in which the cut point value identifies a patient in the cohort population as positive or negative for a diagnostic test.Type: GrantFiled: June 16, 2023Date of Patent: April 30, 2024Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Michael Barnes, Christophe Chefd'hotel, Srinivas Chukka
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Publication number: 20240135532Abstract: Systems and methods described herein relate, among other things, to unmixing more than three stains, while preserving the biological constraints of the biomarkers. Unlimited numbers of markers may be unmixed from a limited-channel image, such as an RGB image, without adding any mathematical complicity to the model. Known co-localization information of different biomarkers within the same tissue section enables defining fixed upper bounds for the number of stains at one pixel. A group sparsity model may be leveraged to explicitly model the fractions of stain contributions from the co-localized biomarkers into one group to yield a least squares solution within the group. A sparse solution may be obtained among the groups to ensure that only a small number of groups with a total number of stains being less than the upper bound are activated.Type: ApplicationFiled: December 19, 2023Publication date: April 25, 2024Applicant: Ventana Medical Systems, Inc.Inventors: Srinivas Chukka, Ting Chen
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Patent number: 11893731Abstract: Systems and methods described herein relate, among other things, to unmixing more than three stains, while preserving the biological constraints of the biomarkers. Unlimited numbers of markers may be unmixed from a limited-channel image, such as an RGB image, without adding any mathematical complicity to the model. Known co-localization information of different biomarkers within the same tissue section enables defining fixed upper bounds for the number of stains at one pixel. A group sparsity model may be leveraged to explicitly model the fractions of stain contributions from the co-localized biomarkers into one group to yield a least squares solution within the group. A sparse solution may be obtained among the groups to ensure that only a small number of groups with a total number of stains being less than the upper bound are activated.Type: GrantFiled: August 2, 2021Date of Patent: February 6, 2024Assignee: Ventana Medical Systems, Inc.Inventors: Srinivas Chukka, Ting Chen
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Publication number: 20240013339Abstract: The disclosure relates to devices, systems and methods for image registration and annotation. The devices include computer software products for aligning whole slide digital images on a common grid and transferring annotations from one aligned image to another aligned image on the basis of matching tissue structure. The systems include computer-implemented systems such as work stations and networked computers for accomplishing the tissue-structure based image registration and cross-image annotation. The methods include processes for aligning digital images corresponding to adjacent tissue sections on a common grid based on tissue structure, and transferring annotations from one of the adjacent tissue images to another of the adjacent tissue images.Type: ApplicationFiled: September 15, 2023Publication date: January 11, 2024Applicant: Ventana Medical Systems, Inc.Inventors: Srinivas Chukka, Anindya Sarkar, Quan Yuan
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Patent number: 11860072Abstract: The subject disclosure presents systems and methods for improved meso-dissection of biological specimens and tissue slides including importing one or more reference slides with annotations, using inter-marker registration algorithms to automatically map the annotations to an image of a milling slide, and dissecting the annotated tissue from the selected regions in the milling slide for analysis, while concurrently tracking the data and analysis using unique identifiers such as bar codes.Type: GrantFiled: October 15, 2021Date of Patent: January 2, 2024Assignee: ROCHE MOLECULAR SYSTEMS, INC.Inventors: Michael Barnes, Christophe Chefd'hotel, Srinivas Chukka, Mohammad Qadri
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Publication number: 20230419489Abstract: Immune context scores are calculated for tumor tissue samples using continuous scoring functions. Feature metrics for at least one immune cell marker are calculated for a region or regions of interest, the feature metrics including at least a quantitative measure of human CD3 or total lymphocyte counts. A continuous scoring function is then applied to a feature vector including the feature metric and at least one additional metric related to an immunological biomarker, the output of which is an immune context score. The immune context score may then be plotted as a function of a diagnostic or treatment metric, such as a prognostic metric (e.g. overall survival, disease-specific survival, progression-free survival) or a predictive metric (e.g. likelihood of response to a particular treatment course). The immune context score may then be incorporated into diagnostic and/or treatment decisions.Type: ApplicationFiled: August 29, 2023Publication date: December 28, 2023Inventors: Michael Barnes, Joerg Bredno, Rebecca C. Bowermaster, Srinivas Chukka, Wen-Wei Liu, Kandavel Shanmugam, Junming Zhu
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Publication number: 20230393036Abstract: The subject disclosure provides systems, computer-implemented methods, and clinical workflows for meso-dissection of biological specimens and tissue slides by incorporating annotation and inter-marker registration modules within digital pathology imaging and meso-dissection (or milling) systems. Images of a reference slide a milling slide may be acquired using the same imaging system, with the annotations on the image associated with the milling slide being based on the inter-marker registration. Each image along with its respective annotations and meta-data may be associated with a project or a case and stored in an image management system. A same-marker registration may be used to map annotations from the annotated image of the milling slide to a live image of the milling slide. The milling slide may be milled based on the annotations, with milled tissue output into a contained that is labeled in association with the labeled input slides.Type: ApplicationFiled: August 16, 2023Publication date: December 7, 2023Inventors: Michael Barnes, Srinivas Chukka, Mohammad Qadri
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Patent number: 11823347Abstract: The disclosure relates to devices, systems and methods for image registration and annotation. The devices include computer software products for aligning whole slide digital images on a common grid and transferring annotations from one aligned image to another aligned image on the basis of matching tissue structure. The systems include computer-implemented systems such as work stations and networked computers for accomplishing the tissue-structure based image registration and cross-image annotation. The methods include processes for aligning digital images corresponding to adjacent tissue sections on a common grid based on tissue structure, and transferring annotations from one of the adjacent tissue images to another of the adjacent tissue images.Type: GrantFiled: March 5, 2021Date of Patent: November 21, 2023Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Srinivas Chukka, Anindya Sarkar, Quan Yuan
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Publication number: 20230352151Abstract: Automated systems and methods are presented for retrospectively analyzing clinical trial data. A plurality of image derived from biological samples of patients in a cohort population are accessed. Image features are computed based on the plurality of images. A diagnostic feature metric is derived based on the computed image features. A cut point value is determined by applying a statistical minimization method using the derived diagnostic feature metric and patient outcome data from the cohort population, in which the cut point value identifies a patient in the cohort population as positive or negative for a diagnostic test.Type: ApplicationFiled: June 16, 2023Publication date: November 2, 2023Applicant: Ventana Medical Systems, Inc.Inventors: Michael BARNES, Christophe Chefd'hotel, Srinivas Chukka
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Patent number: 11783478Abstract: Immune context scores are calculated for tumor tissue samples using continuous scoring functions. Feature metrics for at least one immune cell marker are calculated for a region or regions of interest, the feature metrics including at least a quantitative measure of human CD3 or total lymphocyte counts. A continuous scoring function is then applied to a feature vector including the feature metric and at least one additional metric related to an immunological biomarker, the output of which is an immune context score. The immune context score may then be plotted as a function of a diagnostic or treatment metric, such as a prognostic metric (e.g. overall survival, disease-specific survival, progression-free survival) or a predictive metric (e.g. likelihood of response to a particular treatment course). The immune context score may then be incorporated into diagnostic and/or treatment decisions.Type: GrantFiled: January 5, 2022Date of Patent: October 10, 2023Assignee: Ventana Medical Systems, Inc.Inventors: Michael Barnes, Joerg Bredno, Rebecca C. Bowermaster, Srinivas Chukka, Wen-Wei Liu, Kandavel Shanmugam, Junming Zhu
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Patent number: 11768136Abstract: The subject disclosure provides systems, computer-implemented methods, and clinical workflows for meso-dissection of biological specimens and tissue slides by incorporating annotation and inter-marker registration modules within digital pathology imaging and meso-dissection (or milling) systems. Images of a reference slide a milling slide may be acquired using the same imaging system, with the annotations on the image associated with the milling slide being based on the inter-marker registration. Each image along with its respective annotations and meta-data may be associated with a project or a case, and stored in an image management system. A same-marker registration may be used to map annotations from the annotated image of the milling slide to a live image of the milling slide. The milling slide may be milled based on the annotations, with milled tissue output into a contained that is labeled in association with the labeled input slides.Type: GrantFiled: August 12, 2021Date of Patent: September 26, 2023Assignee: Roche Molecular Systems, Inc.Inventors: Michael Barnes, Srinivas Chukka, Mohammad Qadri
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Patent number: 11756318Abstract: Convolutional neural networks for detecting objects of interest within images of biological specimens are disclosed. Also disclosed are systems and methods of training and using such networks, one method including: obtaining a sample image and at least one of a set of positive points and a set of negative points, wherein each positive point identifies a location of one object of interest within the sample image, and each negative point identifies a location of one object of no-interest within the sample image; obtaining one or more predefined characteristics of objects of interest and/or objects of no-interest, and based on the predefined characteristics, generating a boundary map comprising a positive area around each positive point the set of positive points, and/or a negative area around each negative point in the set of negative points; and training the convolutional neural network using the sample image and the boundary map.Type: GrantFiled: February 3, 2023Date of Patent: September 12, 2023Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Srinivas Chukka, Jianxu Chen
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Patent number: 11721427Abstract: Automated systems and methods are presented for retrospectively analyzing clinical trial data. A plurality of image derived from biological samples of patients in a cohort population are accessed. Image features are computed based on the plurality of images. A diagnostic feature metric is derived based on the computed image features. A cut point value is determined by applying a statistical minimization method using the derived diagnostic feature metric and patient outcome data from the cohort population, in which the cut point value identifies a patient in the cohort population as positive or negative for a diagnostic test.Type: GrantFiled: June 22, 2020Date of Patent: August 8, 2023Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Michael Barnes, Christophe Chefd'Hotel, Srinivas Chukka
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Patent number: 11682192Abstract: Automated systems and methods for training a multilayer neural network to classify cells and regions from a set of training images are presented. Automated systems and methods for using a trained multilayer neural network to classify cells within an unlabeled image are also presented.Type: GrantFiled: June 3, 2020Date of Patent: June 20, 2023Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Srinivas Chukka, Anindya Sarkar, Mohamed Amgad Tageldin
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Publication number: 20230186657Abstract: Convolutional neural networks for detecting objects of interest within images of biological specimens are disclosed. Also disclosed are systems and methods of training and using such networks, one method including: obtaining a sample image and at least one of a set of positive points and a set of negative points, wherein each positive point identifies a location of one object of interest within the sample image, and each negative point identifies a location of one object of no-interest within the sample image; obtaining one or more predefined characteristics of objects of interest and/or objects of no-interest, and based on the predefined characteristics, generating a boundary map comprising a positive area around each positive point the set of positive points, and/or a negative area around each negative point in the set of negative points; and training the convolutional neural network using the sample image and the boundary map.Type: ApplicationFiled: February 3, 2023Publication date: June 15, 2023Applicant: Ventana Medical Systems, Inc.Inventors: Srinivas Chukka, Jianxu Chen
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Patent number: 11657503Abstract: Described herein are computer-implemented methods for analysis of a tissue sample. An example method includes: annotating the whole tumor regions or set of tumorous sub-regions either on a biomarker image or an H&E image (e.g. from an adjacent serial section of the biomarker image); registering at least a portion of the biomarker image to the H&E image; detecting different cellular and regional tissue structures within the registered H&E image; computing a probability map based on the different detected structures within the registered H&E image; deriving nuclear metrics from each of the biomarker and H&E images; deriving probability metrics from the probability map; and classifying tumor nuclei in the biomarker image based on the computed nuclear and probability metrics.Type: GrantFiled: March 16, 2021Date of Patent: May 23, 2023Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Srinivas Chukka, Kien Nguyen, Ting Chen
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Patent number: 11600087Abstract: Convolutional neural networks for detecting objects of interest within images of biological specimens are disclosed. Also disclosed are systems and methods of training and using such networks, one method including: obtaining a sample image and at least one of a set of positive points and a set of negative points, wherein each positive point identifies a location of one object of interest within the sample image, and each negative point identifies a location of one object of no-interest within the sample image; obtaining one or more predefined characteristics of objects of interest and/or objects of no-interest, and based on the predefined characteristics, generating a boundary map comprising a positive area around each positive point the set of positive points, and/or a negative area around each negative point in the set of negative points; and training the convolutional neural network using the sample image and the boundary map.Type: GrantFiled: August 27, 2021Date of Patent: March 7, 2023Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Srinivas Chukka, Jianxu Chen
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Patent number: 11526984Abstract: Automated systems and methods for determining the variability between derived expression scores for a series of biomarkers between different identified cell clusters in a whole slide image are presented. The variability between derived expression scores may be a derived inter-marker heterogeneity metric.Type: GrantFiled: June 2, 2020Date of Patent: December 13, 2022Assignee: VENTANA MEDICAL SYSTEMS, INC.Inventors: Michael Barnes, Srinivas Chukka, Anindya Sarkar
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Publication number: 20220270242Abstract: Immune context scores are calculated for tumor tissue samples using continuous scoring functions. Feature metrics for at least one immune cell marker are calculated for a region or regions of interest, the feature metrics including at least a quantitative measure of human CD3 or total lymphocyte counts. A continuous scoring function is then applied to a feature vector including the feature metric and at least one additional metric related to an immunological biomarker, the output of which is an immune context score. The immune context score may then be plotted as a function of a diagnostic or treatment metric, such as a prognostic metric (e.g. overall survival, disease-specific survival, progression-free survival) or a predictive metric (e.g. likelihood of response to a particular treatment course). The immune context score may then be incorporated into diagnostic and/or treatment decisions.Type: ApplicationFiled: January 5, 2022Publication date: August 25, 2022Inventors: Michael Barnes, Joerg Bredno, Rebecca C. Bowermaster, Srinivas Chukka, Wen-Wei Liu, Kandavel Shanmugam, Junming Zhu
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Patent number: 11417021Abstract: A tissue analysis system and method for the spectral deconvolution of a RGB digital image obtained from a stained biological tissue sample, by estimating the stain component images that are obtained from a staining system configuration, where the reference stain vectors are assumed to be sampled from a known color distribution. The prior knowledge of stain variability of the staining system is adopted as initial reference stain vectors and statistical distribution of their variability. Based on the initial reference stain vectors distribution, the tissue analysis system determines both the reference stain vectors and stain component images of the input image. The image is then deconvoluted based on the reference stain vectors and stain component images.Type: GrantFiled: January 31, 2020Date of Patent: August 16, 2022Assignee: Ventana Medical Systems, Inc.Inventors: Srinivas Chukka, Zhou Lan