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High-throughput biomarker segmentation utilizing hierarchical normalized cuts

A biomarker, hierarchical data technology, applied in the field of high-throughput biomarker segmentation using hierarchical standardized cutting, can solve the problems of inconsistent analysis, inaccuracy, and difficulty in implementation

Inactive Publication Date: 2012-09-19
RUTGERS THE STATE UNIV +3
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  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Human visual analysis of such large amounts of data is not readily available, requires highly trained observers, and is also prone to inaccurate and / or inconsistent analysis for a number of reasons

Method used

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  • High-throughput biomarker segmentation utilizing hierarchical normalized cuts
  • High-throughput biomarker segmentation utilizing hierarchical normalized cuts
  • High-throughput biomarker segmentation utilizing hierarchical normalized cuts

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Embodiment Construction

[0046] The subject matter disclosed in this patent application relates to algorithms and methods that enable rapid quantitative analysis of biomarkers in tissue samples. The disclosed methods and algorithms, and devices implementing such methods and algorithms, are capable of utilizing the iterative frequency-weighted mean shift method as it tends to converge (here defined as meaning that all points reach their associated pattern based on the bandwidth parameter) in each tissue sample Snapshots are taken at each level of color resolution.

[0047] Layers can then be subjected to a normalized cut, e.g. guided by a small swatch of user-specified domain knowledge, which can then be mapped to the final segmentation result. The procedure can be performed in less than a minute to accurately obtain segmented images of stained regions, allowing easy quantification and analysis afterwards. By selecting representative points (pixels) from classes of interest in tissue samples, the syst...

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Abstract

A method and apparatus for obtaining segmented images of the stained regions may comprise quantifying the extent of the presence of staining of a biomarker in an original image of a sample, which may comprise selecting a domain swatch of data based upon a user specified domain knowledge; clustering the data within the original image by conducting a frequency weighted mean shift of the data within the original image to convergence, forming a hierarchical plurality of layers each having a different data resolution to form a hierarchical data pyramid; segmenting the plurality of mean shifted data images to determine in each mean shifted data image within the hierarchical data pyramid data not excluded as outside of the swatch; mapping the data not excluded as outside the swatch spatially back to the original image to create a final image; and, storing the final image on a storage medium for further analysis.

Description

[0001] cross reference [0002] This application claims the benefit of U.S. Provisional Patent Application No. 61 / 294703, filed January 13, 2010, entitled "HIERARCHICAL NORMALIZED CUTS: HIGH-THROUGHPUT BIOMARKER SEGMENTATION," and filed September 18, 2009, entitled "SYSTEM AND METHOD FOR AUTOMATED DETECTION AND IDENTIFICATION OF DISEASE AND DISEASE MARKERS FROM BIOLOGICAL IMAGES", the priority of application No. 61 / 276986, the disclosure of each of which is hereby incorporated by reference in its entirety. [0003] Statement of Government Funding [0004] Said subject was not made with government support. technical field [0005] The disclosed subject matter relates to rapid quantitative analysis of biomarkers in tissue samples by segmentation, particularly biomarker segmentation utilizing hierarchical normalized cuts to provide high throughput analysis. Background technique [0006] With the advent of whole slide digital scanners, histology data became available for digit...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G01N33/483
CPCG06T2207/30072G06T7/0083G06T2207/20016G06K9/6224G06T7/0093G06T2207/30024G06T2207/10056G06T7/12G06T7/162G06V20/695G06V10/7635G06F18/2323
Inventor A·雅诺维茨克S·钱德兰A·马达布什
Owner RUTGERS THE STATE UNIV
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