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Software for Accurate Segmentation of Cell Nuclei in Breast Tissue

Posted Jul 22 2010 5:00pm

Description of Invention:
Automatic segmentation of cell nuclei is critical in several high-throughput cytometry and pathology applications (1), such as spatial analysis of genetic loci by fluorescence in situ hybridization ("FISH"), whereas manual segmentation is laborious (2). Current automated segmentation methods have varying performance in the presence of distortions introduced during sample preparation, non-uniform illumination, clustering of the individual objects of interest (cells or cell nuclei), and seldom assess boundary accuracy.

Researchers at the National Cancer Institute-Frederick, NIH, have developed an automatic algorithm to segment cell nuclei (3) and FISH signals from two-dimensional images of breast tissue. This automated system integrates a series of advanced image processing methods to overcome the delays inherent to current manual methods for segmenting (delineating) individual cell nuclei in tissue samples. The system automatically selects a subset of nuclei that with high likelihood are accurately segmented. This system has been validated using both simulated and actual datasets that have been accurately analyzed by manual methods. The system generalizes to independent analysis of many spatial parameters useful for studying spatial gene positioning in interphase nuclei, and potentially has a wide range of diagnostic pathology, cytological and high throughput screening applications.

Applications:
  • Investigations on genomic organization (nuclear architecture and non-random gene positioning) in the individual nuclei in tissues.
  • Other pathology and cytological and high throughput screening applications requiring precise, quantitative analysis of a subset of cell nuclei in the sample.


Advantages:
  • Automatic
  • Efficient, robust and effective in extracting individual nuclei with FISH labels
  • Facilitates reproducible and unbiased spatial analysis of DNA sequences in interphase nuclei


Development Status:
  • Early stage.
  • Negotiations are underway with several companies to scale up development of the system and to undertake pre-clinical validation for gene positioning in the nuclei of breast sections as a possible early-stage diagnostic or prognostic test for cancer.


Inventors:
Kaustav Nandy (NCI)


Patent Status:
HHS, Reference No. E-106-2010/0

Research Tool -- patent protection is not being pursued for this technology

Relevant Publication:
  1. Gudla PR, Nandy K, Collins J, Meaburn KJ, Misteli T, Lockett SJ. A high-throughput system for segmenting nuclei using multiscale techniques. Cytometry A. 2008 May;73(5):451-466. [ PubMed: 18338778 ]
  2. Meaburn KJ, Gulda PR, Khan S, Lockett SJ, Misteli T. Disease-specific gene repositioning in breast cancer. J Cell Biol. 2009 Dec 14;187(6):801-812. [ PubMed: 19995938 ]
  3. Nandy K, Gudla PR, Meaburn KJ, Misteli T, Lockett SJ. Automatic nuclei segmentation and spatial FISH analysis for cancer detection. Conf Proc IEEE Eng Med Biol Soc 2009;2009:6718-6721. [ PubMed: 19963931 ]


Licensing Status:
Available for licensing.

Collaborative Research Opportunity:
The inventers, working for the Office of the Director, National Cancer Institute, are seeking statements of capability or interest from parties interested in collaborative research (using the Cooperative Research and Development Agreement (CRADA) or Material Transfer Agreement (MTA)) to further develop, evaluate, or commercialize the software for accurate segmentation of cell nuclei and FISH signals in tissue sections. Collaborators working in the field of quantitative and automated pathology may be interested. Please contact John Hewes, Ph.D. at 301-435-3121 or hewesj@mail.nih.gov for more information.


Portfolios:
Devices/Instrumentation
Devices/Instrumentation - Software
Cancer
Cancer - Research Materials



For Additional Information Please Contact:
Patrick McCue Ph.D.
NIH Office of Technology Transfer
6011 Executive Blvd. Suite 325,
Rockville, MD 20852
United States
Email: McCuepat@mail.nih.gov
Phone: 301-496-7057
Fax: 301-402-0220


Ref No: 2137

Updated: 07/2010

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