Quantitative assessment of biological function based on the temporal and spatial organization of subnuclear domains

• US 7,813,881 B2
• Filed: 09/07/2005
• Issued: 10/12/2010
• Est. Priority Date: 09/10/2004
• Status: Active Grant

• Current Assignee: University Of Massachusetts
• Original Assignee: University Of Massachusetts
• Inventors: Zaidi, Sayyed K., Lian, Jane B., Javed, Amjad, Stein, Janet L., Young, Daniel W., Stein, Gary S., Van Wijnen, Andre J.
• Primary Examiner(s): Skowronek; Karlheinz R
• Application Number:
  US11/221,166
• Publication Number:
  US 20060149481A1
• Time in Patent Office: 1,861 Days
• Field of Search: None
• US Class Current: 702/19
• CPC Class Codes: G06T 2207/30004 Biomedical image processing
• CPC Class Codes: G06T 7/0012 Biomedical image inspection
• CPC Class Codes: G06V 20/698 Matching; Classification

Abstract

The present invention provides a method useful for analysis of punctate distribution of supramolecular complexes that are compartmentalized in nuclear microenvironments. In preferred embodiments the method provides quantitative analysis of the assembly of regulatory machinery within the context of nuclear architecture and to provide a mechanistic link with biological control. In other embodiments, the invention provides a method of identifying a molecule by parameters of its subnuclear distribution, comprising the steps of quantifying organizational parameters of domains within subnuclear distributions of a molecule; performing factor analysis on the quantified organizational parameters; performing discriminant analysis on the quantified organizational parameters; comparing the results of the factor analysis and the results of the discriminant analysis to one or more standards, thereby identifying a molecule by parameters of its subnuclear distribution.

Claims

1. A method for quantifying domains within a punctate distribution comprising the steps of:

acquiring at least one digital image of a punctate distribution, wherein the at least one digital image is a fluorescence photomicrographic image of the nucleus of a eukaryotic cell;

performing image segmentation on the at least one digital image to produce a segmented image of the punctate distribution;

identifying domains within the punctate distribution of the segmented image; and

computing at least twenty-five organizational parameters of the domains within the punctate distribution of the segmented image wherein the at least 25 organizational parameters comprise the number of domains, mean domain size, median domain size, standard deviation of domain size, variance of domain size, skewness of domain size, kurtosis of domain size, coefficient of variation of domain size;

index of dispersion of domain size;

mean nearest neighbor distance, median nearest neighbor distance, standard deviation of nearest neighbor distance, variance of nearest neighbor distance, skewness of nearest neighbor distance, kurtosis of nearest neighbor distance, coefficient of variation of nearest neighbor distance;

index of dispersion of nearest neighbor distance, domain density, Re, Ro/Re, Ve, Vo/Ve, Rp, Rd, or Rd/Rp.

2. The method of claim 1, wherein the step of acquiring digital images further comprises the step of deconvoluting the digital image.

3. The method of claim 1 wherein the step of identifying domains further comprises the step of providing a mask of a portion of the digital image.

4. The method of claim 1 wherein the step of identifying domains further comprises the step of producing a masked image.

5. The method of claim 1 wherein the step of performing image segmentation further comprises the step of determining an image threshold.

6. The method of claim 1 wherein the step of performing image segmentation further comprises the step of selecting a threshold that maximizes the number of detectable domains in the segmented image.

7. The method of claim 1 further comprising the step of performing factor analysis on the organizational parameters.

8. The method of claim 1, further comprising performing statistical analysis of organizational parameters.

9. The method of claim 1, wherein the statistical analysis is selected from discriminant analysis, cluster analysis, classification analysis, analysis of variance, a Kruskal-Wallis test, and a multiple-comparison test.

10. The method of claim 1, wherein the at least 25 organizational parameters are selected from parameters that describe (i) domain quantity and nuclear size, (ii) domain size and variability, (iii) domain spatial randomness, and (iv) domain radial position.

11. The method of claim 1, wherein the domains are protein domains.

12. A method for quantifying domains within a punctate distribution comprising the steps of:

acquiring at least one digital image of a punctate distribution, wherein the at least one digital image is a fluorescence photomicrographic image of the nucleus of a eukaryotic cell;

performing image segmentation on the at least one digital image to produce a segmented image of the punctate distribution;

identifying protein domains within the punctate distribution in the segmented image;

computing organizational parameters of the protein domains within the punctate distribution of the segmented image; and

performing statistical analysis of the organizational parameters wherein the organizational parameters comprise the number of domains, mean domain size, median domain size, standard deviation of domain size, variance of domain size, skewness of domain size, kurtosis of domain size, coefficient of variation of domain size;

index of dispersion of domain size;

mean nearest neighbor distance, median nearest neighbor distance, standard deviation of nearest neighbor distance, variance of nearest neighbor distance, skewness of nearest neighbor distance, kurtosis of nearest neighbor distance, coefficient of variation of nearest neighbor distance;

index of dispersion of nearest neighbor distance, domain density, Re, Ro/Re, Ve, Vo/Ve, Rp, Rd, or Rd/Rp.

13. The method of claim 12, wherein the step of acquiring digital images further comprises the step of deconvoluting the digital image.

14. The method of claim 12, wherein the step of identifying domains further comprises the step of providing a mask of a portion of the digital image.

15. The method of claim 12, wherein the step of identifying domains further comprises the step of producing a masked image.

16. The method of claim 12, wherein the step of performing image_segmentation further comprises the step of determining an image threshold.

17. The method of claim 12, wherein the step of performing image segmentation further comprises the step of selecting a threshold that maximizes the number of detectable domains in the segmented image.

18. The method of claim 12, further comprising the step of performing factor analysis on the organizational parameters.

19. A method for quantifying the organization of molecules in a cell, comprising:

acquiring a digital image that comprises fluorescently labeled molecules in a cell, wherein the digital image is a fluorescence photomicrographic image;

segmenting the at least one digital image to produce a segmented image;

detecting, in the segmented image, domains of the molecules in the cell;

determining the number of domains in the cell;

determining the areas of the domains and the centroids of the domains;

determining the locations of the centroids of the domains in pixel coordinates of the segmented image wherein the at least 25 organizational parameters comprise the number of domains, mean domain size, median domain size, standard deviation of domain size, variance of domain size, skewness of domain size, kurtosis of domain size, coefficient of variation of domain size;

index of dispersion of domain size;

mean nearest neighbor distance, median nearest neighbor distance, standard deviation of nearest neighbor distance, variance of nearest neighbor distance, skewness of nearest neighbor distance, kurtosis of nearest neighbor distance, coefficient of variation of nearest neighbor distance;

index of dispersion of nearest neighbor distance, domain density, Re, Ro/Re, Ve, Vo/Ve, Rp, Rd, or Rd/Rp; and

computing at least twenty-five parameters that quantify the organization of the molecule in the cell based, in part, on the areas and the locations of the centroids of the domains.

20. The method of claim 19, wherein the at least 25 parameters are selected from parameters that describe (i) domain quantity and nuclear size, (ii) domain size and variability, (iii) domain spatial randomness, and (iv) domain radial position.

21. The method of claim 19, wherein the molecule is a protein.

22. The method of claim 19, further comprising producing a nuclear mask image and determining the area of the nucleus of the cell in the nuclear mask image, wherein the parameters are based, in further part, on the area of the nucleus.

23. The method of claim 19, further comprising performing factor analysis on the parameters.