Method and system for digital image based flourescent in situ hybridization (FISH) analysis

• US 20050265588A1
• Filed: 02/03/2005
• Published: 12/01/2005
• Est. Priority Date: 02/03/2004
• Status: Abandoned Application

• Current Assignee: BioImagene, Inc. (Roche Holding AG)
• Original Assignee: BioImagene, Inc. (Roche Holding AG)
• Inventors: Jadhav, Prithviraj, Rao, C. V.K., Pardeshi, Deepak M., Gholap, Gauri A., Gholap, Abhijeet S., Vipra, Madhura, Abhyankar, Jayant
• Application Number:
  US11/050,035
• Publication Number:
  US 20050265588A1
• Time in Patent Office: Days
• US Class Current: 382/128
• CPC Class Codes: G06V 20/69 Microscopic objects, e.g. biological cells or cellular parts

Abstract

A method and system for automated digital fluorescent in situ hybridization (FISH) image analysis. Luminance parameters from a digital image of a biological tissue sample to which a fluorescent compound (e.g., LSI-HER-2/neu and CEP-17 dyes) have been applied are analyzed to determine plural regions of interest. Fluorescent color signals in the plural regions of interest including plural cell nuclei are identified, classified and grouped into plural groups. Each of the plural groups is validated based on pre-defined conditions. A medical diagnosis or prognosis or medical, life science or biotechnology experiment conclusion determined using a count of plural ratios of validated fluorescent color signals within each of the cell nuclei within the plural groups.

Claims

1. An automated method for fluorescence in situ hybridization (FISH) analysis, comprising:

selecting a plurality of regions of interest in a digital image of a biological tissue sample to which a fluorescent compound has been applied;

detecting a plurality of luminance signals from a plurality of objects of interest in the selected plurality of regions of interest;

grouping the detected plurality of luminance signals from the plurality of objects of interest into a plurality of sets of signals;

forming a plurality of clusters of signals from the plurality of sets of signals; and

analyzing the plurality of clusters of signals to determine a medical conclusion.

2. The method of claim 1 further comprising a computer readable medium having stored therein instructions for causing one or more processors to execute the steps of the method.

3. The method of claim 1 further comprising:

generating one or more reports related to the medical conclusion;

presenting the digital image and one or more reports generated for the medical conclusion on a graphical user interface.

4. The method of claim 1 wherein the fluorescent compound comprises fluorescent dyes including LSI-HER-2/neu and CEP-17.

5. The method of claim 1 wherein the biological tissue sample includes a plurality of human cells.

6. The method of claim 5 wherein the plurality of human cells potentially includes one or more human cancer cells.

7. The method of claim 6 wherein the one or more human cancer cells are breast cancer cells.

8. The method of claim 1 wherein the luminance signals include orange, red, green or yellow signals.

9. The method of claim 1 wherein the selecting step includes determining region a plurality of regions of interest with:

(x,y)=region of interest if (Rxy, Gxy, Bxy) are such that Colorxy>

meanColor+STDColor/2,

wherein Rxy, Gxy, Bxy, are (x,y) points in red, green and blue color planes respectively for luminance signals in the digital image, meanColor is a mean value in a selected color plane and STDColor is a standard deviation value in the selected color plane.

10. The method of claim 9 wherein a selected color plane for Color is a red color plane and wherein fluorescent compound includes fluorescent dyes comprising LSI-HER-2/neu and CEP-17.

11. The method of claim 1 wherein the selecting step includes determining a region of interest by excluding pixels with a pre-determined threshold which includes determining biological tissue components from background pixels in the digital image.

12. The method of claim 1 wherein the grouping step includes grouping the detected plurality of luminance signals for cell nuclei identified in the plurality of objects of interest that are a pre-determined distant apart.

13. The method of claim 1 wherein the forming step includes:

identifying set of signals independent of color for each cell nucleus identified in the plurality of objects of interest in the digital image; and

determining a plurality of clusters of signals using a pre-determined distance between each of the identified set of signals is used to form groups of signals, wherein the pre-determined distance differentiates between inter-nucleus signals and intra-nucleus signals.

14. The method of claim 1 wherein the forming step includes:

grouping a plurality of colored fluorescent signals into a plurality of component groups if a distance between a pair of the plurality of colored fluorescent signals is less than a pre-determined threshold;

splitting the plurality of component groups into a plurality of clusters for each individual cell nucleus identified from the plurality of objects of interest in the digital image; and

validating the plurality of clusters of signals each individual cell nucleus.

15. The method of claim 1 wherein the analyzing step includes counting pre-determined colored luminance signals from plurality of clusters of signals included within inter-phase cell nuclei identified from the plurality of objects of interest in the digital image.

16. The method of claim 15 wherein the counting step includes counting fluorescence red and orange signals and fluorescence green signals included within an inter-phase cell nuclei from the plurality of objects of interest in the digital image for a biological tissue sample to which LSI-HER-2/neu and CEP-17 fluorescent dyes have been applied.

17. The method of claim 1 wherein the analyzing step includes counting a plurality of ratios of luminescent signals within the plurality of clusters to determine a medical conclusion.

18. An automated method for fluorescence in situ hybridization (FISH) analysis, comprising:

grouping a plurality of colored fluorescent signals in a digital image of a biological tissue sample to which a fluorescent compound has been applied into a plurality of component groups if a distance between a pair of the plurality of colored fluorescent signals is less than a pre-determined threshold;

splitting the plurality of component groups into a plurality of clusters for each individual cell nucleus identified in the digital image; and

validating the plurality of clusters of signals each individual cell nucleus; and

counting a plurality of ratios of colored fluorescent colors signals within the plurality of clusters to determine a medical prognosis or diagnosis.

19. The method of claim 18 further comprising a computer readable medium having stored therein instructions for causing one or more processors to execute the steps of the method.

20. The method of claim 18 wherein the counting step includes counting fluorescence red and orange signals and fluorescence green signals included within an inter-phase cell nuclei in the digital image for a biological tissue sample to which LSI-HER-2/neu and CEP-17 fluorescent dyes have been applied.

21. The method of claim 18 wherein the step of splitting the plurality of component groups into a plurality of clusters for each individual cell nucleus identified in the digital image includes splitting a group of fluorescent signals for each individual nucleus based on a presence of a non-region of interest in between a pair of fluorescent color signals in the group.

22. An automated method for fluorescence in situ hybridization (FISH) analysis, comprising:

analyzing luminance values of a plurality of pixels from a digital image of a biological sample to which a fluorescent compound has been applied to segment the digital image into a plurality of cell nuclei and a background portion;

grouping a plurality of fluorescent color signals from the segmented plurality of cell nuclei into a plurality groups of signals; and

determining a medical conclusion based on different color signals present in each of the plurality of groups of signals.

23. The method of claim 22 further comprising a computer readable medium having stored therein instructions for causing one or more processors to execute the steps of the method.

24. The method of claim 22 wherein the grouping step includes:

identifying one or more color error fluorescent signals within the segmented plurality of cell nuclei related to signal noise or biological tissue artifacts; and

eliminating the one or more identified error color fluorescent signals from further analysis.

25. The method of claim 22 wherein the identifying step includes:

identifying a blue color signal based on pre-determined threshold;

identifying a green color signal based on pre-determined threshold;

identifying a yellow color signal based on pre-determined threshold; and

eliminating the identified blue, green and yellow color signals from further analysis in the segmented plurality of cell nuclei for a biological tissue sample to which LSI-HER-2/neu and CEP-17 fluorescent dyes have been applied.

26. The method of claim 25 wherein eliminating step includes:

eliminating the identified blue, green and yellow color signals color signals based on pre-determined size threshold; and

modifying a color of green color signals adjacent to an yellow color signals.

27. The method of claim 22 wherein the determining step includes counting fluorescence red and orange signals and fluorescence green signals included within a plurality of inter-phase cell nuclei in the segmented plurality of cell nuclei for a biological tissue sample to which LSI-HER-2/neu and CEP-17 fluorescent dyes have been applied.

28. An automated system for fluorescence in situ hybridization (FISH) analysis, comprising, in combination:

a means for selecting a plurality of regions of interest in a digital image of a biological tissue sample to which a fluorescent compound has been applied;

a means for detecting a plurality of luminance signals from a plurality of objects of interest in the selected plurality of regions of interest;

a means for grouping the detected plurality of luminance signals from the plurality of objects of interest into a plurality of sets of signals; and

a means for forming a plurality of clusters of signals from the plurality of sets of signals;

a means for analyzing the plurality of clusters of signals to determine a medical conclusion; and

a means for creating one or more reports related to the medical conclusion, for presenting the digital image and the one or more types of reports generated for the medical conclusion on a graphical user interface.

29. An automated system for fluorescence in situ hybridization (FISH) analysis, comprising, in combination:

a database including a plurality of digital images of a plurality of biological samples to which a fluorescent compound has been applied;

a software module for analyzing luminance values of a plurality of pixels from a digital image of a biological sample to which a fluorescent compound has been applied to segment a digital image into a plurality of cell nuclei and a background portion, for identifying and grouping fluorescent color signals from the segmented plurality of cell nuclei into a plurality groups of signals, for validating the plurality of groups of signals for each cell nucleus in the plurality of cell nuclei and for determining a medical conclusion based on different color signals present in each of the plurality of groups of signals; and

a software module for generating one or more reports related to the medical conclusion, for presenting a digital image and the one or more types of reports generated for the conclusion on a graphical user interface.