System and method for co-registering multi-channel images of a tissue micro array

1. A method for registering images of a biological material, comprising the steps of;

applying one or more molecular probes, adapted to provide fluorescent molecular markers, to said biological material;

obtaining a digital image of said biological material and the fluorescent molecular markers;

applying a morphological stain to said biological material;

obtaining a digital image of said biological material; and

aligning and combining digital images, one of which is a moving image and one of which is a fixed image, into a single digital image, that comprises the fluorescent markers and the morphological stain, whereby aligning the digital images comprises identifying a plurality of feature points of the biological material in the moving image and the fixed image, and aligning one or more pixels in the moving and fixed images that correspond to the identified feature points, wherein the feature points comprise a cellular structure, a subcellular structure, or proteins, or combinations thereof.

2. The method of claim 1 , wherein one or more of said registration metrics comprises mutual information from the first and second images.

3. The method of claim 2 , wherein one or more of said registration metrics comprises, at least in part, feature based information comprising one or more features selected from a group consisting of: nuclei, epithelia and stroma.

4. The method of claim 1 , wherein said one or more of said registration metrics comprises, at least in part, intensity based information.

5. The method of claim 1 , further comprising the step of segmenting at least one of said images into nuclei, epithelia and stroma.

6. The method of claim 1 , further comprising the step of creating a digital mask of at least a portion of cellular stroma.

7. The method of claim 1 , further comprising the step of identifying one or more molecular pathways based on said molecular markers.

8. The method of claim 7 , wherein one or more of said molecular pathways is indicative of a disease.

9. The method of claim 8 , wherein said disease is cancer.

10. The method of claim 9 , wherein said cancer is an epithelial cancer.

11. The method of claim 1 , further comprising the steps of,

segmenting at least one of said images into nuclei, epithelia and stroma; and

identifying one or more molecular pathways based on said molecular markers.

12. The method of claim 11 , further comprising the step of creating a digital mask of said stroma.

13. The method of claim 11 , further comprising the step of quantifying one or more of said identified molecular pathways as a function of one or more morphological structures selected from a group consisting of said nuclei, epithelia and stroma.

14. The method of claim 1 , further comprising the step of viewing one or more of said images with a virtual microscope for communication over a communications network.

15. The method of claim 1 , wherein one or more of said registration metrics is selected from a group consisting of mean square error, joint entropy, mutual information from the first and second images, normalized mutual information from the first and second images, cross-correlation, sum of squared differences, and sum of absolute differences.

16. A system for carrying out the method of claim 1 , comprising

a means for storing the digital images; and

a processor for co-registering said second image with said first image based on one or more registration metrics.

17. A method for registering images of a biological material, comprising the steps of,

providing a digital image of a biological material comprising one or more fluorescent molecular markers;

providing a digital image of said biological material comprising one or more morphological stains;

aligning and combining digital images, one of which is a moving image and one of which is a fixed image, into a single digital image using a processor, that comprises the fluorescent markers and the morphological stain, whereby aligning the digital images comprises identifying a plurality of feature points of the biological material in the moving image and the fixed image, and aligning one or more pixels in the moving and fixed images that correspond to the identified feature points, wherein the feature points comprise a cellular structure, a subcellular structure, or proteins, or combinations thereof; and

displaying one or more of the provided digital images or the single digital image on a display device.

18. A system for carrying out the method of claim 17 , comprising;

a means for storing the digital images; and

a processor for co-registering said first and second images based on said information common to said first and second images.

19. The method of claim 17 , wherein said information common to said first and second images comprises one or more types of feature based information selected from a group consisting of: nuclei, epithelia and stroma.

20. The method of claim 17 , further comprising the steps of:

segmenting said digital images into a plurality of morphological features; and

creating a digital mask of one or more of said morphological features.

21. The method of claim 20 , wherein one or more of said morphological features is selected from group consisting of: nuclei, epithelia, stroma, and extracellular matrix.

22. The method of claim 17 , wherein said information common to said first and second images comprises intensity based information.

23. The method of claim 22 , further comprising the steps of:

segmenting said digital images into a plurality of morphological features; and

creating a digital mask of one or more of said morphological features.

24. A method for registering images of a biological material, comprising the steps of;

applying one or more molecular probes, adapted to provide fluorescent molecular markers, to said biological material;

obtaining a first digital image of said biological material and the fluorescent molecular markers;

identifying one or more molecular pathways corresponding to said molecular markers;

applying a morphological stain to said biological material;

obtaining a second digital image of said biological material;

segmenting said second image to identify one or more morphological features; and

aligning and combining the digital images, one of which is a moving image and one of which is a fixed image, based, at least in part, on said step of segmenting said second image, whereby aligning the digital images comprises identifying a plurality of feature points of the biological material in the first and second images, and aligning one or more pixels in the first and second images that correspond to the identified feature points, wherein the feature points comprise a cellular structure, a subcellular structure, or proteins, or combinations thereof.