Biomarker Evaluation Through Image Analysis

• US 20130108139A1
• Filed: 10/26/2011
• Published: 05/02/2013
• Est. Priority Date: 10/26/2011
• Status: Active Grant

• Current Assignee: Definiens AG (Astrazeneca PLC)
• Original Assignee: Definiens AG (Astrazeneca PLC)
• Inventors: Binnig, Gerd, Athelogou, Maria, Schmidt, Guenter
• Granted Patent: US 9,042,630 B2
• Time in Patent Office: Days
• US Class Current: 382/133
• CPC Class Codes: G06F 18/22 Matching criteria, e.g. proximity measures
• CPC Class Codes: G06T 2207/10024 Color image
• CPC Class Codes: G06T 2207/10056 Microscopic image
• CPC Class Codes: G06T 2207/30024 Cell structures in vitro; Tissue sections in vitro
• CPC Class Codes: G06T 7/0012 Biomedical image inspection
• CPC Class Codes: G06T 7/11 Region-based segmentation
• CPC Class Codes: G06T 7/155 involving morphological operators
• CPC Class Codes: G06T 7/187 involving region growing; involving region merging; involving connected component labelling
• CPC Class Codes: G06T 7/90 Determination of colour characteristics
• CPC Class Codes: G06V 10/26 Segmentation of patterns in the image field; Cutting or merging of image elements to establish the pattern region, e.g. clustering-based techniques; Detection of occlusion
• CPC Class Codes: G06V 20/695 Preprocessing, e.g. image segmentation

Abstract

A method for determining whether a test biomarker is a stain for a type of cell component, such as membrane or nucleus, involves performing various segmentation processes on an image of tissue stained with the test biomarker. One segmentation process searches for a first cell component type, and another segmentation process searches for a second cell component type by segmenting only stained pixels. The test biomarker is identified as a stain for each component type if the process identifies the component based only on stained pixels. Whether the test biomarker is a membrane stain or nucleus stain is displayed on a graphical user interface. In addition, the method identifies stained pixels corresponding to a second cell component using pixels determined to correspond to a first cell component. An expression profile for the test biomarker is then displayed that indicates the proportion of stained pixels in each type of cell component.

Claims

1. A method comprising:

performing a first segmentation process on a digital image that searches for a first cell component type having a predetermined color, wherein the digital image depicts tissue that is stained with a test biomarker to have the predetermined color;

performing a second segmentation process on the digital image that searches for a second cell component type that has the predetermined color;

identifying the test biomarker as a stain for the first cell component type if the first segmentation process identifies the first cell component type;

identifying the test biomarker as a stain for the second cell component type if the second segmentation process identifies the second cell component type, wherein both, neither or only one of the first and second cell component types can be identified; and

displaying on a graphical user interface whether the test biomarker is a stain for the first cell component type and whether the test biomarker is a stain for the second cell component type.

2. The method of claim 1, wherein the first cell component type is a membrane, and wherein the second cell component type is a nucleus.

3. The method of claim 1, wherein the first segmentation process includes:

identifying a starting pixel in the digital image;

expanding from the starting pixel into each successive neighboring pixel so long as the neighboring pixel has a color that is not more dissimilar to the predetermined color than is the previous neighboring pixel; and

halting the expanding into successive neighboring pixels at a boundary at which the neighboring pixel of each boundary pixel has a color that is more dissimilar to the predetermined color than is the boundary pixel.

4. The method of claim 3, wherein the test biomarker is a stain for the first cell component type, and wherein the first cell component type is a membrane.

5. The method of claim 1, wherein the first segmentation process identifies a plurality of cell components of the first cell component type, further comprising:

counting a total number of the plurality of cell components of the first cell component type in the digital image.

6. The method of claim 1, wherein the first segmentation process identifies a plurality of cell components of the first cell component type, further comprising:

determining that the plurality of cell components of the first cell component type are clumped together.

7. The method of claim 1, wherein the first segmentation process identifies a plurality of cell components of the first cell component type, further comprising:

determining that the plurality of cell components of the first cell component type are dispersed throughout the tissue.

8. The method of claim 1, wherein the predetermined color is a range of colors, wherein the first segmentation process searches for cell components of the first cell component type that have colors within the range of colors, and wherein the second segmentation process searches for cell components of the second cell component type that have colors within the range of colors.

9. A method comprising:

staining a tissue with both a test biomarker and a known stain;

acquiring a digital image of the stained tissue;

identifying a first cell component region that is stained by the known stain, wherein the first cell component region corresponds to a first cell component;

identifying a second cell component region using the first cell component region, wherein the second cell component region corresponds to a second cell component;

determining a stained proportion of pixels within the second cell component region whose colors fall within a selected color range, wherein the test biomarker stains tissue to have a color that falls within the selected color range;

identifying the test biomarker as a stain for the second cell component if the stained proportion of pixels whose colors fall within the selected color range exceeds a predetermined proportion; and

displaying on a graphical user interface an indication whether the test biomarker is a stain for the second cell component.

10. The method of claim 9, wherein the first cell component is a nucleus, and the second cell component is a membrane.

11. The method of claim 9, further comprising:

identifying a third cell component region that corresponds to a third cell component; and

displaying on a graphical user interface an expression profile of the test biomarker, wherein the expression profile includes a first proportion of pixels within the first cell component region whose colors fall within the selected color range, a second proportion of pixels within the second cell component region whose colors fall within the selected color range, and a third proportion of pixels within the third cell component region whose colors fall within the selected color range.

12. The method of claim 9, wherein the test biomarker includes a first stain and a second stain.

13. The method of claim 9, further comprising:

performing a segmentation process on the digital image that searches for pixels whose colors fall within the selected color range and that form a shape of the second cell component; and

counting a total number of shapes of the second cell component in the digital image.

14. The method of claim 9, wherein the known stain is taken from the group consisting of:

hematoxylin and eosin (H&

E), Her2/neu cytoplasmic stain, estrogen receptor (ER) stain, progesterone receptor (PR) stain, cluster of differentiation 44 (CD44) antibody stain and CD23 antibody stain.

15. A method comprising:

identifying a first cell component that is stained by a known stain, wherein the first cell component is identified in a digital image of tissue that has been stained with both a test biomarker and the known stain;

identifying a first group of pixels of the digital image that correspond to the first cell component;

identifying a second group of pixels of the digital image that correspond to a second cell component, wherein the second group of pixels is identified using the first group of pixels;

determining a first stained proportion of pixels of the first group of pixels whose colors fall within a selected color range, wherein the test biomarker stains tissue to have a color that falls within the selected color range;

determining a second stained proportion of pixels of the second group of pixels whose colors fall within the selected color range;

displaying on a graphical user interface an expression profile of the test biomarker, wherein the expression profile includes the first stained proportion corresponding to the first cell component and the second stained proportion corresponding to the second cell component.

16. The method of claim 15, wherein the first cell component is a membrane, and wherein the second cell component is a nucleus.

17. The method of claim 15, further comprising:

displaying on the graphical user interface that the test biomarker is a stain for the second cell component.

18. The method of claim 15, wherein the test biomarker includes a first stain and a second stain.

19. The method of claim 15, further comprising:

performing a segmentation process on the digital image that searches for pixels whose colors fall within the selected color range and that form a shape of the second cell component; and

counting a total number of shapes of the second cell component in the digital image.

20. The method of claim 15, wherein the known stain is taken from the group consisting of:

hematoxylin and eosin (H&

E), Her2/neu cytoplasmic stain, estrogen receptor (ER) stain, progesterone receptor (PR) stain, cluster of differentiation 44 (CD44) antibody stain and CD23 antibody stain.

21. A method comprising:

performing a first segmentation process on a digital image that searches for a first cell component type having a predetermined color, wherein the digital image depicts tissue that is stained with a test biomarker to have the predetermined color, and wherein the first segmentation process identifies a plurality of cell components of the first cell component type;

counting a first total number of the plurality of cell components of the first cell component type in an area of the digital image; and

storing the first total number of the plurality of cell components in a database.

22. The method of claim 21, further comprising:

displaying on a graphical user interface an indication of the first total number of the plurality of cell components.

23. The method of claim 21, wherein

performing a second segmentation process on the digital image that searches for a second cell component type that has the predetermined color, wherein the second segmentation process identifies a second plurality of cell components of a second cell component type;

counting a second total number of the second plurality of cell components of the second cell component type in the area of the digital image; and

storing the second total number of the plurality of cell components in the database.

24. The method of claim 23, further comprising

calculating an expression parameter for the test biomarker using the first total number and the second total number;

and

displaying the expression parameter on a graphical user interface.

25. A method comprising:

performing a first segmentation process on a digital image that searches for a first cell component type having a first color, wherein the digital image depicts tissue that is stained with a test biomarker to have the first color and that is stained with a known stain to have a second color, and wherein the first segmentation process identifies a first plurality of cell components of the first cell component type;

performing a second segmentation process on the digital image that searches for a second cell component type that has the second color, wherein the second segmentation process identifies a second plurality of cell components of the second cell component type;

counting a first total number of the first plurality of cell components in an area of the digital image;

counting a second total number of the second plurality of cell components in the area of the digital image;

calculating an expression parameter for the test biomarker using the first total number and the second total number; and

storing the expression parameter in a database.

26. The method of claim 25, further comprising:

displaying the expression parameter on a graphical user interface.