Systems for analyzing microtissue arrays

• US 7,079,673 B2
• Filed: 02/05/2002
• Issued: 07/18/2006
• Est. Priority Date: 02/05/2002
• Status: Expired due to Fees

• Current Assignee: Rutgers University
• Original Assignee: University of Medicine and Dentistry of New Jersey (State of New Jersey)
• Inventors: Foran, David J., Chen, Wenjin
• Primary Examiner(s): Werner, Brian
• Assistant Examiner(s): LAVIN, CHRISTOPHER L
• Application Number:
  US10/072,470
• Publication Number:
  US 20030147552A1
• Time in Patent Office: 1,624 Days
• Field of Search: 382/128
• US Class Current: 382/128
• CPC Class Codes: G06F 18/00 Pattern recognition
• CPC Class Codes: G06T 2207/30072 Microarray; Biochip, DNA array; Well plate
• CPC Class Codes: G06T 7/00 Image analysis
• CPC Class Codes: G06T 7/0012 Biomedical image inspection
• CPC Class Codes: G06T 7/70 Determining position or orientation of objects or cameras camera calibration G06T7/80

Abstract

The systems described herein autonomously image, analyze, and store date for samples in a tissue microarray. The system may include a tissue microarray, a robotic microscope, and an imaging workstation that executes software to automatically control operation of the microscope to capture images from the microarray and analyze image results. A low magnification may be used to register samples within the microarray and obtain coordinates for each tissue specimen. Progressively higher magnifications may be used to analyze images of each registered specimen. Images and quantitative data from the images may then be stored in a relational database for subsequent review. The system may be local, or may be Web-based for distributed control and sharing of results.

Claims

1. A method comprising the steps of:

capturing an image of a tissue microarray at a first magnification, the tissue microarray including a plurality of disks, each disk including a sample of a biological specimen;

locating a first group of disks from the plurality of disks using one or more visual features of the first group of disks, the locating comprising;

generating a disk template that is substantially the same size as the disks in the captured image;

matching the template to the said one or more visual features of said first group of disks; and

determining the coordinates of candidate disk cores;

identifying a grid defined by the first group of disks by locating rows and columns connecting said candidate disk cores;

locating a second group of disks from the plurality of disks using grid intersections in the identified grid to locate disks which were not located using said template and at positions that do not include the one or more visual features of the first group of disks;

capturing an image of each one of the first group of disks and the second group of disks at a second magnification; and

storing the captured images.

2. The method of claim 1 wherein identifying a grid comprises applying a Hough transformation to locate one or more gridlines having one or more intersections.

3. The method of claim 2 wherein locating a second group of disks comprises selecting locations at the one or more intersections which do not include any of the first group of disks.

4. The method of claim 1 wherein locating the first group of disks comprises convolving the image of the tissue microarray with a disk template that includes the one or more visual features.

5. The method of claim 1 further comprising quantitatively analyzing the captured images of each one of the first group of disks and the second group of disks to obtain quantitative data.

6. The method of claim 5 further comprising storing the location and the quantitative data for each one of the first group of disks and the second group of disks in a database.

7. The method of claim 6 further comprising providing access to the database over a network to one or more remote clients.

8. The method of claim 1 wherein capturing the image of the tissue microarray at the first magnification further comprises combining a plurality of images of a plurality of portions of the tissue microarray.

9. The method of claim 1 wherein a robotic microscope is employed to capture the image of the tissue microarray and to capture the image of each one of the first group of disks and the second group of disks.

10. The method of claim 9 wherein the robotic microscope is accessible over a network.

11. The method of claim 1 wherein the method is performed by a robotic microscope under control of a computer program without user intervention to autonomously capture and archive magnified images of each disk in the tissue microarray.

12. The method of claim 11 further comprising autonomously analyzing each captured image and storing a result of each autonomous analysis.

13. The method of claim 1 wherein the one or more visual features include matching to a disk template.

28. The method of claim 1 wherein said one or more visual features comprises one or more visual shape features.

14. A computer readable medium coded with machine-executable instructions for causing a data processing apparatus to perform a method comprising the steps of:

controlling an imaging device to capture an image of a tissue microarray at a first magnification, the tissue microarray including a plurality of disks, each disk including a sample of a biological specimen;

locating a first group of disks from the plurality of disks using one or more visual features of the first group of disks, the locating comprising;

generating a disk template that is substantially the same size as the disks in the captured image;

matching the template to the said one or more visual features of said first group of disks; and

determining the coordinates of candidate disk cores;

identifying a grid defined by the first group of disks by locating rows and columns connecting said candidate disk cores;

locating a second group of disks from the plurality of disks using grid intersections in the identified grid to locate disks which were not located using said template and at positions that do not include the one or more visual features of the first group of disks;

controlling the imaging device to capture an image of each one of the first group of disks and the second group of disks at a second magnification; and

storing the captured images.

15. The computer readable medium of claim 14 wherein in said method said step of identifying a grid comprises applying a Hough transformation to locate one or more gridlines having one or more intersections.

16. The computer readable medium of claim 15 wherein in said method said step of locating a second group of disks comprises selecting locations at the one or more intersections which do not include any of the first group of disks.

17. The computer readable medium of claim 14 wherein in said method said step of locating the first group of disks comprises convolving the image of the tissue microarray with a disk template that includes the one or more visual features.

18. The computer readable medium of claim 14 wherein said method further comprises quantitatively analyzing the captured images of each one of the first group of disks and the second group of disks to obtain quantitative data.

19. The computer readable medium of claim 18 wherein said method further comprises storing the location and the quantitative data for each one of the first group of disks and the second group of disks in a database.

20. The computer readable medium of claim 14 wherein in said method the imaging device is a robotic microscope.

21. A system comprising:

capturing means for capturing an image of a tissue microarray at a first magnification, the tissue microarray including a plurality of disks, each disk including a sample of a biological specimen;

first locating means for locating a first group of disks from the plurality of disks using one or more visual features of the first group of disks, the first locating means comprising;

means for generating a disk template that is substantially the same size as the disks in the captured image;

means for matching the template to the said one or more visual features of said first group of disks; and

means for determining the coordinates of candidate disk cores;

identifying means for identifying a grid defined by the first group of disks by locating rows and columns connecting said candidate disk cores;

second locating means for locating a second group of disks from the plurality of disks using grid intersections in the identified grid to locate disks which were not located using said template and at positions that do not include the one or more visual features of the first group of disks;

the capturing means further for capturing an image of each one of the first group of disks and the second group of disks at a second magnification; and

storing means for storing the captured images.

22. A system comprising an imaging device and a computer, the imaging device responsive to control signals to provide images at a specified magnification and a specified location within a tissue microarray, and the computer providing the control signals to the imaging device and receiving the images provided by the imaging device, the computer being configured to locate a first group of disks from the plurality of disks using one or more visual features of the first group of disks on the tissue microarray within an image of the tissue microarray captured at a first magnification, the locating configuration comprising:

generating a disk template that is substantially the same size as the disks in the captured image;

matching the template to the said one or more visual features of said first group of disks; and

determining the coordinates of candidate disk cores;

the computer being configured to identify a grid defined by the first group of disks by locating rows and columns connecting said candidate disk cores;

and the computer being further configured to locate a second group of disks on the tissue microarray using grid intersections in the identified grid to locate disks which were not located using said template and at positions that do not include the one or more visual feaures of the first group of disks.

23. The system of claim 22 wherein the computer communicates with the imaging device through a local area network.

24. The system of claim 22 wherein the computer communicates with the imaging device through an internetwork.

25. The system of claim 22 wherein the computer includes a voice-activated command system for receiving and processing user input.

26. The system of claim 22 further comprising a database for storing, for each disk of the first group of disks and the second group of disks, an image of the disk, a location of the disk, and a quantitative analysis of the disk.

27. The system of claim 26 wherein the database is accessible from one or more remote computers through an internetwork.