Feature locations in array reading

• US 7,206,439 B2
• Filed: 04/30/2003
• Issued: 04/17/2007
• Est. Priority Date: 04/30/2003
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Zhou, Xiangyang, Troup, Charles D.
• Primary Examiner(s): MARIAM, DANIEL G
• Application Number:
  US10/427,850
• Publication Number:
  US 20040218795A1
• Time in Patent Office: 1,448 Days
• Field of Search: 382128-129, 382/151, 382/291, 702 19- 20
• US Class Current: 382/129
• CPC Class Codes: G06F 18/00 Pattern recognition
• CPC Class Codes: G06T 2207/30072 Microarray; Biochip, DNA array; Well plate
• CPC Class Codes: G06T 7/73 using feature-based methods
• CPC Class Codes: G06V 2201/04 Recognition of patterns in DNA microarrays

Abstract

Feature locations are determined in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array. A complete image of the array or a sub-array is presented on a display. Magnified images of corner regions of the displayed complete image are simultaneously presented on the display with the complete image. A user selection of corners for the array or sub-array are received and an array or sub-array actual outline is generated by linearly connecting the user selected corners. The generated actual outline is presented on the magnified image and may also be simultaneously presented on the complete image. Feature locations in the array or sub-array image may be determined based on the actual outline.

Claims

1. A computer implemented method of determining feature locations in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array, the method comprising:

(a) presenting on a display a complete image of the array or a sub-array;

(b) presenting on the display magnified images of corner regions of the displayed complete image simultaneously with the complete image;

(c) receiving a user selection of corners for the array or sub-array and generating an array or sub-array actual outline by linearly connecting the user selected corners;

(d) presenting the generated actual outline simultaneously on the displayed complete and magnified images; and

(e) after step (d) determining feature locations in the array or sub-array image based on the actual outline.

2. A method according to claim 1 additionally comprising, prior to (c) through (e):

(i) reading an identifier associated with the array;

(ii) retrieving an array layout based on the read identifier; and

(iii) generating, based on the array layout, an array or sub-array expected outline in which the expected location of corners of the array image or sub-array image are linearly connected;

(iv) presenting the expected outline simultaneously on the displayed complete and magnified images.

3. A method according to claim 2 wherein (e) comprises generating a grid based on the actual outline and retrieved array layout and selecting locations in relation to the grid as feature locations.

4. A method according to claim 2 wherein the array comprises at least one sub-arrays and the method additionally comprises:

receiving a user selection of a sub-array prior to (iii); and

repeating (a) through (e) for each sub-arrays.

5. An apparatus for determining feature locations in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array, the apparatus comprising:

an identifier reader to read an identifier associated with the array; and

a computer programmed to execute a method of claim 4.

6. An apparatus for determining feature locations in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array, the apparatus comprising:

an identifier reader to read an identifier associated with the array; and

a computer programmed to execute a method of claim 2.

7. A computer program product comprising a computer readable medium carrying a computer program code which performs the method of claim 2.

8. A method according to claim 1 wherein the user selection is received from a point and select device.

9. A method according to claim 1 wherein the array includes sub-arrays, the method additionally comprising, prior to (c) and (d):

(i) reading an identifier associated with the array;

(ii) retrieving an array layout based on the read identifier; and

(iii) generating, based on the array layout, a sub-array expected outline in which the expected location of corners of the sub-array image are linearly connected;

(iv) presenting the expected outline simultaneously on the displayed complete and magnified images;

(v) following (d) repeating (iii) and (iv) and (a) through (d), for one or more sub-arrays in turn.

10. A method according to claim 1 wherein the array includes sub-arrays, the method additionally comprising receiving a user selection of one of the sub-arrays prior to (c) through (e).

11. A method according to claim 1 additionally comprising reading the array.

12. A method according to claim 1 additionally comprising extracting feature data from the image based on the determined feature locations.

13. A method comprising transmitting a result obtained from the method of claim 12 to a remote location.

14. A method according to claim 1 wherein the array image is obtained from reading a chemical array comprising multiple features arranged in rows and columns.

15. A method comprising receiving a result obtained from the method of claim 14 from a remote location.

16. A computer program product comprising a computer readable medium carrying a computer program code which performs the method of claim 14.

17. An apparatus for determining feature locations in an array image obtained from reading a chemical array comprising multiple features arranged in a polygon and which array optionally includes sub-arrays within the array, the apparatus comprising a computer programmed to execute a method of claim 1.

18. An apparatus according to claim 17 additionally comprising an array reader to read the array.

19. A computer program product comprising a computer readable medium carrying a computer program code which performs the method of claim 1.