Method and system for interactively developing at least one grid pattern and computer-readable storage medium having a program for executing the method

• US 6,754,375 B1
• Filed: 07/16/1999
• Issued: 06/22/2004
• Est. Priority Date: 07/16/1999
• Status: Expired due to Term

• Current Assignee: Packard Bioscience Co. (Massachusetts) (Revvity, Inc.)
• Original Assignee: Packard Bioscience Co. (Massachusetts) (Revvity, Inc.)
• Inventors: Yang, Jun, Stephan, Todd J., Noblett, David A.
• Primary Examiner(s): Mehta, Bhavesh M.
• Assistant Examiner(s): DESIRE, GREGORY M
• Application Number:
  US09/356,168
• Time in Patent Office: 1,803 Days
• Field of Search: 435/6, 435/7.21, 382/128-134, 345/433, 345/619, 345/629, 422/62, 436/43
• US Class Current: 382/129
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/30 Microarray design
• CPC Class Codes: Y10T 436/11 Automated chemical analysis

Abstract

Method and system are disclosed for interactively developing at least one grid pattern, such as a microarray pattern, as well as an array set of such patterns, and a computer-readable storage medium having a program for executing the method given only a few user inputs through the use of a pointing device such as a mouse or trackball on a personal computer or workstation. Each array in the set typically has an identical number of rows and columns of points.

Claims

1. A method for interactively developing a regular pattern of grid patterns including at least one grid pattern from at least one digital image of rows and columns of spots, the regular pattern of grid patterns defining an array set, and the rows and columns of spots defining rows and columns of arrays, the method comprising:

displaying the rows and columns of spots including a corner spot located in one of the rows and columns;

receiving a first set of commands from a user to select an approximate location of the corner spot to obtain pattern origin data;

receiving a second set of commands from the user to select at least one column spot in the same column as the corner spot to obtain column data wherein the at least one column spot includes a spot furthest away from the corner spot, and wherein the column data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern;

receiving a third set of commands from the user to select at least one row corner spot in the row of arrays corresponding to the corner spot of the at least one grid pattern to obtain row array data wherein the at least one row corner spot is in an array furthest from the at least one grid pattern in the same row of arrays as the at least one grid pattern; and

receiving a fourth set of commands from the user to select at least one column corner spot in the column of arrays corresponding to the corner spot of the at least one grid pattern to obtain column array data wherein the at least one column corner spot is in an array furthest from the at least one grid pattern in the same column of arrays; and

processing the at least one digital image and the pattern origin data to obtain the at least one grid pattern, wherein the at least one grid pattern includes rows and columns of grid elements, wherein the step of processing includes the step of calculating the number of rows and columns of grid elements, average spacing between adjacent rows and average spacing between adjacent columns of grid elements, and wherein processing also processes the row array data and the column array data with the spot dimension data, the pattern origin data and the row and column data to obtain the regular pattern of grid patterns.

2. The method as claimed in claim 1 further comprising receiving a fifth set of commands from the user to select at least one edge of one of the spots to obtain spot dimension data, wherein the spot dimension data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern.

3. The method as claimed in claim 2 wherein the step of receiving the fifth set of commands from the user selects two opposite edges of the one of the spots and wherein the spot dimension data is spot diameter data.

4. The method as claimed in claim 2 wherein the step of processing includes the step of processing the spot dimension data and the pattern origin data to obtain a bounded area of image data which encompasses either the row or the column of spots including the corner spot.

5. The method as claimed in claim 4 wherein the step of processing includes the step of performing a profile projection of the image data in the bounded area to obtain profile projection data.

6. The method as claimed in claim 5 wherein the step of processing includes the step of calculating a spot model projection based on the spot dimension data.

7. The method as claimed in claim 6 wherein the step of processing includes the steps of utilizing the spot model projection as a correlation model and comparing the correlation model with sections corresponding to each spot along the profile projection in the bounded area.

8. The method as claimed in claim 7 wherein the step of processing includes the step of calculating a correlation coefficient between the correlation model and each similar feature within the profile projection data to identify features representing spots in the bounded area.

9. The method as claimed in claim 8 wherein the step of processing includes the step of calculating a best fitted pitch value using an outlier removal based line fitting algorithm.

10. The method as claimed in claim 1 further comprising receiving a sixth set of commands from the user to select at least one row spot in the same row as the corner spot to obtain row data wherein the at least one row spot includes a spot furthest away from the corner spot, and wherein the row data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern.

11. The method as claimed in claim 10 wherein the step of receiving the sixth set of commands selects two row spots in the same row as the corner spot to obtain the row data.

12. The method as claimed in claim 1 wherein the step of receiving the second set of commands selects two column spots in the same column as the corner spot to obtain the column data.

13. The method as claimed in claim 1 wherein the at least one grid pattern is a microarray pattern.

14. The method as claimed in claim 1 wherein each of the grid patterns is a microarray pattern.

15. The method as claimed in claim 1 wherein the step of receiving the third set of commands selects two row corner spots in the same row of arrays as the at least one grid pattern to obtain the row array data.

16. The method as claimed in claim 1 wherein the step of receiving the fourth set of commands selects two column corner spots in the same column of arrays as the at least one grid pattern to obtain the column array data.

17. The method as claimed in claim 1 further comprising displaying a value representing distance between columns or rows of spots.

18. The method as claimed in claim 1 wherein the step of processing includes the step of calculating distance between adjacent rows of arrays and distance between adjacent columns of arrays.

19. A system for interactively developing a regular pattern of grid patterns including at least one grid pattern from at least one digital image of rows and columns of spots, the regular pattern of grid patterns defining an array set, and wherein the rows and columns of spots define rows and columns of arrays, the system comprising:

means for displaying the rows and columns of spots including a corner spot located in one of the rows and columns;

means for;

receiving a first set of commands from a user to select an approximate location of the corner spot to obtain pattern origin data;

receiving a second set of commands from a user to select at least one column spot in the same column as the corner spot to obtain column data wherein the at least one column spot includes a spot furthest away from the corner spot, wherein the column data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern;

receiving a third set of commands from the user to select at least one row corner spot in the row of arrays corresponding to the corner spot of the at least one grid pattern to obtain row array data wherein the at least one row corner spot is in an array furthest from the at least one grid pattern in the same row of arrays as the at least one grid pattern; and

receiving a fourth set of commands from the user to select at least one column corner spot in the column of arrays corresponding to the corner spot of the at least one grid pattern to obtain column array data wherein the at least one column corner spot is in an array furthest from the at least one grid pattern in the same column of arrays; and

means for processing the pattern origin data and the at least one digital image to obtain the at least one grid pattern, wherein the at least one grid pattern includes rows and columns of grid elements, the means for processing includes means for calculating the number of rows and columns of grid elements, average spacing between adjacent rows and average spacing between adjacent columns, and wherein the means for processing also processes the row array data and the column array data with the spot dimension data, the pattern origin data and the row and column data to obtain the regular pattern of grid patterns.

20. The system as claimed in claim 19 further comprising means for receiving a fifth set of commands from the user to select at least one edge of one of the spots to obtain spot dimension data, wherein the spot dimension data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern.

21. The system as claimed in claim 20 wherein the fifth set of commands from the user selects two opposite edges of the one of the spots and wherein the spot dimension data is spot diameter data.

22. The system as claimed in claim 20 wherein the means for processing processes the spot dimension data and the pattern origin data to obtain a bounded area of image data which encompasses either the row or the column of spots including the corner spot.

23. The system as claimed in claim 22 wherein the means for processing includes means for performing a profile projection of the image data in the bounded area to obtain profile projection data.

24. The system as claimed in claim 23 wherein the means for processing includes means for calculating a spot model projection based on the spot dimension data.

25. The system as claimed in claim 24 wherein the means for processing utilizes the spot model projection as a correlation model and compares the correlation model with sections corresponding to each spot along the profile projection in the bounded area.

26. The system as claimed in claim 25 wherein the means for processing includes means for calculating a correlation coefficient between the correlation model and each similar feature within the profile projection data to identify features representing spots in the bounded area.

27. The system as claimed in claim 26 wherein the step for processing includes means for calculating a best fitted pitch value using an outlier removal based line fitting algorithm.

28. The system as claimed in claim 19 further comprising means for receiving a sixth set of commands from the user to select at least one row spot in the same row as the corner spot to obtain row data wherein the at least one row spot includes a spot furthest away from the corner spot, wherein the row data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern.

29. The system as claimed in claim 28 wherein the sixth set of commands selects two row spots in the same row as the corner spot to obtain the row data.

30. The system as claimed in claim 28 wherein the means for processing includes the means for calculating distance between adjacent rows of arrays and distance between adjacent columns of arrays.

31. The system as claimed in claim 19 wherein the second set of commands selects two column spots in the same column as the corner spot to obtain the column data.

32. The system as claimed in claim 19 wherein the at least one grid pattern is a microarray pattern.

33. The system as claimed in claim 19 wherein each of the grid patterns is a microarray pattern.

34. The system as claimed in claim 19 wherein the third set of commands selects two row corner spots in the same one of arrays as the at least one grid pattern to obtain the row array data.

35. The system as claimed in claim 19 wherein the fourth set of commands selects two column corner spots in the same column of arrays as the at least one grid pattern to obtain the column array data.

36. The system as claimed in claim 19 further comprising means for displaying a value representing distance between columns or rows of spots.

37. A computer-readable storage medium having stored therein a program which interactively develops a regular pattern of grid patterns including at least one grid pattern from at least one digital image of rows and columns of spots, the regular pattern of grid patterns defining an array set, and the rows and columns of spots defining rows and columns of arrays by executing the steps of:

displaying the rows and columns of spots including a corner spot located in one of the rows and columns;

receiving a first set of commands from a user to select an approximate location of the corner spot to obtain pattern origin data;

receiving a second set of commands from the user to select at least one column spot in the same column as the corner spot to obtain column data wherein the at least one column spot includes a spot furthest away from the corner spot, and wherein the column data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern;

receiving a third set of commands from the user to select at least one row corner spot in the row of arrays corresponding to the corner spot of the at least one grid pattern to obtain row array data wherein the at least one row corner spot is in an array furthest from the at least one grid pattern in the same row of arrays as the at least one grid pattern;

receiving a fourth set of commands from the user to select at least one column corner spot in the column of arrays corresponding to the corner spot of the at least one grid pattern to obtain column array data wherein the at least one column corner spot is in an array furthest from the at least one grid pattern in the same column of arrays; and

processing the pattern origin data and the at least one digital image to obtain the at least one grid pattern, wherein the at least one grid pattern includes rows and columns of grid elements, wherein the step of processing includes the step of calculating the number of rows and columns of grid elements, average spacing between adjacent rows and average spacing between adjacent columns of grid elements, and wherein processing also processes the row array data and the column array data with the spot dimension data, the pattern origin data and the row and column data to obtain the regular pattern of grid patterns.

38. The storage medium as claimed in claim 37 wherein the program further executes the step of receiving a fifth set of commands from the user to select at least one edge of one of the spots to obtain spot dimension data, and wherein the spot dimension data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern.

39. The storage medium as claimed in claim 38 wherein the step of receiving the fifth set of commands from the user selects two opposite edges of the one of the spots and wherein the spot dimension data is spot diameter data.

40. The storage medium as claimed in claim 38 wherein the step of processing includes the step of processing the spot dimension data and the pattern origin data to obtain a bounded area of image data which encompasses either the row or the column of spots including the corner spot.

41. The storage medium as claimed in claim 40 wherein the step of processing includes the step of performing a profile projection of the image data in the bounded area to obtain profile projection data.

42. The storage medium as claimed in claim 41 wherein the step of processing includes the step of calculating a spot model projection based on the spot dimension data.

43. The storage medium as claimed in claim 42 wherein the step of processing includes the steps of utilizing the spot model projection as a correlation model and comparing the correlation model with sections corresponding to each spot along the profile projection in the bounded area.

44. The storage medium as claimed in claim 43 wherein the step of processing includes the step of calculating a correlation coefficient between the correlation model and each similar feature within the profile projection data to identify features representing spots in the bounded area.

45. The storage medium as claimed in claim 44 wherein the step of processing includes the step of calculating a best fitted pitch value using an outlier removal based line fitting algorithm.

46. The storage medium as claimed in claim 37 wherein the program further executes the step of receiving a sixth set of commands from the user to select at least one row spot in the same row as the corner spot to obtain row data wherein the at least one row spot includes a spot furthest away from the corner spot, and wherein the row data is processed with the pattern origin data and the at least one digital image to obtain the at least one grid pattern.

47. The storage medium as claimed in claim 46 wherein the step of receiving the sixth set of commands selects two row spots in the same row as the corner spot to obtain the row data.

48. The storage medium as claimed in claim 37 wherein the step of receiving the second set of commands selects two column spots in the same column as the corner spot to obtain the column data.

49. The storage medium as claimed in claim 41 wherein the at least one grid pattern is a microarray pattern.

50. The storage medium as claimed in claim 37 wherein each of the grid patterns is a microarray pattern.

51. The storage medium as claimed in claim 37 wherein the step of receiving the third set of commands selects two row corner spots in the same one of arrays as the at least one grid pattern to obtain the row array data.

52. The storage medium as claimed in claim 37 wherein the step of receiving the fourth set of commands selects two column corner spots in the same column of arrays as the at least one grid pattern to obtain the column array data.

53. The storage medium as claimed in claim 37 wherein the program further executes the step of displaying a value representing distance between columns or rows of spots.

54. The storage medium as claimed in claim 37 wherein the step of processing includes the step of calculating distance between adjacent rows of arrays and distance between adjacent columns of arrays.