System, method, and computer software product for gain adjustment in biological microarray scanner

• US 20020168094A1
• Filed: 07/17/2001
• Published: 11/14/2002
• Est. Priority Date: 08/22/2000
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Weiner, Nathan K., Kaushikkar, Shantanu V., McKenzie, Eric E., Stephens, John C.
• Granted Patent: US 7,062,092 B2
• Time in Patent Office: Days
• US Class Current: 382/128
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00533 essentially rectangular
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• 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 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• 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: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: C40B 50/14 Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• CPC Class Codes: G01N 2021/6441 with two or more labels
• CPC Class Codes: G01N 2021/6471 Special filters, filter wheel
• CPC Class Codes: G01N 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 2035/0494 Detecting or compensating piositioning errors
• CPC Class Codes: G01N 21/6452 : Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 27/44717 : Arrangements for investigating the separated zones, e.g. localising zones
• CPC Class Codes: G01N 27/44721 : by optical means
• CPC Class Codes: G16B 25/00 : ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 45/00 : ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

Systems, methods, and computer program products are described for adjusting the gain of a scanner. The scanner includes one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain. One described method includes receiving a user-selected gain value, adjusting the first gain based on a first portion of the user-selected gain value, and adjusting the second gain based on a second portion of the user-selected gain value. Another described method includes selecting an auto-gain value, adjusting the first gain based on a first portion of the auto-gain value, adjusting the second gain based on a second portion of the auto-gain value, causing the scanner to collect sample pixel intensity values, determining a comparison measure based on comparing the sample pixel intensity values to desired pixel intensity values, and adjusting the auto-gain value based on the comparison measure.

Claims

1. A computer program product for adjusting the gain of a scanner having one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:

(a) providing a first user interface constructed and arranged to enable a user to select a user-selected gain value;

(b) receiving the user-selected gain value;

(c) adjusting the first gain based, at least in part, on a first portion of the user-selected gain value; and

(d) adjusting the second gain based, at least in part, on a second portion of the user-selected gain value.

2. The computer program product of claim 1, wherein:

step (c) includes the steps of

(i) determining the first portion to be equal to a no-change value when the user-selected gain value is equal to or less than a threshold value, and

(ii) determining the first portion to be equal to an excess of the user-selected gain value over the threshold value, when the user-selected gain value is greater than the threshold value; and

step (d) includes the steps of

(i) determining the second portion to be equal to the user-selected gain value when the user-selected gain value is equal to or less than a threshold value, and

(ii) determining the second portion to be equal to the threshold value when the user-selected gain value is equal to or greater than the threshold value.

3. The computer program product of claim 2, wherein:

the threshold value is predetermined.

4. The computer program product of claim 1, wherein:

step (c) includes the steps of

(i) determining the first portion to be equal to the user-selected gain value when the user-selected gain value is equal to or less than a threshold value, and

(ii) determining the first portion to be equal to the threshold value when the user-selected gain value is equal to or greater than the threshold value; and

step (d) includes the steps of

(i) determining the second portion to be equal to a no-change value when the user-selected gain value is equal to or less than a threshold value, and

(ii) determining the second portion to be equal to an excess of the user-selected gain value over the threshold value, when the user-selected gain value is greater than the threshold value.

5. The computer program product of claim 4, wherein:

the threshold value is predetermined.

6. The computer program product of claim 1, wherein the method further comprises the step of:

(e) receiving a calibration gain for a first of the one or more excitation sources, wherein the calibration gain is based, at least in part, on an output of the emission detector responsive to the first excitation source exciting a calibration source; and

(f) adjusting the first gain, the second gain, or both based, at least in part, on the calibration gain.

7. The computer program product of claim 6, wherein:

the calibration gain is based on a measurement that depends, at least in part, on the output of the emission detector.

8. The computer program product of claim 1, wherein:

the first user interface further is constructed and arranged to enable the user to associate the user-selected gain value with a first of the one or more excitation sources;

step (b) further includes receiving from the first user interface the association of the user-selected gain value with the first excitation source; and

steps (c) and (d) are done when the first excitation source is operational.

9. The computer program product of claim 8, wherein:

the user associates the user-selected gain value with the first excitation source based, at least in part, on identifying a scanning operation in which the first excitation source is operational.

10. The computer program product of claim 1, wherein:

the first user interface further is constructed and arranged to enable the user to associate the user-selected gain value with a first of one or more emission labels;

step (b) further includes receiving from the first user interface the association of the user-selected gain value with the first emission label; and

steps (c) and (d) are done when the first emission label is excited in a scanning operation.

11. The computer program product of claim 1, wherein:

the method further comprises the step of

(e) providing a second user interface constructed and arranged to enable a user to initiate a scanning operation; and

step (b) further comprises the steps of

(i) receiving the user-selected gain value from the first user interface and storing the user-selected gain value in a memory storage unit, and

(ii) retrieving the user-selected gain value from the memory storage unit responsive to the user initiating a scanning operation.

12. The computer program product of claim 1, wherein:

the first and second user interfaces are included in a same user interface.

13. The computer program product of claim 1, wherein:

the emission detector includes a photomultiplier tube.

14. The computer program product of claim 1, wherein:

the first gain amplifies an emission signal based, at least in part, on emissions from an emission label spatially associated with a probe of a probe array.

15. The computer program product of claim 14, wherein:

the probe array is a spotted probe array.

16. The computer program product of claim 14, wherein:

the probe array is a synthesized probe array.

18. The computer program product of claim 17, wherein the method further comprises the steps of:

(d) receiving a calibration gain for a first of the one or more excitation sources, wherein the calibration gain is based, at least in part, on an output of the emission detector responsive to the first excitation source exciting a calibration source; and

(e) adjusting the first gain, the second gain, or both based, at least in part, on the calibration gain.

19. The computer program product of claim 17, wherein:

the user interface further is constructed and arranged to enable the user to associate the first user-selected gain value with a first of the one or more excitation sources;

step (a) further includes receiving from the user interface the association of the first user-selected gain value with the first excitation source; and

steps (b) and (c) are done when the first excitation source is operational.

17. A computer program product for adjusting the gain of a scanner having one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:

(a) receiving one or more user-selected gain values from one or more ranges of gain values;

(b) adjusting the first gain based, at least in part, on a first of the one or more user-selected gain values; and

(c) adjusting the second gain based, at least in part, on a second of the one or more user-selected gain values.

20. A computer program product for adjusting the gain of a scanner having one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:

(a) receiving a user-selected gain value;

(b) adjusting the first gain based, at least in part, on a first portion of the user-selected gain value, including the steps of

(i) determining the first portion to be equal to a no-change value when the user-selected gain value is equal to or less than a threshold value, and

(ii) determining the first portion to be equal to an excess of the user-selected gain value over the threshold value, when the user-selected gain value is greater than the threshold value;

(c) adjusting the second gain based, at least in part, on a second portion of the user-selected gain value;

(d) receiving a calibration gain for a first of the one or more excitation sources, wherein the calibration gain is based, at least in part, on an output of the emission detector responsive to the first excitation source exciting a calibration source; and

(e) adjusting the first gain, the second gain, or both based, at least in part, on the calibration gain.

21. A gain adjustment system, comprising:

(a) a scanner having

(i) one or more excitation sources,

(ii) an emission detector having a first gain, and

(iii) a variable gain element having a second gain;

(b) a computer-implemented user interface constructed and arranged to enable a user to select a user-selected gain value; and

(c) scanner control and analysis control logic comprising

(i) a user-selected gain data manager constructed and arranged to receive the user-selected gain value, and

(ii) a scan gain controller constructed and arranged to adjust the first gain based, at least in part, on a first portion of the user-selected gain value, and to adjust the second gain based, at least in part, on a second portion of the user-selected gain value.

22. The system of claim 21, wherein:

the scan gain controller further is constructed and arranged to determine the second portion to be equal to the user-selected gain value, and the first portion to be a no-change value, when the user-selected gain value is equal to or less than a threshold value; and

to determine the second portion to be equal to the user-selected gain value, and the first portion to be equal to an excess of the user-selected gain value over the threshold value, when the user-selected gain value is greater than the threshold value.

23. The system of claim 21, wherein:

the scan gain controller further is constructed and arranged to determine the first portion to be equal to the user-selected gain value, and the second portion to be a no-change value, when the user-selected gain value is equal to or less than a threshold value; and

to determine the first portion to be equal to the user-selected gain value, and the second portion to be equal to an excess of the user-selected gain value over the threshold value, when the user-selected gain value is greater than the threshold value.

24. The system of claim 21, wherein:

the scan gain controller further is constructed and arranged to receive a calibration gain for a first of the one or more excitation sources, wherein the calibration gain is based, at least in part, on an output of the emission detector responsive to the first excitation source exciting a calibration source; and

to adjust the first gain, the second gain, or both based, at least in part, on the calibration gain.

26. The method of claim 25, wherein:

steps (b) and (c) include the step of allocating the user-selected gain between the first and second portions based, at least in part, on one or more operational characteristics of the emission detector.

27. The method of claim 26, wherein:

the operational characteristics include signal to noise ratio.

29. The computer program product of claim 28, wherein:

steps (b) through (f) are repeated until the comparison measure reaches an acceptance value or range, or until a number of repetitions exceeds an attempt number.

30. The computer program product of claim 29, wherein:

the acceptance value or range, the attempt number, or both are user selected.

31. The computer program product of claim 29, wherein:

the acceptance value or range, the attempt number, or both are predetermined.

32. The computer program product of claim 29, wherein:

the acceptance value or range, the attempt number, or both are calculated.

33. The computer program product of claim 28, wherein:

the comparison measure includes a histogram of the plurality of sample pixel intensity values.

34. The computer program product of claim 33, wherein:

the comparison measure includes a ratio between a first portion of the plurality of sample pixel intensity values in a first number of bins of the histogram and a second portion of the plurality of sample pixel intensity values in a second number of bins of the histogram.

35. The computer program product of claim 28, wherein:

the comparison measure includes a statistical measure.

36. The computer program product of claim 35, wherein:

the statistical measure includes a mean or average of two or more of the plurality of sample pixel intensity values.

37. The computer program product of claim 28, wherein:

the first gain amplifies an emission signal based, at least in part, on emissions from an emission label spatially associated with a probe of a probe array; and

38. The computer program product of claim 37, wherein:

the probe array is a spotted probe array.

39. The computer program product of claim 37, wherein:

the probe array is a synthesized probe array.

40. The computer program product of claim 37, wherein:

the plurality of desired pixel intensity values is determined based, at least in part, on an expected ratio of background pixels on the probe array to probe pixels on the probe array.

41. The computer program product of claim 28, wherein:

step (b) includes the steps of

(i) determining the first portion to be equal to a no-change value when the auto-gain value is equal to or less than a threshold value, and

(ii) determining the first portion to be equal to an excess of the auto-gain value over the threshold value, when the auto-gain value is greater than the threshold value; and

step (c) includes the steps of

(i) determining the second portion to be equal to the auto-gain value when the auto-gain value is equal to or less than a threshold value, and

(ii) determining the second portion to be equal to the threshold value when the auto-gain value is equal to or greater than the threshold value.

42. The computer program product of claim 41, wherein:

the threshold value is predetermined.

43. The computer program product of claim 28, wherein the method further comprises the step of:

(g) receiving a calibration gain for a first of the one or more excitation sources, wherein the calibration gain is based, at least in part, on an output of the emission detector responsive to the first excitation source exciting a calibration source; and

(h) adjusting the first gain, the second gain, or both based, at least in part, on the calibration gain.

44. The computer program product of claim 28, wherein:

the emission detector includes a photomultiplier tube.

47. The method of claim 46, wherein:

steps (b) and (c) include the step of allocating the auto-gain between the first and second portions based, at least in part, on one or more operational characteristics of the emission detector.

48. The method of claim 47, wherein:

the operational characteristics include signal to noise ratio.

25. A method for adjusting the gain of a scanner having one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain, comprising the steps of:

(a) receiving a user-selected gain value;

(b) adjusting the first gain based, at least in part, on a first portion of the user-selected gain value; and

(c) adjusting the second gain based, at least in part, on a second portion of the user-selected gain value.

28. A computer program product for adjusting the gain of a scanner having one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain, wherein the computer program product, when executed on a computer system, performs a method comprising the steps of:

(a) selecting an auto-gain value;

(b) adjusting the first gain based, at least in part, on a first portion of the auto-gain value;

(c) adjusting the second gain based, at least in part, on a second portion of the auto-gain value;

(d) causing the scanner to collect a plurality of sample pixel intensity values using the adjusted first and second gains;

(e) determining a comparison measure based on comparing one or more of the plurality of sample pixel intensity values to one or more of a plurality of desired pixel intensity values; and

(f) adjusting the auto-gain value based on the comparison measure.

45. A gain adjustment system, comprising:

(a) a scanner having

(i) one or more excitation sources,

(ii) an emission detector having a first gain, and

(iii) a variable gain element having a second gain; and

(b) scanner control and analysis control logic comprising a scan gain controller constructed and arranged to

(i) select an auto-gain value,

(ii) adjust the first gain based, at least in part, on a first portion of the auto-gain value;

(iii) adjust the second gain based, at least in part, on a second portion of the auto-gain value;

(iv) cause the scanner to collect a plurality of sample pixel intensity values using the adjusted first and second gains;

(v) determine a comparison measure based on comparing one or more of the plurality of sample pixel intensity values to one or more of a plurality of desired pixel intensity values; and

(vi) adjust the auto-gain value based on the comparison measure.

46. A method for adjusting the gain of a scanner having one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain, comprising the steps of:

(a) selecting an auto-gain value;

(b) adjusting the first gain based, at least in part, on a first portion of the auto-gain value;

(c) adjusting the second gain based, at least in part, on a second portion of the auto-gain value;

(d) causing the scanner to collect a plurality of sample pixel intensity values using the adjusted first and second gains;

(e) determining a comparison measure based on comparing one or more of the plurality of sample pixel intensity values to one or more of a plurality of desired pixel intensity values; and

(f) adjusting the auto-gain value based on the comparison measure.

49. A computer program product, comprising:

(a) a gain-value receiver that receives a user-selected gain value;

(b) a first gain controller that applies a first gain to the emission signal based, at least in part, on a first portion of the user-selected gain value; and

(c) a second gain controller that applies a second gain to the emission signal based, at least in part, on a second portion of the user-selected gain value.

50. A method for adjusting an emission signal, comprising the steps of:

(a) receiving a user-selected gain value;

(b) applying a first gain to the emission signal based, at least in part, on a first portion of the user-selected gain value; and

(c) applying a second gain to the emission signal based, at least in part, on a second portion of the user-selected gain value.

51. A computer program product, comprising:

(a) an auto-gain value selector;

(b) a first gain controller that applies a first gain to the emission signal based, at least in part, on a first portion of the auto-gain value;

(c) a second gain controller that applies a second gain to the emission signal based, at least in part, on a second portion of the auto-gain value;

(d) an intensity manager that determines a plurality of sample pixel intensity values based on the emission signal having applied to it the first and second gains;

(e) a comparison manager that determines a comparison measure based on comparing one or more of the plurality of sample pixel intensity values to one or more of a plurality of desired pixel intensity values; and

(f) an auto-gain adjuster that adjusts the auto-gain value based on the comparison measure.

52. A method for adjusting an emission signal, comprising the steps of:

(a) selecting an auto-gain value;

(b) applying a first gain to the emission signal based, at least in part, on a first portion of the auto-gain value;

(c) applying a second gain to the emission signal based, at least in part, on a second portion of the auto-gain value;

(d) determining a plurality of sample pixel intensity values based on the emission signal having applied to it the first and second gains;

(e) determining a comparison measure based on comparing one or more of the plurality of sample pixel intensity values to one or more of a plurality of desired pixel intensity values; and

(f) adjusting the auto-gain value based on the comparison measure.

53. A gain adjustment system, comprising:

(a) a scanner having one or more excitation sources, an emission detector having a first gain, and a variable gain element having a second gain; and

(b) a scan gain controller that adjusts the first and second gains.