System, method, and product for symmetrical filtering in scanning of biological materials

• US 6,643,015 B2
• Filed: 12/03/2001
• Issued: 11/04/2003
• Est. Priority Date: 04/26/2001
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Weiner, Nathan K.
• Primary Examiner(s): Evans, F. L.
• Assistant Examiner(s): Geisel, Kara
• Application Number:
  US09/683,219
• Publication Number:
  US 20020159058A1
• Time in Patent Office: 701 Days
• Field of Search: 356/318, 702/27, 250/458--46, 422/82-5-, 436/171-172
• US Class Current: 356/318
• 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: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: B82Y 35/00 Methods or apparatus for measurement or analysis of nanostructures
• 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 2035/00158 Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: G01N 2035/0494 Detecting or compensating piositioning errors
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/6456 Spatial resolved fluorescence measurements; Imaging
• 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

Abstract

An apparatus is described that includes an emission signal detector and an emission signal filter. An excitation beam scans an array of biological materials, and the emission signal detector detects an emission signal indicative of an emission beam responsive to the excitation beam. The emission signal filter is a linear-phase filter that provides a filtered emission signal having substantially symmetrical rise and fall edges. A linear-phase excitation signal filter may also be provided that provides a filtered excitation signal having substantially symmetrical rise and fall edges. The emission signal filter and the excitation signal filter may be matched. In some applications, they may be high-order Bessel filters. Linear-phase filtering enables sampling of emission signals to be accomplished consistently irrespective of the scanning direction, and thus is particularly advantageous in bi-directional scanning applications.

Claims

1. A method for analyzing molecules, comprising the steps of:

(1) directing an excitation beam to a plurality of probe locations;

(2) receiving an emission signal;

(3) linear-phase filtering the emission signal to provide a filtered emission signal having substantially symmetrical rise and fall edges; and

(4) analyzing molecules at one or more probe locations based, at least in part, on one or more values of the filtered emission signal.

2. An apparatus comprising:

an excitation beam provider constructed and arranged to direct an excitation beam to a plurality of locations of a probe array;

an emission signal detector constructed and arranged to detect an emission signal from at least one location; and

an emission filter comprising a linear-phase filter constructed and arranged to filter the emission signal to provide a filtered emission signal having substantially symmetrical rise and fall edges.

3. The apparatus of claim 2, further comprising:

an excitation signal detector constructed and arranged to detect an excitation signal; and

an excitation filter constructed and arranged to filter the excitation signal to provide a filtered excitation signal.

4. The apparatus of claim 3, wherein:

the emission filter and the excitation filter are matched with each other.

5. The apparatus of claim 3, wherein:

the emission filter has a first delay function and the excitation filter has a second delay function; and

the apparatus further comprises a delay compensator constructed and arranged to compensate for a difference between the first and second delay functions, if any.

6. The apparatus of claim 3, wherein:

the excitation filter comprises a linear-phase filter constructed and arranged to filter the excitation signal to provide a filtered excitation signal having substantially symmetrical rise and fall edges.

7. The apparatus of claim 6, wherein:

the emission filter and the excitation filter both comprise a high-order Bessel filter.

8. The apparatus of claim 7, wherein:

the Bessel filter is a sixth or higher order Bessel filter.

9. The apparatus of claim 7, wherein:

the Bessel filter is an eleventh or higher order Bessel filter.

10. The apparatus of claim 2, wherein:

the emission filter further is constructed and arranged to normalize the emission signal to avoid aliasing errors.

11. The apparatus of claim 2, wherein:

the emission filter comprises a low-pass, anti-aliasing filter.

12. The apparatus of claim 11, wherein:

one or more characteristics of the emission filter are determined, at least in part, based on a scan rate or a resolution.

13. The apparatus of claim 11, wherein:

a low-pass characteristic of the linear-phase emission filter is determined, at least in part, based on applying the Nyquist criterion to a sampling rate.

14. The apparatus of claim 2, further comprising:

a clock signal generator constructed and arranged to generate a clock signal to digitize the filtered emission signal, thereby providing a plurality of digitized emission values.

15. The apparatus of claim 14, further comprising:

an excitation signal detector constructed and arranged to detect an excitation signal indicative of the excitation beam; and

an excitation filter constructed and arranged to filter the excitation signal to provide a filtered excitation signal;

wherein the clock signal digitizes the filtered excitation signal, thereby providing a plurality of digitized excitation values.

16. The apparatus of claim 15, wherein:

the emission filter and the excitation filter are matched so that the plurality of digitized emission values are spatially correlated with the plurality of digitized excitation values.

17. The apparatus of claim 2, wherein:

the excitation beam provider further is constructed and arranged to direct the excitation beam to the plurality of locations of the probe array so that dx/dt is substantially constant.

18. The apparatus of claim 2, wherein:

the probe array comprises a synthesized probe array.

19. The apparatus of claim 2, wherein:

the probe array comprises a spotted probe array.

20. A method comprising the steps of:

detecting an emission signal from a probe array; and

filtering the emission signal to provide a filtered emission signal having substantially symmetrical rise and fall edges.

21. The method of claim 20, further comprising the step of:

directing an excitation beam to a plurality of locations of the probe array, thereby giving rise to the emission signal.

22. The method of claim 21, further comprising the step of:

detecting an excitation signal indicative of the excitation beam; and

filtering the excitation signal to provide a filtered excitation signal.

23. The method of claim 21, wherein:

filtering the excitation signal includes linear-phase filtering to provide a filtered excitation signal having substantially symmetrical rise and fall edges.

24. The method of claim 20, further comprising the step of:

digitizing the filtered emission signal, thereby providing a plurality of digitized emission values.

25. The method of claim 20, wherein:

the probe array comprises a synthesized probe array.

26. The method of claim 20, wherein:

the probe array comprises a spotted probe array.

27. A noise compensation module comprising:

an excitation signal filter constructed and arranged to filter at least a first and a second excitation signal; and

an emission signal filter constructed and arranged to filter at least a first and a second emission signal;

wherein the excitation signal filter and the emission signal filter are linear-phase filters, the first excitation signal and corresponding first emission signal are derived from a scan in a first direction, and the second excitation signal and corresponding second emission signal are derived from a scan in a second direction that is opposite to the first direction.

28. The noise compensation module of claim 27, wherein:

the excitation signal filter and the emission signal filter are matched with each other.

29. The noise compensation module of claim 27, wherein:

the excitation signal filter and the emission signal filter both comprise a high-order Bessel filter.

30. A method comprising the steps of:

filtering at least a first and a second excitation signal; and

filtering at least a first and a second emission signal;

wherein the filtering characteristics applied to the first and second excitation signals and to the first and second emission signals are linear-phase, the first excitation signal and corresponding first emission signal are derived from a scan in a first direction, and the second excitation signal and corresponding second emission signal are derived from a scan in a second direction that is opposite to the first direction.

31. An apparatus comprising:

an emission signal detector constructed and arranged to detect an emission signal from at least one probe; and

an emission filter constructed and arranged to filter the emission signal to provide a filtered emission signal having substantially symmetrical rise and fall edges.

32. A method comprising the steps of:

detecting an emission signal from at least one probe; and

filtering the emission signal to provide a filtered emission signal having substantially symmetrical rise and fall edges.