Methods and devices for reading microarrays

• US 8,351,026 B2
• Filed: 04/21/2006
• Issued: 01/08/2013
• Est. Priority Date: 04/22/2005
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Stern, David
• Primary Examiner(s): Chowdhury, Tarifur
• Assistant Examiner(s): Nur, Abdullahi
• Application Number:
  US11/379,641
• Publication Number:
  US 20060253035A1
• Time in Patent Office: 2,454 Days
• Field of Search: 356/73, 356/317, 356/73.1, 250/201.2, 250/201.4, 250/201.5, 600/476
• US Class Current: 356/73
• 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

Abstract

An embodiment of a system for acquiring images of a probe array is described that comprises a first light emitting diode that provides light comprising a first range of wavelengths outside of an excitation spectrum; a second light emitting diode that provides light comprising a second range of wavelengths inside of the excitation spectrum; and a detector that detects one or more wavelengths in the first range of wavelengths, wherein the first range of wavelengths comprise light wavelengths emitted from fluorescent molecules associated with one or more probes of the probe array in response to the second range of wavelengths and wavelengths reflected from one or more reflective elements associated with the probe array.

Claims

1. A system for acquiring one or more images of a probe array, the system comprising:

a first light source configured to provide a first set of one or more excitation wavelengths, wherein a first excitation filter is configured to alter the first set of one or more excitation wavelengths, wherein the first light source is a light-emitting diode, and wherein a first lens is configured to collimate illumination from the first light source;

a second light source configured to provide a second set of one or more excitation wavelengths, wherein a second excitation filter is configured to alter the second set of one or more excitation wavelengths, wherein the second light source is a light-emitting diode, and wherein a second lens is configured to collimate illumination from the second light source;

a first detector configured to detect fluorescent emissions from the probe array, wherein a first emission filter is configured to allow transmission of a first set of one or more emission wavelengths to the first detector;

a second detector configured to detect fluorescent emissions from the probe array, wherein a second emission filter is configured to allow transmission of a second set of one or more emission wavelengths to the second detector; and

a stage configured to hold and translate the probe array within the system.

2. The system of claim 1, wherein the first and second light sources and the first and second excitation filters are arranged within an optical train, and wherein the optical train is configured such that illumination from the first and second light sources is combined before the probe array is illuminated when both the first and second light sources are active.

3. The system of claim 1, wherein the optical train comprises one or more beamsplitters configured to combine the illumination from the first and second light sources.

4. The system of claim 1, wherein the first and second detectors are configured to operate simultaneously.

5. The system of claim 1, additionally comprising:

a computer, wherein the computer comprises system memory with a control application stored for execution thereon, and wherein the instrument control application comprises instructions for generating one or more images of the probe array based upon the fluorescent emissions detected by the first and second detectors.

6. The system of claim 5, wherein the first and second detectors are configured to operate simultaneously, and wherein the instructions for generating one or more images of the probe array include instructions for generating one or more images that display data based upon the fluorescent emissions detected by both the first and second detectors within each image.

7. The system of claim 5, wherein the instrument control application additionally comprises instructions for automatic focusing of the probe array during excitation and detection of fluorescent molecules associated with the probe array.

8. The system of claim 7, wherein the instructions for automatic focusing comprise instructions for:

determining positions for the stage to maximize focus for a plurality of areas of the probe array; and

interpolating additional positions for the stage to maximize focus for other areas of the probe array not included within the plurality of areas.

9. The system of claim 1, wherein the first set of one or more excitation wavelengths does not overlap with the second set of one or more excitation wavelengths.

10. The system of claim 1, wherein the first set of one or more emission wavelengths does not overlap with the second set of one or more emission wavelengths.

11. The system of claim 1, wherein one or more filters of the system are positioned within one or more filter wheels, and wherein the one or more filter wheels include two or more different filters.

12. The system of claim 1, wherein the first and second excitation filters are neutral-density filters.

13. The system of claim 1, wherein the stage is additionally configured to tilt the probe array within the system.

14. A system for acquiring one or more images of a probe array, the system comprising:

a first light source configured to provide a first set of one or more excitation wavelengths, wherein a first excitation filter is configured to alter the first set of one or more excitation wavelengths, wherein the first light source is a light-emitting diode, and wherein a first lens is configured to collimate illumination from the first light source;

a second light source configured to provide a second set of one or more excitation wavelengths, wherein a second excitation filter is configured to alter the second set of one or more excitation wavelengths, wherein the second light source is a light-emitting diode, and wherein a second lens is configured to collimate illumination from the second light source;

a first detector configured to detect fluorescent emissions from the probe array, wherein a first emission filter is configured to allow transmission of a first set of one or more emission wavelengths to the first detector;

a second detector configured to detect fluorescent emissions from the probe array, wherein a second emission filter is configured to allow transmission of a second set of one or more emission wavelengths to the second detector, wherein the first and second light sources and the first and second excitation filters are arranged within an optical train, wherein the optical train is configured such that illumination from the first and second light sources is combined before the probe array is illuminated when both the first and second light sources are active, and wherein the first and second detectors are configured to operate simultaneously; and

a stage configured to hold and translate the probe array within the system.

15. The system of claim 14, additionally comprising:

a computer, wherein the computer comprises system memory with a control application stored for execution thereon, and wherein the instrument control application comprises instructions for generating one or more images of the probe array based upon the fluorescent emissions detected by the first and second detectors.

16. The system of claim 15, wherein the instructions for generating one or more images of the probe array include instructions for generating one or more images that display data based upon the fluorescent emissions detected by both the first and second detectors within each image.

17. The system of claim 14, wherein the instrument control application additionally comprises instructions for automatic focusing of the probe array during excitation and detection of fluorescent molecules associated with the probe array.

18. The system of claim 17, wherein the instructions for automatic focusing comprise instructions for:

determining positions for the stage to maximize focus for a plurality of areas of the probe array; and

interpolating additional positions for the stage to maximize focus for other areas of the probe array not included within the plurality of areas.

19. A system for acquiring one or more images of a probe array, the system comprising:

a first light source configured to provide a first set of one or more excitation wavelengths, wherein a first excitation filter is configured to alter the first set of one or more excitation wavelengths, and wherein the first light source is a light-emitting diode, and wherein a first lens is configured to collimate illumination from the first light source;

a second light source configured to provide a second set of one or more excitation wavelengths, wherein a second excitation filter is configured to alter the second set of one or more excitation wavelengths, and wherein the second light source is a light-emitting diode, and wherein a second lens is configured to collimate illumination from the second light source;

a first detector configured to detect fluorescent emissions from the probe array, wherein a first emission filter is configured to allow transmission of a first set of one or more emission wavelengths to the first detector;

a second detector configured to detect fluorescent emissions from the probe array, wherein a second emission filter is configured to allow transmission of a second set of one or more emission wavelengths to the second detector, wherein the first and second light sources and the first and second excitation filters are arranged within an optical train, wherein the optical train is configured such that illumination from the first and second light sources is combined before the probe array is illuminated when both the first and second light sources are active, and wherein the first and second detectors are configured to operate simultaneously;

a stage configured to hold and translate the probe array within the system; and

a computer, wherein the computer comprises system memory with a control application stored for execution thereon, wherein the instrument control application comprises instructions for generating one or more images of the probe array that display data based upon the fluorescent emissions detected by both the first and second detectors within each image, and wherein the instrument control application additionally comprises instructions for automatic focusing of the probe array during excitation and detection of fluorescent molecules associated with the probe array.