Confocal imaging methods and apparatus

• US 8,884,211 B2
• Filed: 03/12/2012
• Issued: 11/11/2014
• Est. Priority Date: 11/23/2005
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Feng, Wenyi, Kotseroglou, Theofilos, Wang, Mark, Triener, Alexander, Che, Diping, Kain, Robert
• Primary Examiner(s): LEE, JOHN R
• Application Number:
  US13/417,474
• Publication Number:
  US 20120168644A1
• Time in Patent Office: 974 Days
• Field of Search: 250/208.1, 250/208.2, 250/458.1, 250/459.1, 250/586, 250/234, 250/235, 250/236
• US Class Current: 250/234
• CPC Class Codes: G01N 2021/6421 Measuring at two or more wavelengths
• 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 21/6458 Fluorescence microscopy fluorescence microscopes per se G02B21/0076 and G02B21/16
• CPC Class Codes: G02B 21/0032 Optical details of illumination, e.g. light-sources, pinholes, beam splitters, slits, fibers G02B21/0036 - G02B21/008; means for illumination of specimens in general G02B21/06
• CPC Class Codes: G02B 21/004 fixed arrays, e.g. switchable aperture arrays

Abstract

The invention provides imaging apparatus and methods useful for obtaining a high resolution image of a sample at rapid scan rates. A rectangular detector array having a horizontal dimension that is longer than the vertical dimension can be used along with imaging optics positioned to direct a rectangular image of a portion of a sample to the rectangular detector array. A scanning device can be configured to scan the sample in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array and the shorter of the two rectangular dimensions for the image are in the scan-axis dimension, and wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis.

Claims

1. A method of detecting features of a microarray, comprising

(a) directing a radiation line to a microarray to simultaneously excite a plurality of fluorescent features in a rectangular or oblong area of the microarray, wherein the radiation line has vertical and horizontal dimensions, the vertical dimension for the radiation line being the shorter dimension, thereby producing simultaneous emission radiation from the plurality of fluorescent features;

(b) detecting the simultaneous emission radiation with a rectangular detector array, wherein the rectangular detector array comprises a plurality of pixel elements in a horizontal dimension and a plurality of pixel elements in a vertical dimension, wherein the horizontal dimension for the rectangular detector array is longer than the vertical dimension for the rectangular detector array, wherein the ratio of the vertical dimension for the radiation line to the quotient of the vertical dimension for the detector array divided by the magnification of the imaging optics is in the range of 0.1 to 10, and wherein the simultaneous emission is detected at a Rayleigh resolution in the range of 0.2 micrometer to 10 micrometers; and

(c) scanning the radiation line across the microarray in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array is in the scan-axis dimension, thereby repeating (a) and (b).

2. The method of claim 1, further comprising directing a second radiation line to the microarray to simultaneously excite a plurality of fluorescent features in a rectangular area of the microarray, wherein the radiation line and the second radiation line excite different fluorophores to produce different emission radiation colors.

3. The method of claim 2, wherein the radiation line and the second radiation line form a spaced multi-line to simultaneously excite the different fluorophores.

4. The method of claim 3, wherein the different emission radiation colors are simultaneously detected by the rectangular detector.

5. The method of claim 2, wherein (b) comprises detecting the different emission radiation colors with different rectangular detector arrays, wherein each rectangular detector array comprises a plurality of pixel elements in a horizontal dimension and a plurality of pixel elements in a vertical dimension, wherein the ratio of the vertical dimension for the radiation line to the quotient of the vertical dimension for the detector array divided by the magnification of the imaging optics is in the range of 0.1 to 10 for each of the different rectangular detector arrays, wherein the horizontal dimension for the rectangular detector array is longer than the vertical dimension for the rectangular detector array, and wherein the emission is detected at a Rayleigh resolution in the range of 0.2 micrometer to 10 micrometers.

6. The method of claim 1, wherein the simultaneous emission radiation is directed to the rectangular detector array as an image of the rectangular area of the microarray, the shorter dimension for the image correlating with the vertical dimension of the rectangular array.

7. The method of claim 1, wherein the aspect ratio of the rectangular detector array is greater than 20.

8. The method of claim 1, wherein the fluorescent features are separated by less than 10 micrometers.

9. The method of claim 1, wherein the radiation line is directed to the surface of the microarray and the rectangular detector array detects the simultaneous emission from the surface of the microarray.

10. The method of claim 1, wherein the detecting comprises collecting electrical responses from a plurality of pixel elements of the vertical dimension in a common bin, and reading the collected electrical responses from the common bin as a single value.

11. The method of claim 1, wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis of the rectangular detector array, wherein the single axis is the vertical dimension for the rectangular detector array.

12. The method of claim 1, further comprising storing a data representation of an image of the microarray in a computer readable memory.

13. The method of claim 1, further comprising displaying a representation of an image of the microarray on a graphical user interface.

14. The method of claim 1, further comprising determining, from the microarray, genetic make-up of a biological sample, number of genes that are expressed in a biological sample, or types of genes that are expressed in a biological sample.

28. The method of claim 1, wherein each of the fluorescent features is homogeneous with respect to having a single species of nucleic acid.

15. A method of detecting features of a microarray, comprising

(a) directing a radiation line to a microarray to simultaneously excite a plurality of fluorescent features in a rectangular area of the microarray, wherein the radiation line has vertical and horizontal dimensions, the vertical dimension for the radiation line being the shorter dimension, wherein the fluorescent features are separated by less than 10 micrometers, thereby producing simultaneous emission radiation from the plurality of fluorescent features;

(b) detecting the simultaneous emission radiation with a rectangular detector array, wherein the rectangular detector array comprises a plurality of pixel elements in a horizontal dimension and a plurality of pixel elements in a vertical dimension, wherein the horizontal dimension for the rectangular detector array is longer than the vertical dimension for the rectangular detector array, wherein the ratio of the vertical dimension for the radiation line to the quotient of the vertical dimension for the detector array divided by the magnification of the imaging optics is in the range of 0.1 to 10, and wherein the emission is detected at a resolution sufficient to distinguish the fluorescent features that are separated by less than 10 micrometers; and

(c) scanning the radiation line across the microarray in a scan-axis dimension, wherein the vertical dimension for the rectangular detector array is in the scan-axis dimension, thereby repeating (a) and (b).

16. The method of claim 15, further comprising directing a second radiation line to the microarray to simultaneously excite a plurality of fluorescent features in a rectangular area of the microarray, wherein the radiation line and the second radiation line excite different fluorophores to produce different emission radiation colors.

17. The method of claim 16, wherein the radiation line and the second radiation line form a spaced multi-line to simultaneously excite the different fluorophores.

18. The method of claim 17, wherein the different emission radiation colors are simultaneously detected by the rectangular detector.

19. The method of claim 16, wherein (b) comprises detecting the different emission radiation colors with different rectangular detector arrays, wherein each rectangular detector array comprises a plurality of pixel elements in a horizontal dimension and a plurality of pixel elements in a vertical dimension, wherein the ratio of the vertical dimension for the radiation line to the quotient of the vertical dimension for the detector array divided by the magnification of the imaging optics is in the range of 0.1 to 10 for each of the different rectangular detector arrays, wherein the horizontal dimension for the rectangular detector array is longer than the vertical dimension for the rectangular detector array, and wherein the emission is detected at a resolution sufficient to distinguish the fluorescent features that are separated by less than 10 micrometers.

20. The method of claim 15, wherein the simultaneous emission radiation is directed to the rectangular detector array as an image of the rectangular area of the microarray, the shorter dimension for the image correlating with the vertical dimension of the rectangular array.

21. The method of claim 15, wherein the aspect ratio of the rectangular detector array is greater than 20.

22. The method of claim 15, wherein the radiation line is directed to the surface of the microarray and the rectangular detector array detects the emission from the surface of the microarray.

23. The method of claim 15, wherein the detecting comprises collecting electrical responses from a plurality of pixel elements of the vertical dimension in a common bin, and reading the collected electrical responses from the common bin as a single value.

24. The method of claim 15, wherein the vertical dimension for the rectangular detector array is short enough to achieve confocality in a single axis of the rectangular detector array, wherein the single axis is the vertical dimension for the rectangular detector array.

25. The method of claim 15, further comprising storing a data representation of an image of the microarray in a computer readable memory.

26. The method of claim 15, further comprising displaying a representation of an image of the microarray on a graphical user interface.

27. The method of claim 15, further comprising determining, from the microarray, genetic make-up of a biological sample, number of genes that are expressed in a biological sample, or types of genes that are expressed in a biological sample.

29. The method of claim 15, wherein each of the fluorescent features is homogeneous with respect to having a single species of nucleic acid.