Hexagonal site line scanning method and system

• US 7,813,013 B2
• Filed: 11/21/2006
• Issued: 10/12/2010
• Est. Priority Date: 11/21/2006
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Kain, Robert
• Primary Examiner(s): Worku; Negussie
• Application Number:
  US11/602,788
• Publication Number:
  US 20080117425A1
• Time in Patent Office: 1,421 Days
• Field of Search: 358/474, 358/482, 358/483, 358512-514, 358/520, 358/1.9, 358/1.15, 382/213, 382/474, 382/275, 382/133, 348/255, 348/229.1, 348/230.1, 348/231.99, 356/455, 435/167, 435/243, 250/235, 250/208.1, 250/234, 250/459.1, 250/307, 359/618, 359/641
• US Class Current: 358/474
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• 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 2021/6439 with indicators, stains, dyes, tags, labels, marks
• 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 2021/6484 Optical fibres
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G02B 13/22 Telecentric objectives or lens systems
• CPC Class Codes: G02B 6/4204 the coupling comprising intermediate optical elements, e.g. lenses, holograms encapsulated active devices H01S5/02208, H01L33/52

Abstract

A scanning technique for imaging sites in an array includes illuminating or irradiating sites in lines of the array, and collecting returned radiation from the sites for imaging. The sites are sequentially scanned by means of confocally directed radiation lines from source optics. The orientation of the radiation lines with respect to the lines of sites in the array is such that the distance between nearest edges of sites in adjacent lines is greater than lines through those edges in a direction parallel to the radiation lines used for scanning. The resulting system experiences less crosstalk and a greater ability to distinguish between neighboring sites in resulting images.

Claims

1. A method for analyzing an array of discrete sites, comprising:

simultaneously irradiating a first plurality of sites in a first line of the array via a first line of radiation;

simultaneously irradiating a second plurality of sites in a second line of the array via a second line of radiation; and

storing data representative of the irradiated first and second plurality of sites;

wherein the second line is generally parallel to the first line, wherein imaginary parallel lines through nearest edges of the sites of the first and second lines of sites and parallel to the first and second lines of radiation are separated by a distance D, wherein nearest edges of adjacent sites within each of the plurality of sites are separated by a distance greater than D, and wherein widths of the first and second lines of radiation are at most approximately 75% of a largest dimension of the sites.

2. The method of claim 1, wherein the array comprises a biological microarray.

3. The method of claim 1, wherein the array comprises discrete sites on a surface.

4. The method of claim 1, wherein the sites have a generally symmetric shape.

5. The method of claim 1, wherein the sites are arranged in a generally hexagonal grid, and wherein the first and second lines are parallel to lines of the grid.

6. The method of claim 1 further comprising returning radiation from the sites to a detector that generates signals for analysis of the sites.

7. The method of claim 1, wherein widths of the first and second lines of radiation are at most approximately 50% of the largest dimension of the sites.

8. The method of claim 1, wherein widths of the first and second lines of radiation are at most approximately 25% of the largest dimension of the sites.

9. A method for analyzing an array of discrete sites comprising:

sequentially irradiating a series of lines of the sites, each line being irradiated with a radiation line; and

storing data representative of the irradiated series of lines of the sites;

wherein the distance between the nearest edges of adjacent sites in each of the adjacent lines of sites is greater than the distance between imaginary parallel lines through the nearest edges of the sites in the adjacent lines of sites, wherein the imaginary parallel lines are parallel to the radiation line, and wherein a width of the radiation line is at most approximately 75% of a largest dimension of the sites.

10. The method of claim 9, wherein the array comprises a biological microarray.

11. The method of claim 9, wherein the array comprises discrete sites on a surface.

12. The method of claim 9, wherein each line is simultaneously irradiated with the radiation line.

13. The method of claim 9, wherein each line is sequentially irradiated with radiation, and wherein return radiation from the sites forms a line at a detector.

14. The method of claim 9, wherein the sites have a generally symmetric shape.

15. The method of claim 9, wherein the sites are arranged in a non-rectangular grid.

16. The method of claim 15, wherein the sites are arranged in a generally hexagonal grid.

17. The method of claim 9, wherein the radiation line is confocally directed to the sites along the adjacent lines of sites.

18. The method of claim 9, wherein the radiation line is substantially continuous along a desired length extending over the plurality of sites.

19. The method of claim 9 further comprising returning radiation from the sites to a detector that generates signals for analysis of the sites.

20. A method for analyzing an array having discrete sites comprising:

(a) irradiating a line of the sites with a radiation line;

(b) repeating step (a) for a plurality of lines of sites;

(c) returning radiation from each of the lines of sites to a detector that generates signals for analysis of the sites; and

(d) storing data representative of the signals generated by the detector;

wherein the sites are disposed in a non-rectangular grid on the array surface, whereby the distance between the nearest edges of adjacent sites in each line of sites is greater than the distance between imaginary parallel lines through the nearest edges of the sites in adjacent lines of the plurality of lines of sites, wherein the imaginary parallel lines are parallel to the radiation line, wherein a width of the radiation line is at most approximately 75% of a largest dimension of the sites, and wherein an image detected by the detector is confocal in the axis orthogonal to the axes along the parallel lines.

21. The method of claim 20, wherein step (a) comprises simultaneously irradiating the line of the sites with the radiation line.

22. The method of claim 20, wherein step (a) comprises sequentially irradiating the line of the sites with radiation, wherein the return radiation from the sites forms a line at a detector.

23. The method of claim 20, wherein the array comprises a biological microarray.

24. The method of claim 20, wherein the array comprises discrete sites on a surface.

25. The method of claim 20, wherein the sites have a generally symmetric shape.

26. The method of claim 20, wherein the sites are disposed in a generally hexagonal grid on the array surface.

27. A system for analyzing an array of discrete sites, the system configured to:

simultaneously irradiate a first plurality of sites in a first line of the array via a first line of radiation; and

simultaneously irradiate a second plurality of sites in a second line of the array via a second line of radiation,

wherein the second line is generally parallel to the first line, wherein imaginary parallel lines through nearest edges of the sites of the first and second lines of sites and parallel to the first and second lines of radiation are separated by a distance D nearest edges of adjacent sites within each of the plurality of sites are separated by a distance greater than D, and wherein widths of the first and second lines of radiation are at most approximately 75% of a largest dimension of the sites.

28. A system for analyzing an array of discrete sites, the system configured to:

sequentially irradiate a series of lines of the sites, each line being irradiated with a radiation line;

wherein the distance between the nearest edges of adjacent sites in each of the adjacent lines of sites is greater than the distance between imaginary parallel lines through the nearest edges of the sites in the adjacent lines of sites, wherein the imaginary parallel lines are parallel to the radiation line, and wherein a width of the radiation line is at most approximately 75% of a largest dimension of the sites.

29. A system for analyzing an array of discrete sites, the system configured to:

(a) simultaneously irradiate a plurality of sites with a line of radiation;

(b) repeat step (a) for a plurality of lines of sites; and

(c) return radiation from each of the pluralities of sites to a detector that generates signals for analysis of the sites;

wherein the sites are disposed in a non-rectangular grid on the array surface, wherein the distance between the nearest edges of adjacent sites in each line of sites is greater than the distance between imaginary parallel lines through the nearest edges of the sites in adjacent lines of the plurality of lines of sites, wherein the imaginary parallel lines are parallel to the line of radiation, wherein a width of the line of radiation is at most approximately 75% of a largest dimension of the sites, and wherein an image detected by the detector is confocal in the axis orthogonal to the axes along the parallel lines.

30. A system for analyzing an array of discrete sites, the system configured to:

(a) sequentially irradiate a plurality of sites with a line of radiation, wherein said sites are disposed along a line,

wherein the return radiation from the plurality of sites forms a line at a detector;

(b) repeat step (a) for a plurality of lines of the sites; and

(c) return radiation from each of the pluralities of sites to a detector that generates signals for analysis of the sites;

wherein the sites are disposed in non-rectangular grid on the array surface,

wherein the distance between the nearest edges of adjacent sites in each line of sites is greater than the distance between imaginary parallel lines through the nearest edges of the sites in adjacent lines of the plurality of lines of sites, wherein the imaginary parallel lines are parallel to the line of radiation, wherein an image detected by the detector is confocal in the axis orthogonal to the axes along the parallel lines, and wherein a width of the line of radiation is at most approximately 75% of a largest dimension of the sites.