Hexagonal site line scanning method and system

• US 8,023,162 B2
• Filed: 09/03/2010
• Issued: 09/20/2011
• 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:
  US12/875,553
• Publication Number:
  US 20100328732A1
• Time in Patent Office: 382 Days
• Field of Search: 358/474, 358/482, 358/483, 358512-514, 358/520, 358/1.9, 382/213, 382/275, 382/254, 359/618, 359/641, 250/235, 250/208.1, 250/234, 250/459.1, 250/307
• 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 of scanning an array of discrete sites, comprising:

(a) providing an array of discrete sites, wherein the sites are arranged in a hexagonal grid; and

(b) scanning the array of discrete sites with a line of radiation using a scanner, wherein distances between nearest neighbor sites that are irradiated simultaneously by the line of radiation at a particular scan position are greater than a distance between any one of the sites being irradiated simultaneously by the line of radiation and a nearest neighbor site that is not one of the sites being irradiated simultaneously by the line of radiation.

2. The method of claim 1, wherein the line of radiation is narrower than the width of the discrete sites in the scan direction.

3. The method of claim 1, wherein the width of the line of radiation is at most 75% of the width of the sites in the scan direction.

4. The method of claim 1, wherein the array of discrete sites comprises a biological microarray.

5. The method of claim 1, wherein the array of discrete sites is on a surface.

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

7. The method of claim 1, wherein the sites have a circular shape.

8. The method of claim 1, wherein the sites comprise beads.

9. The method of claim 1, wherein a laser is positioned to irradiate the array of discrete sites with the line of radiation.

10. The method of claim 1, wherein the discrete sites are separated by a distance less than 50 micrometers.

11. The method of claim 1, further comprising detecting emitted radiation, wherein the emitted radiation emanates from discrete sites that are irradiated by the line of radiation.

12. The method of claim 11, wherein the emitted radiation comprises fluorescence from fluorescent dyes at the discrete sites.

13. The method of claim 11, wherein the emitted radiation is detected at a Rayleigh resolution between 0.2 and 10 micrometers.

14. The method of claim 11, wherein the emitted radiation is detected by a detector array.

15. The method of claim 11, wherein the detector array is a rectangular detector array.

16. The method of claim 11, wherein the detector array uses time delay integration for the detecting of the emitted radiation.

17. The method of claim 1, wherein the discrete sites comprise nucleic acids.

18. A system for analyzing an array of discrete sites, the system comprising:

an array of discrete sites arranged in a hexagonal grid; and

a scanner configured to scan the array of discrete sites with a line of radiation, wherein distances between nearest neighbor sites that are irradiated simultaneously by the line of radiation at a particular scan position are greater than a distance between any one of the sites being irradiated simultaneously by the line of radiation and a nearest neighbor site that is not one of the sites being irradiated simultaneously by the line of radiation.

19. The system of claim 18, wherein the line of radiation is narrower than the width of the discrete sites in the scan direction.

20. The system of claim 18, wherein the width of the line of radiation is at most 75% of the width of the sites in the scan direction.