Wide field of view and high speed scanning microscopy

• US 6,335,824 B1
• Filed: 09/19/2000
• Issued: 01/01/2002
• Est. Priority Date: 03/20/1998
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Genetic MicroSystems, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Overbeck, James W.
• Primary Examiner(s): Spyrou, Cassandra
• Assistant Examiner(s): Treas, Jared
• Application Number:
  US09/665,544
• Time in Patent Office: 469 Days
• Field of Search: 359/210, 359/201, 359/806, 359/813, 359/381, 359/656, 359/661, 359/368, 369/44.17, 369/44.18, 369/44.19, 369/44.21
• US Class Current: 359/368
• CPC Class Codes: B01J 2219/00364 Pipettes
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00691 using robots
• CPC Class Codes: B01L 3/0241 Drop counters; Drop formers making arrays for combinatorial libraries B01J19/0046; automation of dispensing for analysis G01N35/10
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G01N 2021/6419 Excitation at two or more wavelengths
• CPC Class Codes: G01N 2035/1034 Transferring microquantities of liquid
• CPC Class Codes: G01N 2035/1037 Using surface tension, e.g. pins or wires
• CPC Class Codes: G01N 21/6458 Fluorescence microscopy fluorescence microscopes per se G02B21/0076 and G02B21/16
• CPC Class Codes: G01N 35/1065 Multiple transfer devices
• CPC Class Codes: G02B 21/0036 : Scanning details, e.g. scanning stages
• CPC Class Codes: G02B 21/0048 : scanning mirrors, e.g. rotating or galvanomirrors, MEMS mirrors
• CPC Class Codes: G02B 21/0072 : details concerning resolution or correction, including general design of CSOM objectives
• CPC Class Codes: G02B 21/0076 : arrangements using fluorescence or luminescence
• CPC Class Codes: G02B 21/008 : Details of detection or image processing, including general computer control
• CPC Class Codes: G02B 21/34 : Microscope slides, e.g. mounting specimens on microscope slides

Abstract

Limited rotation, micro-lens scanning of DNA arrays, microscope slides, biological materials, etc., is performed by arcuate and translational motion. A scanning system includes an objective lens located on a low moment of inertia oscillating arm, which provides optical coupling to a light source or a light detector arranged for transmission, reflection, or fluorescence microscopy.

Claims

1. A method of scanning by rotating an objective lens on a scan arm, comprising the acts of:

supporting an objective lens on an oscillating support structure constructed for periodic scanning over biological material disposed on a substrate;

scanning said objective lens in scanning arcs over said biological material disposed on said substrate while said objective lens being coupled to a light path partially extending over said oscillating support structure;

said objective lens having a field of view of about twice its spot size; and

employing a translation mechanism constructed for relative linear movement of said substrate and said support structure.

2. The method of claim 1 further comprising collecting by said objective lens fluorescent light emitted from said biological material.

3. The method of claim 2 wherein said collecting said fluorescent light comprises collecting fluorescent light emitted from DNA fragments included in said biological material.

4. The method of claim 3 further including, prior to said scanning, hybridizing said DNA fragments.

5. The method of claim 2 further comprising, prior to said collecting said fluorescent light, focusing by tilting said substrate in at least one direction.

6. The method of claim 1 wherein said scanning includes scanning a microscope slide supporting said biological material.

7. The method of claim 1 wherein said scanning includes scanning a DNA chip supporting said biological material.

8. The method of claim 1 wherein said scanning includes scanning a DNA chip supporting said biological material comprising DNA fragments.

9. The method of claim 8 further including, prior to said scanning, hybridizing said DNA fragments.

10. The method of claim 1 wherein said light path partially extending over said oscillating support structure includes a periscope assembly.

11. The method of claim 1 further comprising detecting radial position of said objective lens using a position detector.

12. The method of claim 1 wherein said scanning includes employing a galvanometer.

13. The method of claim 1 wherein said scanning includes employing a counterweight mounted on said support structure and arranged for balancing said objective lens.

14. A rotary scanning system producing arcuate scan motion comprising:

an oscillating support structure, associated with a driver, constructed to support an objective lens for periodic scanning over biological material disposed on a substrate;

said objective lens coupled to a light path partially extending over said oscillating support structure having a field of view of about twice its spot size;

a translation mechanism constructed for relative linear movement said substrate and said support structure; and

a data collection control arranged to time the data collection during the arcuate scan motion to align data collection points with rows of a predetermined raster grid to which the data is to be converted.

15. The scanning system of claim 14 including a data conversion system arranged to convert data to the raster grid by averaging for each raster point the value of each of the two data points in the row on either side of the raster point, the values weighted by their respective distances from the raster point in question.

16. The scanning system of claim 14 wherein said objective lens is arranged to collect fluorescent light emitted from said biological material.

17. The scanning system of claim 16 wherein said objective lens has a numerical aperture larger than 0.5.

18. The scanning system of claim 16 wherein said substrate includes a DNA chip arranged for hybridization of said biological material prior to scanning.

19. The scanning system of claim 16 wherein said substrate includes a DNA chip comprising said biological material arranged for DNA sequencing.

20. The scanning system of claim 14 wherein said oscillating support structure includes a periscope assembly arranged to provide said light path.

21. The scanning system of claim 14 further comprising a tilting mechanism constructed to tilt said substrate for focusing light passing through said objective lens.

22. The scanning system of claim 21 wherein said substrate includes a microscope slide comprising said biological material.

23. The scanning system of claim 21 wherein said substrate includes a DNA chip comprising said biological material.

24. The scanning system of claim 14 further comprising a position detector for detecting radial position of said objective lens.

25. The scanning system of claim 14 wherein said support structure includes a counterweight mounted for balancing said objective lens during said scanning.

26. An apparatus for scanning an objective lens on a scan arm, comprising:

means for supporting an objective lens on an oscillating support structure constructed for periodic scanning over biological material disposed on a substrate;

means for scanning said objective lens in scanning arcs over said biological material disposed on said substrate while said objective lens being coupled to a light path partially extending over said oscillating support structure;

said objective lens having a field of view of about twice its spot size; and

means for employing a translation mechanism constructed for relative linear movement of said substrate and said support structure.

27. The apparatus of claim 26 includes means for collecting fluorescent light emitted from said biological material.

28. The apparatus of claim 27 wherein said objective lens has a numerical aperture larger than 0.5.

29. The method of claim 28 wherein said objective lens has a numerical aperture larger than 0.5.

30. The apparatus of claim 27, wherein said substrate includes a DNA chip comprising said biological material arranged for hybridization prior to scanning.

31. The apparatus of claim 27, wherein said substrate includes a DNA chip comprising said biological material arranged for DNA sequencing.

32. The apparatus of claim 26 further comprising means for focusing by tilting said substrate in at least one direction.

33. The apparatus of claim 32, wherein said substrate includes a microscope slide comprising said biological material.

34. The apparatus of claim 32, wherein said substrate includes a DNA chip comprising said biological material.

35. The apparatus of claim 26 further comprising means for detecting radial position of said objective lens.