Systems, devices, and methods for improved optical waveguide transmission and alignment

Patent metadata

Field	Value
Publication number	US-11415745-B2
Application number	US-202117201317-A
Country	US
Kind code	B2
Filing date	Mar 15, 2021
Priority date	Nov 3, 2017
Publication date	Aug 16, 2022
Grant date	Aug 16, 2022

Abstract

Provided herein are systems, devices, and methods for improved optical waveguide transmission and alignment in an analytical system. Waveguides in optical analytical systems can exhibit variable and increasing back reflection of single-wavelength illumination over time, thus limiting their effectiveness and reliability. The systems are also subject to optical interference under conditions that have been used to overcome the back reflection. Novel systems and approaches using broadband illumination light with multiple longitudinal modes have been developed to improve optical transmission and analysis in these systems. Novel systems and approaches for the alignment of a target waveguide device and an optical source are also disclosed.

First claim

What is claimed is:

1. A system for optical analysis, the system comprising:
an optical source, the optical source configured to emit an optical excitation beam into free space, and
a removable target waveguide device, comprising:
at least one optical coupler, the at least one optical coupler configured to receive the optical excitation beam through free space from the optical source;
at least one optical waveguide, the at least one optical waveguide comprising a first end; wherein the first end of the optical waveguide is configured to receive an optical excitation signal from the at least one optical coupler;
at least one reaction region, the at least one reaction region optically coupled to the at least one waveguide; and
at least one detector region, the at least one detector region optically coupled to the at least one reaction region and configured to detect an optical alignment signal from the at least one reaction region;

wherein either the target waveguide device or the optical excitation beam is movable relative to the other; and
wherein the system is configured to monitor the optical alignment signal and to move either the target waveguide device or the optical excitation beam relative to one another to increase the optical alignment signal.

2. The system of claim 1 , wherein the system does not include an alignment camera.

3. The system of claim 1 , wherein the system is configured to move either the target waveguide device or the optical excitation beam relative to the other to increase the optical alignment signal to a maximum level.

4. The system of claim 1 , wherein either the target waveguide device or the optical excitation beam is movable in two dimensions.

5. The system of claim 1 , wherein the at least one detector region is configured to detect both an optical alignment signal and an optical emission signal from the at least one reaction region.

6. The system of claim 1 , wherein the optical excitation beam is configured to project at least a coarse illumination spot and a fine illumination spot on the target waveguide device, and wherein the coarse illumination spot is larger than the fine illumination spot.

7. The system of claim 6 , wherein the optical excitation beam is configured to project the coarse illumination spot on the target waveguide device while the target waveguide device or the optical source is moved.

8. The system of claim 1 , wherein the target waveguide device further comprises at least one auxiliary alignment sensor or at least one auxiliary alignment coupler positioned on a surface of the target waveguide device at a distance from the at least one optical coupler.

9. The system of claim 8 , wherein the distance is defined using photolithography during manufacture of the target waveguide device.

10. The system of claim 8 , wherein the at least one auxiliary alignment sensor or the at least one auxiliary alignment coupler is configured for use in a coarse alignment process.

11. The system of claim 8 , wherein the target waveguide device comprises a plurality of auxiliary alignment sensors or a plurality of auxiliary alignment couplers.

12. The system of claim 11 , wherein the plurality of auxiliary alignment sensors or the plurality of auxiliary alignment couplers are arranged in a geometric pattern.

13. The system of claim 12 , wherein the geometric pattern includes the at least one optical coupler that is optically coupled to the at least one reaction region.

14. The system of claim 1 , wherein the target waveguide device comprises at least one alignment feature at a defined location on the device, and wherein the location of the alignment feature is stored in a readable format on the device.

15. The system of claim 1 , further comprising at least one optical element positioned between the optical source and the target waveguide device, wherein the at least one optical element modulates the optical excitation beam between the optical source and the target waveguide device.

16. The system of claim 15 , wherein the at least one optical element is a lens, a polarizer, a wedge, a filter, a prism, a mirror, or a grating.

17. The system of claim 1 , wherein the target waveguide device comprises a plurality of optical waveguides, each optical waveguide configured to receive the optical excitation signal from the optical source.

18. The system of claim 17 , wherein the target waveguide device comprises at least 2, at least 5, at least 10, at least 50, at least 100, at least 500, at least 1,000, at least 5,000, at least 10,000, or at least 50,000 optical waveguides.

19. The system of claim 17 , wherein the target waveguide device comprises no more than 100,000, no more than 50,000, no more than 10,000, no more than 5,000, no more than 1,000, no more than 500, or no more than 100 optical waveguides.

20. The system of claim 17 , wherein the target waveguide device comprises from 1 to 100,000, from 100 to 10,000, or from 500 to 5,000 optical waveguides.

21. The system of claim 1 , further comprising a computer that receives at least one electronic signal from the at least one detector region and analyzes the at least one electronic signal.

22. The system of claim 21 , wherein the analysis comprises obtaining nucleic acid sequencing information.

23. The system of claim 1 , wherein the optical excitation beam has a wavelength of excitation from about 450 nm to about 700 nm.

24. The system of claim 23 , wherein the wavelength of excitation is from about 500 nm to about 650 nm.

25. The system of claim 1 , wherein the at least one optical waveguide comprises a SiON core.

26. The system of claim 25 , wherein the SiON core has a refractive index above about 1.6.

27. The system of claim 1 , wherein the at least one optical waveguide comprises a core surrounded by silicon dioxide.

28. The system of claim 1 , wherein the target waveguide device is fabricated on a silicon chip.

29. The system of claim 1 , wherein the at least one detector region comprises a CMOS sensor.

30. The system of claim 1 , wherein the optical source is coupled to an optical fiber, and the optical excitation beam is emitted from the optical fiber.

31. The system of claim 1 , wherein the optical source is coupled to a planar lightwave circuit through an optical fiber, and the optical excitation beam is emitted from the planar lightwave circuit.

32. The system of claim 1 , wherein the at least one reaction region comprises a nucleic acid sample.

33. The system of claim 1 , wherein the at least one reaction region comprises a nanoscale well.

34. The system of claim 1 , wherein the at least one reaction region comprises a zero mode waveguide.

35. The system of claim 1 , wherein the target waveguide device comprises 2 to 16 couplers.

36. The system of claim 1 , wherein the target waveguide device comprises from 2 to 16 optical splitters.

Assignees

• Pacific Biosciences California Inc

Inventors

• Kuritsyn Alexey
• Mcdonald Mark
• Rulison Aaron
• Berman Russell

Classifications

• G02B6/12016 Primary

  characterised by the input or output waveguides, e.g. tapered waveguide ends, coupled together pairs of output waveguides · CPC title

• G02B2006/1215

  Splitter · CPC title

• G02B2006/12147

  Coupler · CPC title

• G02B27/0955

  Lenses (lenses per se G02B3/00) · CPC title

• G02B6/4224

  using visual alignment markings, e.g. index methods · CPC title