BACKGROUND

High-throughput DNA sequencing can be the basis for genomic analysis and other genetic research. In this and other types of sequencing, characteristics of a sample of genetic material are determined by illuminating the sample, for example using a planar waveguide. Some types of image detection can place particular demands on the sequencing system in order to create an image of the entire sample. For example, with a time-delay and integration (TDI) sensor the image is captured one narrow sliver at a time, involving a scanning operation along the length of the slide. To reduce photodamage to the sample from the illuminating light, it is often desirable to confine the illumination to the sample area being imaged. In some instances, this creates the challenge of ensuring that the illumination is synchronized with the image detection throughout the scanning process.

SUMMARY

In a first aspect, a system includes: an objective lens; a first light source to feed first illuminating light through the objective lens and into a flowcell to be installed in the system, the first illuminating light to be fed using a first grating on the flowcell; and a first image sensor to capture imaging light using the objective lens, wherein the first grating is positioned outside a field of view of the first image sensor.

Implementations can include any or all of the following features. The flowcell is installed in the system. The first grating and a second grating are positioned on the flowcell. The first and second gratings have different coupling angles. The first and second gratings have different grating periods. The flowcell includes a first sample surface parallel to a second sample surface, the first grating to couple a first portion of the first illuminating light to illuminate the first sample surface, and the second grating to couple a second portion of the first illuminating light to illuminate the second sample surface. The system further comprises a first planar waveguide into which the first grating couples the first portion of the first illuminating light, and a second planar waveguide into which the second grating couples the second portion of the first illuminating light. The first grating is offset, relative to the second grating, in a travel direction of the first portion of the first illuminating light. The first and second gratings are positioned on opposite sides of a planar waveguide that illuminates the flowcell, the first grating coupling the first illuminating light into the planar waveguide, and the second grating coupling the first illuminating light out of the planar waveguide. The system further comprises a wall that blocks the first illuminating light coupled out of the planar waveguide by the second grating from entering the objective lens. The first illuminating light comprises a first light beam of a first wavelength, the system further comprising a second light source to feed second illuminating light through the objective lens, the second illuminating light comprising a second light beam of a second wavelength. The second light source is to feed the second illuminating light through the objective lens into the flowcell via the first grating, the first grating having a symmetric coupling angle for the first and second wavelengths. The first light source is directing the first light beam at a first side of the objective lens, and the second light source directing the second light beam at a second side of the objective lens opposite the first side. The system further comprises a first mirror and a tube lens positioned after the first and second light sources and before the objective lens, wherein respective angles of the first and second light beams in propagation from the first mirror to the tube lens reflect corresponding incident angles of the first and second light beams on the first grating. The system further comprises a second mirror positioned after the first light source and before the first mirror, the second mirror to provide a spatial separation of the first and second light beams on the first grating. The flowcell has multiple swaths bounded by respective gratings including the first grating, and wherein the system uses at least one of the respective gratings both as an entry grating and an exit grating. A waveguide material of the flowcell includes Ta2O5. The first image sensor comprises a time delay and integration sensor, the system further comprising a moveable stage holding the flowcell. The system further comprises a thermal stage to hold the flowcell, the thermal stage providing thermal control. The system further comprises a second image sensor that captures images of at least the first grating and a planar waveguide in the flowcell, wherein the system evaluates the images using an alignment criterion. The light has a wavelength to trigger a fluorescent response from a sample in the flowcell.

In a second aspect, a flowcell includes: a substrate to hold a sample; a first planar waveguide to lead first light for the sample; a first grating to couple the first light; a second planar waveguide to lead second light for the sample; and a second grating to couple the second light.

Implementations can include any or all of the following features. The first grating is positioned on the first planar waveguide, and the second grating is positioned on the second planar waveguide. The first and second gratings have different coupling angles. The first and second gratings have different grating periods. The flowcell includes a first sample surface parallel to a second sample surface, the first grating to couple the first light to illuminate the first sample surface, and the second grating to couple the second light to illuminate the second sample surface. The first grating is offset, relative to the second grating, in a travel direction of the first light. The first grating to couple the first light into the first waveguide, the second grating to couple the second light into the second waveguide, the flowcell further comprising a third grating to couple the first light out of the first planar waveguide, and a fourth grating to couple the second light out of the second planar waveguide.

In a third aspect, a method includes: feeding illuminating light through an objective lens and into a flowcell using a first grating positioned outside an image-sensor field of view; and capturing imaging light using the objective lens.

Implementations can include any or all of the following features. The flowcell includes a first sample surface parallel to a second sample surface, the method further comprising directing a first component of the illuminating light to a first grating aligned with the first sample surface, and directing a second component of the illuminating light to a second grating aligned with the second sample surface. The method further comprises adjusting the objective lens to focus on the first sample surface in connection with directing the first component of the illuminating light to the first grating, and adjusting the objective lens to focus on the second sample surface in connection with directing the second component of the illuminating light to the second grating. The illuminating light comprises a first light beam of a first wavelength, and a second light beam of a second wavelength, the method further comprising directing the first light beam at a first side of the objective lens, and directing the second light beam at a second side of the objective lens opposite the first side. The method further comprises blocking the illuminating light, upon the illuminating light exiting the flowcell, from entering the objective lens. A thermal stage holds the flowcell, the method further comprising providing thermal control of the flowcell using the flowcell. The flowcell has multiple swaths bounded by respective gratings including the first grating, the method further comprising using at least one of the respective gratings both as an entry grating and an exit grating. The method further comprises performing an alignment process that evaluates a quality of coupling by the first grating.

It should be appreciated that all combinations of the foregoing concepts and additional concepts discussed in greater detail below (provided such concepts are not mutually inconsistent) are contemplated as being part of the inventive subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are contemplated as being part of the inventive subject matter disclosed herein.

