# US 2019/0170904 A1 · Photonic stucture-based devices and compositions for use in luminescent imaging of multiple sites within a pixel, and methods of using the same

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- Number: US 2019/0170904 A1
- Document ID: US20190170904A1
- Status: Published application
- Kind: A1
- Application number: 16/093,070
- Filed: 2017-04-21
- Published: 2019-06-06
- Earliest claimed: 2016-04-22
- Assignees: Illumina, Inc.
- Applicants: Illumina, Inc.
- Inventors: Juraj TOPOLANCIK; Cheng Frank ZHONG
- Web page: https://patentgrep.com/patent/US20190170904A1

## CPC

- G02B 1/005: {made of photonic crystals or photonic band gap materials (photonic band-gap structures or photonic lattices in integrated optics G02B6/1225; photonic band-gap structures or photonic lattices in optical fibres G02B6/02295)}
- B82Y 20/00: Nanooptics, e.g. quantum optics or photonic crystals
- G01N 21/6454: {using an integrated detector array}
- G01N 21/6456: {Spatial resolved fluorescence measurements; Imaging}
- G01N 21/6458: {Fluorescence microscopy (fluorescence microscopes per se G02B21/0076 and G02B21/16)}
- G02B 1/02: made of crystals, e.g. rock-salt, semi-conductors (G02B1/08 takes precedence)
- G02B 5/3025: {Polarisers, i.e. arrangements capable of producing a definite output polarisation state from an unpolarised input state (G02B5/3008, G02B5/3016 take precedence)}
- G02B 27/285: {comprising arrays of elements, e.g. microprisms}
- H10F 39/80: {Constructional details of image sensors}
- H10F 39/802: {Geometry or disposition of elements in pixels, e.g. address-lines or gate electrodes}
- H10F 39/806: {Optical elements or arrangements associated with the image sensors}
- C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation
- G02B: OPTICAL ELEMENTS, SYSTEMS OR APPARATUS
- B82Y: SPECIFIC USES OR APPLICATIONS OF NANOSTRUCTURES; MEASUREMENT OR ANALYSIS OF NANOSTRUCTURES; MANUFACTURE OR TREATMENT OF NANOSTRUCTURES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)
- H10F: INORGANIC SEMICONDUCTOR DEVICES SENSITIVE TO INFRARED RADIATION, LIGHT, ELECTROMAGNETIC RADIATION OF SHORTER WAVELENGTH OR CORPUSCULAR RADIATION
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES

## Abstract

A device for luminescent imaging includes an array of imaging pixels, a photonic structure over the array of imaging pixels, and an array of features over the photonic structure. A first feature of the array of features is over a first pixel of the array of imaging pixels, and a second feature of the array of features is over the first pixel and spatially displaced from the first feature. A first luminophore is within or over the first feature, and a second luminophore is within or over the second feature. The device includes a radiation source to generate first photons having a first characteristic at a first time, and generate second photons having a second characteristic at a second time. The first pixel selectively receives luminescence emitted by the first and second luminophores responsive to the first photons at the first time and second photons at the second time, respectively.

## Claims

### Claim 1

A device for use in luminescent imaging, the device comprising:
an array of imaging pixels;
a photonic structure disposed over the array of imaging pixels;
an array of features disposed over the photonic structure,
a first feature of the array of features being disposed over a first pixel of the array of imaging pixels,
a second feature of the array of features being disposed over the first pixel and spatially displaced from the first feature;
a first luminophore disposed within or over the first feature;
a second luminophore disposed within or over the second feature; and
a radiation source to generate first photons having a first characteristic at a first time, and to generate second photons having a second characteristic at a second time, the second characteristic being different than the first characteristic, the second time being different than the first time,
the first pixel selectively receiving luminescence emitted by the first luminophore responsive to the first photons at the first time, and selectively receiving luminescence emitted by the second luminophore responsive to the second photons at the second time.

### Claim 2 (depends on 1)

The device of claim 1, wherein the first photons having the first characteristic generate a first resonant pattern within the photonic structure at the first time, the first resonant pattern selectively exciting the first luminophore relative to the second luminophore; and
wherein the second photons having the second characteristic generate a second resonant pattern within the photonic structure at the second time, the second resonant pattern selectively exciting the second luminophore relative to the first luminophore.

### Claim 3 (depends on 1)

The device of claim 1, wherein the array of imaging pixels, the photonic structure, and the array of features are monolithically integrated with one another.

### Claim 4 (depends on 1)

The device of claim 1, wherein the photonic structure comprises a photonic crystal, a photonic superlattice, a microcavity array, or an array of plasmonic nanoantennas.

### Claim 5

(canceled)

### Claim 6

(canceled)

### Claim 7

(canceled)

### Claim 8 (depends on 1)

The device of claim 1, wherein the array of features comprises a plurality of wells, the first feature comprising a first well within which the first luminophore is disposed, the second feature comprising a second well within which the second luminophore is disposed.

### Claim 9 (depends on 1)

The device of claim 1, wherein the array of features comprises a plurality of posts, the first feature comprising a first post upon which the first luminophore is disposed, the second feature comprising a second post upon which the second luminophore is disposed.

### Claim 10 (depends on 1)

The device of claim 1, wherein the first and second characteristics are selected independently from the group consisting of wavelength, polarization, and angle.

### Claim 11

(canceled)

### Claim 12

(canceled)

### Claim 13

(canceled)

### Claim 14 (depends on 1)

The device of claim 1, wherein the first characteristic comprises a first wavelength, and wherein the second characteristic comprises a second wavelength that is different than the first wavelength.

### Claim 15 (depends on 1)

The device of claim 1, wherein the radiation source comprises an optical component,
the device further comprising a controller coupled to the optical component and to control the optical component so as to impose the first characteristic on the first photons and to impose the second characteristic on the second photons.

### Claim 16

(canceled)

### Claim 17

(canceled)

### Claim 18

(canceled)

### Claim 19

(canceled)

### Claim 20 (depends on 1)

The device of claim 1, wherein the second feature is laterally displaced from the first feature.

### Claim 21 (depends on 1)

The device of claim 1, wherein:
a third feature of the array of features is disposed over the first pixel and spatially displaced from each of the first and second features;
the device further comprises a third luminophore disposed within or over the third feature;
the radiation source is to generate third photons having a third characteristic at a third time, the third characteristic being different than the first and second characteristics, the third time being different than the first and second times; and
the first pixel selectively receives luminescence emitted by the third luminophore responsive to the third photons at the third time.

### Claim 22 (depends on 21)

The device of claim 21, wherein:
a fourth feature of the array of features is disposed over the first pixel and spatially displaced from each of the first, second, and third features;
the device further comprises a fourth luminophore disposed within or over the fourth feature;
the radiation source is to generate fourth photons having a fourth characteristic at a fourth time, the fourth characteristic being different than the first, second, and third characteristics, the fourth time being different than the first, second, and third times; and
the first pixel selectively receives luminescence emitted by the fourth luminophore responsive to the fourth photons at the fourth time.

### Claim 23

(canceled)

### Claim 24 (depends on 1)

The device of claim 1, wherein:
a third feature of the array of features is disposed over a second pixel of the array of imaging pixels;
a fourth feature of the array of features is disposed over the second pixel and spatially displaced from the third feature;
the device further comprises a third luminophore disposed within or over the third feature;
the device further comprises a fourth luminophore disposed within or over the fourth feature;
the second pixel selectively receives luminescence emitted by the third luminophore responsive to the first photons at the first time or responsive to the second photons at the second time; and
the second pixel selectively receives luminescence emitted by the fourth luminophore responsive to the first photons at the first time or responsive to the second photons at the second time.

### Claim 25

(canceled)

### Claim 26

(canceled)

### Claim 27 (depends on 1)

The device of claim 1, wherein the photonic structure comprises a hexagonal lattice, and wherein the imaging pixels are rectangular.

### Claim 28

(canceled)

### Claim 29

(canceled)

### Claim 30 (depends on 1)

The device of claim 1, wherein the first and second photons independently have wavelengths between about 300 nm and about 800 nm.

### Claim 31 (depends on 1)

The device of claim 1, wherein the first luminophore is coupled to a first nucleic acid, and wherein the second luminophore is coupled to a second nucleic acid.

### Claim 32 (depends on 1)

The device of claim 1, further comprising at least one microfluidic feature in contact with the array of features and to provide a flow of one or more analytes to the first and second features.

### Claim 33 (depends on 1)

The device of claim 1, wherein the first luminophore is coupled to a first polynucleotide to be sequenced, and the second luminophore is coupled to a second polynucleotide to be sequenced.

### Claim 34

(canceled)

### Claim 35

(canceled)

### Claim 36

(canceled)

### Claim 37

A method for use in luminescent imaging, the method comprising:
providing an array of imaging pixels;
providing a photonic structure disposed over the array of imaging pixels;
providing an array of features disposed over the photonic structure,
a first feature of the array of features being disposed over a first pixel of the array of imaging pixels,
a second feature of the array of features being disposed over the first pixel and spatially displaced from the first feature;
providing a first luminophore disposed within or over the first feature;
providing a second luminophore disposed within or over the second feature;
generating by a radiation source first photons having a first characteristic at a first time; generating by the radiation source second photons having a second characteristic at a second time, the second characteristic being different than the first characteristic, the second time being different than the first time;
selectively receiving by the first pixel luminescence emitted by the first luminophore responsive to the first photons at the first time; and
selectively receiving by the first pixel luminescence emitted by the second luminophore responsive to the second photons at the second time.

### Claim 38 (depends on 37)

The method of claim 37, wherein the first photons having the first characteristic generate a first resonant pattern within the photonic structure at the first time, the first resonant pattern selectively exciting the first luminophore relative to the second luminophore; and
wherein the second photons having the second characteristic generate a second resonant pattern within the photonic structure at the second time, the second resonant pattern selectively exciting the second luminophore relative to the first luminophore.

### Claim 39

(canceled)

### Claim 40 (depends on 37)

The method of claim 37, wherein the photonic structure comprises a photonic crystal, a photonic superlattice, a microcavity array, or an array of plasmonic nanoantennas.

### Claim 41

(canceled)

### Claim 42

(canceled)

### Claim 43

(canceled)

### Claim 44 (depends on 37)

The method of claim 37, wherein the array of features comprises a plurality of wells, the first feature comprising a first well within which the first luminophore is disposed, the second feature comprising a second well within which the second luminophore is disposed.

### Claim 45 (depends on 37)

The method of claim 37, wherein the array of features comprises a plurality of posts, the first feature comprising a first post upon which the first luminophore is disposed, the second feature comprising a second post upon which the second luminophore is disposed.

### Claim 46 (depends on 37)

The method of claim 37, wherein the first and second characteristics are selected independently from the group consisting of wavelength, polarization, and angle.

### Claim 47

(canceled)

### Claim 48

(canceled)

### Claim 49

(canceled)

### Claim 50 (depends on 37)

The method of claim 37, wherein the first characteristic comprises a first wavelength, and wherein the second characteristic comprises a second wavelength that is different than the first wavelength.

### Claim 51 (depends on 37)

The method of claim 37, wherein the radiation source comprises an optical component,
the method further comprising controlling the optical component so as to impose the first characteristic on the first photons and so as to impose the second characteristic on the second photons.

### Claim 52

(canceled)

### Claim 53

(canceled)

### Claim 54

(canceled)

### Claim 55

(canceled)

### Claim 56 (depends on 37)

The method of claim 37, wherein the second feature is laterally displaced from the first feature.

### Claim 57 (depends on 37)

The method of claim 37, wherein a third feature of the array of features is disposed over the first pixel and spatially displaced from each of the first and second features, and the method further comprises:
providing a third luminophore disposed within or over the third feature;
generating third photons having a third characteristic at a third time, the third characteristic being different than the first and second characteristics, the third time being different than the first and second times; and
selectively receiving by the first pixel luminescence emitted by the third luminophore responsive to the third photons at the third time.

### Claim 58

(canceled)

### Claim 59

(canceled)

### Claim 60 (depends on 37)

The method of claim 37, wherein:
a third feature of the array of features is disposed over a second pixel of the array of imaging pixels;
a fourth feature of the array of features is disposed over the second pixel and spatially displaced from the third feature; and
the method further comprises:
providing a third luminophore disposed within or over the third feature;
providing a fourth luminophore disposed within or over the fourth feature;
selectively receiving by the second pixel luminescence emitted by the third luminophore responsive to the first photons at the first time or responsive to the second photons at the second time; and
selectively receiving by the second pixel luminescence emitted by the fourth luminophore responsive to the first photons at the first time or responsive to the second photons at the second time.

### Claim 61

(canceled)

### Claim 62

(canceled)

### Claim 63

(canceled)

### Claim 64 (depends on 37)

The method of claim 37, comprising flood illuminating the photonic structure with the first and second photons.

### Claim 65

(canceled)

### Claim 66

(canceled)

### Claim 67

(canceled)

### Claim 68 (depends on 37)

The method of claim 37, further comprising providing at least one microfluidic feature in contact with the array of features and flowing, by the at least one microfluidic feature, one or more analytes to the first and second features.

### Claim 69

(canceled)

### Claim 70

(canceled)

### Claim 71

(canceled)

### Claim 72

(canceled)

### Claim 73

(canceled)

### Claim 74

(canceled)

### Claim 75

(canceled)

### Claim 76

(canceled)

### Claim 77

(canceled)