阅读说明：本技术 用于集成装置的光学吸收滤光器 (Optical absorption filter for integrated devices ) 是由 迈克尔·贝洛斯 费萨尔·R·阿哈默德 詹姆斯·比奇 迈克尔·库曼斯 沙拉特·侯萨利 阿里· 于 2020-03-03 设计创作，主要内容包括：描述了与衰减入射在用于样品分析的集成装置中的传感器(1-122)上的激发辐射有关的装置和方法。选定材料和晶体形态的至少一个半导体膜(1-336)位于形成在基板(1-105)上的集成器件中的波导(1-115)和传感器(1-122)之间。对于单层半导体材料(1-135)相距40nm的激发和发射波长,可以获得大于100或更高的抑制比。(Devices and methods relating to attenuating excitation radiation incident on a sensor (1-122) in an integrated device for sample analysis are described. At least one semiconductor film (1-336) of a selected material and crystal morphology is located between a waveguide (1-115) and a sensor (1-122) in an integrated device formed on a substrate (1-105). For excitation and emission wavelengths of a single layer of semiconductor material (1-135) 40nm apart, an inhibition ratio of greater than 100 or more can be obtained.)

1. A multilayer absorber filter comprising:

a plurality of absorber layers; and

separating the plurality of absorber layers to form a plurality of layers of dielectric material of a multi-layer stack, wherein there are at least three different layer thicknesses within the multi-layer stack.

2. The filter of claim 1, wherein the plurality of layers of dielectric material comprise at least two different thicknesses.

3. The filter of claim 1 or 2, wherein the plurality of absorber layers comprise at least two different thicknesses.

4. The filter of claim or 2, wherein there are at least four different layer thicknesses within the stack.

5. The filter of claim 1 or 2, wherein some thicknesses within the stack do not correspond to a quarter wavelength of radiation for which the filter is designed to block.

6. The filter according to claim 1 or 2, wherein at least two of the three different layer thicknesses differ by more than 50%.

7. The filter of claim 1 or 2, wherein the absorber layer comprises doped silicon.

8. The filter according to claim 1 or 2, wherein the thickness of the absorber layer is between 20nm and 300 nm.

9. A method of forming a multilayer absorber filter, the method comprising:

depositing a plurality of absorber layers; and

depositing a plurality of layers of dielectric material separating the plurality of absorber layers to form a multi-layer stack, wherein at least three different layer thicknesses are deposited within the multi-layer stack.

10. The method of claim 9, wherein depositing the plurality of absorber layers comprises depositing at least two different thicknesses of absorber that differ by at least 20%.

11. The method of claim 9 or 10, wherein depositing the plurality of absorber layers comprises depositing an absorber layer that is not a quarter wavelength thick.

12. The method of claim 9 or 10, wherein depositing the plurality of layers of dielectric material comprises depositing at least two different thicknesses of dielectric material that differ by at least 20%.

13. The method of claim 9 or 10, wherein depositing the plurality of layers of dielectric material comprises depositing a layer of dielectric material that is not a quarter wavelength thick.

14. A fluorescence detection assembly, comprising:

a substrate on which an optical detector is formed;

a reaction chamber arranged to receive fluorescent molecules;

an optical waveguide disposed between the optical probe and the reaction chamber; and

an optical absorption filter comprising a semiconductor absorption layer disposed between the optical detector and the reaction chamber.

15. The assembly of claim 14, further comprising:

an iris layer having an opening between the reaction chamber and the optical detector;

a first capping layer contacting a first side of the semiconductor absorber layer;

a hole through the first capping layer and the semiconductor absorber layer; and

a conductive interconnect extending through the aperture.

16. The assembly of claim 14 or 15, further comprising at least one dielectric layer disposed in a stack with the semiconductor absorption layer to form an absorptive interference filter, wherein an suppression ratio of the stack is greater than an suppression ratio of the semiconductor absorption layer alone.

17. The assembly of claim 14 or 15, further comprising at least one dielectric layer disposed in a stack with the semiconductor absorber layer and at least one additional semiconductor absorber layer to form an absorptive interference filter, wherein an suppression ratio of the stack is greater than an suppression ratio of the semiconductor absorber layer alone.

18. The assembly of claim 14 or 15, wherein the semiconductor absorption layer comprises a band gap sufficient to absorb excitation radiation of a first wavelength directed to the reaction chamber and transmit emission radiation of a second wavelength from the reaction chamber.

19. The assembly of claim 18, wherein the first wavelength corresponds to the green region of the visible electromagnetic spectrum and the second wavelength corresponds to the yellow or red region of the visible electromagnetic spectrum.

20. The assembly of claim 19, wherein the first wavelength is in a range of 515 nanometers (nm) to 540nm and the second wavelength is in a range of 620nm to 650 nm.

21. The assembly of claim 19, wherein the first wavelength is about 532 nanometers and the second wavelength is about 572 nanometers.

22. The component of claim 18, wherein the bandgap is in a range of 2.2eV to 2.3 eV.

23. The assembly of claim 14, wherein the semiconductor absorber layer comprises a binary II-VI semiconductor.

24. The component of claim 23, wherein the semiconductor absorber layer is zinc telluride.

25. The assembly of claim 23, wherein the semiconductor absorber layer is alloyed with a third element from group II or group VI.

26. The assembly of claim 14, wherein the semiconductor absorber layer comprises a ternary III-V semiconductor.

27. The assembly of claim 26, wherein the semiconductor absorber layer is indium gallium nitride.

28. The assembly of any of claims 14-27, wherein the semiconductor absorber layer is amorphous.

29. The assembly of any one of claims 14 to 27, wherein the semiconductor absorber layer is polycrystalline.

30. The component of any one of claims 14 to 27, wherein the semiconductor absorber layer has an average grain size of not less than 20 nm.

31. The assembly of any one of claims 14 to 27, wherein the semiconductor absorber layer is substantially monocrystalline.

32. The assembly of any one of claims 14 to 31, further comprising a first capping layer contacting the semiconductor absorber layer.

33. The assembly of claim 32, wherein the capping layer prevents diffusion of elements from the semiconductor absorber layer.

34. The assembly of claim 32, wherein the capping layer comprises a refractory metal oxide having a thickness of 5nm to 200 nm.

35. The assembly of claim 34, wherein the refractory metal oxide comprises tantalum oxide, titanium oxide, or hafnium oxide.

36. The assembly of any one of claims 32 to 35, wherein the capping layer reduces light reflection from the semiconductor absorber layer for visible wavelengths between 500nm and 750 nm.

37. The assembly of any one of claims 32 to 36, wherein the cover layer provides increased adhesion of a semiconductor absorber layer in the assembly.

38. The assembly of any one of claims 32 to 36, wherein the cover layer reduces in-plane stress from a semiconductor absorber layer in the assembly.

39. The assembly of any one of claims 14 to 36, further comprising an opening formed through the optical absorption filter and an electrically conductive connection extending through the opening.

40. The assembly of any of claims 14 to 36, wherein the optical absorption filter is formed over a non-planar topography.

41. The assembly of claim 40, further comprising an opening formed through the optical absorption filter and an electrically conductive connection extending through the opening.

42. The assembly of claim 41, wherein the opening is located at a planarized interface between the optical absorption filter and an adjacent layer, and the semiconductor absorption layer has been removed at the planarized interface.

43. An optical absorption filter includes a semiconductor absorption layer formed over a non-planar topography on a substrate.

44. The optical absorption filter according to claim 43 wherein at least a portion of the semiconductor absorption layer has been removed by planarization.

45. The optical absorption filter according to claim 44 further comprising conductive connections extending through openings formed by the removed portions of the semiconductor absorption layer.

46. The optical absorption filter according to any one of claims 43 to 45, wherein the semiconductor absorption layer has a uniform thickness within 10% and conforms to a non-planar topography.

47. The optical absorption filter according to claim 46, wherein portions of the semiconductor absorption layer extend substantially perpendicular to the plane of the substrate.

48. An optical absorption filter includes a ternary III-V semiconductor absorption layer formed in an integrated device on the substrate.

49. The optical absorption filter according to claim 48 wherein the ternary III-V semiconductor absorption layer is monocrystalline.

50. The optical absorbing filter according to claim 48 or 49, wherein the ternary group III-V semiconductor absorbing layer is indium gallium nitride.

51. The optical absorption filter according to any one of claims 48 to 50 wherein the integrated device comprises an optical detector and a reaction chamber located on opposite sides of the optical absorption filter.

52. The optical absorption filter of claim 51, wherein the integrated device further comprises an optical waveguide on the same side of the optical absorption filter as the reaction chamber.

53. The optical absorption filter according to any one of claims 48 to 50 wherein the integrated device comprises an optical detector and an optical waveguide on opposite sides of the optical absorption filter.

54. The optical absorption filter according to any one of claims 48 to 53 further comprising an anti-reflective layer formed adjacent to the semiconductor absorption layer, the anti-reflective layer configured to reduce light reflection from the semiconductor absorption layer for visible wavelengths between 500nm and 750 nm.

55. A method of forming a fluorescence detection device, the method comprising:

forming an optical probe on a substrate;

forming a semiconductor optical absorption filter over an optical detector on the substrate;

forming an optical waveguide over an optical probe on the substrate; and

forming a reaction chamber configured to receive fluorescent molecules over the optical absorption filter and the optical waveguide.

56. The method of claim 55, wherein forming the semiconductor light absorbing filter comprises conformally depositing a semiconductor absorbing layer over a non-planar topography.

57. The method of claim 55 or 56, further comprising forming an oxide or nitride cap layer in contact with the semiconductor absorber layer to prevent diffusion of elements from the semiconductor absorber layer.

58. The method of claim 57, further comprising forming the oxide or nitride cap layer adjacent to the semiconductor absorber layer, the thickness of the oxide or nitride cap layer reducing optical reflection from the semiconductor absorber layer for visible wavelengths between 500nm and 750nm compared to if the oxide or nitride cap layer were not present.

59. A method of improving the signal-to-noise ratio of an optical detector, the method comprising:

transmitting excitation radiation to a reaction chamber using an optical waveguide, wherein the optical waveguide and the reaction chamber are integrated on a substrate;

passing the emitted radiation from the reaction chamber through an optical absorption filter comprising the semiconductor absorption layer;

detecting the emitted radiation through the semiconductor absorbing layer with an optical detector; and

attenuating excitation radiation traveling toward the optical detector with the semiconductor absorption layer.

60. The method of claim 59, further comprising attenuating, with the semiconductor absorption layer, between 10 and 100 times more excitation radiation traveling toward the optical detector than emission radiation that has passed through the semiconductor absorption layer.

61. The method of claim 59, further comprising attenuating, with the semiconductor absorption layer, between 100 and 1000 times more excitation radiation traveling toward the optical detector than emission radiation that has passed through the semiconductor absorption layer.

62. The method of claim 59, further comprising attenuating, with the semiconductor absorption layer, between 1000 and 3000 times more excitation radiation traveling toward the optical detector than emission radiation that has passed through the semiconductor absorption layer.

63. The method of claim 59, wherein the excitation radiation has a first characteristic wavelength in the range of 500nm to 540nm and the emission radiation has a second characteristic wavelength between 560nm to 690 nm.

64. The method of any one of claims 59 to 63, further comprising passing the emitted radiation through a first capping layer contacting the semiconductor absorber layer.

65. The method of claim 64, further comprising reducing reflection of emitted radiation from said semiconductor absorber layer with said first capping layer.

66. The method of any one of claims 59 to 65, wherein the first capping layer comprises a refractory metal oxide having a thickness of 5nm to 200 nm.

67. The method of any one of claims 59 to 66, further comprising reducing in-plane stress from the semiconductor absorber layer with the capping layer.

Technical Field

The present application relates to the use of optical absorption filters to reduce harmful radiation in integrated devices for analyzing samples.

Background

In the field of instruments for sample analysis, micromachined chips may be used to analyze a large number of analytes or samples (contained in one or more samples) in parallel. In some cases, the optical excitation radiation is delivered to a plurality of discrete locations on the chip where individual analyses are performed. The excitation radiation may excite the sample at each location, fluorophores attached to the sample, or fluorophores interacting with the sample. In response to the excitation, radiation may be emitted from the location detected by the sensor. Information obtained from the emitted radiation, or lack thereof, at a location can be used to determine characteristics of the location sample.

Disclosure of Invention

Devices and methods related to attenuating excitation radiation or other harmful radiation incident on sensors in integrated devices, such as devices for sample analysis, are described. In some embodiments, the semiconductor film of the selected material and crystalline morphology is in a material stack on a substrate and is located between a waveguide and a sensor in a pixel of an integrated device. The semiconductor material and crystal morphology are selected to significantly attenuate excitation radiation while delivering more than 75% of the radiation emitted by the reaction chambers in the pixel to the sensor. Wavelength discrimination ratios (also referred to as "suppression ratios" or "extinction ratios") of greater than 100 or greater can be obtained for wavelengths spaced 40nm or about 40nm apart. In some embodiments, the multilayer stack comprises layers of absorbing material separated by layers of dielectric material. The stack may comprise at least three or four layers with different thicknesses. Such a stack may provide an rejection ratio greater than 10000 over a range of incident angles from normal angles to 80 degrees (or any subrange within these angles) for wavelengths spaced at 110nm or about 110 nm.

Some embodiments relate to a multilayer semiconductor absorber filter comprising a plurality of semiconductor absorber layers and a plurality of dielectric material layers separating the plurality of semiconductor absorber layers to form a multilayer stack, wherein there are at least three different layer thicknesses within the multilayer stack.

Some embodiments relate to methods of forming multilayer semiconductor absorber filters. A method may include the steps of: depositing a plurality of semiconductor absorber layers; and depositing a plurality of layers of dielectric material separating the plurality of semiconductor absorber layers to form a multi-layer stack, wherein at least three different layer thicknesses are deposited within the multi-layer stack.

Some embodiments relate to a fluorescence detection assembly comprising: a substrate on which an optical detector is formed; a reaction chamber arranged to receive fluorescent molecules; an optical waveguide disposed between the optical probe and the reaction chamber; and an optical absorption filter comprising a layer of semiconductor material and disposed between the optical detector and the reaction chamber.

Some embodiments relate to an optical absorption filter that includes a semiconductor layer formed on a non-planar topography on a substrate.

Some embodiments relate to an optical absorption filter that includes a ternary III-V semiconductor formed in an integrated device on a substrate.

Some embodiments relate to a method for forming a fluorescence detection device, the method comprising: forming an optical probe on a substrate; forming a semiconductor optical absorption filter over an optical detector on the substrate; forming an optical waveguide over an optical probe on the substrate; and forming a reaction chamber configured to receive fluorescent molecules over the optical absorption filter and the optical waveguide.

The foregoing and other aspects, implementations, actions, functions, features and embodiments of the present teachings can be more fully understood from the following description taken in conjunction with the accompanying drawings.

Drawings

Those skilled in the art will appreciate that the drawings described herein are for illustration purposes only. It is to be understood that in some instances various aspects of the invention may be exaggerated or enlarged to facilitate an understanding of the invention. In the drawings, like reference numbers generally indicate similar features, functionally similar, and/or structurally similar elements throughout the various views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating the principles of the teachings. The drawings are not intended to limit the scope of the present teachings in any way.

Fig. 1-1 depicts an example of a structure at a pixel of an integrated device according to some embodiments.

Fig. 1-2 depict examples of structures at a pixel of an integrated device according to some embodiments.

Fig. 1-3 depict examples of structures at a pixel of an integrated device according to some embodiments.

Figure 2-1 illustrates an example semiconductor absorber structure, according to some embodiments.

Fig. 2-2 depicts the light transmission of a ZnTe semiconductor absorber layer as a function of wavelength, according to some embodiments.

Fig. 2-3 depict the suppression ratio Rr as a function of the thickness of the InGaN semiconductor absorption layer, in accordance with some embodiments.

Fig. 2-4 are transmission electron micrographs of exemplary semiconductor absorber layers.

Fig. 2-5 depict transmittance as a function of wavelength of radiation incident on a multilayer semiconductor absorber, in accordance with some embodiments.

Fig. 2-6A depict examples of multilayer absorber filters according to some embodiments.

2-6B depict another example of transmittance as a function of wavelength of radiation incident on a multilayer semiconductor absorber, according to some embodiments.

Fig. 2-6C depict reflectivity, absorptivity, and transmissivity as a function of angle of s-polarized radiation incident on a multilayer semiconductor absorber, according to some embodiments.

Fig. 2-7 depict another example of a multilayer absorber filter, according to some embodiments.

Figure 3-1 illustrates an exemplary absorber formed on a topography, according to some embodiments.

Fig. 3-2 illustrates an exemplary absorber formed over a topography, according to some embodiments.

Figures 3-3 illustrate exemplary absorbers formed over a topography, according to some embodiments.

Figures 3-4A depict a patterned resist layer that can be used to form a semiconductor absorber on a topography, according to some embodiments.

Figures 3-4B illustrate structures associated with forming a semiconductor absorber topographically, in accordance with some embodiments.

Figures 3-4C illustrate structures associated with forming a semiconductor absorber over a topography, in accordance with some embodiments.

Figures 3-4D illustrate structures associated with forming a semiconductor absorber over a topography, according to some embodiments.

Figures 3-4E illustrate structures associated with forming a semiconductor absorber topographically, in accordance with some embodiments.

Fig. 4 depicts a cut-away perspective view of a portion of an integrated device, according to some embodiments.

Fig. 5-1A is a block diagram depicting an analytical instrument including a compact mode-locked laser module, in accordance with some embodiments.

Fig. 5-1B depicts a compact mode-locked laser module incorporated into an analytical instrument, according to some embodiments.

Fig. 5-2 depicts a train of light pulses according to some embodiments.

Fig. 5-3 depicts an example of parallel reaction chambers that may be excited by a pulsed laser via one or more waveguide lights, and further showing corresponding detectors for each chamber, according to some embodiments.

Fig. 5-4 illustrate optical excitation from a reaction chamber of a waveguide according to some embodiments.

Fig. 5-5 depict further details of an integrated reaction chamber, optical waveguide, and time-binning photodetector according to some embodiments.

Fig. 5-6 depict examples of biological reactions that may occur within a reaction chamber according to some embodiments.

Fig. 5-7 depict emission probability curves for two different fluorophores with different attenuation characteristics.

Fig. 5-8 depict time-binned detection of fluorescence emissions according to some embodiments.

Fig. 5-9 depict time-binning photodetectors according to some embodiments.

Fig. 5-10A depict pulsed excitation and time-binning detection of fluorescence emissions from reaction chambers according to some embodiments.

Fig. 5-10B depict histograms of cumulative fluorescence photon counts in different time bins (bins) after repeated pulse excitation of an analyte, according to some embodiments.

According to some embodiments, fig. 5-11A through 5-11D depict different histograms that may correspond to four nucleotides (T, A, C, G) or nucleotide analogs.

The features and advantages of the present invention will become more apparent from the following detailed description taken in conjunction with the accompanying drawings. Directional references ("above", "below", "top", "bottom", "left", "right", "horizontal", "vertical", etc.) may be used when describing embodiments with reference to the drawings. Such references are intended only to assist the reader in viewing the drawings in a normal orientation. These directional references are not intended to describe preferred or mere orientations of features of the embodied devices. Other directions may be used to implement the device.

Detailed Description

I. Integrated device with semiconductor absorber

Instruments for analyzing samples are constantly being developed, possibly including micro-machined components (e.g., electronic chips, microfluidic chips), which help to reduce the overall size of the instrument. The sample to be analyzed may include air (e.g., to detect harmful gas leaks, combustion byproducts, or toxic chemical components), water or other ingestible liquids, food samples, and biological samples (blood, urine, etc.) collected from a subject. In some cases, a portable hand-held instrument is required to analyze the sample so that a technician or medical staff can easily bring the instrument to a site where service is possible and where rapid, accurate analysis of the sample is required. In a clinical setting, a bench-top instrument may be required for more complex sample analysis, such as human gene sequencing or complete blood count analysis.

In advanced analytical instruments, such as those described in U.S. patent publication 2015/0141267 and U.S. patent 9617594, both of which are incorporated herein by reference, massively parallel sample analysis can be performed using disposable integrated devices (which may be referred to as "chips" and "disposable chips" for brevity). The disposable integrated device may include a packaged biophotonic chip on which a large number of pixels may be present, the pixels having reaction chambers for performing parallel analysis on one sample or different samples. For example, the number of pixels having reaction chambers on the biophotonic chip may be between about 10000 to about 10000000 in some cases, and may be between 100000 to about 100000000 in some cases. In some embodiments, the disposable chip may be mounted into a socket of an advanced analytical instrument and connected with optical and electronic components in the instrument. The user can easily replace the disposable chip for each new sample analysis.

Fig. 1-1 is a simplified diagram depicting some of the components that may be included in a pixel of a bio-optoelectronic chip. The pixel may include reaction chambers 1-130, optical waveguides 1-115, semiconductor absorbers 1-135, and sensors 1-122 formed on substrates 1-105. The waveguides 1-115 can deliver light energy from a remote light source to the pixels and provide excitation radiation to the reaction chambers 1-130. The excitation radiation may excite one or more fluorophores present in the reaction chambers 1-130. Radiation emitted by the fluorophore can be detected by the sensors 1-122. The signal from sensors 1-122, or lack thereof, can provide information about the presence or absence of an analyte in reaction chambers 1-130. In some embodiments, the signals from sensors 1-122 may determine the type of analyte present in the reaction chamber.

For sample analysis, a sample containing one or more analytes can be deposited on reaction chambers 1-130. For example, the sample can be placed in a reservoir or microfluidic channel above the reaction chambers 1-130. In some cases, the sample can be printed as a droplet onto a treated surface including reaction chambers 1-130. During sample analysis, at least one analyte from a sample to be analyzed may enter the reaction chamber 1-130. In some embodiments, the analyte itself may fluoresce when excited by excitation radiation from waveguides 1-115. In some cases, the analyte may carry one or more attached fluorescent molecules. In other cases, the analyte may quench fluorophores already present in the reaction chambers 1-130. When a fluorescent entity enters the reaction chamber and is excited by the excitation radiation, the fluorescent entity may emit radiation at a wavelength different from the excitation radiation, which in turn is detected by the sensors 1-122. The semiconductor absorber 1-135 may preferentially attenuate excitation radiation to a significantly greater extent than emission radiation from the reaction chamber 1-130.

In more detail, the reaction chambers 1-130 may be formed as transparent or translucent layers 1-110. According to some embodiments, the reaction chamber may have a depth of between 50nm and 1 μm. According to some embodiments, the reaction chamber 1-130 may have a minimum diameter between 50nm and 300 μm. If the reaction chambers 1-130 are formed as zero mode waveguides, the minimum diameter may even be less than 50nm in some cases. If larger analytes are to be analyzed, the minimum diameter may be greater than 300 nm. The reaction chamber may be located above the optical waveguides 1-115 such that the bottom of the reaction chamber may be 500nm above the top of the waveguides 1-115. In some cases, the reaction chamber 1-130 bottom can be located in the waveguide or on the waveguide 1-115 top surface. According to some embodiments, the transparent or translucent layers 1-110 may be formed of an oxide or nitride such that excitation radiation from the optical waveguides 1-115 and emission radiation from the reaction chambers 1-130 will pass through the transparent or translucent layers 1-110 without being attenuated by, for example, more than 10%.

In some embodiments, there may be one or more additional transparent or translucent layers 1-137 formed on the substrates 1-105 and located between the substrates and the optical waveguides 1-115. In some embodiments, these additional layers may be formed of oxide or nitride and may be the same type of material as the transparent or translucent layers 1-110. Semiconductor absorbers 1-135 may be formed within these additional layers 1-137 between the waveguides 1-115 and the sensors 1-122. The distance from the bottom of the optical waveguides 1-115 to the sensors 1-122 may be between 500nm and 10 μm.

In various embodiments, the substrates 1-105 may include semiconductor substrates, such as silicon (Si). However, other semiconductor materials may be used in some embodiments. The sensors 1-122 may include semiconductor photodiodes patterned and formed on the substrates 1-105. The sensors 1-122 may be connected to other Complementary Metal Oxide Semiconductor (CMOS) circuitry on the substrate through interconnects 1-170.

Another example of a structure that may be included at a pixel of an integrated device is shown in fig. 1-2. According to some embodiments, one or more light blocking layers 1-250 may be formed over layers 1-110, and reaction chambers 1-230 may be formed in the light blocking layers. In some embodiments, the reaction chamber etching process can begin by opening holes in one or more light blocking layers that will become the top of the reaction chambers 1-230. The light blocking layers 1-250 may be formed of one or more metal layers. In some cases, light blocking layers 1-250 may include semiconductor and/or oxide layers. The light blocking layer 1-250 may reduce or prevent excitation radiation from the optical waveguide 1-115 from propagating into the sample above the reaction chamber 1-230 and exciting an analyte within the sample. In addition, the light blocking layer 1-250 can prevent external radiation from above the reaction chamber from passing through the sensor 1-122. Radiation from outside the reaction chamber can cause unwanted background radiation and signal noise.

In some embodiments, one or more iris layers 1-240 can be formed over sensors 1-122. The iris layer 1-240 may include an opening 1-242 to allow emissions from the reaction chamber 1-230 to pass through to the sensor 1-122 while blocking emissions or radiation from other directions (e.g., from adjacent pixels or scattered excitation radiation). For example, the iris layer 1-240 may be formed of a light blocking material that may prevent excitation radiation scattered at wide angles of incidence from striking the sensor 1-122 and causing background noise.

In some cases, iris layers 1-240 may be formed of a conductive material and provide a potential reference plane or ground plane for circuitry formed on or over substrates 1-105. According to some embodiments, vias or holes 1-237 may be formed in the semiconductor absorber 1-235 (and the capping layer contacting the semiconductor absorber layer, if present) such that the vertical conductive interconnects or vias 1-260 may connect to the iris layer 1-240 without contacting the semiconductor absorber layer 1-235, which may be conductive. In some cases, the semiconductor absorber 1-235 can serve as a potential reference plane or ground plane for circuitry formed on or over the substrate 1-105, and the vertical interconnect can be connected to the semiconductor absorber 1-235 and can be unconnected to the iris layer 1-240. In some cases, the holes 1-237 may include an electrically insulating material (e.g., an oxide) that prevents electrical contact between the conductive vias 1-260 and the semiconductor absorber layers 1-235. In some embodiments, the semiconductor absorber layer 1-235 can have a high resistivity and the holes 1-237 can be filled with a conductive material to provide electrical connections through the semiconductor absorber layer. In an embodiment, there may be additional electronics, such as storage and readout electronics 1-224 formed at each pixel with the sensor on the substrate 1-105. For example, readout electronics may be used to control the signal acquisition and readout of the charge stored at each sensor 1-122. In some embodiments, the holes 1-237 in the semiconductor absorbers 1-235 (and the cover layer) can facilitate electrical connection through the semiconductor layer, for example, by wire bonding, flip chip bonding, or other methods to connect the integrated circuit to external circuitry.

In some cases, there may be multiple layers of semiconductor absorber material, as shown in fig. 1-3. For example, the semiconductor absorber 1-335 may include two, three, or more layers of semiconductor absorber material 1-336 separated by intermediate layers of material 1-334. The intermediate layers 1-334 may have a different index of refraction than the semiconductor absorber material 1-336. The intermediate layers 1-334 may additionally or alternatively have a different transmissivity than the semiconductor absorber materials 1-336. In some cases, the thicknesses of the different semiconductor absorber material layers 1-336 are substantially the same and may be different than the thicknesses of the intermediate layers 1-334, although in some cases the semiconductor absorber material layers 1-336 may have at least two different thicknesses. In some embodiments, the semiconductor absorber material 1-336 may be between 75nm and 90nm thick for silicon-based absorber materials, and the excitation characteristic wavelength is between 515nm and 540 nm. Other thicknesses may be used for other absorbing materials and excitation wavelengths. In some cases, the thickness of the intermediate layers 1-334 is substantially the same and may be different than the thickness of the semiconductor absorber layer 1-336, although in some cases the intermediate layers 1-334 may have at least two different thicknesses. In some embodiments, the thickness of the intermediate layers 1-334 may be between 50nm and 150nm for silicon oxide and the excitation characteristic wavelength is between 515nm and 540 nm. Other thicknesses may be used for other interlayer materials and excitation wavelengths.

By using multiple layers of semiconductor absorber material 1-336 as shown in fig. 1-3, the interlayer optical interference effect can effectively sharpen the band edge steepness of the semiconductor absorber, increasing the rejection ratio of the semiconductor absorber 1-335. Band-edge interference sharpening may allow for lower quality crystallinity of the semiconductor absorber material 1-336. In some embodiments, polycrystalline or amorphous semiconductor materials (e.g., amorphous silicon carbide, amorphous ZnTe, amorphous InGaN, etc.) may be used for the semiconductor absorber 1-335 having the plurality of semiconductor absorber material layers 1-336.

More details of the semiconductor absorber 2-135 are shown in fig. 2-1. In various embodiments, the semiconductor absorber 2-135 comprises a semiconductor absorber layer 2-210. The structure shown in fig. 2-1 may be implemented in a semiconductor absorber having only one layer of semiconductor absorber material, or may be used for one or more layers of a semiconductor absorber having multiple layers of semiconductor absorber material. The semiconductor absorption layer may be formed of a semiconductor material having a band gap. For example, the semiconductor absorption layer may be formed of a compound semiconductor material having a band gap corresponding to the visible range of the spectrum. Example materials include, but are not limited to, zinc telluride, indium gallium nitride, gallium phosphide, vanadium oxide, tantalum nitride, aluminum arsenide, magnesium silicide, aluminum antimonide, silicon arsenide, and indium arsenide. Other materials suitable for some applications include silicon carbide, hydrogen carbon, cadmium sulfide, cadmium oxide, and zinc selenide. Such exemplary materials can be implemented in various stoichiometric ratios. The semiconductor absorber layers 2-210 may be polycrystalline in some embodiments, or may be monocrystalline in some embodiments. In some cases, the average grain size of the polycrystalline semiconductor absorber layers 2-210 may be no less than 20nm, measured in the lateral, in-plane directions. In some cases, the average grain size of the polycrystalline semiconductor absorber layers 2-210 may be no less than 1 μm, measured in the lateral, in-plane directions. In some embodiments, the semiconductor absorber layers 2-210 may comprise amorphous semiconductor material. According to some embodiments, the thickness of the semiconductor absorber layer 2-210 may be between 200nm and 5 μm. In some cases, the thickness of the semiconductor absorber layer 2-210 may be between 1 μm and 2 μm.

The type of semiconductor material used for the semiconductor absorber layers 2-210 can be selected or tailored to provide the desired absorption of excitation radiation and transmission of radiation emitted from the reaction chambers 1-230. For example, the semiconductor material may be selected or tailored to have a band gap such that excitation radiation having photon energies greater than the band gap will be primarily absorbed by the semiconductor material and fluorophore emissions from reaction chambers 1-230 having photon energies less than the band gap will be primarily transmitted by the semiconductor material. In an embodiment, the band gap is selected or adjusted such that the transition between the absorbed wavelength and the transmitted wavelength is between the excitation radiation provided by the optical waveguides 1-115 and the fluorescent emission emitted from the reaction chambers 1-230. The band gap of the semiconductor absorber layers 2-210 can be tuned by changing the composition of the semiconductor (e.g., changing the stoichiometric ratio of In and Ga In InxGa1-xN, where x has a value In the range 0< x < 1).

An example transmittance profile of a semiconductor absorber layer 2-210 formed of ZnTe is shown in fig. 2-2. In some embodiments, the excitation radiation may have a characteristic wavelength of 532nm, and the fluorescent emission may have a characteristic wavelength value between 560nm and 580 nm. For an example in which the excitation radiation has a characteristic wavelength of about 532nm, the semiconductor absorption layers 2-210 transmit an emission radiation (e.g. towards the sensors 1-122) which is about 400 times the excitation radiation (suppression ratio R)_r400). In some embodiments, the excitation radiation may have a characteristic wavelength between 500nm and 540nm, and the emission radiation may have a characteristic wavelength between 560nm and 650 nm. In some cases, the rejection ratio may be higher (e.g., between 400 and 800, between 800 and 1000, or between 1000 and 3000). According to some embodiments, the semiconductor absorber may attenuate desired detected radiation (e.g., from the reaction chamber) by between 5% and 85%, while attenuating unwanted radiation by much more than this amount.

The inventors have recognized and appreciated that the abruptness of the filter cut-off and the ratio of transmitted radiation with wavelengths above the cut-off to absorbed radiation with wavelengths below the cut-off depend on the thickness of the semiconductor absorber layers 2-210, the number of semiconductor absorber layers, the crystalline quality of the semiconductor absorber layers, and the separation of the excitation and emission characteristic wavelengths, and that each of these parameters can be modified to some extent. The thickness of the semiconductor absorber layers 2-210 can be controlled, for example, by adjusting the length of time the semiconductor absorber material is deposited.

In some embodiments, the type of deposition process (e.g., metal organic chemical vapor deposition, molecular beam epitaxy, or physical vapor deposition) may be selected to improve the crystal quality of the semiconductor absorber layers 2-210. In some cases, a seed layer of a different material may be deposited first on the underlying layer to improve the crystalline quality of the subsequently deposited semiconductor absorber layer 2-210. In some embodiments, a post-deposition annealing step may be performed to improve the crystalline quality of the semiconductor absorber layers 2-210. In some embodiments, the semiconductor absorber layers 2-210 may have an average grain size of no less than 20nm, as measured in the plane of the layers. In some cases, the average grain size is not less than 50 nm. In some cases, the average grain size is not less than 100 nm. In some cases, the average grain size is not less than 500 nm. In some cases, the average grain size is between 40nm and 100 nm. In some cases, the average grain size is between 100nm and 500 nm. In some cases, the average grain size is between 100nm and 1 m. In some cases, the average grain size is between 1m and 3 m. In some cases, the average grain size is between 2m and 5 m. In some cases, the average grain size is between 5m and 10 m. According to some embodiments, the semiconductor absorber layer 2-210 may have a larger grain size or may be substantially single crystalline. For example, the semiconductor absorber layers 2-210 may be layered and transferred from a single crystal wafer grown using a handle wafer and deposited by bonding to underlying layers on the substrates 1-105.

In some embodiments, the semiconductor absorber layers 2-210 may have a particular crystalline morphology, such as fibrous, cylindrical, or pancake. The fiber morphology may be represented by fibrous or highly columnar crystals that are oriented vertically in the semiconductor absorber layers 2-210. An example of a fibrous crystal is shown in the transmission electron microscope images of fig. 2-4. The long columnar crystals have a high aspect ratio (e.g., an aspect ratio greater than 10:1), are vertically oriented, and are formed within the zinc telluride layer. The cylindrical morphology may have grains with an aspect ratio between 0.5:1 and 10: 1. The wafer morphology may have grains with aspect ratios less than 0.5: 1.

In some cases, semiconductor absorber layers 2-210 may be formed of an amorphous semiconductor material. For example, any of the semiconductor materials described herein can be deposited as an amorphous material by sputtering, electron beam evaporation, or a chemical vapor deposition process such as Plasma Enhanced Chemical Vapor Deposition (PECVD). Example amorphous semiconductor materials include, but are not limited to, amorphous silicon carbide, amorphous silicon nitride, amorphous silicon oxide, amorphous ZnTe, amorphous InGaN, and alloys thereof. In some embodiments, the amorphous semiconductor material or alloy may be hydrogenated (e.g., amorphous hydrogenated silicon carbide, etc.). In some embodiments, nitrogen may be added to the amorphous semiconductor material or alloy during deposition, for example, during a chemical vapor deposition process. In some cases, nitrogen and/or other elements may be added to the material, such as amorphous silicon, during deposition to adjust the refractive index n and the extinction coefficient k to values required to transmit and block the wavelengths of interest. In some embodiments, the deposited amorphous semiconductor material may include nanocrystals or microcrystals distributed throughout the amorphous semiconductor material. The amorphous semiconductor absorber layer 2-210 can be used in any of the semiconductor absorber structures described herein. In practice, it may be easier and less costly to fabricate the amorphous semiconductor absorber layer 2-210 on a substrate using existing casting tools and processes. In some cases, deposition of amorphous semiconductor or other materials may be achieved at lower temperatures (e.g., below 500℃.), for example, compatible with CMOS processes. Although amorphous semiconductor materials may not provide as steep a band edge as the same type of polycrystalline or crystalline semiconductor materials, a band edge may be sufficient when there is a large difference in characteristic excitation and emission wavelengths. However, some micromachining processes may use polycrystalline or crystalline semiconductor materials in a manner compatible with CMOS structures.

An advantage of an absorption layer, such as the semiconductor absorption layer 2-210, is that it may have more wavelength filtering than other typesHigher angular tolerances for optical devices such as multilayer dielectric filters. In a dielectric filter, each layer absorbs negligible amounts of radiation (e.g., less than one percent of the incident radiation). For example, a multilayer dielectric filter (e.g., a distributed Bragg reflector) having a thickness of about 2 microns may provide an suppression ratio R of about 800 at normal incidence_r. Suppression ratio R_rIs the ratio of the transmitted intensity at the emission wavelength (572nm for the example structure) to the transmitted intensity at the excitation wavelength (532 nm for the example structure). Suppression ratio R at 30 degree incident angle_rAnd down to 110. In contrast, a ZnTe semiconductor absorber layer 2-210 of 2.0 microns thickness provides a suppression ratio R in excess of 800 at all angles of incidence_r. Thus, the micron-scale thin-film absorbing layer or semiconductor absorbing layer 2-210 may outperform micron-scale thin-film multilayer dielectric filters in terms of angular tolerance and, in addition, be compatible with widely available CMOS processing equipment. For example, the semiconductor absorber layers 2-210 may include one or several layers that may not have the tight dimensional tolerances required for multilayer dielectric filters.

According to some embodiments, the semiconductor absorption layers 2-210 may be formed of InGaN, which may provide tunability of the bandgap over a wide range. For example, by varying the concentration ratio of In and Ga, the band gap can be adjusted from 0.8eV to 3.4eV, covering the entire visible wavelength range. InGaN can be grown epitaxially as a single crystal material on a crystalline substrate, and can also be deposited in polycrystalline form by various chemical and physical deposition methods, including Metal Organic Chemical Vapor Deposition (MOCVD), Molecular Beam Epitaxy (MBE), sputtering, reactive sputtering, and other established methods. In some embodiments, the band gap may be adjusted by alloying or otherwise combining a binary semiconductor with group iii II and/or VI elements. Some examples of the resulting ZnTe semiconductor compositions include, but are not limited to, ZnTeO and CdZnTe.

Modeling of single crystal InGaN shows that for a layer thickness of 1.5 microns, an suppression ratio R of greater than 3000 can be obtained_r(572nm/532 nm). In some embodiments, the semiconductor absorber 2-135 may include a semiconductor absorber layer 2-210 formed of InGaN. The thickness of the absorption layer may be between 200nm and 3 microns and the suppression ratio R of the layer_rMay be between 20 and 100000. The suppression ratio R of single crystal InGaN is depicted in FIGS. 2-3_rExemplary profile as a function of layer thickness.

In some embodiments, one or more capping layers 2-220 may be formed adjacent to the semiconductor absorber layers 2-210. In some cases, there may be a capping layer 2-220 on one side of the semiconductor absorber layer 2-210. In other cases, there may be a cover layer on each side of the semiconductor absorber layers 2-210, e.g., the top and bottom sides. According to some embodiments, the capping layers 2-220 may comprise at least one thin layer having a thickness between 20nm and 100nm, although thicker layers may be used in some cases. In some embodiments, the capping layer 2-220 on one side of the semiconductor absorber layer 2-210 may comprise multiple layers of different materials. Exemplary materials that may be used for capping layers 2-220 include, but are not limited to, silicon nitride, aluminum oxide, titanium oxide, hafnium oxide, and tantalum oxide.

One or more capping layers 2-220 may be included to prevent diffusion of the semiconductor absorber layer 2-210 into adjacent materials or to prevent release of the semiconductor absorber material into the environment. In some embodiments, the capping layer 2-220 may additionally or alternatively provide improved adhesion to an immediately adjacent layer as compared to the adhesion provided by the semiconductor absorber layer 2-210 alone. In some embodiments, the one or more capping layers 2-220 may reduce or induce stress in the semiconductor absorber layers 2-210 and/or improve crystallinity of the semiconductor absorber layers 2-210. In some cases, the capping layer 2-220 may reduce stress from the semiconductor absorber layer 2-210 in the assembly by providing a compensating type of stress (e.g., providing a tensile stress if the semiconductor absorber layer has a compressive stress).

Additionally or alternatively, in some embodiments, a capping layer may be formed to reduce optical reflection from the semiconductor absorber layers 2-210. In some cases, the semiconductor absorber layers 2-210 may have a significantly different index of refraction than adjacent layers, which may result in a significant amount of reflected radiation from the interface between the semiconductor absorber layer 2-210 and the adjacent layers. In this regard, one or more of the cover layers 2-220 may be formed as an anti-reflective coating to the semiconductor absorber layers 2-210 and reduce optical reflection at one or more wavelengths in a range of wavelengths. For example, the cover layer 2-220 may reduce reflection of emitted radiation and/or reflection of excitation radiation from the reaction chamber 1-230. For semiconductor absorber layers 2-210 formed of ZnTe and having adjacent silicon oxide layers, the reflection at 532nm and 572nm may be about 14% and 10%, respectively. These reflections can be reduced to below 1% by adding a 63nm thick silicon nitride capping layer 2-220. According to some embodiments, the oxide or nitride cap layer formed adjacent to the semiconductor absorber layer reduces optical reflection from the semiconductor absorber layer for visible wavelengths between 500nm and 750nm compared to the absence of the oxide or nitride cap layer. The thickness of the oxide or nitride cap layer may be selected to reduce optical reflection at the desired wavelength.

According to some embodiments, the semiconductor absorber layer 2-210 may be incorporated into a stack comprising one or more dielectric layers having different optical properties than the semiconductor absorber layer 2-210, either alone or in combination with one or more capping layers 2-220, for example, as shown in fig. 1-3. The thickness of the one or more dielectric layers, the semiconductor absorber layer 2-210 and the one or more cover layers 2-220 (if present) may be selected to provide optical interference of the excitation radiation and/or the emission radiation. Thus, the semiconductor absorber layers 2-210 and one or more dielectric layers may form a hybrid absorbing interference filter with a suppression ratio R of the individual semiconductor absorbers 1-235_rIn contrast, the hybrid absorption interference filter can further increase the suppression ratio R of the stack_r. In some cases, such a multilayer stack may include one or more semiconductor absorber layers 2-210 formed of polycrystalline or amorphous semiconductor material. In some cases, the multilayer stack may include one or more absorber layers formed of polycrystalline or amorphous materials that are not semiconductors.

The inventors have further recognized and appreciated that the emitted radiation can be transferred to longer wavelengths using the Dexter Energy Transfer (DET) and/or Foster Resonance Energy Transfer (FRET) processes. For example, there may be two fluorophores associated with the analyte or sample. The first of the two fluorophores can be excited more efficiently than the second fluorophore by the excitation radiation delivered to the reaction chamber. The second fluorophore may be attached with a chemical linker so that it is not far away from the first fluorophore (e.g., less than 10 nm). Thus, the emission energy from the first fluorophore can be transferred from the first fluorophore to the second fluorophore and excite the second fluorophore such that it emits radiation at a longer characteristic wavelength than the first fluorophore and is detected by the sensors 1-122. As one example, a first fluorophore may emit a characteristic wavelength in the yellow region of the spectrum and a second fluorophore may emit a characteristic wavelength that is red-shifted, e.g., a characteristic wavelength in the yellow-red or red region of the spectrum. In some cases, the energy transfer from the first fluorophore to the second fluorophore can be a non-radiative DET or FRET process. The energy transfer of the emitted radiation and the transfer to a longer characteristic wavelength results in a larger effective stokes shift than the stokes shift of a single fluorophore. This increased effective stokes shift can shift the emitted radiation from the band edge of the semiconductor absorber to a more distant location where the semiconductor absorber absorbs less of the emitted wavelength than the first fluorophore.

In general, it is desirable to use fluorophores with a large separation between the excitation and emission wavelengths. For a single electron transition in a fluorophore, this separation is referred to as the "stokes shift". In some embodiments, multiple fluorophores can be used in FRET or DET methods as described above to achieve greater separation between excitation and emission wavelengths. This large separation between excitation and emission wavelengths due to the use of multiple fluorophores is referred to herein as the "effective stokes shift".

Fig. 2-5 depict calculated transmission results for a multilayer semiconductor absorber as a function of wavelength for five different angles of incidence. The multilayer semiconductor absorber consisted of four layers of amorphous silicon, each about 85nm thick, separated by three layers of silicon oxide, each about 110nm thick. The multilayer semiconductor absorber is embedded in silicon oxide. The refractive index of amorphous silicon is about 4.3 at a wavelength of 532nm, the value of which depends on the wavelength of the radiation, while the refractive index of silicon oxide is about 1.5 at a wavelength of 532nm, the value of which also depends on the wavelength of the radiation incident on the semiconductor absorber. For this calculation, the excitation radiation has a characteristic wavelength of approximately 532nm, and the emission characteristic wavelength is shifted to a value in the range between 620nm and 690nm using two fluorophores as described above. Calculations indicate that suppression ratios greater than 1000 can be achieved using a multilayer semiconductor absorber.

The results depicted in fig. 2-5 also show that the rejection ratio remains the same or in some cases even higher for non-normal incidence angles. This behavior is different from the angle dependence of a multilayer dielectric bandpass filter, and the rejection ratio is significantly reduced for non-normal incidence angles. In an integrated device comprising a plurality of pixels, it may be advantageous to maintain a high rejection ratio at large angles of incidence. For example, a filter with a high rejection ratio at large angles of incidence may allow pixels to be packed more closely together because the filter may better block or reduce oblique radiation from neighboring pixels that would be detected by sensors 1-122 as crosstalk noise.

In some cases, just maintaining a high suppression of excitation radiation at larger non-normal angles of incidence may be sufficient to increase pixel density. For example, in fig. 2-5, excitation radiation with a characteristic wavelength of 532nm is gradually suppressed at non-normal angles up to 60 degrees or more. This behavior may improve the suppression of excitation radiation of neighboring pixels. In some embodiments, a semiconductor absorber that increases suppression of emitted radiation at large non-normal angles of incidence may be further beneficial. The results of fig. 2-5 show that the emitted radiation at 60 degrees is attenuated more than the emitted radiation at 35 degrees. This behavior may improve the suppression of emitted radiation from neighboring pixels. According to some embodiments, the center-to-center pixel pitch of the plurality of pixels in the integrated device may have a value in a range between 2 microns and 50 microns, although smaller or larger pitches are possible in some cases.

Another example of a multilayer semiconductor absorber filter 2-600 is depicted in fig. 2-6A. The semiconductor absorber filter 2-600 may include a plurality of semiconductor absorber layers 2-630 separated by a plurality of layers of dielectric material 2-620. In the example shown, the multilayer semiconductor absorber filter 2-600 includes seven layers of semiconductor absorbers 2-630 or films separated by six layers of dielectric material 2-620. The semiconductor absorber layer 2-630 may absorb significantly more radiation (e.g., at least twice as much radiation) than the dielectric material layer 2-620. By way of example, the semiconductor absorber 2-630 may be formed of nitrogen-doped amorphous silicon and the layer of dielectric material 2-620 may comprise an oxide, such as silicon dioxide. "doping" herein refers to adding impurities to adjust the optical properties (e.g., refractive index, extinction coefficient) of the absorber. The multilayer semiconductor absorber filter 2-600 may further be integrated in a stack of surrounding materials 2-610, 2-640 on the substrate. The surrounding material may be the same or different material as the dielectric material layers 2-620. In some embodiments, fewer or more layers of semiconductor absorbers 2-630 than are shown in figures 2-6A may be used.

Although the example filters depicted in fig. 2-6A include semiconductor absorbers, other materials may be used in other embodiments. For example, doped glass, oxide or nitride may be used as the absorber layer. In some cases, semiconductor absorbers have greater light absorption below a particular wavelength and may therefore be preferred for some applications. Some absorbing materials may have a sharp transition in light absorption near 530 nm. Amorphous materials can have a wide transition in their light absorption curve. Amorphous silicon is a semiconductor material with a wide transition in light absorption. It may be advantageous to adjust the optical properties (e.g., refractive index, extinction coefficient, absorption rate) by introducing nitrogen or other elements as dopants into the amorphous silicon or selected absorbing materials. In some cases, the resulting material forms an amorphous alloy of the absorber material and a dopant or dopant compound (e.g., amorphous silicon and silicon nitride). Although the alloying process is referred to herein as "doping," it should be understood that the dopant does not necessarily behave as a semiconductor dopant. In some embodiments, the electrical behavior of the resulting alloy may be characterized as a dielectric absorbing material rather than a semiconductor. For the multilayer absorber filter of this embodiment, the absorbing layer exhibits an optical absorption of at least twice that of the intermediate dielectric layer, and may further include a refractive index difference from the intermediate layer of more than ten percent or Δ n ≧ 0.1.

In many conventional multilayer dielectric filters, the layers in the filter stack are quarter-wave layers, and the same is used for each material throughout the stackThickness such that the stack has a very regular repeating structure (e.g. t)₁、t₂、t₁、t₂、t₁、t₂、t₁、t₂) Wherein t is₁Is the thickness of the first dielectric material in the stack and t2 is the thickness of the second dielectric material in the stack. For the multilayer semiconductor absorber filters 2-600, the inventors have found that layer thicknesses and non-uniform thicknesses other than a quarter wavelength can improve filter characteristics. For example, the semiconductor absorber layers 2-630 may all have the same thickness t_aAnd the layers 2-620 of dielectric material may have different thicknesses greater than a quarter wavelength. Improvements may also be obtained when the thickness of the absorbing layer is greater than a quarter wavelength rather than a multiple of a quarter wavelength. In some cases, there may be at least three or four layers of different thicknesses within the stack. E.g. thickness t₁May be different from the thickness t₂And both thicknesses may be different from thickness t₃As depicted in the illustrations of fig. 2-6A. In other cases, the thickness t of the semiconductor absorber 2-630_s1、t_s2、…t_s8And thickness t of dielectric material layer 2-620_d1、t_d2、…t_d8May vary within the stack as shown by the multilayer semiconductor absorber filters 2-700 of fig. 2-7. Furthermore, some layer thicknesses may not correspond to a quarter wavelength of radiation that the filter is designed to block or pass. The thickness of the quarter wavelength is determined within the layer in consideration of the refractive index of the layer. The thickness variation of the same material and/or different materials within the stack may be greater than 20% in some cases, greater than 50% in some cases, and still greater than 100% in some cases, but may be less than a factor of 10.

According to some embodiments, the thickness of the semiconductor absorber 2-630 may be between 20nm and 300nm in a multilayer semiconductor absorber filter. The thickness of the layer of dielectric material 2-620 may be between 40nm and 300 nm. In some cases, the semiconductor absorber 2-630 may be formed of doped or alloyed amorphous silicon or other semiconductor materials described above. One advantage of using amorphous silicon is that it can be deposited at a temperature low enough to be compatible with other CMOS processes, such as processes that form back-end metallization. In some embodiments, nitrogen may be used as a dopant or additive, although other dopants or additives (e.g., carbon, phosphorus, germanium, arsenic, etc.) may be used in some getters. For the case of nitrogen-doped amorphous silicon, the amount of nitrogen added during amorphous silicon deposition may be between 0 and 40 atomic percent. This range of doping levels can yield a range of refractive index values between 2.6 and 4.3 and a range of extinction coefficient values between 0.01 and 0.5. Other dopants, semiconductor materials, and doping ranges may be used in other embodiments to obtain different refractive index and extinction coefficient values for particular wavelength ranges (e.g., green, blue, or ultraviolet or infrared wavelengths).

Fig. 2-6B depict calculated transmission results for a multilayer semiconductor absorber 2-600, as shown in fig. 2-6A, as a function of five different incident angle wavelengths. The multi-layer semiconductor absorber consists of seven layers of nitrogen-doped amorphous silicon absorbers 2-630. For this example, each layer of semiconductor absorbers 2-630 is approximately 30nm thick. Thickness t of outermost layer of dielectric material 2-620₁Approximately 67 nm. The next layer of dielectric material 2-620 moving towards the center of the stack has a thickness of approximately 108 nm. The thickness t3 of the innermost layer of dielectric material 2-620 is approximately 95 nm. The multilayer semiconductor absorption filter 2-600 is embedded in silicon oxide. The refractive index of the doped amorphous silicon is about 3.6 at a wavelength of 532nm, the value of which depends on the wavelength of the radiation. The extinction coefficient k of the doped amorphous silicon is about 0.2 at a wavelength of 532nm and has wavelength dependence. The refractive index of silicon oxide is about 1.5 at a wavelength of 532nm, the value of which also depends on the wavelength of the radiation incident on the semiconductor absorber.

For the results shown in fig. 2-6B, the filter design was adapted for excitation radiation with a characteristic wavelength of about 532nm (indicated by the hatched bars on the left side of the figure). Furthermore, two fluorophores are used as described above to increase the effective stokes shift of the FRET and/or DET process and to shift the emission characteristic wavelength to a value in the range between 640nm and 700nm (indicated by the shaded area on the right in the figure). The results show that rejection ratios greater than 24000 can be obtained when the absorbing filter includes layers that are not quarter-wavelength thick. The results also show a very good angular dependence of the filter, maintaining a high rejection ratio for incident angles up to 60 degrees.

Further details of the angular dependence are shown in fig. 2-6C for the multilayer semiconductor absorber filters 2-600 described in connection with fig. 2-6B. The plots are plotted for s-polarized radiation of characteristic wavelength 532nm incident on the filter at different angles. The results for p-polarized radiation show a small angular tolerance. The top trace plots the reflectivity R of the incident radiation. The middle trace plots the absorption a of the incident radiation and the lower trace plots the transmission T of the incident radiation. The angular tolerance for s-polarized radiation is very good, up to about 80 degrees, which is not achievable with conventional multilayer dielectric filters. For example, the suppression ratio remains above 10000 for incident angles between 0 and 80 degrees. In some embodiments, the variation in the reflectivity of the filter may be less than 20% of its average over the same range of incident angles. In a stack comprising layers of non-uniform thickness, the inventors did not initially anticipate such a high rejection rate and such a wide angular tolerance.

It will be appreciated that the performance of the optical filter may differ depending on the materials surrounding the optical filter (e.g., above and below the optical filter when integrated into a substrate, as shown in fig. 1-3). For example, when integrated on a substrate, reflections from other materials on the substrate may change the reflection, absorption, and transmission characteristics of the filter, and these calculations are shown in fig. 2-6B and 2-6C.

Fig. 2-7 illustrate another example of a multilayer semiconductor absorber filter 2-700. The filter design includes thickness variations of both the semiconductor absorber layer 2-630 and the dielectric material layer 2-620. In an example embodiment, the thickness of the semiconductor absorber layers 2-630 is about 32nm, about 153nm, about 145nm, about 32nm, about 145nm, and about 133nm (from ts1 to ts8, respectively). In the embodied devices, the thickness may be exactly as listed or within ± 5nm of these values. The thickness of the layer of dielectric material 2-620 is (from td1 to td7, respectively) about 56nm, about 100nm, about 79nm, about 100nm, about 79nm and about 100 nm. In the embodied devices, the thickness may be exactly as listed or within ± 5nm of these values. The filter designs shown in fig. 2-7 may be suitable for applications using a single fluorophore (e.g., without using FRET or DET).

The multilayer absorber filter can be formed by sequential timed deposition of absorbing and dielectric materials. The deposition may be timed to achieve the desired thickness of each layer. A chemical vapor deposition process may be used. A preferred deposition method is Plasma Enhanced Chemical Vapor Deposition (PECVD). In some embodiments, the number of absorber layers deposited may be less than 20, in some embodiments less than 10, and in some embodiments also less than 5. According to some embodiments, the absorption layer may be located at a region in the integrated stack, the region comprising a portion of one or more electric field peaks within the stack for excitation radiation. In some cases, the absorbing layer may be remote from the electric field peak used to emit the radiation.

Although the semiconductor absorbers 1-235 are shown as planar layers in fig. 1-2, the present invention is not limited to only planar semiconductor absorbers. In some cases, and referring now to FIG. 3-1, a semiconductor absorber 3-135 can be formed on the first layer 3-110 to have a topographical structure. According to some embodiments, the height h of the topographic structure may be between 100nm and 2000 nm. In some cases, the height h may be between 1.5 and 3 times the thickness t of the semiconductor absorber. According to some embodiments, the width w of the depression 3-113 or the peak 3-114 in the topology may have any value between 50nm and 500 microns. As shown in fig. 3-1, a second layer 3-112 can be deposited on the semiconductor absorber to fill the topography.

The topography in the semiconductor absorber 3-135 may be included to relieve in-plane stress in the semiconductor absorber 3-135. In some cases, the semiconductor absorber material may accumulate in-plane stress due to the deposition process. Such stress, if severe enough, can cause the substrate to warp and, in some cases, can cause cracking and/or delamination of the semiconductor layers. The topography can allow stress to be relieved and prevent warping, cracking, and delamination. In some embodiments, there may be one or more topographical features in the region of the semiconductor absorber 3-135 between the reaction chamber 1-230 and the corresponding sensor 1-122. In some cases, there may be no topography between the reaction chamber 1-230 and the sensor 1-122, and the topography may be in adjacent areas within a pixel or between pixels. In some embodiments, the topographical features in the semiconductor absorbers 3-135 can be spaced apart by a distance greater than 500 micrometers (e.g., up to 1 millimeter or more), and in some cases, the topographical features can be located outside of the pixel area and sufficient to relieve stress in the pixel area.

In some cases, the topography in the semiconductor absorber 3-135 may provide additional improvements. For example, the topography may increase the overall absorption of the filter, as longer paths through the absorber will be presented to some incident radiation. In addition, the crystallinity of the deposited semiconductor absorber layer can be enhanced by morphology (e.g., by inducing or relieving film stress), resulting in steeper filter cut-off and better rejection ratio.

In some cases, the semiconductor absorber 3-135 including topography can be etched back after deposition to form one or more insulating vias 3-210 through the semiconductor absorber, as shown in FIG. 3-2. In this example, the vertical interconnects 2-160 may pass through the insulating vias 3-210 without electrically connecting to the semiconductor absorber 3-135. Within a pixel there may be one or more insulating vias 3-210 and vertical interconnects 2-160. The vertical interconnects may be connected to potential reference planes above and/or below other in-plane interconnects 2-170 or semiconductor absorbers 3-135. In some embodiments, filler material 3-230 may be added to fill the recessed regions in the semiconductor absorber 3-135. The filler material 3-230 may be the same or a different material as the second layer 3-112 formed above the remaining semiconductor absorber 3-135.

In some embodiments, there may be no vertical interconnects within a pixel. Instead, holes may be opened through the semiconductor absorbers 1-235, 3-135 and within the insulating vias 3-210 so that contact pads beneath the semiconductor absorbers 3-135 may be wire bonded. For example, the wire bonds may be located outside the pixel region. The holes for wire bonding can be opened by patterning a photoresist or hard mask and etching the semiconductor absorber in the exposed areas not covered by the photoresist or hard mask. The etched semiconductor absorber may or may not have a topographic structure prior to etching.

Fig. 3-3 depict another embodiment of a semiconductor absorber 3-135 formed with a topographical structure above the first layer 3-110. In this embodiment, the insulating vias 3-310 are formed only in the regions through which the vertical interconnects 2-160 pass. Unlike the structure shown in fig. 3-2, the adjacent regions may include features that are not interrupted in the semiconductor absorber 3-135. According to this embodiment, the second layer 3-312 may be formed over a region of the semiconductor absorber adjacent to the insulating via 3-310. The second layer 3-312 may be of the same material or a different material than the third layer 3-314 formed on the second layer 3-312. In an embodiment, first layer 3-110, second layer 3-312, and third layer 3-314 may comprise a transparent or translucent material as described above in connection with FIG. 1-1.

Structures associated with an exemplary method for forming a semiconductor absorber 3-135 having a topography and a single insulating via 3-310 are shown in fig. 3-4A through 3-4E. According to some embodiments, a first resist 3-410 may be deposited and patterned on the first layer 3-110 of transparent or translucent material. The first patterned resist 3-410 may be located where a single insulated via 3-310 is to be formed. In some embodiments, the first patterned resist 3-410 may be a soft resist, such as a polymer resist. According to some embodiments, a second resist 3-420 may be deposited and patterned on the first layer 3-310. Some of the second patterned resist 3-420 may remain over the first patterned resist 3-410 after exposure and development. The second patterned resist 3-420, which is located over the first patterned resist 3-410, may define the size and location of the insulating via 3-310 to be formed. According to some embodiments, the second patterned resist may be a hard resist, such as a nitride, oxide or metal resist layer. According to some embodiments, the second resist 3-420 exhibits etch selectivity over the first resist 3-410 and over the underlying first layer 3-110. The structure after patterning the first resist 3-410 and the second resist 3-420 may be as shown in fig. 3-4A.

In a subsequent step of the process, an etching step may be performed to etch away the areas of the first layer 3-110 not covered by the first patterned resist 3-410 and the second patterned resist 3-420. In some cases, a preliminary etch may be performed to etch away portions of the first patterned resist 3-410 not covered by the second patterned resist 3-420. As shown in fig. 3-4B, the etching may result in an etch chamber 3-430 having a chamber wall 3-435. After etching, some of the top surface 3-437 of the first layer 3-110 is not etched.

In a subsequent process step, the second patterned resist 3-420 is removed, leaving the first patterned resist 3-410. A second etching step may then be performed to further etch the first layer 3-110 as shown in fig. 3-4C. In this second etch, the top surfaces of the etch cavities 3-430 and the first layers 3-437 are both etched back, without etching the top surfaces of the pillars 3-440 below the first patterned resist 3-410. The resulting pillars 3-440 after the second etch are completed may be higher in profile than the surrounding.

After the topography is etched into the first layer 3-110, the first patterned resist 3-410 can be removed from the first layer 3-110 and the surface of the layer cleaned in preparation for deposition of the semiconductor absorber 3-135. One or more layers of semiconductor absorber 3-135 may then be deposited over the topography of the first layer 3-110. In some cases, the deposition may be conformal such that the conformal layer has a uniform thickness (within 10%) over the horizontal and sloped surfaces of the first layers 3-110, as measured perpendicular to the contact surface. For example, the semiconductor absorbers 3-135 may be deposited by a plasma deposition process or an atomic layer deposition process or any other suitable deposition process. Other example deposition processes that may be used to deposit one or more layers of the semiconductor absorber 3-135 include, but are not limited to, sputtering, molecular beam epitaxy, pulsed laser deposition, confined space sublimation, electron beam evaporation, vapor deposition, chemical vapor deposition, plasma enhanced chemical vapor deposition, electrodeposition, and metal organic chemical vapor deposition. In some embodiments where the semiconductor absorber 1-235 is planar, the semiconductor absorber may be deposited by wafer transfer. In some embodiments where the semiconductor absorber 3-135 has a topography, the semiconductor absorber and one or more adjacent layers may be deposited by wafer transfer. In some cases, the semiconductor absorber layers 3-135 may be annealed after deposition to improve the crystallinity of the semiconductor absorber layers. Subsequently, a second layer 3-312 may be deposited over the semiconductor absorber 3-135, resulting in the structure shown in FIGS. 3-4D. The thickness of the second layer 3312 may be greater than the variation in the topography h of the semiconductor absorber 3-135 and the first layer 3-110. As described above, the second layer 3-312 may be of the same type as the first layer 3-110, for example, a translucent material such as an oxide or nitride.

Chemical Mechanical Polishing (CMP) may then be used to planarize the structure as shown in fig. 3-4E. In this step, polishing may remove a portion of the second layer 3-312 and the highest features of the semiconductor absorber 3-135 to open the insulating via 3-310, as shown in fig. 3-4E. Additional photolithography steps may be used to form conductive vertical interconnects through the insulating vias. A third layer 3-314 may be deposited over the second layer 3-312 to form the structure shown in fig. 3-3. The first resist 3-410 is not used in order to obtain the structure shown in fig. 3-2.

Exemplary structures 4-100 of disposable chips are shown in FIG. 4, according to some embodiments. The disposable chip structure 4-100 may include a bio-optoelectronic chip 4-110 having a semiconductor substrate 4-105 and including a plurality of pixels 4-140 formed on the substrate. Each pixel 4-140 may have the structure and embodiment of a semiconductor absorber as described above in connection with fig. 1-1 through 3-4E. In an embodiment, row and column waveguides 4-115 providing excitation radiation to a row or column of pixels 4-140 may be present. The excitation radiation may be coupled into the waveguide, for example, through optical ports 4-150. In some embodiments, a grating coupler may be formed on the surface of the bio-optoelectronic chip 4-110 to couple excitation radiation from the focused beam into one or more receiving waveguides connected to the plurality of waveguides 4-115.

The disposable chip structure 4-100 may further include a wall 4-120 formed around the pixel region on the bio-photoelectric chip 4-110. The wall 4-120 may be part of a plastic or ceramic housing that supports the bio-optoelectronic chip 4-110. The walls 4-120 may form at least one receptacle 4-130 in which at least one sample may be placed and in direct contact with the reaction chamber 1-130 on the surface of the biophotonic chip 4-110. For example, the walls 4-120 may prevent the sample in the reservoir 4-130 from flowing into the area containing the optical port 4-150 and the grating coupler. In some embodiments, the disposable chip structure 4-100 may also include electrical contacts on the outer surface of the disposable chip and interconnects within the package so that electrical connections can be made between circuitry on the bio-optoelectronic chip 4-110 and circuitry in the instrument in which the disposable chip is mounted.

In some embodiments, the semiconductor absorber 2-135 may be integrated at each pixel in a disposable chip structure as shown in FIG. 4, however the semiconductor absorber 2-135 is not limited to being integrated only in the components shown and described herein. The semiconductor absorber of this embodiment may also be integrated into other semiconductor devices that may not include an optical waveguide and/or may not include a reaction chamber. For example, the semiconductor absorber of the present embodiments may be integrated into an optical sensor for which it may be desirable to suppress one or more wavelengths over a range. In some embodiments, the semiconductor absorber of the present embodiments can be incorporated into a CCD and/or CMOS imaging array. For example, a semiconductor absorber can be formed over a photodiode at one or more pixels in an imaging array such that the absorber filters radiation received by the photodiode. Such an imaging array may be used, for example, for fluorescence microscopy, in which excitation radiation is preferentially attenuated by a semiconductor absorber. Such imaging arrays may be used in night vision goggles where visible radiation is preferentially attenuated while infrared radiation is passed to prevent bright visible light sources (such as LEDs) from blinding the goggles.

Suppression ratio R of semiconductor absorbers 2-135 integrated into an assembly according to some embodiments_rMay have a value between 10 and 100. In some embodiments, the suppression ratio R_rMay have a value between 100 and 500. In some cases, the suppression ratio R_rMay have a value between 500 and 1000. In some implementations, the suppression ratio R_rMay have a value between 1000 and 2000. In some embodiments, the suppression ratio R_rMay have a range of between 2000 and 5000A value in between. An advantage of the semiconductor absorber is that by selecting the thickness of the semiconductor absorption layer, the suppression ratio R can be selected more easily than in multilayer filters_rThis can be seen in fig. 2-3. Another advantage of semiconductor absorbers is that scattered excitation radiation can be absorbed instead of reflected (as is the case with multilayer filters), thereby reducing cross-talk between pixels. Another advantage is that the effective thickness of the semiconductor absorber can be significantly greater than the actual thickness of the semiconductor absorber layer for light rays incident at angles away from the normal to the surface of the semiconductor absorber layer. Furthermore, as described above, due to micro-machining tolerances, the performance of the semiconductor absorber is much less sensitive to thickness variations of the semiconductor absorber layer than the performance of the multilayer filter depends on the thicknesses of the constituent layers.

Exemplary bioanalytical applications

An example of a bioanalytical application is described in which integrated semiconductor absorbers 1-135 may be used to improve the detection of radiation emitted from reaction chambers on disposable chips for advanced analytical instruments. For example, the semiconductor absorber 1-135 can significantly reduce excitation radiation incident on the sensor 1-122, thereby significantly reducing detected background noise that might otherwise overwhelm radiation emitted from the reaction chamber 1-130. In some cases, as explained above in connection with fig. 2-2, the suppression of excitation radiation may be 800 times the attenuation of emission radiation, resulting in a significant improvement in the signal-to-noise ratio from sensors 1-122.

When installed in the socket of the instrument, the disposable chip can be in optical and electronic communication with the optical and electronic equipment within the advanced analytical instrument. The instrument may include hardware for an external interface so that data from the chip may be transferred to an external network. In embodiments, the term "optical" may refer to ultraviolet, visible, near-infrared, and short wavelength infrared bands. Although various types of analysis can be performed on various samples, the following explanation describes gene sequencing. However, the present invention is not limited to an apparatus configured for gene sequencing.

In summary, referring to fig. 5-1A, a portable advanced analysis instrument 5-100 may include one or more pulsed light sources 5-108 mounted as replaceable modules within the instrument 5-100 or otherwise coupled to the instrument 5-100. The portable analytical instrument 5-100 may include a light coupling system 5-115 and an analysis system 5-160. The optical coupling system 5-115 may include some combination of optical components (e.g., may not include, may include, one or more of lenses, mirrors, filters, attenuators, beam steering components, beam shaping components) and is configured to operate on and/or couple the output optical pulses 5-122 from the pulsed optical source 5-108 to the analysis system 5-160. The analysis system 5-160 may include a plurality of components arranged to direct light pulses to at least one reaction chamber for sample analysis, receive one or more optical signals (e.g., fluorescence, backscatter radiation) from the at least one reaction chamber, and generate one or more electrical signals representative of the received optical signals. In some embodiments, the analysis system 5-160 may include one or more photodetectors and may also include signal processing electronics (e.g., one or more microcontrollers, one or more field programmable gate arrays, one or more microprocessors, one or more digital signal processors, logic gates, etc.) configured to process electrical signals from the photodetectors. The analysis system 5-160 may also include data transmission hardware configured to transmit data to and receive data from external devices (e.g., one or more external devices on a network to which the instrument 5-100 may be connected via one or more data communication links). In some embodiments, the analysis system 5-160 may be configured to receive a bio-optoelectronic chip 5-140, which holds one or more samples to be analyzed.

Fig. 5-1B depicts a more detailed example of a portable analytical instrument 5-100 including a compact pulsed light source 5-108. In this example, pulsed light source 5-108 comprises a compact passive mode-locked laser module 5-110. The passive mode-locked laser can autonomously generate optical pulses without applying an external pulse signal. In some embodiments, the module may be mounted to an instrument chassis or frame 5-102 and may be located inside the housing of the instrument. According to some embodiments, pulsed light sources 5-108 may include additional components that may be used to operate the light sources and operate on the output beams from light sources 5-108. The mode-locked lasers 5-110 may include elements (e.g., saturable absorber, acousto-optic modulator, kerr lens) in or coupled to the laser cavity that cause phase locking of the longitudinal frequency mode of the laser. The laser cavity may be defined in part by end mirrors 5-111, 5-119. This locking of the frequency modes results in pulsed operation of the laser (e.g., intra-cavity pulses 5-120 bounce back and forth between the end-of-cavity mirrors) and produces a stream of output optical pulses 5-122 from the partially launched end-of-cavity mirror 5-111.

In some cases, the analytical instrument 5-100 is configured to receive a removable, packaged, bio-optoelectronic or optoelectronic chip 5-140 (also referred to as a "disposable chip"). The disposable chip may comprise a bio-optoelectronic chip 4-110, as shown in fig. 4, comprising a plurality of reaction chambers, an integrated optical assembly arranged to transfer optical excitation energy to the reaction chambers, and an integrated photodetector arranged to detect fluorescent emissions from the reaction chambers. In some embodiments, the chip 5-140 may be disposable after a single use, while in other embodiments, the chip 5-140 may be reused two or more times. When the chip 5-140 is received by the instrument 5-100, it may be in electro-optical communication with the pulsed light source 5-108 and the devices in the analysis system 5-160. For example, electrical communication may be through electrical contacts on the chip package.

In some embodiments and referring to fig. 5-1B, the disposable chips 5-140 may be mounted (e.g., connected by a socket) on an electronic circuit board 5-130, such as a Printed Circuit Board (PCB) that may include additional instrumentation electronics. For example, the PCB 5-130 may include circuitry configured to provide power, one or more clock signals, and control signals to the chip 5-140, as well as signal processing circuitry configured to receive signals representative of fluorescent emissions detected from the reaction chamber. The data returned from the chips 5-140 may be partially or fully processed by the electronics on the instruments 5-100, although in some embodiments the data may be transmitted over a network connection to one or more remote data processors. The PCB 5-130 may also include circuitry configured to receive a feedback signal from the chip related to the optical coupling and power level of the optical pulses 5-122 coupled into the waveguide of the chip 5-140. A feedback signal may be provided to one or both of the pulsed light source 5-108 and the optical system 5-115 to control one or more parameters of the output beam of the light pulses 5-122. In some cases, the PCB 5-130 may provide or route power to the pulsed light source 5-108 to operate the light source and associated circuitry in the light source 5-108.

According to some embodiments, pulsed light source 5-108 includes a compact mode-locked laser module 5-110. The mode-locked laser may include a gain medium 5-105 (which may be a solid state material in some embodiments), an output coupler 5-111, and a laser cavity end mirror 5-119. The optical cavity of the mode-locked laser may be confined by an output coupler 5-111 and an end mirror 5-119. The optical axis 5-125 of the laser cavity may have one or more folds (turns) to increase the length of the laser cavity and provide a desired pulse repetition rate. The pulse repetition rate is determined by the length of the laser cavity (e.g., the time for a light pulse to round trip within the laser cavity).

In some embodiments, additional optical elements (not shown in fig. 5-1B) may be in the laser cavity for beam shaping, wavelength selection, and/or pulse formation. In some cases, end mirrors 5-119 include Saturable Absorbing Mirrors (SAMs) that cause passive mode-locking of longitudinal cavity modes and result in pulsed operation of the mode-locked laser. The mode-locked laser module 5-110 may also include a pump source (e.g., a laser diode, not shown in fig. 5-1B) for exciting the gain medium 5-105. More details of Mode-Locked Laser modules 5-110 may be found in U.S. patent application 15/844,469 entitled "Compact Mode-Locked Laser Module" filed on 12, 15, 2017, which is incorporated herein by reference.

When laser 5-110 is mode-locked, intracavity pulse 5-120 may cycle between end mirror 5-119 and output coupler 5-111, and a portion of the intracavity pulse may be transmitted as output pulse 5-122 through output coupler 5-111. Thus, when the intra-cavity pulse 5-120 is at output coupler 5-111 and end mirror 5-119 in the laser cavity.

Fig. 5-2 depicts the temporal intensity distribution of output pulses 5-122, although the illustration is not to scale.In some embodiments, the peak intensity values of the transmit pulses may be approximately equal, and the profile may have a gaussian time profile, but such as sech²Other profiles of the profile are also possible. In some cases, the pulses may not have a symmetrical temporal distribution and may have other temporal shapes. The duration of each pulse may be characterized by a Full Width Half Maximum (FWHM) value, as shown in fig. 5-2. According to some embodiments of a mode-locked laser, the ultrashort optical pulses may have a FWHM value of less than 100 picoseconds (ps). In some cases, the FWHM value may be between about 5ps and about 30 ps.

The output pulses 5-122 may be separated by regular intervals T. For example, T may be determined by the round trip time between the output coupler 5-111 and the cavity end mirror 5-119. According to some embodiments, the pulse separation interval T may be between about 1ns and about 30 ns. In some cases, the pulse separation interval T may be between about 5ns to about 20ns, corresponding to a laser cavity length (approximate length of the optical axis 5-125 within the laser cavity) of between about 0.7 meters to about 3 meters. In an embodiment, the pulse separation interval corresponds to the round trip time in the laser cavity, such that a cavity length of 3 meters (6 meters round trip distance) provides a pulse separation interval T of about 20 ns.

According to some embodiments, the desired pulse separation interval T and laser cavity length may be determined by a combination of the number of reaction chambers on the chip 5-140, the fluorescence emission characteristics, and the speed of the data processing circuitry used to read data from the chip 5-140. In embodiments, different fluorophores can be distinguished by their different fluorescence decay rates or characteristic lifetimes. Therefore, there needs to be enough pulse separation intervals T to collect enough statistics of the selected fluorophores to distinguish them from different decay rates. Furthermore, if the pulse separation interval T is too short, the data processing circuitry cannot keep up with the large amount of data collected by a large number of reaction chambers. A pulse separation interval T between about 5ns and about 20ns is suitable for fluorophores with decay rates up to about 2ns and for processing data from between about 60000 and 10000000 reaction chambers.

According to some embodiments, the beam steering module 5-150 may receive output pulses from the pulsed light source 5-108 and be configured to adjust at least the position and angle of incidence of the optical pulses on an optical coupler (e.g., grating coupler) of the chip 5-140. In some cases, the output pulses 5-122 from the pulsed light sources 5-108 may be operated by the beam control modules 5-150 to additionally or alternatively change the beam shape and/or beam rotation of the optical couplers on the chips 5-140. In some embodiments, beam steering modules 5-150 may further provide focusing and/or polarization adjustment of the output pulsed light beam onto the optical coupler. One example of a beam steering module is described in U.S. patent application 15/161,088 entitled "Pulsed Laser and Bioanalytical System" filed on 5/20/2016, which is incorporated herein by reference. Another example of a Beam Steering module is described in separate U.S. patent application 62/435,679 entitled "Compact Beam Shaping and Steering Assembly," filed on 12, 16, 2016, which is hereby incorporated by reference.

Referring to fig. 5-3, for example, output pulses 5-122 from a pulsed light source may be coupled into one or more optical waveguides 5-312 on a disposable biophotonic chip 5-140. In some embodiments, the optical pulses may be coupled to one or more waveguides through grating couplers 5-310, but in some embodiments ends coupled to one or more optical waveguides on chip 5-140 may be used. According to some embodiments, the quad detector 5-320 may be located on a semiconductor substrate 5-305 (e.g., a silicon substrate) to help align the optical pulse beam 5-122 with the grating coupler 5-310. One or more waveguides 5-312 and reaction chambers or chambers 5-330 may be integrated on the same semiconductor substrate with a dielectric layer (e.g., a silicon dioxide layer) interposed between the substrate, waveguides, reaction chambers and photodetectors 5-322.

Each waveguide 5-312 may include a tapered section 5-315 below the reaction chamber 5-330 to equalize the optical power coupled into the reaction chamber along the waveguide. The reduced taper can force more light energy out of the core of the waveguide, increasing coupling with the reaction chamber and compensating for optical losses along the waveguide, including losses of radiation coupling into the reaction chamber. A second grating coupler 5-317 may be located at the end of each waveguide to guide the optical energy to the integrated photodiode 5-324. For example, an integrated photodiode may detect the amount of power coupled along the waveguide and provide the detected signal to a feedback circuit that controls the beam steering modules 5-150.

Reaction chamber 5-330 or reaction chamber 5-330 may be aligned with the tapered portion 5-315 of the waveguide and recessed into basin 5-340. For each reaction chamber 5-330, a photodetector 5-322 may be disposed on the semiconductor substrate 5-305. In some embodiments, a semiconductor absorber (shown in fig. 5-5 as filters 5-530) may be located between the waveguide and the photodetector 5-322 at each pixel. A metallic coating and/or a multi-layer coating 5-350 can be formed around the reaction chamber and over the waveguide to prevent photo-excitation of fluorophores that are not in the reaction chamber (e.g., dispersed in a solution over the reaction chamber). The metallic coating and/or multi-layer coating 5-350 may be raised above the edge of the basin 5-340 to reduce the absorption loss of optical energy in the waveguides 5-312 at the input and output ends of each waveguide.

The chips 5-140 may have multiple rows of waveguides, reaction chambers, and time-binning photodetectors thereon. For example, in some embodiments, there may be 128 rows, each row having 512 reaction chambers, for a total of 65536 reaction chambers. Other embodiments may include fewer or more reaction chambers, and may include other layout configurations. The optical power from the pulsed optical source 5-108 may be distributed to the plurality of waveguides 5-312 by one or more star couplers or multimode interference couplers, or by any other means located between the optical coupler 5-310 and the chip 5-140.

Fig. 5-4 shows the coupling of light energy from the light pulse 5-122 in the tapered portion of the waveguide 5-315 to the reaction chamber 5-330. The figure is generated from an electromagnetic field simulation of light waves, which takes into account the waveguide dimensions, the reaction chamber dimensions, the optical properties of the different materials and the distance of the tapered part of the waveguide 5-315 from the reaction chamber 5-330. For example, the waveguide may be formed of silicon nitride in a surrounding medium 5-410 of silicon dioxide. The waveguide, surrounding medium and reaction chamber can be formed by micromachining processes described in U.S. patent application 14/821,688 entitled "Integrated Device for binding, Detecting and Analyzing Molecules," filed on 8/7/2015. According to some embodiments, the evanescent optical field 5-420 couples the optical energy transmitted by the waveguide into the reaction chamber 5-330.

Non-limiting examples of biological reactions occurring in reaction chambers 5-330 are depicted in FIGS. 5-5. This example describes the sequential incorporation of nucleotides or nucleotide analogs into a growing strand that is complementary to a target nucleic acid. Sequential incorporation can be performed in reaction chambers 5-330 and can be detected by advanced analytical instrumentation to sequence the DNA. The reaction chamber may have a depth of between about 150nm and about 250nm and a diameter of between about 80nm and about 160 nm. Metallization layers 5-540 (e.g., metallization for a reference potential) may be patterned over the photodetectors 5-322 to provide apertures or apertures to block stray radiation from other unwanted radiation sources in adjacent reaction chambers. According to some embodiments, polymerase 5-520 may be located within reaction chamber 5-330 (e.g., attached to the bottom of the reaction chamber). The polymerase can take up the target nucleic acid 5-510 (e.g., a portion of a nucleic acid derived from DNA) and sequence the growing strand of complementary nucleic acid to produce a growing strand of DNA 5-512. Nucleotides or nucleotide analogs labeled with different fluorophores can be dispersed in solution above and within the reaction chamber.

When the labeled nucleotide or nucleotide analog 5-610 is incorporated into the growing strand of complementary nucleic acid, as shown in FIGS. 5-6, one or more attached fluorophores 5-630 can be repeatedly excited by pulses of optical energy coupled from the waveguide 5-315 to the reaction chamber 5-330. In some embodiments, one or more fluorophores 5-630 can be attached to one or more nucleotides or nucleotide analogs 5-610 through any suitable linker 5-620. The merge event may last for a period of up to about 100 milliseconds. During this time, for example, the fluorescence emission pulse generated by the pulsed excitation of the fluorophore from the mode-locked laser can be detected with the time-binning photodetector 5-322. In some embodiments, there may be one or more additional integrated electronics 5-323 at each pixel for signal processing (e.g., amplification, readout, routing, signal pre-processing, etc.). According to some embodiments, each pixel may include at least one filter 5-530 (e.g., a semiconductor absorber) that passes fluorescent emissions and reduces transmission of radiation from the excitation pulse. Some embodiments may not use filters 5-530. By linking fluorophores with different emission characteristics (e.g., fluorescence decay rate, intensity, fluorescence wavelength) to different nucleotides (A, C, G, T), different emission signatures are detected and distinguished when the DNA strands 5-512 comprise nucleic acids, and the genetic sequence of the growing DNA strand can be determined.

According to some embodiments, an advanced analytical instrument 5-100 configured to analyze a sample based on fluorescence emission characteristics may detect differences in fluorescence lifetime and/or intensity between different fluorescent molecules, and/or differences in lifetime and/or intensity between the same fluorescent molecules in different environments. By way of illustration, FIGS. 5-7 plot two different fluorescence emission probability curves (A and B), which may represent, for example, fluorescence emissions from two different fluorescent molecules. With reference to curve A (dashed line), the probability p of fluorescence emission from a first molecule after excitation by a short or ultrashort light pulse_A(t) may decay over time as shown. In some cases, the reduction in photon emission probability over time may be performed using an exponential decay functionIs represented by the formula, wherein P_AoIs the initial emission probability, τ₁Is a time parameter associated with the first fluorescent molecule that characterizes the probability of emission decay. Tau is₁May be referred to as the "fluorescence lifetime", "emission lifetime" or "lifetime" of the first fluorescent molecule. In some cases, τ₁Can be changed by the local environment of the fluorescent molecule. Other fluorescent molecules may have different emission characteristics than that shown in curve a. For example, another fluorescent molecule may have a decay curve that is different from a single exponential decay, the lifetime of which may be characterized by a half-life value or some other metric.

The second fluorescent molecule may have an exponential decay curve p_B(t) but with a distinctly different lifetime τ₂As shown by curve B in fig. 5-7. In the example shown, the lifetime of the second fluorescent molecule of curve B is shorter than the lifetime of curve A, and the emission probability p after excitation of the second molecule_B(t) is higher than curve A. In some embodiments, the different fluorescent groupsThe lifetime or half-life value of the optical molecule ranges from about 0.1ns to about 20 ns.

Differences in fluorescence emission lifetimes may be used to distinguish between the presence or absence of different fluorescent molecules and/or to distinguish between different environments or conditions in which the fluorescent molecules are located. In some cases, discrimination of fluorescent molecules based on lifetime (rather than emission wavelength) may simplify various aspects of the analytical instrument 5-100. For example, wavelength identification optics (e.g., wavelength filters, dedicated detectors for each wavelength, dedicated pulsed light sources of different wavelengths, and/or diffractive optics) may be reduced or eliminated when discriminating fluorescent molecules based on lifetime. In some cases, a single pulsed light source operating at a single characteristic wavelength may be used to excite different fluorescent molecules that emit in the same wavelength region of the spectrum, but have measurably different lifetimes. An analytical system that uses a single pulsed light source to excite and identify different fluorescent molecules emitted in the same wavelength region, rather than multiple light sources operating at different wavelengths, is less complex to operate and maintain, more compact, and can be manufactured at lower cost.

Although analysis systems based on fluorescence lifetime analysis have certain advantages, the amount of information obtained by the analysis system and/or the accuracy of detection may be increased by allowing the use of additional detection techniques. For example, some analysis systems 5-160 may also be configured to identify one or more characteristics of the sample based on the fluorescence wavelength and/or fluorescence intensity.

Referring again to fig. 5-7, according to some embodiments, photodetectors configured to time bin fluorescent emission events after fluorescent molecule excitation may be used to distinguish between different fluorescence lifetimes. Temporal binning may occur during a single charge accumulation period of the photodetector. The charge accumulation period is the interval between readout events during which photogenerated carriers accumulate in the binning of the time-binning photodetector. The concept of determining fluorescence lifetime by time binning of emission events is graphically illustrated in fig. 5-8. At t₁Previous time t_eExcitation of fluorescent molecules or fluorescent molecules of the same type (e.g., of the type corresponding to curve B of FIGS. 5-7) by short or ultrashort light pulsesA set of children. For macromolecular ensembles, the emission intensity may have a time distribution similar to curve B, as shown in fig. 5-8.

However, for a single molecule or a small number of molecules, for this example, emission of fluorescence photons occurs according to the statistics of curve B in fig. 5-7. The time-binned photodetectors 5-322 may accumulate carriers generated from emission events into discrete time bins. Three bins are indicated in fig. 5-8, but fewer or more bins may be used in embodiments. The bin is the excitation time t relative to the fluorescent molecule_eResolved in time. For example, the first bin may accumulate at time t₁And t₂Carriers generated during the interval between, occurring at time t_eAfter the firing event. The second bin may accumulate at time t₂And t₃The third bin may accumulate carriers generated during the interval between, at time t₃And t₄Carriers generated during the interval therebetween. When summing a large number of emission events, the carriers accumulated in the time bins can approximate the decaying intensity curves shown in fig. 5-8, and the cell signals can be used to distinguish between different fluorescent molecules or different environments in which the fluorescent molecules are located.

Examples of time-Binning photodetectors 5-322 are described in U.S. patent application No. 14/821,656 entitled "Integrated Device for Temporal Binning of Received Photons" filed on 8/7/2015 and U.S. patent application No. 15/852,571 entitled "Integrated photon with Direct Binning Pixel" filed on 2/22/2017, the entire contents of which are incorporated herein by reference. For purposes of explanation, non-limiting embodiments of time-binning photodetectors are depicted in fig. 5-9. The single time-binned photodetector 5-322 may include a photon absorption/carrier generation region 5-902, a carrier discharge channel 5-906, and a plurality of carrier storage bins 5-908a, 5-908b, all formed on a semiconductor substrate. A carrier transport channel 5-907 may be connected between the photon absorption/carrier generation region 5-902 and the carrier storage bins 5-908a, 5-908 b. In the illustrated example, two carrier storage bins are shown, but there may be more or fewer. There may be one readout channel 5-910 connected to the carrier reservoir. The photon absorption/carrier generation regions 5-902, carrier discharge channels 5-906, carrier storage bins 5-908a, 5-908b and readout channels 5-910 may be formed by locally doping the semiconductor and/or forming adjacent insulating regions to provide photo-detectivity, confinement and transport of carriers. The time-binning photodetector 5-322 may further comprise a plurality of electrodes 5-920, 5-921, 5-922, 5-923, 5-924 formed on the substrate, the electrodes being configured to generate an electric field in the device for transporting charge carriers through the device.

In operation, a portion of the excitation pulse 5-122 from the pulsed light source 5-108 (e.g., a mode-locked laser) is transmitted to the reaction chamber 5-330 through the time-binning photodetector 5-322. Initially, some of the excitation radiation photons 5-901 may reach the photon absorption/carrier generation region 5-902 and generate carriers (shown as light shaded circles). It is also possible that some fluorescence emitting photons 5-903 arrive together with excitation radiation photons 5-901 and generate corresponding carriers (shown as dark shaded circles). Initially, the number of carriers generated by the excitation radiation may be too large compared to the number of carriers generated by fluorescence emission. For example, the time interval can be determined by_e–t₁The initial carriers generated during l are gated to the carrier discharge channel 5-906 with the first electrode 5-920 to reject them.

Later, most of the fluorescence emitting photons 5-903 reach the photon absorption/carrier generation region 5-902 and generate carriers (represented by dark shaded circles) that provide a useful and detectable signal representative of the fluorescence emission from the reaction chamber 5-330. According to some detection methods, the second electrode 5-921 and the third electrode 5-923 may be gated at a later time to be at a later time (e.g., at a second time interval | t |)₁–t₂|) the generated carriers are directed to the first carrier storage 5-908 a. Subsequently, the fourth electrodes 5-922 and the fifth electrodes 5-924 may be at a later time (e.g., at a third time interval | t)₂–t₃During) is gated to direct carriers to the second carrier storage bin 5-908 b. After a large number of excitation pulses have been excited, the charge can continue in this wayTo accumulate a significant number of carriers and signal levels in each carrier bin 5-908a, 5-908 b. Later, the signal can be read out of the bin. In some embodiments, the time interval corresponding to each bin is on a sub-nanosecond timescale, although in some embodiments a longer timescale may be used (e.g., in embodiments where the fluorophore has a longer decay time).

The process of generating and binning the carriers after an excitation event (e.g., an excitation pulse from a pulsed light source) may occur once after a single excitation pulse or repeated multiple times after multiple excitation pulses during a single charge accumulation period of the time-binned photodetectors 5-322. After charge accumulation is complete, carriers can be read out of the storage bins through the readout channels 5-910. For example, an appropriate sequence of bias voltages can be applied to electrodes 5-923, 5-924 and at least to electrodes 5-940 to remove carriers from memory bins 5-908a, 5-908 b. The charge accumulation and readout processes may occur in massively parallel operations on chips 5-140, producing data frames.

Although the examples described in connection with fig. 5-9 include multiple charge stores 5-908a, 5-908b, in some cases a single charge store may be used instead. For example, only bin 1 may be present in the time-binned photodetectors 5-322. In this case, the individual bins 5-908a may operate in a variable time-gated manner to see different time intervals after different firing events. For example, after a pulse in the first series of excitation pulses, the electrodes of memory bin 5-908a can be gated to collect data during a first time interval (e.g., at a second time interval | t)₁–t₂I period), and the accumulated signal may be read out after a first predetermined number of pulses. Following a pulse in a subsequent series of excitation pulses for the same reaction chamber, the same electrode of storage bin 5-908a can be gated to collect data during a different interval (e.g., at a third time interval | t)₂–t₃I period), and the accumulated signal may be read out after a second predetermined number of pulses. In a similar manner at later intervals if desiredCarriers are collected. In this way, signal levels corresponding to fluorescent emissions during different time periods after the excitation pulse reaches the reaction chamber can be generated using a single carrier reservoir.

Regardless of how the charge accumulation is performed at different time intervals after excitation, for example, the read-out signal may provide a histogram representing the decay characteristic of the fluorescence emission. 5-10A and 5-10B illustrate an exemplary process in which two charge storage bins are used to obtain fluorescent emissions from the reaction chamber. The bins of the histogram may indicate the number of photons detected in each time interval after excitation of the fluorophore in the reaction chamber 5-330. In some embodiments, as depicted in fig. 5-10A, the signals for the bins will be accumulated after a large number of excitation pulses. The excitation pulses may be at times T separated by pulse interval times T_e1、t_e2、t_e3、…t_eNAnd (c) occurs. In some cases, for a single event observed in the reaction chamber (e.g., a single nucleotide incorporation event in a DNA assay), during the accumulation of a signal in the electronic reservoir, 10 can be applied to the reaction chamber⁵To 10⁷Excitation pulses 5-122 (or portions thereof). In some embodiments, one bin (bin 0) may be configured to detect the amplitude of the excitation energy delivered with each light pulse, and may be used as a reference signal (e.g., to normalize the data). In other cases, the excitation pulse amplitude may be stable, determined one or more times during signal acquisition, and not determined after each excitation pulse, such that no bin0 signal acquisition follows each excitation pulse. In this case, carriers generated by the excitation pulse may be rejected and dumped from photon absorption/carrier generation region 5-902, as described above in connection with fig. 5-9.

In some embodiments, as shown in fig. 5-10A, only a single photon may be emitted from the fluorophore after the excitation event. At time t_e1After the first firing event of (c), at time t_f1The emitted photons may occur within a first time interval (e.g., at time t)₁And t₂In between) so that the resulting electronic signals accumulate in the first electronic storage bin (contributing to the accumulation of the electronic signals in the first electronic storage bin)Bin 1). At time t_e2In a subsequent firing event of (a), at time t_f2The emitted photon may occur within a second time interval (e.g., at time t)₂And t₃In between) the resulting electronic signal contributes to bin 2. At time t_e3May occur within a first time interval, at a time t_f3And (4) transmitting.

In some embodiments, there may be no emitted and/or detected fluorescence photons after each excitation pulse is received at the reaction chamber 5-330. In some cases, only one fluorescence photon may be detected in the reaction chamber per 10000 excitation pulses sent to the reaction chamber. One advantage of implementing mode-locked lasers 5-110 as pulsed excitation sources 5-108 is that mode-locked lasers can be at high pulse repetition rates (e.g., between 50MHz and 250 MHz). At such high pulse repetition rates, the number of excitation pulses in the 10 millisecond charge accumulation interval can reach 50000 to 250000, allowing accumulation of detectable signals.

After a number of excitation events and carrier accumulation, the carrier storage bins of the time-binned photodetectors 5-322 can be read out to provide multi-valued signals (e.g., two or more valued histograms, N-dimensional vectors, etc.) to the reaction chambers. The signal value for each bin may depend on the decay rate of the fluorophore. For example, and referring again to fig. 5-8, the ratio of signal in bin 1 to bin 2 will be higher for fluorophores with attenuation curve B as compared to fluorophores with attenuation curve a. The values from the bins can be analyzed and compared to calibration values and/or to each other to determine the particular fluorophores present. For example, for sequencing applications, recognition of a fluorophore can determine the nucleotide or nucleotide analog incorporated into the growing DNA strand. For other applications, identifying the fluorophore may determine the identity of the molecule or sample of interest, which may be attached to or labeled with the fluorophore.

To further aid in understanding the signal analysis, the accumulated multi-bin values may be plotted as a histogram, for example as shown in fig. 5-10B, or may be recorded as a vector or location in an N-dimensional space. Calibration runs can be performed separately to obtain calibration values for multivalued signals (e.g., calibration histograms) of four different fluorophores attached to four nucleotides or nucleotide analogs. For example, the calibration histogram can be as shown in FIGS. 5-11A (fluorescent tag associated with T nucleotide), 5-11B (fluorescent tag associated with A nucleotide), 5-11C (fluorescent tag associated with C nucleotide), and 5-11D (fluorescent tag associated with G nucleotide). The identity "T" of the nucleotide or nucleotide analog incorporated into the growing strand of DNA can be determined by comparing the measured multi-valued signal (corresponding to the histograms of FIGS. 5-10B) with the calibration multi-valued signal (FIGS. 5-11A).

In some embodiments, fluorescence intensity may additionally or alternatively be used to distinguish between different fluorophores. For example, some fluorophores may emit at significantly different intensities or have significant differences in their probability of excitation (e.g., differences of at least about 35%), even though their decay rates may be similar. By referencing the binned signal (bin 5-3) with the measured excitation energy and/or other acquired signals, different fluorophores can be distinguished according to intensity level.

In some embodiments, different numbers of fluorophores of the same type can be attached to different nucleotides or nucleotide analogs, such that the nucleotides can be identified based on fluorophore intensity. For example, two fluorophores can be attached to a first nucleotide (e.g., "C") or nucleotide analog, and four or more fluorophores can be attached to a second nucleotide (e.g., "T") or nucleotide analog. Different nucleotides may have different excitation and fluorophore emission probabilities due to the different number of fluorophores. For example, there may be more emission events for a "T" nucleotide or nucleotide analog during the signal accumulation interval, and thus the apparent intensity of the bin is significantly higher than for a "C" nucleotide or nucleotide analog.

Distinguishing between nucleotides or any other biological or chemical sample based on fluorophore decay rate and/or fluorophore intensity can simplify the optical excitation and detection system in the analytical instrument 5-100. For example, optical excitation may be performed with a single wavelength source (e.g., a source that produces one characteristic wavelength rather than multiple sources or sources operating at multiple different characteristic wavelengths). In addition, wavelength discrimination optics and filters may not be required in the detection system to distinguish between fluorophores of different wavelengths. In addition, a single photodetector may be used for each reaction chamber to detect emissions from different fluorophores.

The phrase "characteristic wavelength" or "wavelength" is used to refer to a center or dominant wavelength within a limited bandwidth of radiation (e.g., a center or peak wavelength within a 20nm bandwidth of pulsed light source output). In some cases, "characteristic wavelength" or "wavelength" may be used to refer to a peak wavelength within the total bandwidth of radiation output by the source.

Fluorophores with emission wavelengths in the range of about 560nm to about 900nm can provide a sufficient amount of fluorescence to be detected by a time-binned photodetector (which can be fabricated on silicon using CMOS processes). These fluorophores can be attached to a biomolecule of interest, such as a nucleotide or nucleotide analog for gene sequencing applications. Fluorescence emission in this wavelength range can be detected with higher responsivity in silicon-based photodetectors than for longer wavelengths. In addition, fluorophores and associated linkers in this wavelength range may not interfere with the incorporation of nucleotides or nucleotide analogs into the growing DNA strand. In some embodiments, fluorophores having emission wavelengths in the range between about 560nm and about 660nm can be optically excited with a single wavelength source. An exemplary fluorophore in this range is Alexa Fluor 647, available from Thermo Fisher Scientific Inc. of Waltham, Mass. Excitation energy of shorter wavelengths (e.g., between about 500nm and about 650 nm) can be used to excite fluorophores that emit at wavelengths between about 560nm and about 900 nm. In some embodiments, the time-binning photodetector may effectively detect longer wavelength emissions from the reaction chamber, for example, by incorporating other materials (e.g., Ge) into the active region of the photodetector. .

Embodiments of the absorption filter and related methods are possible in various configurations as described further below. Exemplary device configurations include combinations of configurations (1) to (8) described below.

(1) A multilayer absorber filter comprising: a plurality of semiconductor absorber layers, such as semiconductor absorbers; and a plurality of dielectric material layers separating the plurality of semiconductor absorber layers to form a multilayer stack, wherein there are at least three different layer thicknesses within the multilayer stack. The absorber may be a semiconductor absorber.

(2) The filter of configuration (1), wherein the plurality of layers of dielectric material comprise at least two different thicknesses.

(3) The filter of configurations 1 or 2, wherein the plurality of absorber layers comprise at least two different thicknesses.

(4) The filter according to any of configurations (1) to (3), wherein there are at least four different layer thicknesses within the stack.

(5) The filter of any of configurations (1) through (4), wherein some thicknesses within the stack do not correspond to a quarter wavelength of radiation for which the filter is designed to block.

(6) The filter according to any of configurations (1) to (5), wherein at least two of the three different layer thicknesses differ by more than 50%.

(7) The optical filter of any of configurations (1) through (6), wherein the absorber layer comprises doped silicon.

(8) The optical filter according to any of configurations (1) to (7), wherein the thickness of the absorber layer is between 20nm and 300 nm.

The method of manufacturing the absorber filter may include various processes. An example method includes a combination of processes (9) to (13) described below. These processes may be used, at least in part, to manufacture an absorption filter having the above-described configuration.

(9) A method of forming a multilayer absorber filter, the method comprising: depositing a plurality of absorber layers; and depositing a plurality of layers of dielectric material separating the plurality of absorber layers to form a multi-layer stack, wherein at least three different layer thicknesses are deposited within the multi-layer stack.

(10) The method of (9), wherein depositing the plurality of absorber layers comprises depositing at least two different thicknesses of absorber that differ by at least 20%.

(11) The method of (9) or (10), wherein depositing the plurality of absorber layers comprises depositing an absorber layer that is not a quarter-wavelength thick.

(12) The method of any of (9) to (11), wherein depositing the plurality of layers of dielectric material comprises depositing at least two different thicknesses of dielectric material that differ by at least 20%.

(13) The method of any of (9) to (12), wherein depositing the plurality of layers of dielectric material comprises depositing a layer of dielectric material that is not a quarter wavelength thick.

Embodiments of the absorption filter may be included in a fluorescence detection assembly. Examples of such embodiments are listed in configurations (14) to (42).

(14) A fluorescence detection assembly, comprising: a substrate on which an optical detector is formed; a reaction chamber arranged to receive fluorescent molecules; an optical waveguide disposed between the optical probe and the reaction chamber; and an optical absorption filter comprising a semiconductor absorption layer disposed between the optical detector and the reaction chamber.

(15) The assembly according to configuration (14), further comprising: an iris layer having an opening between the reaction chamber and the optical detector; a first capping layer contacting a first side of the semiconductor absorber layer; a hole through the first capping layer and the semiconductor absorber layer; and a conductive interconnect extending through the aperture.

(16) The assembly of configuration (14) or (15), further comprising at least one dielectric layer disposed in a stack with the semiconductor absorber layer to form an absorptive interference filter, wherein a rejection ratio of the stack is greater than a rejection ratio of the semiconductor absorber layer alone.

(17) The assembly of any of configurations (14) through (16), further comprising at least one dielectric layer disposed in a stack with the semiconductor absorber layer and at least one additional semiconductor absorber layer to form an absorptive interference filter, wherein a rejection ratio of the stack is greater than a rejection ratio of the semiconductor absorber layer alone.

(18) The component of any of configurations (14) to (17), wherein the semiconductor absorption layer comprises a bandgap sufficient to absorb excitation radiation of a first wavelength directed to the reaction chamber and transmit emission radiation of a second wavelength from the reaction chamber.

(19) The assembly according to configuration (18), wherein the first wavelength corresponds to the green region of the visible electromagnetic spectrum and the second wavelength corresponds to the yellow or red region of the visible electromagnetic spectrum.

(20) The assembly of configuration (19), wherein the first wavelength is in a range from 515 nanometers (nm) to 540nm and the second wavelength is in a range from 620nm to 650 nm.

(21) The assembly of configuration (19), wherein the first wavelength is approximately 532 nanometers and the second wavelength is approximately 572 nanometers.

(22) The component according to configuration (18), wherein the bandgap is in a range of 2.2eV to 2.3 eV.

(23) The assembly of any of configurations (14) through (22), wherein the semiconductor absorber layer comprises a binary II-VI semiconductor.

(24) The assembly of configuration (23), wherein the semiconductor absorber layer is zinc telluride.

(25) The assembly of configuration (23), wherein the semiconductor absorber layer is alloyed with a third element from group II or group VI.

(26) The assembly of any of configurations (14) through (22), wherein the semiconductor absorber layer comprises a ternary III-V semiconductor.

(27) The assembly of configuration (26), wherein the semiconductor absorber layer is indium gallium nitride.

(28) The assembly of any of configurations (14) through (27), wherein the semiconductor absorber layer is amorphous.

(29) The assembly of any of configurations (14) to (27), wherein the semiconductor absorber layer is polycrystalline.

(30) The component of any of configurations (14) to (27), wherein the semiconductor absorber layer has an average grain size of not less than 20 nm.

(31) The assembly of any of configurations (14) through (27), wherein the semiconductor absorber layer is substantially monocrystalline.

(32) The assembly of any of configurations (14) through (31), further comprising a first capping layer contacting the semiconductor absorber layer.

(33) The assembly of configuration (32), wherein the capping layer prevents diffusion of elements from the semiconductor absorber layer.

(34) The assembly of configuration (32) or (33), wherein the capping layer comprises a refractory metal oxide having a thickness of 5nm to 200 nm.

(35) The assembly of configuration (34), wherein the refractory metal oxide comprises tantalum oxide, titanium oxide, or hafnium oxide.

(36) The assembly of any of configurations (32) through (35), wherein the capping layer reduces light reflection from the semiconductor absorber layer for visible wavelengths between 500nm and 750 nm.

(37) The assembly according to any of configurations (32) through (36), wherein the cover layer provides increased adhesion of a semiconductor absorber layer in the assembly.

(38) The assembly of any of configurations (32) through (37), wherein the cover layer reduces in-plane stress from a semiconductor absorber layer in the assembly.

(39) The assembly of any of configurations (14) through (38), further comprising an opening formed through the optical absorption filter and an electrically conductive connection extending through the opening.

(40) The assembly of any of configurations (14) through (39), wherein the optical absorption filter is formed over a non-planar topography.

(41) The assembly of configuration (40), further comprising an opening formed through the optical absorption filter and an electrically conductive connection extending through the opening.

(42) The assembly of configuration (41), wherein the opening is located at a planarized interface between the optical absorption filter and an adjacent layer, and the semiconductor absorption layer has been removed at the planarized interface.

Additional embodiments of the optical absorption filter are described in configurations (43) to (54).

(43) An optical absorption filter includes a semiconductor absorption layer formed over a non-planar topography on a substrate.

(44) The optical absorption filter according to configuration (43), wherein at least a portion of the semiconductor absorption layer has been removed by planarization.

(45) The optical absorption filter according to configuration (44), further comprising an electrically conductive connection extending through an opening formed by the removed portion of the semiconductor absorption layer.

(46) The optical absorption filter according to any one of configurations (43) to (45), wherein the semiconductor absorption layer has a uniform thickness within 10% and conforms to a non-planar topography.

(47) The optical absorption filter according to configuration (46), wherein portions of the semiconductor absorption layer extend substantially perpendicular to the plane of the substrate.

(48) An optical absorption filter includes a ternary III-V semiconductor absorption layer formed in an integrated device on the substrate.

(49) The optical absorption filter according to configuration (48), wherein the ternary group III-V semiconductor absorption layer is monocrystalline.

(50) The optical absorption filter according to configuration (48) or (49), wherein the ternary group III-V semiconductor absorption layer is indium gallium nitride.

(51) The optical absorption filter according to any one of configurations (48) to (50), wherein the integrated device comprises an optical detector and a reaction chamber located on opposite sides of the optical absorption filter.

(52) The optical absorption filter of configuration (51), wherein the integrated device further comprises an optical waveguide located on the same side of the optical absorption filter as the reaction chamber.

(53) The optical absorption filter according to any one of configurations (48) to (50), wherein the integrated device comprises an optical detector and an optical waveguide located on opposite sides of the optical absorption filter.

(54) The optical absorption filter according to any one of configurations (48) to (53), further comprising an anti-reflection layer formed adjacent to the semiconductor absorption layer, the anti-reflection layer configured to reduce light reflection from the semiconductor absorption layer for visible wavelengths between 500nm and 750 nm.

Various methods of forming a fluorescence detection device are possible. An example method includes a combination of processes (55) to (58) described below. These processes may be used, at least in part, to manufacture a fluorescence detection device configured as described above.

(55) A method of forming a fluorescence detection device, the method comprising: forming an optical probe on a substrate; forming a semiconductor optical absorption filter over an optical detector on the substrate; forming an optical waveguide over an optical probe on the substrate; and forming a reaction chamber configured to receive fluorescent molecules over the optical absorption filter and the optical waveguide.

(56) The method of (55), wherein forming the semiconductor light absorbing filter comprises conformally depositing a semiconductor absorbing layer over a non-planar topography.

(57) The method of (55) or (56), further comprising forming an oxide or nitride cap layer in contact with the semiconductor absorber layer to prevent diffusion of elements from the semiconductor absorber layer.

(58) The method of (57), further comprising forming an oxide or nitride cap layer adjacent to the semiconductor absorber layer, the oxide or nitride cap layer having a thickness that reduces optical reflection from the semiconductor absorber layer for visible wavelengths between 500nm and 750nm as compared to if the oxide or nitride cap layer were not present.

Various methods for improving the signal-to-noise ratio of the optical detector are possible. An example method includes a combination of processes (59) to (66) as described below.

(59) A method of improving the signal-to-noise ratio of an optical detector, the method comprising: transmitting excitation radiation to a reaction chamber using an optical waveguide, wherein the optical waveguide and the reaction chamber are integrated on a substrate; passing the emitted radiation from the reaction chamber through an optical absorption filter comprising the semiconductor absorption layer; detecting the emitted radiation through the semiconductor absorbing layer with an optical detector; and attenuating excitation radiation traveling toward the optical detector with the semiconductor absorption layer.

(60) The method of (59), further comprising attenuating, with the semiconductor absorption layer, the excitation radiation traveling toward the optical detector by between 10 to 100 times more than the emission radiation that has passed through the semiconductor absorption layer.

(61) The method of (59), further comprising attenuating, with the semiconductor absorption layer, the excitation radiation traveling toward the optical detector by between 100 to 1000 times more than the emission radiation that has passed through the semiconductor absorption layer.

(62) The method of (59), further comprising attenuating, with the semiconductor absorber layer, the excitation radiation traveling toward the optical detector by between 1000 to 3000 times more than the emission radiation that has passed through the semiconductor absorber layer.

(63) The method of any of (59) to (62), wherein the excitation radiation has a first characteristic wavelength in the range of 500nm to 540nm and the emission radiation has a second characteristic wavelength between 560nm to 690 nm.

(64) The method of any of (59) to (63), further comprising passing the emitted radiation through a first capping layer contacting the semiconductor absorber layer.

(65) The method of (64), further comprising reducing reflection of emitted radiation from the semiconductor absorber layer with the first capping layer.

(66) The method of any one of (59) to (65), wherein the first capping layer comprises a refractory metal oxide having a thickness of 5nm to 200 nm.

(67) The method of any of (59) to (66), further comprising reducing in-plane stress from the semiconductor absorber layer with the capping layer.

Conclusion III

Having thus described several aspects of several embodiments of the system architecture of the advanced analysis system 5-100, it is to be appreciated various alterations, modifications, and improvements will readily occur to those skilled in the art. Such alterations, modifications, and improvements are intended to be part of this disclosure, and are intended to be within the spirit and scope of the invention. While the present teachings have been described in conjunction with various embodiments and examples, the present teachings are not limited to these embodiments or examples. On the contrary, the teachings of the present invention include various alternatives, modifications, and equivalents, as will be appreciated by those skilled in the art.

While several inventive embodiments have been described and illustrated herein, those of ordinary skill in the art will readily envision a variety of other means and/or structures for performing the function and/or obtaining the results and/or one or more of the advantages described, and each of such variations and/or modifications is deemed to be within the scope of the inventive embodiments described herein. More generally, those skilled in the art will readily appreciate that all parameters, dimensions, materials, and configurations described herein are meant to be exemplary and that the actual parameters, dimensions, materials, and/or configurations will depend upon the specific application or applications for which the teachings of the present invention is/are used. Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described herein. It is, therefore, to be understood that the foregoing embodiments are presented by way of example only and that, within the scope of the appended claims and equivalents thereto. Embodiments of the invention may be practiced other than as specifically described and claimed. Inventive embodiments of the present invention may be directed to each individual feature, system upgrade, and/or method described herein. Moreover, combinations of two or more such features, systems and/or methods, if such combinations are not mutually inconsistent, are included within the scope of the present invention.

Moreover, while some advantages of the invention may be indicated, it should be understood that not every embodiment of the invention will include every advantage described. Some embodiments may not implement any features described as advantageous. Accordingly, the foregoing description and drawings are by way of example only.

All documents and similar materials cited in this application, including but not limited to patents, patent applications, articles, books, treatises, and web pages, are expressly incorporated by reference in their entirety regardless of the format in which such documents and similar materials are presented. If one or more of the incorporated documents and similar materials differ or contradict the present application, including but not limited to defined terms, usage of terms, described techniques, etc., the present application controls.

The section headings used are for organizational purposes only and are not to be construed as limiting the subject matter described in any way.

Further, the described technology may be embodied as a method, at least one example of which has been provided. The actions performed as part of the method may be ordered in any suitable way. Accordingly, embodiments may be constructed to perform acts in an order different than illustrated, which may include performing some acts simultaneously, even though shown as sequential acts in illustrative embodiments.

All definitions, as defined and used herein, should be understood to control dictionary definitions, definitions in documents incorporated by reference and/or ordinary meanings of the defined terms.

The values and ranges may be expressed as approximations or as precise values or ranges in the specification and claims. For example, in some cases, the terms "about," "approximately," and "substantially" may be used to refer to a value. Such references are intended to include reference to the value and reasonable variations of the value. For example, the phrase "between about 10 and about 20" is intended to mean "exactly between 10 and 20" in some embodiments, and "between 10 ± δ 1 and 20 ± δ 2" in some embodiments. The amount of change δ 1, δ 2 in the value may be less than 5% of the value in some embodiments, less than 10% of the value in some embodiments, and also less than 20% of the value in some embodiments. In embodiments where a wide range of values is given, for example, a range comprising two or more orders of magnitude, the amount of change δ 1, δ 2 may be as high as 50%. For example, if the operable range extends from 2 to 200, "about 80" may encompass a value between 40 and 120, and the range may be as large as between 1 and 300. The term "exactly" is used when an exact value is required, e.g. "exactly between 2 and 200".

The term "adjacent" may refer to two elements that are disposed in close proximity to one another (e.g., within a distance of less than about one-fifth of the lateral or vertical dimension of the larger of the two elements). In some cases, there may be intermediate structures or layers between adjacent elements. In some cases, adjacent elements may be directly adjacent to each other without intervening structures or elements.

The indefinite articles "a" and "an" used in the specification and claims should be understood to mean "at least one" unless specifically indicated to the contrary.

The phrase "and/or" as used in the specification and claims should be understood to mean "one or two" of the elements so combined, i.e., elements that are present in combination in some cases and not present in combination in other cases. Multiple elements listed with "and/or" should be construed in the same manner, i.e., "one or more" of such connected elements. In addition to elements specifically identified by the "and/or" clause, other elements may optionally be present, whether related or unrelated to those specifically identified elements. Thus, as a non-limiting example, when used in conjunction with open language such as "including," references to "a and/or B" may refer in one embodiment to only a (optionally including elements other than B); in another embodiment, only B (optionally including elements other than a); in yet another embodiment, to both a and B (optionally including other elements); and so on.

As used in the specification and claims, "or" should be understood to have the same meaning as "and/or" as defined above. For example, when separating items in a list, "or" and/or "should be interpreted as being inclusive, i.e., including at least one, but also including multiple elements or elements of the list, as well as (optionally) other unlisted items. To the contrary, terms such as "only one" or "exactly one," or "consisting of," when used in the claims, are intended to mean that there is exactly one element in a quantity or list of elements. In general, when preceding an exclusive term, such as "or", "one of", "only one of", or "exactly one of", the use of the term "or" is to be interpreted merely as indicating an exclusive alternative (i.e. "one or the other, but not both"). "consisting essentially of … …" when used in a claim shall have the ordinary meaning in the patent law field.

As used in this specification and the claims, the phrase "at least one" referring to a list of one or more elements should be understood as at least one element selected from any one or more of the elements in the list of elements, but not necessarily including at least one of each element specifically listed in the list of elements, nor excluding any combination of elements in the list of elements. The definition also allows that elements may optionally be present other than the explicitly identified elements in the list of elements to which the phrase "at least one" refers, whether or not those elements are related to the explicitly identified elements. Thus, as a non-limiting example, "at least one of a and B" (or, equivalently, "at least one of a or B," or, equivalently "at least one of a and/or B") may refer, in one embodiment, to at least one (optionally including a plurality of) a, with no B (optionally including elements other than B); in another embodiment, at least one, optionally including more than one, B, and a is absent (and optionally includes elements other than a); in yet another embodiment, at least one, optionally including more than one a, and at least one, optionally including more than one B (and optionally including other elements); and so on.

In the claims, as well as in the specification above, all transitional phrases such as "comprising," including, "" carrying, "" having, "" containing, "" involving, "" holding, "" consisting of … … and the like are to be understood to be open-ended, i.e., to mean including but not limited to. Only the transition phrases "consisting of … …" and "consisting essentially of … …" are closed or semi-closed transition phrases, respectively.

The claims should not be read as limited to the described order or elements unless stated to that effect. It will be understood by those of ordinary skill in the art that various changes in form and details may be made therein without departing from the spirit and scope of the appended claims. All embodiments that come within the spirit and scope of the following claims and equivalents thereto are claimed.