Waveguide excitation uniformity

Abstract

Systems and methods for substantially uniform optical power distribution within an integrated device across multiple sample wells and / or other photonic elements. The integrated device and related instruments and systems may be used to analyze samples in parallel. The integrated device may include a grating coupler configured to optically couple with multiple waveguides (2-104), which are configured to receive light from an excitation source and couple to the sample wells (2-102). The vertical extent of the optical mode of each waveguide may be modified to adjust the confinement of light within the waveguides (2-104). This modification may enable a more uniform distribution of excitation light across the sample wells (2-102), improving excitation efficiency and preventing excess power over an area of ​​the integrated device.

Description

Technical Field

[0001] This application generally relates to devices, methods, and techniques for coupling light energy to an integrated device and distributing the light energy to multiple regions of the device. The integrated device can be used for performing parallel quantitative analysis of biological and / or chemical samples, including nucleic acid sequencing and protein sequencing.

Background Art

[0002] Devices capable of large-scale parallel analysis of biological or chemical samples are typically limited to laboratory environments due to several factors, including their large size, lack of portability, the need for skilled technicians to operate the devices, power requirements, the need for a controlled operating environment, and cost. Further, some analyses of biological or chemical samples are performed collectively, and large quantities of specific types of samples are required for detection and quantification.

[0003] Analysis of a biological or chemical sample can include tagging the sample with a luminescent marker that emits light at a specific wavelength, irradiating the tagged sample with a light source, and detecting the emitted light with a photodetector. Such techniques conventionally require expensive laser light sources and systems for irradiating the tagged sample, as well as complex detection optics and electronics for collecting the light emitted from the tagged sample.

Summary of the Invention

[0004] Some embodiments are systems comprising an array of reaction chambers comprising a plurality of reaction chambers, and a waveguide for delivering excitation light to at least a portion of the array of reaction chambers, wherein a vertical extent of an optical mode of the waveguide is varied to adjust confinement of light within the waveguide.

[0005] In some embodiments, the vertical extent of the optical mode is varied by varying a thickness of a waveguide core layer along a length of the waveguide. In some embodiments, the vertical range of the optical mode is changed by varying the refractive index of the waveguide core material or the waveguide cladding material along the length of the waveguide.

[0006] In some embodiments, the thickness of the waveguide core layer along the length of the waveguide changes by transferring the topography of the photoresist layer. In some embodiments, a plurality of waveguides having a uniform width and a plurality of dummy structures having a tapered width are provided, and the plurality of waveguides and the plurality of dummy structures are arranged alternately.

[0007] In some embodiments, the plurality of waveguides and the plurality of dummy structures are in the waveguide core layer. Some embodiments relate to a system comprising an array of reaction chambers comprising a plurality of reaction chambers and a waveguide for delivering excitation light to at least a portion of the reaction chambers, wherein the distance between the waveguide and the reaction chambers is changed to compensate for waveguide losses.

[0008] In some embodiments, the thickness of the cladding layer of the waveguide is controlled to change the distance between the waveguide and the reaction chamber. In some embodiments, a plurality of waveguides having a uniform width and a plurality of dummy structures having a tapered width are provided, and the plurality of waveguides and the plurality of dummy structures are arranged alternately.

[0009] In some embodiments, a plurality of waveguides having a tapered width and a plurality of dummy structures having a tapered width are provided, and the plurality of waveguides and the plurality of dummy structures are arranged alternately.

[0010] In some embodiments, a plurality of waveguides having a tapered width in a first direction and a plurality of dummy structures having a tapered width in a second direction opposite to the first direction are provided, and the plurality of waveguides and the plurality of dummy structures are arranged alternately.

[0011] Some embodiments relate to a method comprising: providing a waveguide for delivering excitation light to an array of reaction chambers comprising a plurality of reaction chambers; and a changing step of changing a vertical range of an optical mode of the waveguide so as to adjust optical confinement within the waveguide.

[0012] In some embodiments, the changing step includes changing a thickness of a waveguide core layer along the length of the waveguide. In some embodiments, the changing step includes changing a refractive index of a waveguide core material or a waveguide cladding material.

[0013] Some embodiments relate to a method comprising: providing a waveguide for delivering excitation light to an array of reaction chambers comprising a plurality of reaction chambers; and a changing step of changing a distance between the waveguide and the reaction chambers.

[0014] In some embodiments, the changing step includes a control step of controlling a thickness of a cladding layer of the waveguide. In some embodiments, the control step includes providing a tapered thickness to the cladding layer by flattening a material for the cladding layer on a changed waveguide patterning.

[0015] In some embodiments, the control step includes providing a tapered thickness to the cladding layer by depositing a material for the cladding layer on a changed waveguide patterning.

[0016] In some embodiments, the control step includes providing a tapered thickness to the cladding layer by transferring a topography of a photoresist layer to the cladding layer. Some embodiments are methods comprising forming an array of reaction chambers comprising a plurality of reaction chambers, forming a waveguide for delivering excitation light to the reaction chambers, and a modifying step of modifying the waveguide so as to deliver excitation light that is nearly the same amount to each reaction chamber.

[0017] The modifying step includes a step of modifying a vertical range of the optical mode of the waveguide. The modifying step includes a step of modifying a thickness along the length of the waveguide. The modifying step includes a step of modifying a distance from each reaction chamber along the length of the waveguide.

[0018] Some embodiments are methods comprising exciting a sample within each of a plurality of reaction chambers with excitation light delivered through a waveguide, the waveguide being modified such that substantially the same amount of light is delivered to each reaction chamber.

[0019] The above summary is provided for purposes of illustration and is not intended to be limiting. Various aspects and embodiments of the present application are described with reference to the drawings. It is understood that the drawings are not necessarily drawn to scale. Elements appearing in multiple figures are indicated by the same reference numeral in all figures in which they appear.

Brief Description of the Drawings

[0020]

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Mode for Carrying Out the Invention

[0021] I. Introduction Aspects of the present application relate to integrated devices, instruments, and related systems capable of analyzing samples in parallel, including the identification and nucleic acid sequencing of single molecules. Such instruments are compact, portable, and easy to operate, allowing physicians or other providers to easily use the instrument and transport it to the desired location where care may be needed. Analysis of the sample may include labeling the sample with one or more fluorescent markers, which may be used for detection of the sample and / or identification of single molecules of the sample (e.g., individual nucleotide identification as part of nucleic acid sequencing). The fluorescent marker may be excited in response to irradiation with excitation light (e.g., light having a characteristic wavelength capable of exciting the fluorescent marker to an excited state), and when the fluorescent marker is excited, emits emission light (e.g., light having a characteristic wavelength emitted by the fluorescent marker upon returning from the excited state to the ground state). Detection of the emission light can enable identification of the fluorescent marker and thus identification of the sample or molecules of the sample labeled with the fluorescent marker. According to some embodiments, the instrument is capable of large-scale parallel sample analysis and can be configured to process tens of thousands or more samples simultaneously.

[0022] The inventors have recognized and understood that an integrated device having sample wells (also referred to as reaction chambers) configured to receive samples and an integrated optical system formed on the integrated device, and an instrument configured to interface with the integrated device, can be used to achieve analysis of this number of samples. The instrument can include one or more excitation light sources, and the integrated device can interface with the instrument such that excitation light is delivered to the sample wells using integrated optical components (e.g., waveguides, optical couplers, optical splitters) formed on the integrated device. The optical components can improve the uniformity of irradiation across the sample wells of the integrated device and otherwise reduce the number of external optical components that may be required. Further, the inventors have recognized and understood that by integrating photodetectors on the integrated device, the detection efficiency of fluorescence emission from the sample wells can be improved and otherwise reduce the number of light collection components that may be required.

[0023] According to some embodiments, an integrated device includes an array of sample wells that enables multiplex analysis of a plurality of samples across the array, and an optical system configured to deliver excitation light to the array of sample wells. The performance of the integrated device can depend on the ability of the integrated device to deliver excitation light across the array of sample wells using the optical system. Further, the performance of the integrated device can be related to the ability of the optical system to deliver excitation light to individual sample wells in a substantially uniform manner, such as by delivering a relatively constant intensity or electric field strength to the individual sample wells. Specifically, the performance-related factors associated with the optical system can include light losses resulting from scattering and / or absorption by the sample wells, the coupling efficiency of an optical coupler (e.g., a grating coupler configured to receive light from an external light source), light losses resulting from splitting the excitation light between a plurality of waveguides, and the coupling efficiency between the plurality of sample wells and the individual waveguides.

[0024] To increase the multiplexing ability of an integrated device, it may be desirable to increase the number of sample wells in an array to enable the analysis of more samples at any given time while using the integrated device. When the integrated device is scaled by an increase in the number of sample wells, issues in the performance of the integrated device may arise due to one or more of these factors. For example, rows of sample wells can receive light by coupling to waveguides of an optical system such that as light propagates along the waveguide, the sample wells in the row receive a portion of the light. Light loss can occur from individual sample wells scattering and / or absorbing the light, such that cumulatively, the last sample well in the row (e.g., furthest from the light input end of the waveguide) can receive a lower intensity or electric field strength than the first sample well in the row (e.g., the sample well next to the light input end of the waveguide). Such light loss can affect the signal-to-noise ratio of measurements performed using the integrated device. As more sample wells are added to the array, these light losses can lead to a further decrease in the signal-to-noise ratio and thus potentially affect the quality and reliability of the analysis performed.

[0025] Accordingly, aspects of the present application relate to optical components and particular arrangements for inclusion in an optical system of an integrated device that can enable improved distribution of light between arrays of sample wells. These optical components and arrangements can enable light to be delivered in a substantially uniform manner such that individual sample wells, including those in the same row, receive similar intensities and / or electric field strengths. The optical components and arrangements described herein can enable the implementation of an integrated device having a greater number of sample wells in an array, as well as the desired performance in the analysis of samples across the array.

[0026] Additional considerations as part of increasing the number of sample wells in the array may include manufacturing costs and constraints. Accordingly, aspects of the present application relate to optical components and systems that take into account manufacturing costs and constraints (e.g., by reducing the number or complexity of manufacturing steps) while enabling the resulting integrated device to achieve the desired optical performance.

[0027] Some aspects of the present application relate to waveguide configurations that may enable substantially uniform illumination of a number of sample wells and / or other photonic elements. In particular, some aspects are directed to changing the vertical extent of the optical mode of a waveguide so as to adjust the confinement within and along the length of the waveguide. This change may compensate for optical losses. This change enables a more uniform distribution of the excitation light with respect to the sample wells, improves the excitation efficiency, and prevents excessive power to the area of the integrated device. The change may be achieved by varying the thickness and / or width of the waveguide, varying the refractive index of the waveguide and / or the refractive index of the cladding material of the waveguide, or any suitable combination of the techniques described herein.

[0028] Other aspects are directed to changing the distance between the waveguide and the sample wells to compensate for optical losses. This change in distance may be accomplished by controlling the thickness of the cladding layer of the waveguide. Accordingly, aspects of the present application relate to techniques for controlling the thickness of the cladding layer of a waveguide along the length of the waveguide. In some embodiments, the technique includes changing the waveguide pattern density. In some embodiments, the technique includes changing the topography of the cladding layer. In some embodiments, the technique includes changing the lateral position of the sample wells with respect to the waveguide. In some embodiments, those techniques may be used alone or in any suitable combination.

[0029] Additional systems and methods for delivering uniform excitation light to an array of sample wells are described in U.S. Patent Application No. 16 / 733,296, entitled "OPTICAL WAVEGUIDES AND COUPLERS FOR DELIVERING LIGHT TO AN ARRAY OF PHOTONIC ELEMENTS," which is hereby incorporated by reference in its entirety.

[0030] The techniques for optical systems as described in this application are discussed in the context of delivering excitation light to an array of sample wells, but it is understood that one or more of these techniques may be used, alone or in combination, in other contexts including distributing light to an array of photonic elements within an integrated device. For example, the techniques of this application may be implemented in an array of optical components such as an array of sensors. In other words, rather than or in addition to providing a technique for delivering uniform excitation light to an array of sample wells, the techniques may be utilized to address non-uniformities in excitation light delivery within optical components used to deliver or receive emitted light from an excited sample within a sample well. Also, the techniques described herein are not limited to the context of analyzing biological or chemical samples, but rather may be implemented in applications where it is desired to distribute light among a number of photonic elements in a substantially uniform manner.

[0031] The aspects and embodiments described above and additional aspects and embodiments are further described below. These aspects and / or embodiments may be used individually, all together, or in any combination of two or more, and the present application is not limited in this regard.

[0032] II. Integrated Device A. Overview A schematic cross-sectional view of an integrated device 1-102 showing the rows of pixels 1-112 is shown in FIG. 1-1. The integrated device 1-102 can include a coupling region 1-201, a routing region 1-202, and a pixel region 1-203. As discussed in the present specification, the optical system of the integrated device can include different types of optical components that can be located within regions 1-201, 1-202, and 1-203 of the integrated device. The coupling region 1-201 can include a grating coupler 1-216, which can be configured to receive excitation light (shown as a dashed line) and propagate the excitation light to one or more optical components within the routing region 1-202. The routing region 1-202 can include an optical routing network configured to split light among a plurality of waveguides 1-220 configured to propagate the light to the pixel region 1-203. The pixel region 1-203 can include a plurality of pixels 1-112 having sample wells 1-108 disposed on a surface at a location different from the coupling region 1-201 where excitation light (shown as a dashed arrow) couples to the integrated device 1-102. The sample wells 1-108 can be formed through a metal layer 1-106. One pixel 1-112, shown by a dotted rectangle, is a region of the integrated device 1-102 that includes a sample well 1-108 and a photodetector region having one or more photodetectors 1-110.

[0033] FIG. 1-1 shows the path of excitation (shown by the dashed line) by coupling the beam of the excitation light to the coupling region 1-201 and the sample well 1-108. The rows of the sample wells 1-108 shown in FIG. 1-1 can be arranged to be optically coupled to the waveguide 1-220. The excitation light can irradiate the sample located within the sample well. The sample can reach an excited state in response to being irradiated by the excitation light. When the sample is in the excited state, the sample can emit emission light that can be detected by one or more photodetectors associated with the sample well. FIG. 1-1 schematically shows the path of the emission light (shown as a solid line) from the sample well 1-108 to the photodetector 1-110 of the pixel 1-112. The photodetector 1-110 of the pixel 1-112 can be configured and arranged to detect the emission light from the sample well 1-108. Examples of suitable photodetectors are described in U.S. Patent Application No. 14 / 821,656, entitled "INTEGRATED DEVICE FOR TEMPORAL BINNING OF RECEIVED PHOTONS" (which is incorporated herein by reference in its entirety). Further examples of suitable photodetectors are described in U.S. Patent Application No. 15 / 852,571, entitled "INTEGRATED PHOTODETECTOR WITH DIRECT BINNING PIXEL", which is incorporated herein by reference in its entirety. For each individual pixel 1-112, the sample well 1-108 and its respective photodetector 1-110 can be aligned along a common axis (along the y direction shown in FIG. 1-1). In this way, the photodetector can overlap with the sample well within the pixel 1-112.

[0034] A plan view of the integrated device 1-102 showing 5 rows of pixels is shown in FIG. 1-2. As shown in FIG. 1-2, the sample wells 1-108a and 1-108b are in the same row, and the sample wells 1-108c and 1-108d are in the same row. Aspects of the present application relate to techniques for receiving excitation light incident on the coupling region 1-201 and propagating the excitation light to an array of sample wells 1-108. These techniques may include one or more grating couplers disposed in the coupling region 1-201 and a waveguide architecture disposed in the routing region 1-202 and / or the pixel region 1-203 to deliver the excitation light from the coupling region 1-201 to the individual sample wells 1-108.

[0035] B. Waveguide Architecture Some embodiments relate to waveguides configured to couple excitation energy generated by an excitation source to individual samples in sample wells, for example, by evanescent coupling, substantially uniformly. In some embodiments, the sample wells may be arranged in an array having rows and columns, and the individual waveguides may be configured to deliver the excitation energy to the sample wells in the corresponding rows and columns. In some embodiments, the waveguides may be configured to provide the excitation energy substantially uniformly between sample wells in a row or column and / or in multiple rows or columns (e.g., with an intensity deviation of less than 50%, in some embodiments less than 20%, and in some embodiments less than 10%). In some embodiments, the number of sample wells along the waveguide may exceed 500, for example, in the range of 500 to 5000.

[0036] The waveguide may be configured to compensate for optical losses. The optical losses can cause non-uniform excitation within the array and / or can result in a quasi-optimal excitation efficiency that can be called the number of measurements enabled by the optical power. Without compensation, the power in the waveguide decreases exponentially, for example, with respect to the distance across the waveguide array. Embodiments of the waveguide are configured to improve the uniformity of excitation and the excitation efficiency across a large array of sample wells and to prevent excess power in regions of an integrated device comprising the large array of sample wells.

[0037] The vertical extent of the optical mode of an individual waveguide can be adjusted for confinement within and along the length of the waveguide. In some embodiments, the thickness and / or width of an individual waveguide may be varied along the length of the individual waveguide. In some embodiments, the refractive index of the waveguide and / or the refractive index of the cladding material of the waveguide may be varied.

[0038] In some embodiments, the distance between the waveguide and each sample well may be varied to adjust the excitation of the sample well along the waveguide. In some embodiments, the distance between the waveguide and each sample well may be varied by adjusting the thickness of the cladding layer of the waveguide along the length of the waveguide. In some embodiments, the distance between the waveguide and each sample well may be varied by changing the lateral position of the sample well relative to the waveguide along the length of the waveguide. For example, the sample wells may be arranged such that, along the length of the waveguide, the sample wells closer to the excitation source are displaced more from the waveguide than the sample wells farther from the excitation source. The displacement may be in a direction perpendicular to the direction in which the waveguide extends (e.g., as shown in FIGS. 2-8). In some embodiments, the techniques described herein may be used alone or in any suitable combination.

[0039] In some embodiments, the thickness profile of the cladding layer at the top of the waveguide array may be modified. FIG. 2-1 shows a schematic plan view of a waveguide array 2-100 according to some embodiments. The waveguide array 2-100 may extend from an array start end 2-108 to an array end 2-110. The array start end 2-108 may be closer to the excitation source than the array end 2-110 in terms of distance. The waveguide array 2-100 may include a dummy structure 2-106 disposed between adjacent waveguides 2-104. The waveguides 2-104 and the dummy structure 2-106 may be waveguide core layers. For example, the waveguide core layer may be deposited on a substrate and patterned into waveguides and the dummy structure. The sample well 2-102 may be disposed on top of the waveguide 2-104. There may be no sample well on top of the dummy structure 2-106. Such a configuration allows the dimensions of the dummy structure 2-106 (e.g., width) to be adapted according to the requirements of subsequent fabrication processes while the dimensions of the waveguide 2-104 remain adapted to change the vertical range of the optical mode of the waveguide so as to adjust the confinement of light within the waveguide and along the length of the waveguide. For example, the results of some subsequent fabrication processes such as chemical mechanical polishing (CMP) and high density plasma chemical vapor deposition (HDP) may depend on the patterning density of the underlying layer. The addition of the dummy structure enables the change in the patterning density of the photolithography mask designed for the waveguide 2-104 to achieve the desired patterning density for subsequent fabrication processes by changing the dimensions of the dummy structure 2-106 without changing the dimensions of the waveguide 2-104 that are adapted to the changed vertical range of the optical mode.

[0040] The waveguide array 2-100 may have a modified patterning density. The patterning density may be configured to decrease as the distance to the excitation source increases. In the illustrated embodiment, the waveguide 2-104 has a constant width along the length of the waveguide that may be configured to maintain a sharp decay rate of the evanescent field. In the illustrated embodiment, the dummy structure 2-106 has a tapered width along the length of the dummy structure, which results in a decrease in the waveguide patterning density from the array start end 2-108 to the array end 2-110.

[0041] The distance between the waveguide 2-104 and the sample well 2-102 may be modified, at least in part, based on the modified waveguide patterning density. The distance between the waveguide 2-104 and the row of sample wells 2-102 at the top of the waveguide may be configured to decrease as the waveguide extends away from the excitation source. FIG. 2-2 shows a cross-sectional view of the waveguide array 2-100 along the line labeled "2-2" in FIG. 2-1, according to some embodiments. The cladding layer 2-112 may be formed on top of the waveguide 2-104. The thickness dc of the cladding layer 2-112 may be modified along the length of the waveguide 2-104. As shown, the thickness dc of the cladding layer 2-112 gradually narrows from the array start end 2-108 to the array end 2-110. The sample well 2-102 may be formed in the cladding layer 2-112, for example, by photolithography and etching. Since the depth dw of the sample well 2-102 may be substantially constant to define the position of the sample, the distance between the sample well 2-102 and the waveguide 2-104 may thus decrease along the length of the waveguide 2-104. The decrease in the distance from the sample to the waveguide can compensate for the power loss in the waveguide as the excitation energy traverses the waveguide away from the excitation source and enables approximately the same amount of light to interact with the sample in the sample well along the length of the waveguide and / or over various ranges of the waveguide array.

[0042] In some embodiments, the waveguide array 2-100 may be fabricated by a first method shown in FIGS. 2-3A through 2-4C. FIGS. 2-3A through 2-3C show cross-sectional views of the waveguide array 2-100 along the line marked "2-3" near the array start end 2-108 in FIG. 2-1, according to some embodiments. FIGS. 2-4A through 2-4C show cross-sectional views of the waveguide array 2-100 along the line marked "2-4" near the array end 2-110 in FIG. 2-1, according to some embodiments.

[0043] In the fabrication process shown in FIGS. 2-3A and 2-4A, the waveguides 2-104 and the dummy structures 2-106 may be fabricated by depositing a layer of waveguide core material on a substrate and patterning the layer of waveguide core material by lithography and etching.

[0044] In the fabrication process shown in FIGS. 2-3B and 2-4B, the cladding layer 2-114 may be deposited on top of the patterned layer of waveguide core material using a deposition process (e.g., plasma-enhanced chemical vapor deposition (PECVD)) that is substantially independent of the underlying patterning density. As shown, the thickness dd of the cladding layer 2-114 may be substantially constant from the array start end 2-108 to the array end 2-110.

[0045] In the fabrication process shown in FIGS. 2-3C and 2-4C, the cladding layer 2-112 may be formed by polishing / planarizing the deposited cladding layer 2-114 using, for example, a chemical mechanical polishing (CMP) process. The CMP process may be configured such that regions having a low waveguide patterning density are polished faster than regions having a high waveguide patterning density. As shown, the thickness d1 of the cladding layer 2-112 at the array start end 2-108 is greater than the thickness d2 of the cladding layer 2-112 at the array end 2-110.

[0046] In some embodiments, the waveguide array 2-100 may be fabricated by a second method as shown in FIGS. 2-5A through 2-6B. FIGS. 2-5A through 2-5B show cross-sectional views of the waveguide array 2-100 along the line marked "2-3" near the array start end 2-108 in FIG. 2-1, according to some embodiments. FIGS. 2-6A through 2-6B show cross-sectional views of the array 2-100 along the line marked "2-4" near the array start end 2-108 in FIG. 2-1, according to some embodiments.

[0047] Similar to the fabrication processes shown in FIGS. 2-3A and 2-4A, in the fabrication processes shown in FIGS. 2-5A and 2-6A, the waveguides 2-104 and the dummy structures 2-106 may be fabricated by depositing a layer of waveguide core material on a substrate and patterning the layer of waveguide core material by lithography and etching.

[0048] Unlike the fabrication processes shown in FIGS. 2-3B and 2-4B, in the fabrication processes shown in FIGS. 2-5B and 2-6B, the cladding layer 2-116 may be deposited on top of the patterned layer of waveguide core material using a deposition process that depends on the underlying patterning density (e.g., high density plasma chemical vapor deposition (HDP)). As shown, the thickness dd1 of the deposited cladding layer 2-116 at the array start end 2-108 is greater than the thickness dd2 of the deposited cladding layer 2-112 at the array end 2-110.

[0049] After the processing steps shown in FIGS. 2-5B and 2-6B, similar to the fabrication processes shown in FIGS. 2-3C and 2-4C, the cladding layer 2-112 may be formed by polishing / planarizing the deposited cladding layer 2-116, for example, using a CMP process. The thickness profile of the deposited cladding layer 2-116 may be maintained or enhanced when transferred to the cladding layer 2-112 by the polishing / planarization process.

[0050] The vertical extent of the optical mode of the waveguide may be altered by a tapered cladding layer (e.g., the cladding layer 2-112 shown in FIG. 2-2). FIG. 2-7A is an enlarged view of the region marked "2-7" in FIG. 2-3C according to some embodiments. FIG. 2-7B is a schematic diagram showing the intensity of the optical mode field within and near the waveguide 2-104 according to some embodiments. The intensity of the optical mode field of the waveguide 2-104 may depend on the width w and thickness t of the waveguide. As shown, the optical mode is approximately elliptical, and the intensity of the field decreases as the distance from the center of the optical mode increases. The intensity of the field may be of another shape depending on the configuration of the integrated device.

[0051] In FIG. 2-7A, the shape 2-118 is shown as an example of a position having a uniform field intensity. The field may decay rapidly in the vertical direction parallel to the thickness of the waveguide. Also, as the waveguide traverses away from the excitation source, the power at the center of the waveguide decays in the horizontal direction parallel to the length of the waveguide and perpendicular to the width w and thickness t of the waveguide. Altering the vertical extent of the optical mode of the waveguide along its length may bring a sample well far from the excitation source closer to the waveguide, and thus, along the length of the waveguide and / or across various regions of the array, enable delivering light as close as possible to the same amount to the sample well as close as possible.

[0052] In some embodiments, the vertical extent of the optical mode may be altered by varying the thickness t of the waveguide along its length. For example, the thickness t of the waveguide may increase as the waveguide extends away from the excitation source, such that the waveguide is brought closer to the sample well far from the excitation source. In some embodiments, the thickness t of the waveguide may be altered by transferring the topography of the photoresist layer to the waveguide core layer. The photoresist layer may be deposited on top of the waveguide core layer, and the photoresist layer may be provided with a desired surface profile after gray scale lithography. The desired surface profile of the photoresist layer may then be transferred to the waveguide core layer after non-selective etching. The foregoing is provided as an example, and it is understood that any other suitable fabrication process may be used to provide the waveguide with a desired varying thickness along its length.

[0053] In addition to, or alternatively to, this, in some embodiments, the refractive index of the waveguide and / or the refractive index of the cladding material surrounding the waveguide may be altered. For example, an ion implantation method may be used to vary the local composition of the waveguide core layer and / or the cladding layer, thereby altering the refractive index.

[0054] The waveguide may be made of a waveguide core material that is transparent in the waveguide for the excitation energy (e.g., having a transmission loss of 2 dB / m). For example, silicon nitride may be used as the material for guiding the excitation energy. Other materials that may be suitable for forming the waveguide core include silicon carbide and alloys of silicon nitride and silicon carbide. The waveguide core layer may be made of a transparent material that provides a desired attenuation rate for the waveguide core material. For example, silicon dioxide may be used as the material for the cladding layer. These waveguide core and cladding materials may be deposited by methods such as plasma enhanced chemical vapor deposition (PECVD), and the optical properties of the materials may be tuned by adjusting the deposition parameters.

[0055] In some embodiments, the distance between the waveguide and each sample well may be changed by varying the lateral position of the sample well relative to the waveguide along the length of the waveguide. FIG. 2-8 shows an example of this. As shown, sample well 2-102 may be arranged such that sample wells closer to the start end 2-108 of waveguide array 2-100 along the length of waveguide 2-104 are displaced from the centerline of the waveguide more than sample wells closer to the array end 2-110 of waveguide array 2-100. The displacement may be in a direction perpendicular to the direction in which the waveguide extends. As a result, sample wells farther from the excitation source are closer to the waveguide than sample wells closer to the excitation source. The foregoing is provided as an example, and any suitable arrangement of the sample wells relative to the waveguide may be configured to vary the distance between the waveguide and each sample well.

[0056] In some embodiments, the vertical extent of the optical mode of the waveguide may be changed by a waveguide having a tapered width along the length of the waveguide. FIG. 2-1 shows a schematic plan view of a waveguide array 3-100 according to some embodiments. Waveguide array 3-100 may extend from an array start end 3-108 to an array end 3-110. The array start end 3-108 may be closer to the excitation source than the array end 3-110. Waveguide array 3-100 may include a dummy structure 3-106 disposed between adjacent waveguides 3-104. Sample well 3-102 may be disposed on top of waveguide 3-104. There may be no sample well on top of dummy structure 3-106.

[0057] The waveguide array 3-100 may have a modified patterning density. In the illustrated embodiment, the waveguide 3-104 has a tapered width along the length of the waveguide. The tapered waveguide may be configured to provide a weak evanescent field near the excitation source and a strong evanescent field far from the excitation source. The tapered waveguide may give rise to a phenomenon of waveguide patterning density that can affect the results of subsequent fabrication processes from the array start 3-108 to the array end 3-110. In the illustrated embodiment, the dummy structure 3-106 has a tapered width along the length of the dummy structure, which increases the reduction of the waveguide patterning density from the array start 3-108 to the array end 3-110.

[0058] As shown, the degree of taper, which can be measured by the slope along the respective length of the contour of the waveguide 3-104 or the dummy structure 3-106, may be modified to allow for a substantially uniform distribution of the excitation energy. In the illustrated embodiment, the degree of taper for the dummy structure 3-106 is steeper than the degree of taper for the waveguide 3-104. It is understood that the waveguide 3-104 may have the same degree of taper as the dummy structure 3-106 or a steeper degree of taper than the dummy structure 3-106.

[0059] The waveguide array 3-100 may be fabricated by a method similar to the first method shown in FIGS. 2-3A through 2-4C, a method similar to the second method shown in FIGS. 2-5A through 2-6B, or any suitable combination of the steps of the first method and the second method. The resulting waveguide array 3-100 may have a tapered cladding layer similar to the cladding layer 2-112 shown in FIG. 2-2.

[0060] In some embodiments, the waveguide and the dummy structure may be tapered in opposite directions so as to provide substantially uniform patterning across the array of waveguides. FIG. 4-1 shows a schematic plan view of an array of waveguides according to some embodiments. The waveguide array 4-100 may extend from an array start end 4-108 to an array end 4-110. The array start end 4-108 may be closer to the excitation source than the array end 4-110 in distance. The waveguide array 4-100 may include a dummy structure 4-106 disposed between adjacent waveguides 4-104. The sample well 4-102 may be disposed on top of the waveguide 4-104. There may be no sample well on top of the dummy structure 4-106.

[0061] In some embodiments, the waveguide array 4-100 may be fabricated by the method shown in FIGS. 4-2A to 4-2B. FIGS. 4-2A to 4-2B are cross-sectional views of the waveguide array 4-100 along the line marked "4-2" according to some embodiments.

[0062] Prior to the fabrication process shown in FIGS. 4-2A to 4-2B, similar to the fabrication process shown in FIGS. 2-3A and 2-4A, the waveguide 4-104 and the dummy structure 4-106 may be fabricated by depositing a layer of waveguide core material on a substrate and patterning the layer of waveguide core material by lithography and etching. Similar to the fabrication process shown in FIGS. 2-3B and 2-4B, the cladding layer may be deposited on top of the patterned layer of waveguide core material using a deposition process (e.g., PECVD) that is substantially independent of the lower patterning density. Similar to the fabrication process shown in FIGS. 2-3C and 2-4C, the cladding layer may be formed, for example, using a chemical mechanical polishing (CMP) process, prior to polishing / planarizing the deposited cladding layer. The polished cladding layer may have a substantially flat surface so that the waveguide array 4-100 has substantially uniform patterning across the array.

[0063] In the fabrication process shown in FIG. 4-2A, the photoresist layer 4-144 may be deposited on top of the polished cladding layer 4-116, and the photoresist layer 4-144 may be provided with a tapered surface profile after gray-scale lithography. In the fabrication process shown in FIG. 4-2B, the tapered surface profile of the photoresist layer 4-144 may be transferred to the cladding layer 4-112 after non-selective etching. The resulting waveguide array 4-100 may have a tapered cladding layer similar to the cladding layer 2-112 shown in FIG. 2-2.

[0064] Although the process of creating a waveguide array has been described, it is understood that the fabrication process may be processed in any suitable combination and / or in any suitable order and may have any other suitable processes added to the present specification.

[0065] C. Grating Coupler As discussed in connection with FIG. 1-1, the integrated device can include a grating coupler, such as grating coupler 1-216, which is configured to receive light from a light source and direct the light to a waveguide configured to optically couple with a sample well array. The inventors have recognized and understood that some grating coupler configurations provide one or more advantages to the integrated device, including higher coupling efficiency of light to other optical components within the device and a wider tolerance to the angle of incident light. The grating coupler includes a plurality of material structures, i.e., grating teeth, separated by gaps filled with a material. The material structures may have a higher refractive index than the gap material (e.g., a material structure formed of silicon nitride and a gap formed of silicon oxide). Parameters that can affect the coupling efficiency of the grating coupler include the width of the material structure, the number of material structures, the width of the gap, and the filling ratio, which is the ratio of the width of the material structure to the width of the gap.

[0066] Some embodiments relate to an integrated device having an apodized grating coupler configured to receive light incident on the integrated device. The apodized grating coupler can have material structures spaced apart from each other by a variable fill factor. In some embodiments, the material structures can be spaced apart from each other by gaps having variable widths. In some embodiments, the material structures can have variable widths.

[0067] Some embodiments relate to a grating coupler having a material structure that is asymmetric with respect to a plane substantially parallel to the surface of the integrated device. In some embodiments, the grating coupler can have multiple layers. A blazed grating coupler includes a combination of grating couplers, and the layer proximate to the surface has a material structure with a narrower width than another layer. According to some embodiments, the blazed grating coupler can have a sawtooth material structure. A two-layer grating coupler includes a combination of two grating couplers offset from each other.

[0068] For some grating couplers, the range of coupling efficiency and incident angle at which a desired coupling efficiency can be achieved can depend on the bandwidth of the incident light, where the performance of the grating coupler can degrade over a wider wavelength band. The inventors have recognized and understood that by varying the refractive index of the material structure, a wider band can be accommodated, resulting in a broadband grating coupler. In some embodiments, multiple materials may be used to control the refractive index of the diffraction grating. For example, when silicon oxide and silicon nitride are used to form the grating structure of the grating coupler, the grating structure may be discretized into sub-wavelength elements (e.g., less than 200 nm). The effective refractive index n eff can depend on both the filling factors of the two silicon oxides, f ox and f SiN , as well as the refractive index n ox of silicon oxide and the refractive index n SiN of silicon nitride. Specifically,

[0069]

Equation

[0070] It is understood that a grating coupler having a configuration as described in the present specification may be coupled to any suitable number of waveguides and may have output light in one or more directions. In some embodiments, the grating coupler can have a plurality of output waveguides substantially parallel in one direction.

[0071] III. Additional Aspects of the System The system can include an integrated device and a device configured to interface with the integrated device. The integrated device can include an array of pixels, and the pixels can include sample wells and one or more photodetectors. The surface of the integrated device can have a plurality of sample wells, and the sample wells are configured to receive a sample from a sample placed on the surface of the integrated device. The sample can include a plurality of samples and, in some embodiments, can include different types of samples. The plurality of sample wells can have appropriate sizes and shapes such that at least a portion of the sample wells receive one sample from the sample. In some embodiments, the number of samples in the sample wells can be distributed among the plurality of sample wells such that one sample well contains one sample and other sample wells contain zero or two or more samples.

[0072] In some embodiments, the sample may include a plurality of single-stranded DNA templates, and individual sample wells on the surface of the integrated device are sized and shaped to receive the sequencing template. The sequencing template may be distributed among a plurality of sample wells of the integrated device such that at least a portion of the plurality of sample wells of the integrated device contain the sequencing template. The sample can include labeled nucleotides, which then enter the sample well and are incorporated into a DNA strand complementary to the single-stranded DNA template in the sample well, enabling identification of the nucleotides. In such an example, the "sample" can refer to both the sequencing template and the labeled nucleotides currently being incorporated by the polymerase. In some embodiments, the sample can include the sequencing template, and then the labeled nucleotides can be introduced into the sample well when the nucleotides are incorporated into the complementary strand within the sample well. Thus, the timing of nucleotide incorporation can be controlled by when the labeled nucleotides are introduced into the sample wells of the integrated device.

[0073] The excitation light is supplied from an excitation source located remotely from the pixel array of the integrated device. The excitation light is directed, at least in part, by elements of the integrated device toward one or more pixels to irradiate an illumination region within the sample well. Then, the marker can emit emitted light in response to being irradiated with the excitation light when located within the illumination region. In some embodiments, one or more excitation sources are part of the apparatus of the system, and the components of the apparatus and the integrated device are configured to direct the excitation light toward one or more pixels.

[0074] The emission light emitted by the sample can then be detected by one or more photodetectors within the pixels of the integration device. The characteristics of the detected emission light can provide an indicator for identifying markers associated with the emission light. Such characteristics can include any suitable type of characteristics, including the arrival time of photons detected by the photodetector, the amount of photons accumulated by the photodetector over time, and / or the distribution of photons across two or more photodetectors. In some embodiments, the photodetector can be configured to enable the detection of one or more timing characteristics (e.g., fluorescence lifetime) associated with the emission light of the sample. The photodetector can detect the distribution of photon arrival times after a pulse of excitation light has propagated through the integration device, and the distribution of arrival times can provide an indicator of the timing characteristics of the emission light of the sample (e.g., instead of the fluorescence lifetime). In some embodiments, one or more photodetectors provide an indicator of the probability of the emission light emitted by the marker (e.g., fluorescence intensity). In some embodiments, multiple photodetectors may be dimensioned and arranged to capture the spatial distribution of the emission light. Then, the output signal from one or more photodetectors may be used to distinguish markers from among the multiple markers, and the multiple markers may be used to identify the sample within the sample. In some embodiments, the sample may be excited by multiple excitation energies, and the markers may be distinguished from among the multiple markers by the emission light emitted by the sample in response to the multiple excitation energies and / or the timing characteristics of the emission light.

[0075] A schematic diagram of system 5-100 is shown in FIG. 5-1A. The system includes both an integrated device 5-102 that interfaces with device 5-104. In some embodiments, device 5-104 may include one or more excitation sources 5-106 integrated as part of device 5-104. In some embodiments, the excitation source may be external to both device 5-104 and integrated device 5-102, and device 5-104 may be configured to receive excitation light from the excitation source and direct the excitation light towards the integrated device. The integrated device can interface with the device using any suitable socket for holding the integrated device while being precisely optically aligned with the excitation source that receives the integrated device. Excitation source 5-106 may be configured to provide excitation light to integrated device 5-102. As schematically shown in FIG. 5-1A, integrated device 5-102 has a plurality of pixels 5-112, and at least some of the pixels may perform independent analysis of a sample. Such pixels 5-112 may be referred to as "passive source pixels" because the pixel receives excitation light from a light source 5-106 remote from the pixel and the excitation light from the source excites some or all of pixel 5-112. Excitation source 5-106 may be any suitable light source. An example of a suitable excitation source is described in U.S. Patent Application No. 14 / 821,688, filed Aug. 7, 2015, entitled "INTEGRATED DEVICE FOR PROBING, DETECTING AND ANALYZING MOLECULES" (which is incorporated by reference in its entirety). In some embodiments, excitation source 5-106 includes a plurality of excitation sources combined to deliver excitation light to integrated device 5-102. The plurality of excitation sources may be configured to generate a plurality of excitation energies or wavelengths.

[0076] Pixels 5-112 have a sample well 5-108 configured to receive a sample and a photodetector 5-110 for detecting emitted light emitted by the sample in response to irradiating the sample with excitation light provided by an excitation source 5-106. In some embodiments, the sample well 5-108 can hold the sample in proximity to the surface of the integrated device 5-102, thereby facilitating delivery of excitation light to the sample and detection of emitted light from the sample.

[0077] Optical elements for coupling excitation light from the excitation light source 5-106 to the integrated device 5-102 and guiding the excitation light to the sample well 5-108 are disposed on both the integrated device 5-102 and the instrument 5-104. The optical elements from the excitation source to the well can include one or more grating couplers located on the integrated device 5-102 to couple the excitation light to the integrated device and a waveguide for delivering the excitation light from the instrument 5-104 to the sample well within the pixel 5-112. One or more optical splitter elements can be disposed between the grating coupler and the waveguide. The optical splitter can couple the excitation light from the grating coupler and deliver the excitation light to one or more of the waveguides. In some embodiments, the optical splitter can have a configuration that enables substantially uniform delivery of excitation light across all waveguides such that each waveguide receives substantially the same amount of excitation light. Such embodiments can improve the performance of the integrated device by improving the uniformity of the excitation light received by the sample wells of the integrated device.

[0078] The sample wells 5-108, a portion of the optical components from the excitation source to the wells, and the optical components from the sample wells to the photodetector are located in the integrated device 5-102. The excitation source 5-106, and a portion of the components from the excitation source to the wells are located in the instrument 5-104. In some embodiments, a single component can serve both to couple the excitation light to the sample well 5-108 and to deliver the emitted light from the sample well 5-108 to the photodetector 5-110. Examples of suitable components for inclusion in the integrated device for coupling the excitation light to the sample well and / or for directing the emitted light to the photodetector are described in U.S. Patent Application No. 14 / 821,688, filed Aug. 7, 2015, entitled "INTEGRATED DEVICE FOR PROBING, DETECTING AND ANALYZING MOLECULES," and U.S. Patent Application No. 14 / 543,865, filed Nov. 17, 2014, entitled "INTEGRATED DEVICE WITH EXTERNAL LIGHT SOURCE FOR PROBING, DETECTING, AND ANALYZING MOLECULES," each of which is hereby incorporated by reference in its entirety.

[0079] Pixels 5-112 are associated with their own individual sample wells 5-108 and one or more photodetectors 5-110. The plurality of pixels of integrated device 5-102 can be arranged to have any suitable shape, size, and / or dimensions. The integrated device 5-102 can have any suitable number of pixels. The number of pixels within integrated device 2-102 can be in the range of approximately 10,000 pixels to 1,000,000 pixels, or any value or range of values within that range. In some embodiments, the pixels can be arranged in an array of 512 pixels × 512 pixels. The integrated device 5-102 can interface with the device 5-104 in any suitable manner. In some embodiments, the device 5-104 can have an interface that detachably couples to the integrated device 5-102, and thus, a user can attach the integrated device 5-102 to the device 5-104 to analyze a sample using the integrated device 5-102, and remove the integrated device 5-102 from the device 5-104 to allow another integrated device to be attached. The interface of the device 5-104 can be arranged to position the integrated device 5-102 to couple to the circuitry of the device 5-104 and enable a readout signal from one or more photodetectors to be transmitted to the device 5-104. The integrated device 5-102 and the device 5-104 can comprise a multi-channel high-speed communication link to handle data associated with a large (e.g., greater than 10,000 pixel) pixel array.

[0080] A schematic cross-sectional view of the integrated device 5-102 showing the rows of pixels 5-112 is shown in FIG. 5-1B. The integrated device 5-102 can include a coupling region 5-201, a routing region 5-202, and a pixel region 5-203. The pixel region 5-203 can include a plurality of pixels 5-112 having sample wells 5-108 disposed on a surface at a position different from the coupling region 5-201 where the excitation light (indicated by the dashed arrow) couples to the integrated device 5-102. The sample well 5-108 may be formed through the metal layer 5-116. One pixel 5-112 indicated by the dotted rectangle is a region of the integrated device 5-102 that includes the sample well 5-108 and a photodetector region having one or more photodetectors 5-110.

[0081] FIG. 5-1B shows the path of excitation (shown by the dashed line) by coupling the beam of the excitation light to the coupling region 5-201 and to the sample well 5-108. The rows of the sample wells 5-108 shown in FIG. 5-1B can be arranged to be optically coupled to the waveguide 5-220. The excitation light can irradiate the sample located within the sample well. The sample can reach an excited state in response to being irradiated by the excitation light. When the sample is in the excited state, the sample can emit emitted light that can be detected by one or more photodetectors associated with the sample well. FIG. 5-1B schematically shows the path of the emitted light (shown as a solid line) from the sample well 5-108 to the photodetector 5-110 of the pixel 5-112. The photodetector 5-110 of the pixel 5-112 can be configured and arranged to detect the emitted light from the sample well 5-108. Examples of suitable photodetectors are described in U.S. Patent Application No. 14 / 821,656, entitled "INTEGRATED DEVICE FOR TEMPORAL BINNING OF RECEIVED PHOTONS", which is incorporated herein by reference in its entirety. Further examples of suitable photodetectors are described in U.S. Patent Application No. 15 / 852,571, filed on Dec. 22, 2017, entitled "INTEGRATED PHOTODETECTOR WITH DIRECT BINNING PIXEL" (which is incorporated herein by reference in its entirety). For each individual pixel 5-112, the sample well 5-108 and its respective photodetector 5-110 can be aligned along a common axis (along the y-direction shown in FIG. 5-1B). In this way, the photodetector can overlap with the sample well within the pixel 5-112.

[0082] The directivity of the emitted light from sample well 5-108 may depend on the arrangement of the sample within sample well 5-108 such that metal layer 5-116 may act to reflect the emitted light. Thus, the distance between metal layer 5-116 and the fluorescent marker disposed within sample well 5-108 may affect the efficiency of photodetector 1-110 within the same pixel as the sample well for detecting the light emitted by the fluorescent marker. The distance between metal layer 5-116 and the bottom surface of sample well 5-106, proximate to where the sample can be positioned during operation, may range from 100 nm to 500 nm, or any value or range of values within that range. In some embodiments, the distance between metal layer 5-116 and the bottom surface of sample well 5-108 is about 300 nm.

[0083] The distance between the sample and the photodetector may also potentially affect the efficiency of detecting the emitted light. By reducing the distance that the light has to travel between the sample and the photodetector, the detection efficiency of the emitted light can be improved. Also, when the distance between the sample and the photodetector is smaller, the pixel can occupy a smaller footprint area of the integrated device, which may enable more pixels to be included in the integrated device. The distance between the bottom surface of sample well 5-108 and the photodetector may range from 1 μm to 15 μm, or any value or range of values within that range.

[0084] The photonic structure 5-230 can be arranged between the sample well 5-108 and the photodetector 5-110, or otherwise configured to reduce or prevent the arrival of excitation light, which may contribute to signal noise when detecting the emitted light, at the photodetector 5-110. As shown in FIG. 5-1B, one or more photonic structures 5-230 can be arranged between the waveguide 5-220 and the photodetector 5-110. The photonic structure 5-230 can include one or more light-removing photonic structures including a spectral filter, a polarization filter, and a spatial filter. The photonic structure 5-230 can be arranged to align with the individual sample wells 5-108 and their respective photodetectors 5-110 along a common axis. According to some embodiments, a metal layer 5-240 that can act as a circuit for the integrated device 5-102 can also act as a spatial filter. In such embodiments, one or more metal layers 5-240 can be arranged to prevent some or all of the excitation light from reaching the photodetector 5-110.

[0085] The coupling region 5-201 can include one or more optical components configured to couple excitation light from an external excitation source. The coupling region 5-201 can include a grating coupler 5-216 arranged to receive some or all of the beam of excitation light. An example of a suitable grating coupler is described in U.S. Patent Application No. 15 / 844,403, filed Dec. 15, 2017, entitled "OPTICAL COUPLER AND WAVEGUIDE SYSTEM" (which is hereby incorporated by reference in its entirety). The grating coupler 5-216 can couple the excitation light to a waveguide 5-220 configured to propagate the excitation light in the vicinity of one or more sample wells 5-108. Alternatively, the coupling region 5-201 can include other well-known structures for coupling light into a waveguide.

[0086] Components located remotely from the integrated device can be used to position and align the excitation source 5-106 relative to the integrated device. Such components can include optical components such as lenses, mirrors, prisms, windows, apertures, attenuators, and / or optical fibers. Additional mechanical components may be included in the device to enable control of one or more alignment components. Such mechanical components can include actuators, stepper motors, and / or knobs. Examples of suitable excitation sources and alignment mechanisms are described in U.S. Patent Application No. 15 / 161,088, filed May 20, 2016, entitled "PULSED LASER AND SYSTEM" (which is incorporated herein by reference in its entirety). Another example of a beam steering module is described in U.S. Patent Application No. 15 / 842,720, filed December 14, 2017, entitled "COMPACT BEAM SHAPING AND STEERING ASSEMBLY" (which is incorporated herein by reference in its entirety).

[0087] The sample to be analyzed may be introduced into the sample well 5-108 of the pixel 5-112. The sample can be any other suitable sample, such as a biological sample or a chemical sample. The sample can contain multiple molecules, and the sample well can be configured to isolate a single molecule. In some examples, the dimensions of the sample well can act to confine a single molecule within the sample well, enabling measurements to be made on the single molecule. The excitation light can be delivered to the sample well 5-108 to excite the sample or one or more fluorescent markers attached to or otherwise associated with the sample while the sample is within the illumination region in the sample well 5-108.

[0088] During operation, parallel analysis of the sample in the well is performed by exciting some or all of the sample in the well using excitation light and detecting a signal from the sample luminescence with a photodetector. The emitted light from the sample can be detected by a corresponding photodetector and converted into one or more electrical signals. The electrical signals may be transmitted along conductive lines (e.g., metal layer 5-240) in the circuit of the integrated device, and the conductive lines may be connected to a device that interfaces with the integrated device. The electrical signals can subsequently be processed and / or analyzed. The processing or analysis of the electrical signals can be performed by a suitable computing device located on or away from the device.

[0089] Device 5-104 can comprise a user interface to control the operation of device 5-104 and / or integrated device 5-102. The user interface can be configured to enable a user to input information such as commands and / or settings used to control the functions of the device. In some embodiments, the user interface can include buttons, switches, dials, and a microphone for voice commands. The user interface can enable a user to receive feedback regarding the performance of the device and / or integrated device, such as information obtained by appropriate alignment and / or readout signals from photodetectors on the integrated device. In some embodiments, the user interface can provide feedback using a speaker to provide audible feedback. In some embodiments, the user interface can include indicator lights and / or a display screen to provide visual feedback to the user.

[0090] In some embodiments, the device 5-104 can include a computer interface configured to connect to a computing device. The computer interface can be a USB interface, a FireWire® interface, or any other suitable computer interface. The computing device can be any general-purpose computer, such as a laptop or desktop computer. In some embodiments, the computing device can be a server (e.g., a cloud-based server) accessible via a wireless network using a suitable computer interface. The computer interface can facilitate communication of information between the device 5-104 and the computing device. Input information for controlling and / or configuring the device 5-104 can be provided to the computing device and transmitted to the device 5-104 via the computer interface. Output information generated by the device 5-104 can be received by the computing device via the computer interface. The output information can include feedback regarding the performance of the device 5-104, the performance of the integrated device 5-112, and / or data generated from the readout signal of the photodetector 5-110.

[0091] In some embodiments, the apparatus 5-104 can comprise a processing device configured to analyze data received from one or more photodetectors of the integrated device 5-102 and / or to send control signals to the excitation source 5-106. In some embodiments, the processing device can include a general-purpose processor and a specially adapted processor (e.g., a central processing unit (CPU) such as one or more microprocessors or microcontroller cores, a field programmable gate array (FPGA), an application specific integrated circuit (ASIC), a custom integrated circuit, a digital signal processor (DSP), or a combination thereof). In some embodiments, the processing of data from one or more photodetectors can be performed by both the processing device of the apparatus 5-104 and an external computing device. In other embodiments, the external computing device may be omitted, and the processing of data from one or more photodetectors can be performed by the processing device of the integrated device 5-102 only.

[0092] A non-limiting example of a biological reaction taking place within sample well 5-330 is shown in FIG. 5-2. In this example, the continuous incorporation of nucleotides and / or nucleotide analogs into an extension strand that is complementary to the target nucleic acid is taking place within the sample well. Continuous incorporation can be detected in order to sequence a series of nucleic acids (e.g., DNA, RNA). The sample well can have a depth within the range of about 150 nm to about 500 nm or any value or range of values within that range, and a diameter within the range of about 80 nm to about 200 nm. A metallization layer 5-540 (e.g., metallization for a reference potential) can be patterned above the photodetector in order to provide an aperture that blocks stray light from adjacent sample wells and other unwanted light sources. According to some embodiments, polymerase 5-520 can be positioned within sample well 5-330 (e.g., attached to the base of the sample well). The polymerase can incorporate a target nucleic acid (e.g., a portion of a nucleic acid derived from DNA) and sequence an extension strand of a complementary nucleic acid to generate an extension strand of DNA 5-512. Nucleotides and / or nucleotide analogs labeled with different fluorophores can be dispersed within the solution above and within the sample well.

[0093] As shown in FIG. 5-3, when the labeled nucleotide and / or nucleotide analog 5-610 is incorporated into the growing strand of the complementary nucleic acid, one or more attached fluorophores 5-630 can be repeatedly excited by a pulse of light energy coupled from the waveguide 5-315 into the sample well 5-330. In some embodiments, one or more fluorophores 5-630 can be attached to one or more nucleotides and / or nucleotide analogs 5-610 using any suitable linker 5-620. The incorporation event can continue for a period of up to about 100 ms. During this time, pulses of fluorescence emission resulting from excitation of the fluorophores by pulses from the mode-locked laser can be detected using the time-binning photodetector 5-322. By attaching fluorophores having different emission characteristics (e.g., fluorescence decay rate, intensity, fluorescence wavelength) to different nucleotides (A, C, G, T) and detecting and discriminating the different emission characteristics while a strand of DNA 5-512 incorporates the nucleic acid and enables determination of the nucleotide sequence of the growing strand of the DNA.

[0094] According to some embodiments, an instrument 5-104 configured to analyze a sample based on fluorescence emission characteristics can detect differences in fluorescence lifetime and / or intensity between different fluorescent molecules and / or differences in lifetime and / or intensity of the same fluorescent molecule in different environments. By way of illustration, FIG. 5-4 plots two different fluorescence emission probability curves (A and B) that can represent, for example, fluorescence emission from two different fluorescent molecules. Referring to curve A (dashed line), after excitation by a short or ultrashort light pulse, the probability p A (t) of fluorescence emission from the first molecule can decay with time as shown. In some cases, the decrease in the probability of photons being emitted over time is an exponential decay function

[0095] [Number] that can be represented by, where P A0 is the initial emission probability and τ Ais a time parameter associated with a first fluorescent molecule that characterizes the probability of luminescence decay. τ A may be referred to as the "fluorescent lifetime", "luminescence lifetime", or "lifetime" of the first fluorescent molecule. In some cases, τ A The value of can be altered by the local environment of the fluorescent molecule. Other fluorescent molecules may have emission characteristics different from those shown by curve A. For example, other fluorescent molecules may have a decay profile different from a single exponential decay, and their lifetimes may be characterized by a half-life value or some other measure.

[0096] The second fluorescent molecule can have a decay profile that is exponential but has a measurably different lifetime τ B as shown by curve B in FIG. 5-4. In the example shown, the lifetime of the second fluorescent molecule in curve B is shorter than the lifetime of curve A, and the probability of luminescence is higher for the second molecule immediately after excitation than in the case of curve A. In some embodiments, different fluorescent molecules may have lifetimes or half-life values in the range of about 0.1 ns to about 20 ns.

[0097] The inventors have recognized and understood that differences in fluorescence emission lifetimes can be used to discriminate the presence or absence of different fluorescent molecules and / or to discriminate different environments or conditions to which the fluorescent molecules are exposed. In some cases, the operation of apparatus 5-104 can be simplified by discriminating fluorescent molecules based on lifetime (e.g., rather than emission wavelength). As an example, when discriminating fluorescent molecules based on lifetime, the number of wavelength discrimination optical systems (wavelength filters, dedicated detectors for each wavelength, dedicated pulsed light sources at different wavelengths, and / or diffractive optical systems) can be reduced or eliminated. In some cases, a single pulsed light source operating at a single unique wavelength can be used to excite different fluorescent molecules that emit within the same wavelength region of the optical spectrum but have different measurable lifetimes. An analysis system that uses a single pulsed light source rather than multiple light sources operating at different wavelengths to excite and discriminate different fluorescent molecules that emit within the same wavelength region can be less complex to operate and maintain, can be made more compact, and can be manufactured at lower cost.

[0098] Analysis systems based on fluorescence lifetime analysis can have certain advantages, but the amount of information and / or detection accuracy obtained by the analysis system can be improved by enabling additional detection techniques. For example, some analysis systems 5-160 can be further configured to discriminate one or more characteristics of a sample based on fluorescence wavelength and / or fluorescence intensity.

[0099] Referring again to FIG. 5-4, according to some embodiments, different fluorescence lifetimes can be distinguished using a photodetector configured to time-bin fluorescence emission events after excitation of the fluorescent molecules. Time binning can occur during a single charge accumulation cycle of the photodetector. The charge accumulation cycle is the interval between readout events during which the optically generated carriers are accumulated in the bins of the time-binning photodetector. The concept of determining fluorescence lifetime by time binning of the emission events is introduced graphically in FIG. 5-5. The time t immediately prior to t1 eIn this case, a fluorescent molecule or a collection of fluorescent molecules of the same type (e.g., the type corresponding to curve B in FIG. 5-4) is excited by a short or ultrashort light pulse. In the case of a large collection of molecules, the intensity of the emission can have a time profile similar to curve B as shown in FIG. 5-5.

[0100] However, in the case of a single molecule or a small number of molecules, the emission of fluorescent photons occurs, in this example, according to the statistics of curve B in FIG. 5-4. The time-binning photodetector 5-322 can accumulate carriers generated from the emission events into individual time bins (three are shown in FIG. 5-5) that are time-resolved with respect to the excitation time of the fluorescent molecules. When a large number of emission events are summed, the carriers accumulated in the time bins can approximate the decay intensity curve shown in FIG. 5-5, and the binned signals can be used to distinguish different fluorescent molecules or different environments in which the fluorescent molecules are located. Examples of time-binning photodetectors are described in U.S. Patent Application No. 14 / 821,656, filed Aug. 7, 2015, entitled "INTEGRATED DEVICE FOR TEMPORAL BINNING OF RECEIVED PHOTONS", which is incorporated herein by reference in its entirety. Further examples of time-binning photodetectors are described in U.S. Patent Application No. 15 / 852,571, filed Dec. 22, 2017, entitled "INTEGRATED PHOTODETECTOR WITH DIRECT BINNING PIXEL", which is incorporated herein by reference in its entirety.

[0101] In some embodiments, a time-binning photodetector can generate charge carriers in a photon absorption / carrier generation region and directly transfer the charge carriers to charge carrier storage bins within a charge carrier storage region. Such a time-binning photodetector may be referred to as a "direct-binning pixel". An example of a direct-binning pixel is described in U.S. Patent Application No. 15 / 852,571, filed on December 22, 2017, entitled "INTEGRATED PHOTODETECTOR WITH DIRECT BINNING PIXEL" (which is hereby incorporated by reference in its entirety). For illustration purposes, non-limiting embodiments of a time-binning photodetector are shown in FIGS. 5-6. As shown in FIGS. 5-6, the time-binning photodetector 5-950 includes a photon absorption / carrier generation region 5-952, bins of a charge carrier storage region 5-958, and a readout circuit 5-960 that reads signals from the bins of the charge carrier storage region 5-958. The bin to which the charge carriers are transferred is based on the arrival time of photons in the photon absorption / carrier generation region 5-952 that generate the charge carriers. FIGS. 5-6 show an example of a time-binning photodetector having two bins in the charge carrier storage region 5-958, namely bin 0 and bin 1. In some cases, bin 0 can aggregate charge carriers received during one period after a trigger event (e.g., a pulse of excitation light), and bin 1 can aggregate charge carriers received during a later time period relative to the trigger event. However, the charge storage region 5-958 can have any number of bins, such as one bin, three bins, four bins, or more. The time-binning photodetector 5-950 can include electrodes 5-953, 5-955, and 5-956 that can be configured to apply a voltage to establish an electric potential gradient to direct the charge carriers. The time-binning photodetector 5-950 can include a removal region 5-965, which can act as a drain or can be configured to discard charge carriers generated in the photon absorption / carrier generation region 5-952.The time period during which charge carriers are removed by the removal region 5-965 can be timed to occur during a trigger event such as an excitation light pulse.

[0102] Since the excitation light pulse may generate some unwanted charge carriers in the photon absorption / carrier generation region 5-952, a potential gradient is established at pixel 5-950 and such charge carriers can be drained to the removal region 5-965 during the removal period. As an example, the removal region 5-965 can include a high potential diffusion area where electrons are drained to the supply voltage. The removal region 5-965 can comprise an electrode 5-956 that directly charge-couples region 5-952 to the removal region 5-965. The voltage of the electrode 5-956 can be varied to establish a desired potential gradient in the photon absorption / carrier generation region 5-952. During the removal period, the voltage of the electrode 5-956 can be set to a level that draws carriers from the photon absorption / carrier generation region 5-952 to the electrode 5-956 and out to the supply voltage. For example, the voltage of the electrode 5-956 can be set to a positive voltage to attract electrons such that the electrons are pulled away from the photon absorption / carrier generation region 5-952 to the removal region 5-965. The removal region 5-965 can be considered a "lateral removal region" since it enables carriers to be transferred laterally from region 5-952 to the drain.

[0103] After the removal period, the optically generated charge carriers generated in the photon absorption / carrier generation region 5-952 can be time binned. Individual charge carriers can be directed to bins based on their arrival times. To do so, the potential between the photon absorption / carrier generation region 5-952 and the charge carrier accumulation region 5-958 can be varied for respective time periods to establish a potential gradient that directs the optically generated charge carriers to respective time bins. For example, during a first time period, the barrier 5-962 formed by the electrode 5-953 can be lowered, and a potential gradient from the photon absorption / carrier generation region 5-952 to bin 0 can be established, such that carriers generated during this period are transferred to bin 0. Next, during a second time period, the barrier 5-964 formed by the electrode 5-955 can be lowered, and a potential gradient from the photon absorption / carrier generation region 5-952 to bin 1 can be established, such that carriers generated during this subsequent period are transferred to bin 1.

[0104] In some implementations, as shown in FIG. 5-7A, on average only a single photon can be emitted from the fluorophore after an excitation event. At time t e1 after the first excitation event, the photons emitted at time t f1 can occur within a first time interval, and the resulting electronic signal is accumulated in the first electronic storage bin (contributing to bin 1). At time t e2 in a subsequent excitation event, the photons emitted at time t f2 can occur within a second time interval, and the resulting electronic signal contributes to bin 2.

[0105] After a number of excitation events and signal accumulation, the electronic storage bins of the time-binning photodetector 5-322 are read out, providing a multi-valued signal (e.g., a histogram of two or more values, an N-dimensional vector, etc.) for the sample well. The signal value of each bin can depend on the decay rate of the fluorophore. For example, referring again to FIG. 5-4, a fluorophore having decay curve B has a higher signal ratio from bin 1 to bin 2 than a fluorophore having decay curve A. The values from the bins are analyzed and compared against calibration values and / or against each other to determine a particular fluorophore, which in turn can identify the nucleotide or nucleotide analog (or any other molecule or sample of interest) that is bound to the fluorophore when it is in the sample well.

[0106] To further aid in the understanding of signal analysis, the accumulated multi-bin values can be plotted as a histogram, as shown for example in FIG. 5-7B, or recorded as a vector or position in N-dimensional space. Calibration can be performed separately to obtain calibration values for the multi-valued signals (e.g., calibration histograms) of four different fluorophores bound to four nucleotides or nucleotide analogs. As an example, calibration histograms can appear as shown in FIG. 5-8A (fluorescent label associated with the T nucleotide), FIG. 5-8B (fluorescent label associated with the A nucleotide), FIG. 5-8C (fluorescent label associated with the C nucleotide), and FIG. 5-8D (fluorescent label associated with the G nucleotide). By comparing the measured multi-valued signal (corresponding to the histogram of FIG. 5-7B) to the calibrated multi-valued signal, the identity "T" (FIG. 5-8A) of the nucleotide or nucleotide analog incorporated into the growing strand of DNA can be determined.

[0107] In some implementations, fluorescence intensity can be used additionally or alternatively to distinguish different fluorophores. For example, some fluorophores may emit at significantly different intensities, or may have a large difference (e.g., at least about 35% difference) in their excitation probabilities, even if their decay rates are similar. Based on the intensity levels, it may be possible to distinguish different fluorophores by referring to the binned signals (bins 1-3) for the measured excitation light bin 0.

[0108] In some embodiments, different numbers of the same type of fluorophore can be attached to different nucleotides or nucleotide analogs, such that the nucleotides can be identified based on fluorescence 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. Due to the different numbers of fluorophores, there can be different excitation and fluorophore emission probabilities associated with different nucleotides. For example, there may be more emission events for the "T" nucleotide or nucleotide analog during the signal accumulation interval, such that the apparent intensity of these bins may be significantly higher than for the "C" nucleotide or nucleotide analog.

[0109] The inventors have recognized and understood that by distinguishing nucleotides or any other biological or chemical sample based on the decay rate of the fluorophore and / or the intensity of the fluorophore, it is possible to simplify the photoexcitation and detection system in apparatus 5-104. For example, photoexcitation may be performed using a single wavelength source (e.g., a source that generates one unique wavelength, rather than multiple light sources or light sources operating at multiple different unique wavelengths). Also, a wavelength discrimination optical system and filters may not be required in the detection system. Additionally, a single photodetector may be used for each sample well to detect emission from different fluorophores.

[0110] The terms "intrinsic wavelength" or "wavelength" are used to refer to the central wavelength or dominant wavelength within a limited emission bandwidth (e.g., the central wavelength or peak wavelength within a 20 nm bandwidth output by a pulsed light source). In some instances, "intrinsic wavelength" or "wavelength" may be used to refer to the peak wavelength within the entire emission bandwidth of the radiation output by a light source.

[0111] The inventors have recognized and understood that fluorophores having emission wavelengths in the range between about 560 nm and about 900 nm can provide a sufficient amount of fluorescent emission to be detected by a time-binning photodetector (which can be fabricated on a silicon wafer using a CMOS process). These fluorophores can be conjugated to target biomolecules such as nucleotides or nucleotide analogs. Fluorescent emission in this wavelength range can be detected with higher responsiveness in a silicon-based photodetector than fluorescent emission at longer wavelengths. Also, the fluorophores and associated linkers in this wavelength range can be ones that do not interfere with the incorporation of nucleotides or nucleotide analogs into an elongating strand of DNA. The inventors have also recognized and understood that fluorophores having emission wavelengths in the range from about 560 nm to about 660 nm can be photoexcited using a single wavelength source. An exemplary fluorophore within this range is Alexa Fluor 647 available from Thermo Fisher Scientific Inc., located in Waltham, Massachusetts. The inventors have also recognized and understood that excitation light at shorter wavelengths (e.g., between about 500 nm and about 650 nm) may be required to excite fluorophores that emit light at wavelengths between about 560 nm and about 900 nm. In some embodiments, the time-binning photodetector can efficiently detect emission at longer wavelengths from a sample, for example, by incorporating another material such as Ge into the photodetector active region.

[0112] In some embodiments, the sample can be labeled with one or more markers, and the emission associated with the marker can be distinguishable by the device. For example, a photodetector can be configured to convert photons from the emitted light into electrons to form an electrical signal that can be used to determine the lifetime that depends on the emitted light from a particular marker. By labeling the sample with markers of different lifetimes, a particular sample can be identified based on the resulting electrical signal detected by the photodetector.

[0113] The sample can contain multiple types of molecules, and different emission markers can be uniquely associated with the molecular type. The emission marker can emit emitted light during or after excitation. One or more characteristics of the emitted light can be used to identify one or more types of molecules in the sample. The characteristics of the emitted light used to distinguish the types of molecules can include fluorescence lifetime values, intensity, and / or emission wavelength. The photodetector can detect photons (including photons of the emitted light) and provide an electrical signal indicating one or more of these characteristics. In some embodiments, the electrical signal from the photodetector can provide information regarding the distribution of photon arrival times over one or more time intervals. The distribution of photon arrival times can correspond to when photons are detected after a pulse of excitation light is emitted by the excitation source. The value for a time interval can correspond to the number of photons detected during that time interval. The relative values over multiple time intervals can provide an indication of the temporal characteristics (e.g., lifetime) of the emitted light. Analyzing the sample can include distinguishing the markers by comparing the values for two or more different time intervals within the distribution. In some embodiments, an indication of intensity can be provided by determining the number of photons over all time bins within the distribution.

[0114] IV. Conclusion Although some aspects and embodiments of the technology of the present application have been described as above, it is understood that various changes, modifications, and improvements can be easily conceived by those skilled in the art. Such changes, modifications, and improvements are intended to be within the spirit and scope of the technology described in the present application. Therefore, the above-described embodiments are presented only as examples, and it is understood that within the scope of the appended claims and their equivalents, the embodiments of the invention can be implemented in a manner different from that specifically described. Also, any combination of two or more features, systems, articles, materials, kits, and / or methods described in the present specification is included within the scope of the invention of the present disclosure, provided that such features, systems, articles, materials, kits, and / or methods do not conflict with each other.

[0115] Also, as described, some aspects can be embodied as one or more methods. The operations performed as part of the method may be ordered in any suitable way. Accordingly, embodiments may be configured in which the operations are performed in an order different from that illustrated, which may include performing several operations simultaneously, even if they are shown as sequential operations in the exemplary embodiments.

[0116] All definitions defined and used in the present specification are understood to take precedence over dictionary definitions, definitions in the documents incorporated by reference in the present specification, and / or the ordinary meaning of the defined terms.

[0117] As used in the present specification and the claims, the indefinite articles "a" and "an" are understood to mean "one or more" unless clearly indicated otherwise. The phrase "and / or" as used in the present specification and the claims is understood to mean "either or both" of the elements so combined, i.e., elements that exist conjunctively in some cases and disjunctively in other cases.

[0118] As used in the specification and claims of this application, the phrase "one or more," referring to a list of one or more elements, means one or more elements selected from any one or more of the elements in the list of elements, but does not necessarily include one or more of all the elements specifically recited in the list of elements, nor does it exclude any combination of elements in the list of elements. It is understood that this definition allows for the optional presence of elements other than those specifically identified in the list of elements referred to by the phrase "one or more," whether or not those other elements are related to the specifically identified elements.

[0119] In the claims and the above specification of this application, all transitional phrases such as "comprises," "includes," "carries," "has," "contains," "accompanies," "holds," "consists of," etc. are to be understood as non-limiting, i.e., meaning including but not limited to. The transitional phrases "consisting of" and "consisting essentially of" are to be considered exclusive or semi-exclusive transitional phrases, respectively.

Claims

1. A system comprising: an array of reaction chambers comprising a plurality of reaction chambers; a plurality of waveguides configured to deliver excitation light to at least a portion of the array of reaction chambers; a plurality of dummy structures having a tapered width; wherein a vertical range of an optical mode of a waveguide among the plurality of waveguides is changed to adjust light confinement within the waveguide and along a length of the waveguide; and wherein the plurality of waveguides and the plurality of dummy structures are arranged alternately.

2. The system according to claim 1, wherein the vertical range of the optical mode is changed by varying a thickness of a waveguide core layer along the length of the waveguide.

3. The system according to claim 1, wherein the vertical range of the optical mode is changed by varying a refractive index of a waveguide core material or a waveguide cladding material along the length of the waveguide.

4. The system according to claim 1, wherein the plurality of waveguides have a tapered width.

5. The system according to claim 1, wherein the plurality of waveguides have a uniform width.

6. The system according to claim 5, wherein the plurality of waveguides and the plurality of dummy structures are in a waveguide core layer.

7. A system comprising: an array of reaction chambers comprising a plurality of reaction chambers; a plurality of waveguides configured to deliver excitation light to at least a portion of the array of reaction chambers; a plurality of dummy structures having a tapered width; wherein a distance between a waveguide among the plurality of waveguides and the reaction chamber is changed to compensate for waveguide loss; and wherein the plurality of waveguides and the plurality of dummy structures are arranged alternately.

8. The system according to claim 7, wherein a thickness of a cladding layer of the waveguide is controlled to change the distance between the waveguide and the reaction chamber.

9. The system according to claim 7, wherein the plurality of waveguides have a uniform width.

10. The system according to claim 7, wherein the plurality of waveguides have a tapered width.

11. A plurality of waveguides having a tapered width in a first direction; a plurality of dummy structures having a tapered width in a second direction opposite to the first direction; and wherein the plurality of waveguides and the plurality of dummy structures are arranged alternately.

12. A method comprising: Providing a plurality of waveguides for delivering excitation light to an array of reaction chambers comprising a plurality of reaction chambers; Providing a plurality of dummy structures having a tapered width and arranged alternately with the plurality of waveguides; A method comprising: a changing step of changing a vertical range of an optical mode of a waveguide of the plurality of dummy structures so as to adjust light confinement within the waveguide and along a length of the waveguide.

13. The method according to claim 12, wherein the changing step includes a step of changing a thickness of a waveguide core layer along the length of the waveguide.

14. The method according to claim 12, wherein the changing step includes a step of changing a refractive index of a waveguide core material or a waveguide cladding material.

15. A method, comprising: Providing a plurality of waveguides for delivering excitation light to an array of reaction chambers comprising a plurality of reaction chambers; Providing a plurality of dummy structures having a tapered width and arranged alternately with the plurality of waveguides; A method comprising: a changing step of changing a distance between a waveguide of the plurality of waveguides and the reaction chamber.

16. The method according to claim 15, wherein the changing step includes a controlling step of controlling a thickness of a cladding layer of the waveguide.

17. The method according to claim 16, wherein the controlling step includes a step of providing a tapered thickness to the cladding layer by planarizing a material for the cladding layer on a changed waveguide patterning.

18. The method according to claim 17, wherein the controlling step includes a step of providing a tapered thickness to the cladding layer by depositing a material for the cladding layer on a changed waveguide patterning.

19. The method according to claim 17, wherein the controlling step includes a step of providing a tapered thickness to the cladding layer by transferring a topography of a photoresist layer to the cladding layer.

20. A method, comprising: Forming an array of reaction chambers comprising a plurality of reaction chambers; Forming a plurality of waveguides for delivering excitation light to the reaction chambers; Forming a plurality of dummy structures having a tapered width and arranged alternately with the plurality of waveguides; A method comprising: a changing step of changing a waveguide of the plurality of waveguides so as to deliver excitation light having a nearly equal amount to each reaction chamber.

21. The method according to claim 20, wherein the changing step includes a step of changing a vertical range of an optical mode of the waveguide. **Claim 22** The method according to claim 20, wherein the changing step includes a step of changing a thickness along the length of the waveguide. **Claim 23** The method according to claim 20, wherein the changing step includes a step of changing a distance from each reaction chamber along the length of the waveguide. **Claim 24** A method comprising: exciting a sample in each of a plurality of reaction chambers with excitation light delivered through a waveguide among the plurality of waveguides; the waveguide being modified such that substantially the same amount of light is delivered to each reaction chamber; a method in which a plurality of dummy structures having a taper width are arranged alternately with the plurality of waveguides.

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