Optical arrangement for compensating for thermally astigmatism of lens

Abstract

An apparatus includes a sample stage region, an optical assembly, and a camera assembly. The optical assembly includes an objective element, a barrel lens, and a compensation element. The objective element provides a field of view within which at least a portion of the sample stage region is located. The objective lens element has variable astigmatism. The barrel lens is configured to receive light transmitted through the objective element and further transmit the light through an image space. The compensation element is located in the image space. The compensation element is configured to cause a second astigmatism. The second astigmatism is configured to counteract the variable astigmatism. The camera assembly is configured to receive light transmitted from the compensation assembly.

Description

[0001] priority

[0002] This application claims priority to U.S. Provisional Patent Application No. 63 / 463,601, filed on May 3, 2023, entitled “Optical Arrangement for Compensation of Thermally-Induced Astigmatism of Lens,” the disclosure of which is incorporated herein by reference in its entirety. Background Art

[0003] Aspects of the present disclosure are generally related to providing a device, system and method for biological or chemical analysis. Various schemes in biological or chemical research involve carrying out a large number of controlled reactions on a local support surface or in a predefined reaction chamber. The specified reaction can then be observed or detected, and subsequent analysis can help identify or reveal the properties of the chemicals involved in the reaction. For example, in some multiple determinations, an unknown analyte with an identifiable marker (e.g., a fluorescent marker) can be exposed to thousands of known probes under controlled conditions. Each known probe can be placed in the corresponding hole of a circulation cell channel. Any chemical reaction occurring between the known probe and the unknown analyte in the observation hole can help identify or reveal the properties of the analyte. Other examples of such schemes include known DNA sequencing processes, such as sequencing by synthesis (SBS) or cycle array sequencing.

[0004] Although a variety of devices, systems, and methods have been made and used to perform biological or chemical analyses, it is believed that no one prior to the inventors has made or used the devices and techniques described herein. BRIEF DESCRIPTION OF THE DRAWINGS

[0005] Figure 1 Depicted is a schematic diagram of an example of a system that can be used to provide biological or chemical analysis.

[0006] Figure 2 Describes how they can work together to provide Figure 1 A schematic diagram of an example of a set of components of a fluid path in a system.

[0007] Figure 3 Depicted is a schematic diagram of another example of a system that can be used to provide biological or chemical analysis.

[0008] Figure 4 Describes the Figure 1 A cross-sectional view of an example of a flow cell used in the system.

[0009] Figure 5 Describes the Figure 1A cross-sectional view of another example of a flow cell used in a system.

[0010] Figure 6 Depicted Figure 5 A top plan view of a flow cell with the upper chip omitted to show the lower chip.

[0011] Figure 7 Depicted is a schematic diagram of another example of a system that can be used to provide biological or chemical analysis.

[0012] Figure 8 Describes the integration into Figure 7 Schematic diagram of an example of imaging components in a system.

[0013] Fig. 9 Describes the integration into Figure 7 Schematic diagram of another example of an imaging component in a system.

[0014] Fig.10 Describes the integration into Figure 7 Schematic diagram of another example of an imaging component in a system.

[0015] Fig.11A A schematic diagram depicting an example of an arrangement of imaging components, including an example of an astigmatism compensation assembly in a first operational state.

[0016] Fig. 11B Depicted Fig.11A Schematic diagram of the arrangement of imaging components, wherein the astigmatism compensation component is in a second operating state.

[0017] Fig.12 A schematic diagram of an example of an arrangement of imaging components, including an example of an astigmatism compensation assembly and a first example of an actuation arrangement, is depicted.

[0018] Fig.13 A schematic diagram of an example of an arrangement of imaging components, including an example of an astigmatism compensation assembly and a second example of an actuation arrangement, is depicted.

[0019] Fig.14A A schematic diagram depicting an example of an arrangement of imaging components including another example of an astigmatism compensation assembly in a first operational state.

[0020] Fig. 14B Depicted Fig.14A Schematic diagram of the arrangement of imaging components, wherein the astigmatism compensation component is in a second operating state.

[0021] Fig.15A A schematic diagram depicting an example of an arrangement of imaging components including another example of an astigmatism compensation assembly in a first operational state.

[0022] Fig. 15B Depicted Fig.15A Schematic diagram of the arrangement of imaging components, wherein the astigmatism compensation component is in a second operating state.

[0023] Fig.16A A schematic diagram depicting an example of an arrangement of imaging components including another example of an astigmatism compensation assembly in a first operational state.

[0024] Fig. 16B Depicted Fig.16A Schematic diagram of the arrangement of imaging components, wherein the astigmatism compensation component is in a second operating state.

[0025] Fig.17 A schematic diagram depicting an example of an arrangement of imaging components, including another example of an astigmatism compensation assembly.

[0026] Fig.18 A graph representing an example of astigmatism caused by a glass sheet depending on the angle of incidence is depicted.

[0027] Fig.19 A perspective view depicting an example of an astigmatism compensation component.

[0028] Fig. 20 Depicted Fig.19 Another perspective view of the astigmatism compensation component.

[0029] Fig.21 Depicted Fig.19 Exploded perspective view of the astigmatism compensation components.

[0030] Fig. 22 Depicted Fig.19 Another exploded perspective view of the astigmatism compensation assembly, with the housing components omitted for clarity.

[0031] Fig.23A Depicted Fig.19 A bottom plan view of an astigmatism compensation assembly with housing components omitted for clarity and with the astigmatism compensation assembly in a first operating state.

[0032] Fig. 23B Depicted Fig.19 A bottom plan view of an astigmatism compensation assembly with housing components omitted for clarity and with the astigmatism compensation assembly in a second operating state.

[0033] Fig.24A Depicted Fig.19 A top plan view of an astigmatism compensation assembly with housing components omitted for clarity and wherein the astigmatism compensation assembly is in a first operating state.

[0034] Fig. 24B Depicted Fig.19 A top plan view of an astigmatism compensation assembly with housing components omitted for clarity and with the astigmatism compensation assembly in a second operating state. DETAILED DESCRIPTION

[0035] The following detailed description of certain examples will be better understood when read in conjunction with the following drawings. To the extent that the drawings illustrate diagrams of functional blocks of various examples, the functional blocks do not necessarily indicate a division between hardware components. Thus, for example, one or more of the functional blocks (e.g., a processor or memory) may be implemented in a single-chip hardware (e.g., a general-purpose signal processor or random access memory, a hard disk, etc.). Similarly, the programs may be stand-alone programs, may be incorporated into an operating system as subroutines, may be functions in an installed software package, etc. It should be understood that the various examples are not limited to the arrangements and tools shown in the drawings.

[0036] I. Overview of Systems for Biological or Chemical Analysis

[0037] Examples described herein can be used in various biological or chemical processes and systems for academic analysis, commercial analysis or other analysis. More specifically, examples described herein can be used in various processes and systems for events, attributes, quality or characteristics of desired detection indications of specified reactions. Bioassay systems (such as those described herein) can be configured to perform multiple specified reactions that can be detected individually or together. For example, bioassay systems can be used for sequencing dense arrays of nucleic acid features through iterative cycles of enzyme manipulation and image acquisition. In some examples, nucleic acids can be attached to surfaces and amplified. Examples of such amplification are described in the following patent applications: U.S. Patent No. 7,741,463, entitled “Method of Preparing Libraries of Template Polynucleotides,” published on June 22, 2010, the disclosure of which is incorporated herein by reference in its entirety; and / or U.S. Patent No. 7,270,981, entitled “Recombinase Polymerase Amplification,” published on September 18, 2007, the disclosure of which is incorporated herein by reference in its entirety.

[0038] The components used in the bioassay system may include one or more microfluidic channels that deliver reagents or other reaction components to the reaction sites. The reaction sites may be randomly distributed on a substantially planar surface; or may be patterned across a substantially flat surface. Each of the reaction sites may be imaged to detect light from the reaction site. A signal indicating photons emitted from the reaction site and detected by an image sensor may provide an illumination value. These illumination values ​​may be combined into an image indicating photons detected from the reaction site. These images may be further analyzed to identify the composition, reaction, condition, etc. at each reaction site.

[0039] II. Examples of Fluid Devices and Fluid Flow Paths

[0040] A. Example of a system with higher volume throughput

[0041] Figure 1 A schematic diagram of an example of a system (100) that can be used to analyze one or more samples of interest is illustrated. In some embodiments, the sample can include one or more nucleotide (e.g., DNA) clusters that have been linearized to form single-stranded DNA (sstDNA). In the embodiment shown, the system (100) is configured to receive a flow cell box assembly (102) including a flow cell assembly (103) and a sample box (104). The system (100) includes a flow cell receptacle (122) that receives the flow cell box assembly (102), a vacuum chuck (124) that supports the flow cell assembly (103), and a flow cell interface (126) for establishing a fluid connection between the system (100) and the flow cell assembly (103). The flow cell interface (126) can include one or more manifolds. The system (100) also includes an aspirator manifold assembly (106), a sample loading manifold assembly (108), and a pump manifold assembly (110). The system (100) also includes a drive assembly (112), a controller (114), an imaging system (116), and a waste reservoir (118). The controller (114) is electrically and / or communicatively coupled to the drive assembly (112) and the imaging system (116); and is configured to cause the drive assembly (112) and / or the imaging system (116) to perform various functions as disclosed herein.

[0042] In this example, the circulation cell assembly (103) includes a circulation cell (128) having a channel (130) and defining a plurality of first openings (132) that are fluidically coupled to the channel (130) and disposed on a first side (134) of the channel (130). The circulation cell (128) also includes a plurality of second openings (136) that are fluidically coupled to the channel (130) and disposed on a second side (138) of the channel (130). Thus, a fluid can flow through the circulation cell (128) via the channel. Although the circulation cell (128) is shown as including one channel (130), the circulation cell (128) may include two or more channels (130). The circulation cell assembly (103) also includes a circulation cell manifold assembly (140) that is coupled to the circulation cell (128) and has a first manifold fluid line (142) and a second manifold fluid line (144). The flow cell manifold assembly (140) may be in the form of a laminate comprising a plurality of layers, as discussed in more detail below.

[0043] In the illustrated implementation, the first manifold fluid line (142) has a first fluid line opening (146) and is fluidically coupled to each of the first openings (132) of the flow cell (128); and the second manifold fluid line (144) has a second fluid line opening (148) and is fluidically coupled to each of the second openings (136). As shown, the flow cell assembly (103) includes a gasket (150) coupled to the flow cell manifold assembly (140) and fluidically coupled to the fluid line openings (146, 148). In some implementations where the flow cell (128) includes multiple channels (130), the flow cell manifold assembly (140) may include an additional fluid line (152) that couples the first fluid line opening (146) to a single manifold port (154). In such a specific implementation, a single gasket (150) can be coupled to a circulation cell manifold assembly (140) that surrounds a manifold port (154) and is in fluid communication with a plurality of channels (130). In operation, a circulation cell interface (126) engages with a corresponding gasket (150) to establish a fluid connection between the system (100) and the circulation cell (128). The engagement between the circulation cell interface (126) and the gasket (150) reduces or eliminates fluid leakage between the circulation cell interface (126) and the circulation cell (128).

[0044] In the illustrated implementation, the first manifold fluid line (142) has a portion (156) that is substantially parallel to the longitudinal axis (158) of the channel (130); and the second manifold fluid line (144) has a portion (160) that is substantially parallel to the longitudinal axis (158) of the channel (130). Additionally, the first manifold fluid line (142) is shown at least partially adjacent to the first end (162) of the flow cell (128) and spaced apart from the second end (164) of the flow cell (128); and the second manifold fluid line (144) is shown at least partially adjacent to the second end (164) of the flow cell (128) and spaced apart from the first end (162). However, other arrangements of the manifold fluid lines (142, 144) may prove suitable.

[0045] In the illustrated embodiment, the system (100) includes a sample box receptacle (166) that receives a sample box 104 carrying one or more samples of interest (e.g., analytes). The system (100) also includes a sample box interface (168) that establishes a fluid connection with the sample box (104). The sample loading manifold assembly (108) includes one or more sample valves (170). The pump manifold assembly (110) includes one or more pumps (172), one or more pump valves (174), and a cache (176). The valves (170, 174) and the pump (172) can take any suitable form. The cache (176) can include a serpentine cache and can temporarily store one or more reaction components during bypass manipulation of the system (100). While cache (176) is shown as being included in pump manifold assembly (110), cache (176) may alternatively be located elsewhere (eg, in extractor manifold assembly (106) or in another manifold downstream of bypass fluid line (178), etc.).

[0046] The sample loading manifold assembly (108) and the pump manifold assembly (110) allow one or more samples of interest to flow from the sample cartridge (104) to the flow cell cartridge assembly (102) via fluid lines (180). In some implementations, the sample loading manifold assembly (108) can individually load / address each channel (130) of the flow cell (128) with a corresponding sample of interest. The process of loading the channels 130 with samples of interest can occur automatically using the system (100). Figure 1As shown, the sample box (104) and the sample loading manifold assembly (108) are positioned downstream of the circulation cell box assembly (102). In the specific implementation shown, the sample loading manifold assembly (108) is connected between the circulation cell box assembly (102) and the pump manifold assembly (110). In order to draw the sample of interest from the sample box (104) and toward the pump manifold assembly (110), the sample valve (170), the pump valve (174) and / or the pump (172) can be selectively actuated to push the sample of interest toward the pump manifold assembly (110). The sample box (104) can include a plurality of sample reservoirs that can be selectively fluidly accessed via corresponding sample valves (170). In order to cause the sample of interest to flow individually toward the channel (130) of the circulation pool (128) and away from the pump manifold assembly (110), the sample valve (170), the pump valve (174) and / or the pump (172) can be selectively actuated to push the sample of interest toward the circulation pool box assembly (102) and into the corresponding channel (130) of the circulation pool (128).

[0047] The drive assembly (112) is connected to the aspirator manifold assembly (106) and the pump manifold assembly (110) to flow one or more reagents that interact with the sample in the circulation pool (128). In some cases, a reversible terminator is attached to the reagent to allow a single nucleotide to bind to the growing DNA chain. In some such specific implementations, one or more nucleotides have a unique fluorescent label that emits a color when excited. The color (or the absence of color) is used to detect the corresponding nucleotide. In the specific implementation shown, the imaging system (116) excites one or more identifiable labels in the identifiable label (e.g., fluorescent label) and then obtains image data of the identifiable label. The label can be excited by incident light and / or laser, and the image data can include one or more colors emitted by the corresponding label in response to the excitation. The image data (e.g., detection data) can be analyzed by the system (100). Examples of features and functionality that can be incorporated into the imaging system (116) will be described in more detail below.

[0048] After obtaining the image data, the drive assembly (112) interfaces with the aspirator manifold assembly (106) and the pump manifold assembly (110) to flow another reaction component (e.g., a reagent) through the circulation pool (128), which is then received by the waste reservoir (118) via the main waste fluid line (182) and / or otherwise exhausted by the system (100). Some of the reaction components can perform a flushing operation that chemically cleaves the fluorescent label and reversible terminator from the sstDNA. Subsequently, the sstDNA can be ready for another cycle.

[0049] The main waste fluid line (182) is coupled between the pump manifold assembly (110) and the waste reservoir (118). In some embodiments, the pump (172) and / or pump valve (174) of the pump manifold assembly (110) selectively causes the reaction components to flow from the circulation cell box assembly (102) through the fluid line (180) and the sample loading manifold assembly (108) to the main waste fluid line (182). The circulation cell box assembly (102) is coupled to the central valve (184) via the circulation cell interface (126). The central valve (184) is coupled to the circulation cell interface (126) via a fluid line (185). The auxiliary waste fluid line (186) is coupled to the central valve (184) and the waste reservoir (118). In some embodiments, the auxiliary waste fluid line (186) receives excess fluid of the sample of interest from the circulation cell box assembly (102) via the central valve (184) and causes the excess fluid of the sample of interest to flow to the waste reservoir (118) when the sample of interest is reverse loaded into the circulation cell (128), as described herein.

[0050] The extractor manifold assembly (106) includes a shared pipeline valve (188) and a bypass valve (190). The shared pipeline valve (188) can be referred to as a reagent selection valve. The valves (188, 190) of the central valve (184) and the extractor manifold assembly (106) can be selectively actuated to control fluid flow through the fluid pipeline (192, 194, 196). The extractor manifold assembly (106) can be connected to a corresponding number of reagent reservoirs (198) via a reagent extractor (200). The reagent reservoir (198) can accommodate fluid (e.g., reagent and / or another reaction component). In some specific implementations, the extractor manifold assembly (106) includes a plurality of ports. Each port of the extractor manifold assembly (106) can receive a reagent extractor in the reagent extractor (200). The reagent extractor (200) can be referred to as a fluid pipeline. Some forms of the reagent pipette (200) may include an array of pipette tubes extending downwardly along the z dimension from a port in the body of the pipette manifold assembly (106). The reagent reservoirs (198) may be disposed in the cartridge, and the tubes of the reagent pipette (200) may be configured to be inserted into corresponding reagent reservoirs (198) in the reagent cartridge so that liquid reagent may be drawn from each reagent reservoir (198) into the pipette manifold assembly (106).

[0051] The shared line valve (188) of the aspirator manifold assembly (106) is coupled to the central valve (184) via a shared reagent fluid line (196). Different reagents may flow through the shared reagent fluid line (196) at different times. In some versions, when performing a flushing operation prior to changing between one reagent and another, the pump manifold assembly (110) may draw wash buffer through the shared reagent fluid line (196), the central valve (184), and the flow cell cartridge assembly (102).

[0052] The bypass valve (190) of the extractor manifold assembly (106) is connected to the central valve (184) via dedicated reagent fluid lines (194, 196). Each of the dedicated reagent fluid lines (194, 196) can be associated with a single reagent. The fluid that can flow through the dedicated reagent fluid lines (194, 196) can be used during the sequencing operation and can include a cutting reagent, an integration reagent, a scanning reagent, a cutting detergent, and / or a washing buffer.

[0053] The bypass valve (190) is also connected to the cache (176) of the pump manifold assembly (110) via the bypass fluid line (178). The bypass fluid line (178) can be used to perform one or more reagent perfusion operations, hydration operations, mixing operations and / or transfer operations. The perfusion operation, hydration operation, mixing operation and / or transfer operation can be performed independently of the circulation cell box assembly (102). Therefore, the operation using the bypass fluid line (178) can occur during the incubation of one or more samples of interest in the circulation cell box assembly (102), for example. That is, the shared pipeline valve (188) can be utilized independently of the bypass valve (190), so that the bypass valve (190) can utilize the bypass fluid line (178) and / or the cache (176) to perform one or more operations, while the shared pipeline valve (188) and / or the central valve (184) perform other operations simultaneously, substantially simultaneously or offset synchronously.

[0054] The drive assembly (112) includes a pump drive assembly (202) and a valve drive assembly (204). The pump drive assembly (202) can be adapted to interface with one or more pumps (172) to pump fluid through the circulation pool (128) and / or load one or more samples of interest into the circulation pool (128). The valve drive assembly (204) can be adapted to interface with one or more of the valves (170, 174, 184, 188, 190) to control the position of the corresponding valve (170, 174, 184, 188, 190).

[0055] Figure 2An example of a fluid arrangement (220) that can be incorporated into a variation of the system (100) is shown. The example fluid arrangement (220) includes a pump manifold assembly (222) that can operate similarly to the pump manifold assembly (110) described above, a sample loading manifold assembly (228) that can operate similarly to the sample loading manifold assembly (108) described above, a flow cell interface (240) that can operate similarly to the flow cell interface (126) described above, an aspirator manifold assembly (250) that can operate similarly to the aspirator manifold assembly (106) described above, and a waste reservoir (270) that can operate similarly to the waste reservoir (118) described above. The pump manifold assembly (222) is coupled to the port assembly (258) of the aspirator manifold assembly (250) via a fluid line (224), which may be similar to the fluid line (178); and is coupled to the sample loading manifold assembly (228) via a fluid line (226). The sample loading manifold assembly (228) is coupled to the circulation cell interface (240) via a fluid line (230), which may be similar to the fluid line (180); and is coupled to the port assembly (258) via fluid lines (232, 234). The circulation cell interface (240) is coupled to the aspirator manifold assembly (250) via a fluid line (242), which may be similar to the fluid line (185). The aspirator manifold assembly (250) includes a manifold body (252) and a common output port (256), which provides fluid communication via the fluid line (185). The valve assembly (254) controls fluid flow through the common output port (256) and can operate similarly to the central valve (184). The port assembly (258) of the extractor manifold assembly (250) is coupled to the waste reservoir (270) via a fluid line (272), which can be similar to the fluid line (186).

[0056] A plurality of reagent pipettes (260) extend from the manifold body (252) and are fluidly coupled to the valve assembly (254) via corresponding fluid channels (262) in the manifold body (252). The reagent pipettes (260) can operate similarly to the reagent pipettes (200). The valve assembly (254) can be operated to selectively couple the fluid channels (262) to the circulation cell interface (240) via a common output port (256) and a fluid line (230), thereby selectively providing various reagents to the circulation cell interface (240). In other words, when each reagent pipette (260) is disposed in a different corresponding reagent (e.g., in a corresponding reagent reservoir (198)), the circulation cell (e.g., like the circulation cell (128)) coupled to the circulation cell interface (240) can selectively receive those different reagents based on control of the valve assembly (254).

[0057] The port assembly (258) can provide a fluid interface between the pump manifold assembly (222) and the aspirator manifold assembly (250), thereby allowing the aspirator manifold assembly (250) to receive pressurized fluid from the pump manifold assembly (222). The port assembly (258) can also provide a fluid interface between the sample loading manifold assembly (228) and the aspirator manifold assembly (250), thereby allowing the aspirator manifold assembly (250) to receive sample fluid from the sample loading manifold assembly (228). In addition, the port assembly (258) can provide a fluid interface between the waste reservoir (270) and the aspirator manifold assembly (250), thereby allowing the aspirator manifold assembly (250) to transfer waste fluid to the waste reservoir (270). The fluid communication performed via the port assembly (258) can be at least partially regulated by the valve assembly (254).

[0058] Re-reference Figure 1 , the controller (114) of this example includes a user interface (206), a communication interface (208), one or more processors (210), and a memory (212) storing instructions that can be executed by the one or more processors (210) to perform various functions including the disclosed specific implementation. The user interface (206), the communication interface (133), and the memory (212) are electrically and / or communicatively coupled to the one or more processors (210). The user interface (206) can be adapted to receive input from a user and provide information associated with the operation of the system (100) and / or the ongoing analysis to the user. The user interface (206) can include a touch screen, a display, a keyboard, a speaker, a mouse, a trackball, and / or a voice recognition system.

[0059] The communication interface (208) is adapted to enable communication between the system (100) and a remote system (e.g., a computer) via a network (e.g., the Internet, an intranet, a local area network (LAN), a wide area network (WAN), a coaxial cable network, a wireless network, a wired network, a satellite network, a digital subscriber line (DSL) network, a cellular network, a Bluetooth connection, a near field communication (NFC) connection, etc.). Some of the communications provided to the remote system may be associated with analysis results, imaging data, etc. generated or otherwise obtained by the system (100). Some of the communications provided to the system (100) may be associated with fluid analysis operations, patient records, and / or protocols to be executed by the system (100).

[0060] The one or more processors (210) and / or the system (100) may include one or more of a processor-based system or a microprocessor-based system. In some implementations, the one or more processors (210) and / or the system (100) include one or more of a programmable processor, a programmable controller, a microprocessor, a microcontroller, a graphics processing unit (GPU), a digital signal processor (DSP), a reduced instruction set computer (RISC), an application specific integrated circuit (ASIC), a field programmable gate array (FPGA), a field programmable logic device (FPLD), a logic circuit, and / or another logic-based device that performs various functions including the functions described herein.

[0061] The memory (212) may include one or more of the following: semiconductor memory, magnetically readable memory, optical memory, a hard disk drive (HDD), an optical storage drive, a solid-state storage device, a solid-state drive (SSD), flash memory, read-only memory (ROM), erasable programmable read-only memory (EPROM), electrically erasable programmable read-only memory (EEPROM), random access memory (RAM), non-volatile RAM (NVRAM) memory, a compact disk (CD), a compact disk read-only memory (CD-ROM), a digital versatile disk (DVD), a Blu-ray disk, a redundant array of independent disks (RAID) system, a cache, and / or any other storage device or storage disk in which information is stored for any duration (e.g., permanently, temporarily, for a long period of time, for buffering, for caching).

[0062] B. Example of a System with Lower Volume Throughput

[0063] Figure 3 A schematic diagram of another example of a system (300) that can be used to perform analysis on one or more samples of interest is illustrated. Unless otherwise described below, the system (300) of this example can be similar to the system (300) described above with reference to Figure 1The system (100) described herein is configured and operated as described above. In some cases, the system (100) is used to provide a higher volume throughput; while the system (300) is used to provide a lower volume throughput. Alternatively, the system (100, 300) can provide any other suitable amount or degree of throughput. The system (300) of this example receives a reagent kit (302) and includes, in part, a gas source (304), a drive assembly (306), a controller (308), an imaging system (310), and a waste reservoir (312). The reagent kit (302) can be referred to as a consumable, a reagent reservoir, or a reagent assembly. The controller (308) is electrically and / or communicatively coupled to the drive assembly (306) and the imaging system (310), and causes the drive assembly (306) and / or the imaging system (310) to perform various functions as disclosed herein.

[0064] The kit (302) in the illustrated embodiment includes a well assembly (314) having a body (316). The body (316) has a first wall (318) defining a well (320) having a port (322). The first wall (318) has a distal end (324) defining an opening (326) having an opening perimeter (328). The second wall (330) surrounds the first wall (318) and has a distal end (332). The distal end (332) can be referred to as an edge or outer edge. The cover (334) is coupled to the distal end (324) of the first wall (318) and covers the opening (326) along the opening perimeter (328) at a connected portion (336); and is separated from the distal end (324) of the first wall (318) at an unconnected portion (338). The connected portion (336) may be referred to as a connected segment or a connected fragment, and the unconnected portion (338) may be referred to as an unconnected segment or an unconnected fragment. The first wall (318) has a height, and the second wall (330) has a height greater than the height of the first wall (318). The first hole (318) and the second hole (330) may alternatively have the same or similar heights. The impermeable barrier (340) is coupled to the distal end (332) of the second wall (330) and covers the hole (320). The impermeable barrier (340) may be a metal sheet, plastic, etc., and may prevent or inhibit moisture from penetrating into the hole (320) of the test kit (302).

[0065] The unattached portion (338) of the cover (334) forms a vent (342) that allows air to flow out of the hole (320). The dried reagent (348) is contained within the hole (320), and the vent (342) is sized to substantially retain the dried reagent (348) within the hole (320). The body (316) may include a plurality of holes (320), and Figure 3One hole (320) is shown. In practice, liquid (346) can flow into hole (320) via port (322) to rehydrate dried reagent (348). Vent (342) can exhaust gas from hole (320) when liquid (346) flows into hole (320); and cover (334) prevents or inhibits reagent (348) and / or liquid (346) from escaping from hole (320). In other words, vent (342) keeps reagent (348) and / or liquid (346) within hole (320); and prevents or inhibits reagent (348) and / or liquid (346) from migrating out of hole (320). When reagent kit (302) includes more than one hole (320), vent (342) and cover (334) prevent or inhibit cross contamination between reagents. Liquid (346) and dry reagent (348) can flow into and out of hole (320) to mix liquid (346) and dry reagent (348) from liquid reservoir (362). In some embodiments, system (300) and / or test kit (302) can include a mixing chamber for mixing liquid (346) and dry reagent (348). Impermeable barrier (340) can be pierced before liquid (346) flows into hole (320).

[0066] A gas source (304) can be used to pressurize the liquid reservoir (362) to cause the liquid (346) to flow into the hole (320); and / or a pump (350) can draw the liquid (346) from the liquid reservoir (362) and cause the liquid (346) to flow into the hole (320) to rehydrate the reagent (348). The gas source (304) can be provided by the system (300) and / or can be carried by the reagent kit (302). Alternatively, the gas source (304) can be omitted. The pump (350) can be implemented by a syringe pump, a peristaltic pump, a diaphragm pump, etc. Although the pump (350) can be positioned downstream of the circulation pool (368) as shown, the pump (350) can be positioned upstream of the circulation pool (368) or omitted entirely.

[0067] The test kit (302) and / or the system (300) includes a valve (352) that can be selectively actuated to control fluid flow through a fluid line (356). Such a valve (352) can be implemented by a valve manifold, a rotary valve, a selector valve, a pinch valve, a flat valve, a solenoid valve, a check valve, a piezoelectric valve, etc. A regulator (354) can be positioned between the gas source (304) and the valve (352); and regulate the pressure of the gas provided to the valve (352). The regulator (354) can include a valve that controls the flow of gas from the gas source (304).

[0068] The body (316) of the aperture assembly (314) has an edge (364); and the impermeable barrier (340) can be sealingly connected to the body (316) along the edge (364). The impermeable barrier (340) can include a metal sheet, a plastic, and / or any other suitable material. The system (300) can pierce the impermeable barrier (340), the impermeable barrier (340) can be pierced by an individual prior to use, or the impermeable barrier (340) can be pierced by some other structure or method. In the illustrated embodiment, the system (300) includes an actuator assembly (360) that interfaces with the impermeable barrier (340) to pierce the impermeable barrier (340). The system (300) can include a protrusion (such as a column having a blunt end or a sharp end) that can be moved by the actuator assembly (360) to pierce the impermeable barrier (340). The impermeable barrier (340) may alternatively be pierced by an operator prior to positioning the reagent kit (302) in the system (300). The system (300) also includes a liquid reservoir (362) containing a liquid (346). The liquid (346) may include a rehydration liquid, a wash buffer, and / or any other suitable type of liquid.

[0069] The system (300) also includes a circulation cell receptacle (366) that receives a circulation cell (368). The circulation cell (368) can be configured and operated like the circulation cell (128). In some variations, the circulation cell (368) is carried by and / or integrated into the reagent box (302). The circulation cell (368) can carry a sample of interest. The gas source (304) and / or pump (350) can flow the liquid (346) to rehydrate the dried reagent (348) and flow one or more liquid reagents that interact with the sample through the reagent box (302). The imaging system (310) can be configured and operated like the imaging system (116) so that the imaging system (310) can be used to obtain image data from the circulation cell (368). After obtaining the image data, the drive assembly (306) can be connected to the reagent box (302) to flow another reaction component (e.g., a reagent) through the circulation pool (368), which is then received by the waste reservoir (312) and / or otherwise exhausted by the reagent box (302). In this example, the drive assembly (306) includes a pump drive assembly (370), a valve drive assembly (372), and an actuator assembly (360). The pump drive assembly (370) is connected to the pump (350) to pump the fluid through the reagent box (302) and / or the circulation pool (368); and the valve drive assembly (372) is connected to the valve (352) to control the position of the valve (352).

[0070] The controller (308) of this example includes a user interface (374), a communication interface (376), a processor (378), and a memory (380). The user interface (374) can be configured and operated like the user interface (206) of the system (100). The communication interface (376) can be configured and operated like the communication interface (208) of the system (100). The processor (378) can be configured and operated like the processor (210) of the system (100). The memory (380) can be configured and operated like the memory (212) of the system (100).

[0071] Further examples and details of how various features of each system (100, 300) may be configured and operated are described below. By way of further example only, various features of system (100, 300) may be configured and operated in accordance with at least some of the teachings of: International Publication No. WO 2023 / 055873, entitled “Flow Cells and Related Flow Cell Manifold Assemblies and Methods,” published on April 6, 2023, the disclosure of which is incorporated herein by reference in its entirety; U.S. Patent No. 9,958,465, issued on May 1, 2018, entitled “Detection Apparatus having a Microfluorometer, a Fluidic System, and a Flow Cell Latch Clamp Module,” the disclosure of which is incorporated herein by reference in its entirety; and / or U.S. Patent No. 9,958,465, filed on March 30, 2022, entitled “Well Assemblies and Related Systems and Methods.” Methods)", the disclosure of which is incorporated herein by reference in its entirety.

[0072] III. Examples of Flow Cell Configurations

[0073] As described above, the system (100, 300) can perform reactions in the flow cell (128, 368) and / or perform analysis on one or more samples of interest in the flow cell (128, 368). Examples of forms that such flow cells (128, 368) can take are described below, and it should be understood that the flow cell (128, 368) can take various other forms and have various other features in addition to or in place of the features described below.

[0074] A. Example of a single-surface patterned flow cell

[0075] Figure 4 An example of a flow cell (400) is shown, which includes a patterned substrate (402) including a recessed portion (404) separated by a void region (406) and a surface chemical substance (410, 412) positioned in the recessed portion (404). The recessed portion (404) can be in the form of a micropore or a nanopore. The recessed portion (404) can be configured to accommodate a nucleic acid chain or other oligonucleotides, and thereby provide a reaction site for SBS and / or other types of processes. In some versions, each recessed portion (404) has a cylindrical configuration with a generally circular cross-sectional profile. In some other versions, each recessed portion (404) has a polygonal (e.g., hexagonal, octagonal, square, rectangular, elliptical, etc.) cross-sectional profile. Alternatively, the recessed portion (404) can have any other suitable configuration. It should also be understood that the recessed portion (404) can be arranged in any suitable pattern (including but not limited to a grid pattern).

[0076] The surface chemicals (410, 412) of this example include a functionalized coating layer (410) and a primer (412). Although not shown, it should be understood that the recessed portion (404) may also have a surface preparation or treatment chemical (e.g., silane or silane derivative) positioned between the substrate (402) and the functionalized coating layer (410). This same surface preparation or treatment chemical may also be positioned on the gap area (406). In this example, the hydrogel (440) is applied before the cover (420) is bonded to the substrate (402). The hydrogel (440) covers the surface chemicals (410, 412) in the recessed portion (404) and at least a portion of the patterned substrate (402) (e.g., those gap areas (406) that are not also bonding areas (422)). By way of example only, the hydrogel (440) may include PAZAM, cross-linked polyacrylamide, agarose gel, etc.

[0077] The flow cell (400) of this example also includes a cover (420) bonded to the bonding area (422) of the patterned substrate (402). Figure 4In the example shown, the cover (420) includes a top portion (424) connected to a number of side walls (426), and these parts (424, 426) define a portion of each of the six flow channels (430A, 430B, 430C, 430D, 430E, 430F). The corresponding side wall (426) separates one flow channel (430A, 430B, 430C, 430D, 430E, 430F) from each adjacent flow channel (430A, 430B, 430C, 430D, 430E, 430F). Each flow channel (430A, 430B, 430C, 430D, 430E, 430F) is selectively fluidly connected to a corresponding set of recesses (404).

[0078] The cover (420) may be bonded to the bonding region (422) of the substrate (402) using any suitable technique, such as laser bonding, diffusion bonding, anodic bonding, eutectic bonding, plasma activated bonding, glass frit bonding, or other methods known in the art. In some versions, a spacer layer (428) may be used to bond the cover (420) to the bonding region (422). The spacer layer (428) may include any material that seals at least some of the gap regions (404) of the substrate (402) (e.g., the bonding region (422)) and the cover (420) together. Although not shown, the cover (420) or patterned substrate (402) can include inlet ports and outlet ports that fluidly engage other ports (not shown), such as ports of the sample cartridge interface (168), for directing fluids (e.g., from a reagent cartridge or other fluid storage system) into the respective flow channels (430A, 430B, 430C, 430D, 430E, 430F) and out of the flow channels (e.g., to a waste reservoir (118) or another waste removal system). The flow channels (430A, 430B, 430C, 430D, 430E, 430F) can be used, for example, to selectively introduce reaction components or reactants into the hydrogel (440) and the underlying surface chemistry (410, 412) to initiate a specified reaction in / at the recess (404).

[0079] While the flow cell (400) includes a pattern of recesses (404) to provide an array of reaction sites, other variations may provide reaction sites on or at various other types of structural features, including but not limited to continuous flat surfaces and / or protruding surfaces, etc. By way of further example only, the flow cell (400) may be constructed and operated in accordance with at least some of the teachings of U.S. Patent No. 10,919,033, issued on February 16, 2021, entitled “Flow Cells with Hydrogel Coating,” the disclosure of which is incorporated herein by reference in its entirety.

[0080] B. Example of a dual-surface patterned flow cell

[0081] Although Figure 4 An example of a flow cell (400) having a single surface patterned with reaction sites (i.e., recesses (404) formed in substrate (402)) is shown, but in some cases it may be desirable to provide a variation of flow cell (400) that provides two surfaces patterned with reaction sites. Figures 5 and 6 An example of a dual-surface patterned flow cell (450) is shown. In this example, the flow cell (450) includes a pair of wafers (452, 454) bonded together with a spacer layer (456) interposed between the wafers (452, 454). Each wafer (452, 454) is patterned to provide a corresponding plurality of recesses (462, 464) such that when the flow cell (450) is assembled, the recesses (462) of the wafer (452) are aligned with the recesses (464) of the wafer (454). The recesses (462) are separated from each other by gap regions (466); and the recesses (464) are separated from each other by gap regions (468). In this example, the spacer layer (456) does not contact the gap regions (466, 468).

[0082] The recesses (462, 464) of the flow cell (450) can be configured and operated like the recesses (404) of the flow cell (400) described above. Each recess (462, 464) of this example includes a graft coating (470), which can be similar to the functionalized coating layer (410); and a primer (472), which can be similar to the primer (412) described above. Each recess (462, 464) can also include a hydrogel (such as hydrogel (440)) and / or any other suitable feature. Figures 5 and 6As shown, recesses (462, 464) are disposed within a plurality of flow channels (480A, 480B, 480C, 480D). The flow channels (480A, 480B, 480C, 480D) are separated from each other by walls (458) and ends (459) formed by a spacer layer (456). Figure 6 In the example shown, the circulation cell (450) provides four flow channels (480A, 480B, 480C, 480D), wherein each flow channel (480A, 480B, 480C, 480D) accommodates a number of rows and columns of recesses (462, 464). When the circulation cell (450) is used in the system (100, 300), the flow channels (480A, 480B, 480C, 480D) can be used, for example, to selectively introduce reaction components or reactant surface chemicals (470, 472) to initiate a specified reaction in / at the recesses (462, 464). In some cases, since each wafer (452, 454) has its own set of recesses (462, 464) providing corresponding reaction sites, the circulation cell (450) can provide twice as many reactions as a similarly sized circulation cell (400) during a given time period.

[0083] Figure 6 The dashed lines in the figure indicate how the flow cell (450) can be cut to effectively form smaller flow cells (450A, 450A), each of which has its own corresponding pair of flow channels (480A, 480B, 480C, 480D). However, in this example, a single flow cell (450) has more than two flow channels (480A, 480B, 480C, 480D). Although the flow cell (450) includes a pattern of recessed portions (462, 464) to provide an array of reaction sites, other variations may provide reaction sites on or at various other types of structural features (including but not limited to continuous flat surfaces and / or protruding surfaces, etc.). By way of further example only, the flow cell (450) can be constructed and operated in accordance with at least some of the teachings of U.S. Patent No. 10,955,332, issued on March 23, 2021, entitled "Flow Cell Package and Method for Making the Same," the disclosure of which is incorporated herein by reference in its entirety.

[0084] IV. Examples of Imaging System Features

[0085] As described above, the system (100, 300) includes an imaging system (116, 310) that excites one or more identifiable markers (e.g., fluorescent markers) in a sample in a reaction site provided by a recess (404, 462, 464) of a circulation cell (128, 368, 400, 450); and then obtains image data of the identifiable markers. The image data is used to identify nucleotides as part of a nucleic acid sequencing process. Alternatively, the image data can be used for a variety of other purposes. The following description provides details on how some versions of the imaging system (116, 310) can be configured and operated.

[0086] Figure 7 A schematic diagram of another example of a system (500) that can be used to perform analysis on one or more samples of interest is illustrated. Unless otherwise described below, the system (500) of this example can be configured and operated like the system (100,300) described above. The system (500) is configured to perform a large number of parallel reactions in a circulation cell (510). The circulation cell (510) can be configured and operated like the circulation cell (400,450) described above, or can have any other suitable configuration. Therefore, the circulation cell (510) can include one or more flow channels that receive a solution from the system (500) and guide the solution toward the reaction site of the circulation cell (510).

[0087] The system (500) includes a system controller (520) that can communicate with various components, assemblies, and subsystems of the system (500). The controller (520) can be configured and operated as the controllers (114, 308) described above. The imaging assembly (522) of the system (500) includes a light emitting assembly (550) that emits light that reaches reaction sites on the circulation pool (510). The light emitting assembly (550) can include an incoherent light emitter (e.g., emitting a light beam output by one or more excitation diodes) or a coherent light emitter (such as an emitter of light output by one or more lasers or laser diodes). In some specific implementations, the light emitting assembly (550) can include a plurality of different light sources (not shown), each emitting light of a different wavelength range. Some versions of the light emitting assembly (550) can also include one or more collimating lenses (not shown), light structuring optical components (not shown), projection lenses (not shown) operable to adjust the shape and path of the structured light beam, epifluorescence microscope components, and / or other components. Although the system (500) is illustrated as having a single light emitting assembly (550), in some other implementations multiple light emitting assemblies (550) may be included.

[0088] In this example, light from the light emitting assembly (550) is directed by the dichroic mirror assembly (546) through the objective lens assembly (542) to the sample of the circulation pool (510) positioned on the motion stage (570). In the case of fluorescence microscopy of the sample, the fluorescent element associated with the sample of interest fluoresces in response to the excitation light, and the resulting light is collected by the objective lens assembly (542) and directed to the image sensor of the camera system (540) to detect the emitted fluorescence. In some specific implementations, the barrel lens assembly can be positioned between the objective lens assembly (542) and the dichroic mirror assembly (546) or between the dichroic mirror (546) and the image sensor of the camera system (540). The movable lens element can be capable of translating along the longitudinal axis of the barrel lens assembly to resolve the focus on the upper inner surface or the lower inner surface of the circulation pool (510) and / or spherical aberration introduced by the movement of the objective lens assembly (542).

[0089] In this example, the filter switching assembly (544) is interposed between the dichroic mirror assembly (546) and the camera system (540). The filter switching assembly (544) includes one or more emission filters that can be used to pass a specific range of emission wavelengths and block (or reflect) emission wavelengths in other ranges. For example, the emission filter can be used to direct emission light of different wavelength ranges to different image sensors of the camera system (540) of the imaging assembly (522). For example, the emission filter can be implemented as a dichroic mirror that directs emission light of different wavelengths from the circulation pool (510) to different image sensors of the camera system (540). In some variations, the projection lens is interposed between the filter switching assembly (544) and the camera system (540). In some versions, the filter switching assembly (544) can be omitted.

[0090] The system (500) can include a fluid delivery assembly (590) that can direct reagents (e.g., fluorescently labeled nucleotides, buffers, enzymes, cleavage reagents, etc.) to (and through) the flow cell (510) and the waste valve (580). The fluid delivery assembly (590) can be described above in Figures 1 to 3 The system (500) of this example also includes a temperature station actuator (530) and a heater / cooler (532), which can optionally adjust the condition temperature of the fluid in the circulation cell (510). In some specific implementations, the heater / cooler (532) can be fixed to the sample stage (570) on which the circulation cell (510) is placed and / or can be integrated into the sample stage (570).

[0091] The circulation cell (510) can be removably mounted on a sample stage (570) that can provide movement and alignment of the circulation cell (510) relative to the objective lens assembly (542). The sample stage (570) can have one or more actuators to allow the sample stage (570) to move in any of three dimensions. For example, actuators can be provided to allow the sample stage (570) to move in the x-direction, y-direction, and z-direction relative to the objective lens assembly (542), tilt relative to the objective lens assembly (542), and / or otherwise move relative to the objective lens assembly (542). Movement of the sample stage (570) can allow one or more sample locations on the circulation cell (510) to be positioned to be optically aligned with the objective lens assembly (542). Movement of the sample stage (570) relative to the objective lens assembly (542) can be accomplished by moving the sample stage (570) itself, by moving the objective lens assembly (542), by moving some other component of the imaging assembly (522), by moving some other component of the system (500), or any combination of the foregoing. For example, in some implementations, the sample stage (570) can be actuated in the x-direction and the y-direction relative to the objective lens assembly (542), while the focusing component (562) or the z-stage can move the objective lens assembly (542) along the z-direction relative to the sample stage (570).

[0092] In some implementations, a focusing component (562) can be included to control the positioning of one or more elements of the objective lens assembly (542) relative to the flow cell (510) in a focusing direction (e.g., along the z-axis or z-dimension). The focusing component (562) can include one or more actuators that are physically coupled to the objective lens assembly (542), the optical table, the sample stage (570), or a combination thereof to move the flow cell (510) on the sample stage (570) relative to the objective lens assembly (542) to provide appropriate focus for imaging operations. In this example, the focusing component (562) utilizes a focus tracking module (560) that is configured to detect displacement of the objective lens assembly (542) relative to a portion of the circulation pool (510) and output data indicating a focus position to the focusing component (562) or a component thereof, or is operable to control the focusing component (562) (such as a controller (520)) to move the objective lens assembly (542) to position a corresponding portion of the circulation pool (510) at the focus of the objective lens assembly (542).

[0093] In some implementations, the actuator of the focusing component (562) or for the sample stage (570) can be physically coupled to the objective lens assembly (542), the optical table, the sample stage (570), or a combination thereof, such as, for example, being directly or indirectly attached or contacted to the table or a portion thereof by mechanical, magnetic, fluidic, or other means. The actuator of the focusing component (562) can be configured to move the objective lens assembly (542) in the z-direction while maintaining the sample stage (570) in the same plane (e.g., maintaining a horizontal or horizontal attitude perpendicular to the optical axis). In some implementations, the sample stage (570) includes an x-direction actuator and a y-direction actuator to form an xy stage. The sample stage (570) can also be configured to include one or more flip or tilt actuators to flip or tilt the sample stage (570) and / or a portion thereof to account for any slope on its surface.

[0094] The camera system (540) may include one or more image sensors to monitor and track imaging (e.g., sequencing) of the circulation pool (510). The camera system (540) may be implemented as, for example, a CCD or CMOS image sensor camera, although other image sensor technologies (e.g., active pixel sensors) may be used. By way of further example only, the camera system (540) may include a dual sensor time delay integration (TDI) camera, a single sensor camera, a camera with one or more two-dimensional image sensors, and / or other types of camera technologies. Although the camera system (540) and associated optical components are generally Figure 7 500 is shown as being positioned above the flow cell (510), but one or more image sensors or other camera components may be incorporated into the system (500) in a variety of other ways, as will be apparent to those skilled in the art in view of the teachings herein. For example, one or more image sensors may be positioned below the flow cell (510), such as within or below the sample stage (570); or may even be integrated into the flow cell (510).

[0095] Figure 8 Examples of various components that may be integrated into the imaging assembly (522) of the system (500) are shown. Specifically, Figure 8 The arrangement shown may represent a variation of the light emitting assembly (550). Figure 8 The arrangement shown may be particularly useful where the camera system (540) includes a TDI camera. Figure 8In the illustrated arrangement, a line generation module (LGM) (602) and an emission optics module (EOM) (604) are aligned and mechanically coupled to a precision mounting plate (610) and to each other. The EOM (604) includes an objective lens assembly (606) that is aligned with a tube lens (620) via a reflector (608), which in turn is optically coupled to the LGM (602). The LGM (602) may include one or more light sources (e.g., coherent light sources, such as laser diodes). In some examples, the LGM (602) may include: a first light source configured to emit light at a red wavelength; and a second light source configured to emit light at a green wavelength. The LGM (602) may also include optical components, such as focusing surfaces, lenses, reflective surfaces, or reflectors. The optical components may be positioned within the housing of the LGM (602) to direct and focus light emitted from the one or more light sources into adjacent module subassemblies. One or more of the optical components of the LGM (602) may also be configured to shape light emitted from one or more light sources into a desired pattern. For example, in some implementations, the optical components may shape the light into a line pattern (e.g., by using one or more Powell lenses or other beam shaping lenses, diffractive components, or scattering components). In some variations, the LGM (602) may include one or more laser modules that may be individually removed from the LGM (602) and replaced.

[0096] A light beam generated by the LGM (602) is transmitted through an interface baffle between the LGM (602) and the EOM (604), through an objective lens assembly (606), and strikes an optical target (e.g., a flow cell (510)). In some versions, the interface baffle includes an aperture shaped to enable light to pass through its center while shielding interference from external light sources. Responsive light radiation from the target can pass back through the objective lens assembly (606) and enter a tube lens (622). A lens element (622), which can form a portion of the tube lens (620), is configured to be articulated along an axis (e.g., a z-axis) to correct for spherical aberration artifacts introduced by imaging the objective lens assembly (606) through different thicknesses of the flow cell (510) components. As shown, the lens element (622) can be articulated closer to or farther away from the objective lens assembly (606) to adjust the beam shape and path. The objective lens assembly (606) can emit excitation light toward an optical target (e.g., a flow cell (510)) and receive fluorescent emissions from the optical target. The actuator can be configured to position the objective lens assembly (606) to a region of interest adjacent to the optical target. Subsequently, a processor of the controller (520) can execute program instructions for detecting fluorescent emissions from the optical target.

[0097] Fig. 9An example of another configuration that can be provided in the imaging assembly (522) is shown. Specifically, Fig. 9 An imaging assembly (650) is shown positioned relative to a circulation cell (670). The circulation cell (670) can represent any of the various variations of the circulation cells (128, 368, 400, 450, 510) described herein. The circulation cell (670) has an upper layer (671) and a lower layer (673) separated by a fluid-filled channel (675). In the configuration shown, the upper layer (671) is optically transparent, and the imaging assembly (650) is focused on an area (676) on an inner surface (672) of the upper layer (671). In other variations, the imaging assembly (650) can be focused on an inner surface (674) of the lower layer (673). One or both of the surfaces (672, 674) can include array features that will be detected by the imaging assembly (650).

[0098] The imaging assembly (650) includes an objective lens assembly (666) configured to direct excitation radiation from the light emitting assembly (652) to a circulation cell (670); and to direct emission from the circulation cell (670) to a detector (664). In the illustrated arrangement, the excitation radiation from the light emitting assembly (652) passes through a lens (658), through a beam splitter (660), and through an objective lens assembly (666) to the circulation cell (670). In this example, the light emitting assembly (652) includes two light emitting diodes (LEDs) (656, 654) that generate radiation of different wavelengths from each other. Emission radiation from the circulation cell (670) is captured by the objective lens assembly (666) and reflected by the beam splitter (660) through the conditioning optics (662) and to the detector (664) (e.g., a CMOS sensor). The beam splitter (660) is used to direct the emission radiation in a direction orthogonal to the path of the excitation radiation. The position of the objective lens assembly (666) can be moved in the z dimension to change the focus of the imaging assembly (650). The imaging assembly (650) can be moved back and forth in the y direction to capture images of several areas of at least one inner surface (672, 674) of the flow cell (670).

[0099] In this example, a single imaging assembly (650) includes two LEDs (656, 654) that emit light at two different corresponding wavelengths, wherein a single detector (664) detects light emitted by a fluorophore label in a flow cell (670) in response to illumination at the two different wavelengths. In some other versions, there are two or more imaging assemblies (650), wherein each imaging assembly (650) includes a single LED (656, 654) and a single detector (664), such that each imaging assembly (650) provides illumination at only a single corresponding wavelength. As another variation, the two or more detectors (664) may receive excitation radiation from a common light emitting assembly (652).

[0100] Fig.10 An example of another configuration that can be provided in the imaging assembly (522) is shown. Specifically, Fig.10 An imaging assembly (700) is shown positioned relative to a circulation cell (774). The circulation cell (774) can represent any of the various variations of the circulation cells (128, 368, 400, 450, 510) described herein. The circulation cell (770) has a translucent cover (772), a substrate (774), and a liquid layer (776) interposed between the cover (772) and the substrate (774). The biological sample can be located on the inner surface of the cover (772) (above the liquid layer (776)) and / or on the inner surface of the substrate (774) (below the liquid layer (776)).

[0101] The imaging assembly (700) of this example includes an LGM (710) having two light sources (712, 714) disposed therein. The light sources (712, 714) may include laser diodes, diode-pumped solid-state lasers, or other light sources known in the art that output laser beams of different wavelengths (e.g., red light or green light). The light beams output from the light sources (712, 714) are directed through one or more beam shaping lenses 716. In some implementations, one or more beam shaping lenses may be used to shape the light beams output from each or both light sources. The LGM (710) may use one or more Powell lenses to expand and / or shape the laser beam from a single-mode laser source or a near-single-mode laser source. Other beam shaping optics (such as active beam expanders, attenuators, a relay lens, cylindrical lenses, actuated mirrors, diffraction elements, and scattering components) may be used to control uniformity and increase tolerance. The laser beams may intersect at the back focus of the objective lens to provide better tolerance on the surface of the flow cell (770).

[0102] The LGM (710) of this example also includes reflectors (718, 720). The light beam generated by the light source (712) is reflected by the reflector (718) so as to be directed through an aperture or semi-reflective surface of the reflector (720) and directed into the EOM (740) through a single interface port. Similarly, the light beam generated by the light source (714) is reflected by the reflector (720) so as to be directed into the EOM (740) through a single interface port. In some examples, an additional set of articulated reflectors can be incorporated near the reflectors (718, 720) to provide an additional tuning surface. A dichroic mirror (720) can be used to combine the two light beams. The reflectors (718, 720) can each be configured to be articulated using manual control or automatic control to align the light beams from the light sources (712, 714). In this example, the light beam also passes through a shutter element (722).

[0103] The EOM (740) includes an objective lens assembly (756) and a z-stage (758) that moves the objective lens assembly (756) longitudinally closer to or farther away from the circulation cell (770). The LGM (710) is configured to produce uniform line illumination through the objective lens assembly (756). Subsequently, the z-stage (758) can move the objective lens assembly (756) to focus the light beam onto any of the inner surfaces of the circulation cell (770) (e.g., focusing on the biological sample). In some specific implementations, the objective lens assembly (756) can be configured to focus the light beam at a focal point outside the circulation cell (770), such as to increase the line width of the light beam at the surface of the circulation cell (770).

[0104] The EOM (740) of this example also includes a semi-reflective mirror (754) to guide light through the objective lens assembly (756) while allowing light returning from the circulation pool (774) to pass through. The EOM (740) also includes a tube lens (744) and a correction lens (748). The correction lens (748) can be longitudinally hinged closer to or farther away from the objective lens assembly (756) by the z stage (746) to ensure accurate imaging (e.g., to correct spherical aberration caused by moving the objective lens assembly (756); and / or spherical aberration caused by imaging through a thicker substrate, etc.). Light transmitted through the correction lens (748) and the tube lens (744) passes through the filter element (742) and enters the camera system (730). The camera system (730) includes one or more optical sensors (732) to detect light emitted from the biological sample in response to the incident light beam.

[0105] In this example, the EOM (740) further includes a semi-reflective mirror (752) to reflect the focus tracking beam emitted from the focus tracking module (FTM) (760) onto the flow cell (774), and then reflect the light returned from the flow cell (774) back into the FTM (760). The FTM (760) may include a focus tracking optical sensor to detect the characteristics of the returned focus tracking beam and generate a feedback signal to optimize the focus of the objective lens assembly (756) on the flow cell (774).

[0106] The direction, size and / or polarization of the laser beam can be adjusted by using lenses, reflectors and / or polarizers. Optical lenses (e.g., cylindrical, spherical or aspherical) can be used to actively adjust the illumination focus on the dual surfaces of the flow cell (770) target. The LGM (710) can also include multiple units, each of which is designed for a specific / different wavelength and polarization. Stacking multiple units can be used to increase laser power and increase wavelength options. Two or more laser wavelengths can be combined with a dichroic mirror and a polarizer.

[0107] By way of example only, the focus tracking module (560) and / or other components of the imaging assembly (522) may be constructed and operated in accordance with at least some of the teachings of: U.S. Patent No. 10,416,428, entitled “Systems and Methods for Improved Focus Tracking Using a Light Source Configuration,” issued on September 17, 2019, the disclosure of which is incorporated herein by reference in its entirety; U.S. patent application No. 63 / 300,531, entitled “Dynamic Detilt Focus Tracking,” filed on January 18, 2022, the disclosure of which is incorporated herein by reference in its entirety; and / or U.S. patent application No. 63 / 410,961, entitled “Spot Error Handling for Focus Tracking,” filed on September 28, 2022, the disclosure of which is incorporated herein by reference in its entirety. By way of further example only, components of the imaging assembly (522) may be configured and operated in accordance with at least some of the teachings of: U.S. Patent No. 10,774,371, issued on September 15, 2020, entitled "Laser Line Illuminator for High Throughput Sequencing," the disclosure of which is incorporated herein by reference in its entirety; and / U.S. Patent No. 9,958,465, issued on May 1, 2018, entitled "Detection Apparatus having a Microfluorometer, a Fluidic System, and a Flow Cell Latch Clamp Module," the disclosure of which is incorporated herein by reference in its entirety.

[0108] V. Examples of Optical Arrangements for Compensating for Thermally Induced Astigmatism of a Lens

[0109] During operation of a system, such as any of the systems (100, 300, 500) described herein, one or more components may tend to heat up, particularly during an initial stage of use of the system. In some such cases, the heated component may deform or experience some other structural change, and such deformation or other structural change may affect the performance characteristics of the component. For example, as described above, an imaging system (116, 310) or imaging assembly (522, 700) may include an objective lens assembly (542, 606, 666, 756). Such an objective lens assembly (542, 606, 666, 756) may include one or more objective lens elements that heat up during operation of the system (100, 300, 500). Such heating of the objective lens elements may be caused by heat generated by incident light from a light emitting assembly (550, 652), heat generated by incident light from a line generation module (LGM) (602, 710), and / or some other heat source.

[0110] Heating of an objective lens element during operation of a system, such as any of the systems (100, 300, 500) described herein, may tend to dynamically generate aberrations (e.g., astigmatism) in the objective lens element; or otherwise dynamically modify aberrations already present in the objective lens element. For example, heating of the objective lens element may cause changes in the refractive index gradient and / or thermal expansion coefficient of the objective lens element; and these physical changes may provide a corresponding generation or change in the astigmatism of the objective lens element. In some cases, such thermal induction or thermal change of aberrations may tend to occur during an initial heating phase of the objective lens element; subsequently, when the objective lens element maintains a substantially stable operating temperature, the generated / modified aberrations may tend to be substantially stable.

[0111] As described above, the objective lens assembly (542, 606, 666, 756) can provide an image of a reaction site on a circulation cell (128, 368, 400, 450, 510) during operation of the system (100, 300, 500), wherein high image quality is desired to obtain precise and accurate information about the real-time characteristics of a small data point (e.g., a nucleotide) at the reaction site. In the case where the objective lens element has a dynamically changing aberration profile, the dynamically changing aberration profile may tend to dynamically affect the image quality in an unfavorable manner unless there is some dynamic compensation for the dynamically changing aberration profile. To the extent that it may be possible to provide some degree of dynamic compensation for the thermally induced dynamically changing aberration profile of the objective lens element through image processing techniques, it may be desirable to provide an optical hardware-based solution to provide dynamic compensation for the thermally induced dynamically changing aberration profile of the objective lens element. Several examples of optical solutions are described below that can be used to provide dynamic compensation for the thermally induced dynamically changing aberration profile of the objective lens element.

[0112] A. Example of an optical arrangement with two pivot compensation elements

[0113] 1. Overview

[0114] FIG. 11A to FIG. 11B An example of an arrangement (800) that can be integrated into an imaging system (116, 310) or an imaging assembly (522, 700) is shown. The arrangement (800) of the example includes a circulation cell (810), an objective lens element (820), a tube lens (830), a compensation assembly (840), and a camera (850). The objective lens element (820) is positioned above the circulation cell (810), which can be configured and operated as any of the variations of the circulation cells (128, 368, 400, 450, 510) described herein. In this example, fluorescent markers at reaction sites on the circulation cell (810) emit light in response to excitation from one or more excitation light sources (not shown); and the emission light beam is transmitted from the circulation cell (810) through the objective lens element (820) to the tube lens (830). In addition to the emission light beam passing through the objective lens element (820), the excitation light beam can also pass through the objective lens element (820) to reach the circulation cell (820). The excitation beam may cause heating of the objective lens element (820), as described herein. As further described herein, the excitation beam may be emitted from a light emitting assembly (550, 652), from a line generation module (LGM) (602, 710), or from some other light source.

[0115] The emission beam from the circulation pool (810) is usually emitted along the image axis (IA), wherein the objective lens element (820) is centered along the image axis (IA). In this example, the image axis (IA) is parallel to the z-axis. The objective lens element (820) of this example is configured to collimate the emission beam substantially. Although only one objective lens element (820) is shown in this example, such representation is intended to be a schematic representation only. It should be understood that the objective lens element (820) can actually include a lens assembly, which is formed by a plurality of lens elements and / or other optical features.

[0116] The tube lens (830) is also centered along the image axis (IA) so that the collimated emission beam from the objective lens element (820) passes through the tube lens (830) into the converging image space. Although only one lens element is shown in this example to represent the tube lens (830), such representation is intended to be a schematic representation only. It should be understood that the tube lens (820) can actually include a lens assembly formed by multiple and / or other optical features.

[0117] The compensation assembly (840) is positioned on an image axis (IA) in a converging image space between a tube lens (830) and a camera (850). The compensation assembly (840) of this example includes a first compensation plate (842) and a second compensation plate (844). In this example, each compensation plate (842, 844) includes a flat plate formed of a light-transmitting material (e.g., glass); although other configurations may also be used. The first compensation plate (842) is located at a longitudinal position along the image axis (IA) where a first vertical reference plane (R1) intersects the image axis (IA). The second compensation plate (844) is located at a longitudinal position along the image axis (IA) where a second vertical reference plane (R2) intersects the image axis (IA). Therefore, the first compensation plate (842) is longitudinally interposed between the second compensation plate (844) and the tube lens (830); and the second compensation plate (844) is longitudinally interposed between the first compensation plate (842) and the camera (850).

[0118] In this example, the first compensation plate (842) has the same structural configuration as the second compensation plate (844), such that the compensation plates (842, 844) have the same material composition, thickness, etc. However, the compensation plates (842, 844) are positioned at different angular orientations along the image axis (IA). Specifically, Fig.11A In the illustrated operating state, the first compensation plate (842) is positioned along a first plate plane (P1) that is tilted at a first tilt angle (θ1) in a clockwise direction relative to a first reference plane (R1) about a tilt axis parallel to the x-axis. Fig.11A In the same operating state shown, the second compensation plate (844) is positioned along a second plate plane (P2) that is tilted at a first tilt angle (θ1) in a counterclockwise direction relative to a second reference plane (R2) about a tilt axis parallel to the x-axis. In other words, the compensation plates (842, 844) are oriented at equal and opposite tilt angles about respective tilt axes parallel to the x-axis.

[0119] The compensation assembly (840) is configured to compensate for any astigmatism that may be provided by the combination of the objective lens element (820) and the tube lens (830). Specifically, the first compensation plate (842) may be configured to cause a first astigmatism that partially offsets the astigmatism provided by the combination of the objective lens element (820) and the tube lens (830); and the second compensation plate (842) may be configured to cause a second astigmatism that completes the offset of the astigmatism provided by the combination of the objective lens element (820) and the tube lens (830). The first astigmatism caused by the first compensation plate (842) may be a function of the thickness, refractive index, and incident angle (based on the tilt angle (θ)) of the first compensation plate (842); and the second astigmatism caused by the second compensation plate (844) may be a function of the thickness, refractive index, and incident angle (based on the tilt angle (θ)) of the second compensation plate (844).

[0120] The image axis (IA) may tend to shift slightly in a first direction along the y dimension after the emitted light passes through the first compensation plate (842); then, shift slightly in a second direction along the y dimension again after passing through the second compensation plate (844). Fig.11A This shift is not depicted. In this example, because the compensation plates (842, 844) are oriented at equal and opposite tilt angles, the image shift caused by the second compensation plate (844) is equal and opposite to the image shift caused by the first compensation plate (842). Therefore, the image axis (IA) in the space between the second compensation plate (844) and the camera (850) is aligned with the image axis (IA) in the space between the flow cell (810) and the first compensation plate (842).

[0121] It should be understood from the foregoing that the compensating plates (842, 844) work together to counteract or compensate for any astigmatism that may be provided by the combination of the objective lens element (820) and the tube lens (830); while also providing an image from the circulation cell (810) to the camera (850) along the aligned image axis (IA). The camera (850) captures the image transmitted from the compensation assembly (840). The camera (850) may be configured and operated like any of the camera systems (540, 730) described herein; and may include a CCD or CMOS image sensor camera, an active pixel sensor camera, a dual sensor time delay integration (TDI) camera, a single sensor camera, a camera with one or more two-dimensional image sensors, and / or other types of camera technology. The images captured using the camera (850) may be analyzed to evaluate the characteristics of the reaction sites on the circulation cell (810), as described herein.

[0122] As described above, before the excitation light is activated and incident on the objective lens element (820), the temperature of the objective lens element (820) may have a first value. After the excitation light is activated and incident on the objective lens element (820) during the initial stage of operation, the temperature of the objective lens element (820) may increase and eventually stabilize at or near a second temperature value. During continued operation, the temperature of the objective lens element (820) may remain substantially constant at or near the second temperature value because the excitation light remains activated and incident on the objective lens element (820). Also as described above, when the temperature of the objective lens element (820) increases from the first temperature to the second temperature, the increase in temperature may generate an aberration (such as astigmatism) in the objective lens element (820) or cause the aberration to change. In other words, the objective lens element (820) may have thermally induced dynamic aberrations during the initial heating period. In this example, the temperature of the tube lens (830) does not substantially change during operation, so that any changes in aberrations of the tube lens (830) during operation can be considered negligible. In some other versions, temperature changes may induce or otherwise change aberrations in the tube lens (830) and / or other optical components of the imaging system (116, 310) or imaging assembly (522, 700).

[0123] Since the compensation assembly (840) is configured to counteract or compensate for any astigmatism that may be provided by the combination of the objective lens element (820) and the tube lens (830), it may be desirable to dynamically adjust the compensation assembly (840) to "keep up" with thermally induced dynamic aberrations of the objective lens element (820) and / or other optical components during the initial heating cycle. In other words, it may be desirable to provide dynamic adjustment to the compensation assembly (840) to dynamically counteract or compensate for thermally induced dynamic aberrations of the objective lens element (820) and / or other optical components during the initial heating cycle. Such adjustment may be performed by pivoting each compensation plate (842, 844) about its respective pivot axis, since the counteracted astigmatism of each compensation plate (842, 844) may be a function of the tilt angle (θ) of each compensation plate (842, 844).

[0124] Although the examples herein are provided in the context of dynamic aberrations of an objective lens element (820), the teachings herein may also be applied to situations where one or more other optical components of an imaging system (116, 310) or imaging assembly (522, 700) provide dynamic aberrations (regardless of whether the objective lens element (820) also provides dynamic aberrations or does not provide dynamic aberrations. In other words, the teachings herein do not necessarily rely on the objective lens element (820) being the source of dynamic aberrations. Compensation plates (842, 844) may be utilized to correct aberrations from any source that may otherwise reach the camera (850).

[0125] FIG. 11A to FIG. 11B An example of pivoting movement of the compensation plates (842, 844) to simultaneously adjust the tilt angle (θ) of each compensation plate (842, 844) is shown together. Fig.11A In the embodiment, the first compensation plate (842) is tilted at a first tilt angle (θ1) in a clockwise direction around its tilt axis relative to a first reference plane (R1); and the second compensation plate (844) is tilted at a first tilt angle (θ1) in a counterclockwise direction around its tilt axis relative to a second reference plane (R2). Fig. 11B In the embodiment of the present invention, the first compensation plate (842) is tilted at a second tilt angle (θ2) about its tilt axis in a clockwise direction relative to a first reference plane (R1); and the second compensation plate (844) is tilted at a second tilt angle (θ2) about its own tilt axis in a counterclockwise direction relative to the second reference plane (R2). Therefore, the compensation plates (842, 844) pivot about their respective tilt axes in opposite angular directions to transition from the first tilt angle (θ1) to the second tilt angle (θ2). The astigmatism induced by the compensation plates (842, 844) at the second tilt angle (θ2) will be different compared to the astigmatism induced by the compensation plates (842, 844) at the first tilt angle (θ1). This is due to the difference in the incident angle on the compensation plates (842, 844) at the second tilt angle (θ2) relative to the incident angle on the compensation plates (842, 844) at the first tilt angle (θ1), because the induced astigmatism is at least partially affected by the incident angle.

[0126] In some cases, the astigmatism induced by the compensation plates (842, 844) at a first tilt angle (θ1) cancels the astigmatism provided by the combination of the objective lens element (820) and the tube lens (830) at an initial lower temperature; and the astigmatism induced by the compensation plates (842, 844) at a second tilt angle (θ2) cancels the astigmatism provided by the combination of the objective lens element (820) and the tube lens (830) at a higher operating temperature. The rate at which the compensation plates (842, 844) pivot from the first tilt angle (θ1) to the second tilt angle (θ2) can be selected to track the rate at which the astigmatism provided by the combination of the objective lens element (820) and the tube lens (830) changes due to an increase in the temperature of the objective lens element (820). In other words, when the compensation plates (842, 844) are pivoted from the first tilt angle (θ1) to the second tilt angle (θ2), the compensation assembly (840) can dynamically compensate for dynamic changes in astigmatism provided by the combination of the objective lens element (820) and the tube lens (830) when the objective lens element (820) heats up. To the extent that the temperature of the objective lens element (820) remains substantially stable after warming to a normal operating temperature, the compensation plates (842, 844) can remain fixed at the second tilt angle (θ2) so that the compensation assembly (840) maintains a fixed astigmatism offset.

[0127] It should be understood that when the compensation plates (842, 844) pivot from the first tilt angle (θ1) to the second tilt angle (θ2), the image shift caused by the compensation plates (842, 844) along the y dimension can move accordingly along the y dimension. However, because the compensation plates (842, 844) rotate at the same rate in opposite directions around parallel axes, the light can continue to be centered along the aligned image axis (IA) in the space between the second compensation plate (844) and the camera (850). Although in some versions the compensation plates (842, 844) rotate simultaneously at the same rate in opposite directions around parallel axes, there may be situations where one compensation plate (842, 844) pivots independently relative to the other compensation plate (842, 844). Such independent pivoting of a single compensation plate (842, 844) may be provided (e.g., while the other compensation plate (842, 844) remains stationary) to adjust the beam position in the y-direction to maintain a desired alignment of the beam axis on the image sensor of the camera (850).

[0128] It should also be understood that the compensating assembly (840) can be positioned anywhere along the image axis (IA) within the converging image space between the tube lens (830) and the camera (850). FIG. 11A to FIG. 11B closer to the tube lens (830) than FIG. 11A to FIG. 11BShown closer to camera (850). Additionally, compensation plates (842, 844) may be positioned any suitable distance apart from one another.

[0129] 2. Example of a method of operating a compensation component

[0130] Some versions of the arrangement (800) can provide real-time tracking of thermally induced or thermally variable astigmatism of the objective lens element (820); and dynamically adjust the tilt angle (θ) of the compensation plate (842, 844) in real-time through a feedback loop. In some such cases, image processing techniques can be used to achieve real-time tracking of changes in thermally induced or thermally variable astigmatism of the objective lens element (820). For example, an algorithm executed by the controller (114, 308, 520) can provide analysis of images captured by the camera (850) during an initial stage of operation as the objective lens element (820) heats up from an initial resting temperature to a normal stable operating temperature, thereby tracking the thermally induced or thermally variable astigmatism of the objective lens element (820) in real-time. By way of example only, the image analysis algorithm can track full width at half maximum (FWHM) values ​​associated with images captured along the x-dimension and FWHM values ​​associated with images captured along the y-dimension to assess the astigmatism of the objective lens element (820). The same algorithm may further drive one or more actuators, etc., to provide pivotal movement of the compensation plates (842, 844) in real time via a feedback loop based on the tracked astigmatism of the objective lens element (820). In some versions using a real-time feedback loop to drive the pivotal movement of the compensation plates (842, 844), such pivotal movement of the compensation plates (842, 844) may be varied each time the arrangement (800) is used to the extent that the dynamically changing aberration profile of the objective lens element (820) may vary between different uses of the arrangement (800) (e.g., due to environmental factors, equipment age factors, different types of excitation light profiles used, etc.).

[0131] As an alternative to using a temporary real-time feedback loop to drive the pivotal movement of the compensation plates (842, 844) each time the arrangement (800) is used, the pivotal movement of the compensation plates (842, 844) can be provided based on a predetermined adjustment profile. In other words, the controller (114, 308, 520) does not need to process the captured images each time the arrangement (800) is used to track changes in thermally induced astigmatism or thermally variable astigmatism of the objective lens element (820). Instead, the controller (114, 308, 520) can be programmed with only a predetermined adjustment profile; and can execute only the predetermined adjustment profile on a consistent basis each time the arrangement (800) is used. The predetermined adjustment profile can be established by a calibration process. The calibration process can be performed at a facility where the arrangement (800) is manufactured. Alternatively, the calibration process can be performed at the location where the arrangement (800) will ultimately be used, such as during an initialization process when a consumer first uses the arrangement (800).

[0132] Regardless of where the calibration process is performed, the calibration process may include a series of the following operations: allowing the objective lens element (820) to warm up from an initial resting temperature to a normal stable operating temperature; tracking the dynamic astigmatism of the objective lens element (820) in real time through image processing techniques as described above; and driving the pivotal movement of the compensation plates (842, 844) based on the tracked dynamic astigmatism of the objective lens element (820). In some cases, after a first calibration run, the controller (114, 308, 520) may deactivate the excitation light source and allow the temperature of the objective lens element (820) to return to the initial resting temperature; then, repeat the process to perform a second calibration run. This may be repeated as many times as desired. The controller (114, 308, 520) may ultimately determine an optimal adjustment profile for the pivotal movement of the compensation plates (842, 844), and thereby establish the optimal adjustment profile as a predetermined adjustment profile for subsequent use of the arrangement (800).

[0133] 3. Example of a compensation assembly with dual actuators

[0134] Fig.12An example of an arrangement (900) is shown in which dual actuators (970, 980) are used to drive a compensation assembly (940). Unless otherwise described below, the arrangement (900) is substantially the same as the arrangement (800). The arrangement (900) includes a circulation pool (910), an objective lens element (920), a tube lens (930), a compensation assembly (940), and a camera (950). The compensation assembly (940) includes a first compensation plate (942) and a second compensation plate (944). The arrangement (900) of this example differs from the arrangement (800) in that the arrangement (900) is shown to include a controller (960), a first actuator (980), and a second actuator (970). The controller (960) can be configured and operated like any other controller (114, 308, 520) described herein, so that the controller (960) can be operated to process images captured by the camera (950), process other data, and control the operation of other components. To this end, controller (960) is further operable to control actuators (970, 980) to drive movement of compensation plates (942, 944) by activating actuators (970, 980), as described herein.

[0135] A first actuator (980) is coupled to the first compensation plate (942) such that the first actuator (980) is operable to drive pivotal movement of the first compensation plate (942). A second actuator (970) is coupled to the second compensation plate (944) such that the second actuator (970) is operable to drive pivotal movement of the second compensation plate (944). In some versions, each actuator (970, 980) includes a motor such that activation of the actuator (970, 980) rotates a drive shaft of the motor and thereby drives pivotal movement of the compensation plates (942, 944). In some other versions, each actuator (970, 980) includes a solenoid or a voice coil. Alternatively, the actuators (970, 980) may take any other suitable form. In the present example, each compensation plate (942, 944) has its own dedicated actuator (970, 980), so that it is theoretically possible to independently activate the actuators (970, 980) and thereby independently drive the pivotal movement of the compensation plates (942, 944). For example, there may be a situation where one compensation plate (942, 944) pivots independently relative to another compensation plate (942, 944). Such independent pivoting of a single compensation plate (942, 944) can be provided (e.g., while the other compensation plate (942, 944) remains stationary) to adjust the beam position in the y direction, thereby maintaining the desired alignment of the beam axis on the image sensor of the camera (950). However, in the present example, the controller (960) is configured to activate the actuators (970, 980) synchronously with each other.

[0136] 4. Example of a compensation assembly with a single actuator and linkage

[0137] Fig.13 An example of an arrangement (1000) is shown in which a single dual actuator (1070) is used to drive a compensation assembly (1040). Unless otherwise described below, the arrangement (1000) is substantially the same as the arrangement (800). The arrangement (1000) includes a circulation cell (1010), an objective lens element (1020), a tube lens (1030), a compensation assembly (1040), and a camera (1050). The compensation assembly (1040) includes a first compensation plate (1042) and a second compensation plate (1044). The arrangement (1000) of this example differs from the arrangement (1000) in that the arrangement (1000) is shown as including a controller (1060), an actuator (1070), and a linkage (1080). The controller (1060) can be configured and operated like any other controller (114, 308, 520) described herein, such that the controller (1060) is operable to process images captured by the camera (1050), process other data, and control the operation of other components. To this end, the controller (1060) is also operable to control the actuator (1070) by activating the actuator (1070) to drive the movement of the compensation plates (1042, 1044), as described herein.

[0138] The linkage (1080) is coupled to the actuator (1070) and to the two compensation plates (1042, 1044). The linkage (1080) of this example includes a mechanical assembly that is configured to drive simultaneous synchronous pivotal movement of the compensation plates (1042, 1044) in opposite directions when the linkage (1080) is activated by the actuator (1070). By way of example only, the linkage (1080) may include a plurality of rods, bars, or other links pivotally engaged together. By way of further example only, the linkage (1080) may include a plurality of gears meshed together. By way of further example only, the linkage (1080) may include a set of cams that provide a combination of engaged drive surfaces and load-bearing surfaces. Alternatively, the linkage (1080) may take any other suitable form. Similarly, the actuator (1070) may take any suitable form, including but not limited to a motor, a solenoid, a voice coil, and the like.

[0139] B. Example of an optical arrangement with a single pivot compensation element

[0140] In some circumstances, it may be desirable to provide variations of the compensation assembly (840, 940, 1040) having only one compensation element. FIG. 14A to FIG. 14BAn example of such an arrangement (1100) is shown. The arrangement (1100) of this example includes a circulation cell (1110), an objective lens element (1120), a tube lens (1130), a compensation assembly (1140), and a camera (1150). The circulation cell (1110), the objective lens element (1120), the tube lens (1130), and the camera (1150) can be configured and operated like the circulation cell (810), the objective lens element (820), the tube lens (830), and the camera (850) described above. Unless otherwise described below, the compensation assembly (1140) can be configured and operated like the compensation assembly (840).

[0141] The compensation assembly (1140) of this example includes only one compensation plate (1142). Similar to the compensation plates (842, 844), the compensation plate (1142) is configured to compensate (by itself) for any astigmatism that may be provided by the combination of the objective lens element (1120) and the tube lens (1130). Similarly, the compensation plate (1142) is capable of rotating between different tilt angles (θ1, θ2) about a pivot axis to adjust its own astigmatism, thereby dynamically compensating for thermally induced changes in the astigmatism of the objective lens element (1120) as the objective lens element (1120) heats up from an initial resting temperature to a normal stable operating temperature. However, since there is only one compensation plate (1142) in the compensation assembly (1140), when the compensation plate (1142) pivots about a pivot axis parallel to the z-axis, the image axis (IA) will shift along the y-dimension. Fig. 14B This displacement is shown where the image axis (IA2) in the space between the compensation plate (1142) and the camera (1150) is displaced relative to the image axis (IA) in the space between the flow cell (1110) and the compensation plate (1142). It should be understood that for illustrative purposes, FIG. 14A to FIG. 14B The shifts shown in the transitions can be considered as magnifications.

[0142] In the arrangement (1100) of this example, the shift in the image axis (IA, IA2) is accounted for by movement of the camera (1150) such that the camera (1150) moves with the image axis (IA, IA2) to remain centered along the image axis (IA2). FIG. 14A to FIG. 14B. Such movement of the camera (1150) can be provided in various ways. By way of example only, a dedicated actuator (not shown) can drive the camera (1150) to move along the y dimension. Such an actuator can be configured and operated like any of the other actuators (970, 980, 1070) described herein. As another variation, a single actuator (not shown) can be coupled to a linkage (not shown); and the linkage can be coupled to both the compensation plate (1142) and the camera (1150). As another variation, the camera (1150) can be sized and configured to allow image movement due to movement of the compensation plate (1142). The combination of the actuator and the linkage can provide simultaneous, synchronized pivotal movement of the compensation plate (1142) and the camera (1150). The linkage can be configured and operated similarly to the linkage (1080) described above. Alternatively, pivotal movement of the compensation plate (1142) may be provided in any other suitable manner; and movement of the camera (1150) in the y-dimension may be provided in any other suitable manner.

[0143] FIG. 15A to FIG. 15B Another example of how to solve the image shift caused by the movement of a single compensation plate is shown. Specifically, FIG. 15A to FIG. 15B An arrangement (1200) is shown, which includes a flow cell (1210), an objective lens element (1220), a tube lens (1230), a compensation assembly (1240), a camera (1250), and a reflective element (1260). The arrangement (1200) is configured and operates substantially similar to the arrangement (1100). However, unlike the camera (1150) of the arrangement (1100), the camera (1250) of the arrangement is in a fixed position, wherein the reflective element (1260) is interposed between the compensation plate (1242) of the compensation assembly (1240) and the camera (1250). The reflective element (1260) reflects light from the compensation plate (1242) toward the camera (1250). Although the camera (1250) is shown as facing the y dimension, this is merely an example, and the camera (1250) may alternatively be oriented in any other suitable direction.

[0144] Similar to the compensation plate (1142) of the arrangement (1100), the compensation plate (1242) of the arrangement (1200) is configured to compensate (by itself) for any astigmatism that may be provided by the combination of the objective lens element (1220) and the tube lens (1230). Similarly, the compensation plate (1242) is capable of rotating between different tilt angles (θ1, θ2) about the pivot axis to adjust its own astigmatism, thereby dynamically compensating for thermally induced changes in the astigmatism of the objective lens element (1220) as the objective lens element (1220) heats up from an initial resting temperature to a normal stable operating temperature. Also similar to the compensation plate (1142) of the arrangement (1100), after the compensation plate (1242) is pivoted, the compensation plate (1242) of the arrangement (1200) provides a shifted image axis (IA2).

[0145] In the arrangement (1200) of this example, the shift in the image axis (IA, IA2) is accounted for by movement of the reflective element (1260) such that the reflective element (1260) pivots about an axis parallel to the x-axis, thereby redirecting light from the compensation plate (1242) to ensure that the light continues to be centered on the camera (1250). FIG. 15A to FIG. 15B . This pivotal movement of the reflective element (1260) is shown in the transition of . Such movement of the reflective element (1260) can be provided in various ways. By way of example only, a dedicated actuator (not shown) can drive the pivotal movement of the reflective element (1260). Such an actuator can be configured and operated like any of the other actuators (970, 980, 1070) described herein. As another variation, a single actuator (not shown) can be coupled to a linkage (not shown); and the linkage can be coupled to both the compensation plate (1242) and the reflective element (1260). The combination of the actuator and the linkage can provide simultaneous, synchronized pivotal movement of the compensation plate (1242) and the reflective element (1260). The linkage can be configured and operated similarly to the linkage (1080) described above. Alternatively, the pivotal movement of the compensation plate (1242) can be provided in any other suitable manner; and the pivotal movement of the reflective element (1260) can be provided in any other suitable manner. In some variations, the reflective element (1260) is configured to deform rather than rotate in order to controllably redirect light toward the camera (1250).

[0146] As another example of a variation, the reflective element (1260) can translate along a path parallel to the z-axis. Such movement of the reflective element (1260) can move the image on the image sensor of the camera (1250) to correct for the offset caused by the compensation plate (1242).

[0147] C. Examples of Optical Arrangements with Distortion Compensation Elements

[0148] FIG. 16A to FIG. 16B Another example of an arrangement (1300) that can be integrated into an imaging system (116, 310) or an imaging assembly (522, 700) is shown. The arrangement (1300) of this example includes a circulation cell (1310), an objective lens element (1320), a tube lens (1330), a compensation assembly (1340), and a camera (1350). The circulation cell (1310), the objective lens element (1320), the tube lens (1330), and the camera (1350) can be configured and operated like the circulation cell (810), the objective lens element (820), the tube lens (830), and the camera (850) described above. Unless otherwise described below, the compensation assembly (1340) can be configured and operated like the compensation assembly (840).

[0149] The compensation assembly (1340) of this example includes a single compensation element (1342). The compensation element (1342) of this example is configured to selectively deform in response to a control signal. For example, Fig.16A The compensating element (1342) is shown in a substantially undeformed state, wherein the compensating element is substantially flat and positioned along a vertical reference plane (R1) that intersects the image axis (IA). Fig. 16B A compensating element (1342) is shown in a deformed state, wherein the compensating element is deformed relative to a reference plane (R1). In the example shown, the compensating element (1342) is deformed along the z dimension. In some versions, the compensating element (1342) is deformed along one or more other dimensions in addition to being deformed along the z dimension. By way of example only, the compensating element (1342) may include a membrane and a plurality of electrodes, wherein the electrodes may be selectively activated to drive the deformation of the membrane in a controlled manner. Some such versions may be configured similarly to the Delta 7 phase modulator of Phaseform GmbH of Freiburg, Germany. Some such deformable versions of the compensating element (1342) may also include a liquid or gel. Alternatively, the deformable compensating element (1342) may take any other suitable form.

[0150] As the compensating element (1342) deforms, the astigmatism caused by the compensating element (1342) may change accordingly. Thus, the compensating element (1342) may be controllably deformed to dynamically change the astigmatism caused by the compensating element (1342). The controlled deformation (and therefore, the changed astigmatism) may be provided in such a way as to counteract or compensate for the astigmatism caused by the combination of the objective lens element (1320) and the tube lens (1342). Furthermore, since the astigmatism of the objective lens element (1320) changes dynamically as the objective lens element (1320) heats up from an initial resting temperature to a normal stable operating temperature, the deformation of the compensating element (1342) may be adjusted accordingly to "keep up" with the thermally induced dynamic aberrations of the objective lens element (1342) during the initial heating period (i.e., to dynamically correct the thermally induced dynamic aberrations of the objective lens element (1342)).

[0151] It should be understood that a controller, such as controllers (114, 308, 520), can be used to drive the compensation element (1342) according to any of the control schemes described herein. In other words, the compensation element (1342) can be driven based on a temporary real-time feedback loop, based on a predetermined adjustment profile, or based on any other suitable basis.

[0152] exist FIG. 16A to FIG. 16B In the example shown, deformation of the objective lens element (1342) does not cause any displacement of the image axis (IA). In some other variations, deformation of the compensation element (1342) may cause any displacement of the image axis (IA). In such cases, the camera (1350) may be operated in a manner similar to that described above with reference to FIG. 14A to FIG. 14B Alternatively, a movable reflective element may be interposed between the compensation element (1342) and the camera (1350), and the movable reflective element may be moved in a manner similar to that described above with reference to FIG. 15A to FIG. 15B The objective lens element (1342) is moved in a certain manner to track the shifted image axis (IA). Alternatively, any other suitable components and configurations may be used to address the shift of the image axis (IA) caused by deformation of the objective lens element (1342).

[0153] D. Example of an Optical Arrangement with a Cylinder Compensation Element

[0154] Although the above examples include flat plates and deformable members as examples of compensating elements (842, 844, 942, 944, 1042, 1044, 1142, 1242, 1342), other types of components may be used. For example, Fig.17An example of an arrangement (1400) is shown, which includes a circulation cell (1410), an objective lens element (1420), a tube lens (1430), a compensation assembly (1440), and a camera (1450). The circulation cell (1410), the objective lens element (1420), the tube lens (1430), and the camera (1450) can be configured and operated like the circulation cell (810), the objective lens element (820), the tube lens (830), and the camera (850) described above. Unless otherwise described below, the compensation assembly (1440) can be configured and operated like the compensation assembly (840).

[0155] The compensation assembly (1440) of this example includes a plurality of compensation elements (1442). Each compensation element (1442) of this example is configured as a cylindrical lens element, wherein a convex surface (1444) faces the tube lens (1430) and a flat surface (1446) faces the camera (1450). Each compensation element (1442) can provide a discrete degree of astigmatism compensation. Each compensation element (1442) can also be selectively positioned in or away from the image axis (IA). Thus, while in Fig.17 Only one compensating element (1442) is shown as being positioned along the image axis (IA), but other situations may provide two or more compensating elements (1442) positioned along the image axis (IA). In some versions, any compensating element (1442) not positioned along the image axis (IA) may be positioned along a lateral axis (LA) that is laterally spaced from the image axis (IA). Alternatively, any compensating element (1442) not positioned along the image axis (IA) may be positioned and arranged in any other suitable manner.

[0156] Since each compensating element (1442) in this example provides a discrete degree of astigmatism compensation, the compensating elements (1442) can be selectively clustered along the image axis (IA) to provide varying, collective degrees of astigmatism compensation. For example, when the combination of the objective lens element (1420) and the tube lens (1430) is at an initial, relatively low temperature, a first number of compensating elements (1442) can be positioned along the image axis (IA). As the temperature of the objective lens element (1420) and the tube lens (1430) increases during an initial stage of operation (wherein the thermally induced astigmatism of the objective lens element (1420) changes accordingly), the number of compensating elements (1442) along the image axis (IA) can be dynamically varied to track the changing astigmatism of the objective lens element (1420) until the combination of the objective lens element (1420) and the tube lens (1430) reaches a stable operating temperature. In other words, the compensation component (1440) can provide dynamically adjustable astigmatism compensation by selectively changing the number of compensation elements (1442) along the image axis (IA).

[0157] It should be understood that a controller (such as controller (114, 308, 520)) can be used to drive movement of the compensation element (1442) according to any of the control schemes described herein. In other words, the compensation element (1442) can be driven based on a temporary real-time feedback loop, based on a predetermined adjustment profile, or based on any other suitable basis. It should also be understood that one or more actuators (not shown) can be used to drive such movement of the compensation element 1442. Such actuators can include pneumatic actuators, solenoids, voice coils, electric rack and pinion assemblies, electric crankshaft assemblies, and / or any other suitable components and arrangements. In addition, the compensation elements (1442) can be driven independently relative to each other so as to be positioned in or away from the image axis (IA).

[0158] As Fig.17 In another variation of the illustrated example, different compensating elements (1442) of the compensating assembly (1440) may have different respective radii of curvature at the curved surface (1444). Thus, each compensating element (1442) may provide a degree of astigmatism compensation that is different from the astigmatism compensation provided by the other compensating elements (1442). In some such variations, only one compensating element (1442) may be positioned on the image axis (IA) at a given time, wherein such compensating element (1442) is selected based on the particular degree of astigmatism compensation provided by that particular compensating element (1442). However, there may be other situations in which two or more compensating elements (1442) having different respective radii of curvature are selectively positioned simultaneously along the image axis (IA) to collectively provide a desired degree of astigmatism compensation.

[0159] Fig.18 An example of how the parameters of astigmatism can vary depending on the angle of incidence is shown using a compensating element (e.g., a glass plate) such as the various compensating elements described herein. Specifically, Fig.18 A graph (1475) is shown having a curve (1481) of the effective optical path length along the sagittal plane, a curve (1483) of the effective optical path length along the tangential plane, and a curve (1485) representing the difference between the curves (1481, 1483). Fig.18 In the depicted example, the thickness of the compensating element is 1 mm; and the refractive index (n) is 1.5. In the tangential plane, the transfer matrix can be defined as follows, where t is the plate thickness, n is the refractive index, and T is the angle of incidence:

[0160]

[0161] The transfer matrix for the longitudinal plane can be defined as follows:

[0162]

[0163] VI. Example of an Astigmatism Compensation Assembly Having a Housing Component and an Actuation Assembly

[0164] Figures 19 to 21 An example of an astigmatism compensation assembly (1500) that can be incorporated into any of the various arrangements (800, 900, 1000, 1100, 1200) described above is shown. For example, the compensation assembly (1500) of the example can represent a variation of the compensation assembly (840); or more specifically, a variation of the compensation assembly (1040). The compensation assembly (1500) of the example includes an upper housing element (1502), a first side housing element (1504), a second side housing element (1506), a third side housing element (1508), a fourth side housing element (1510), and a bottom plate (1520). The upper housing element (1502) is fixed to the upper end of the housing elements (1504, 1506, 1508, 1510). The lower end of the housing elements (1504, 1506, 1508, 1510) is fixed to the bottom plate (1520). The housing elements (1502, 1504, 1506, 1508, 1510) and the base plate (1520) cooperate to form a box shape.

[0165] The annular element (1512) is coupled to the fourth side housing element (1510). In some versions, the annular element (1512) structurally facilitates the physical coupling or integration of the compensation assembly (1500) with other components of the arrangement (800, 900, 1000, 1100, 1200). The annular element (1512) may also be coupled to the fourth side housing element (1510) using a sliding sealing ring to provide a seal from external light and contamination while allowing for axial length adjustment to match other system components.

[0166] like Figures 22 to 24B As shown, the compensation assembly (1500) further includes an actuator (1530) and a fixed frame plate (1560). The actuator (1530) includes a body (1532) and a shaft (1534). The body (1532) is fixed to the fixed frame plate (1560) via a clamp assembly (1562). The actuator (1530) is operable to drive the linear movement of the shaft (1534) relative to the body (1532) and the linear movement relative to the fixed frame plate (1560), as shown in FIG. Fig.23A and Fig. 23B as shown in the transition between Fig.24A and Fig. 24B. In some versions, actuator (1530) comprises a stepper motor coupled to a mechanical assembly (e.g., a rack and pinion, a helical gear and a nut, etc.) operable to convert the rotation of the motor shaft into the linear movement of shaft (1534). Alternatively, actuator (1530) may take any other suitable form.

[0167] Likewise Figures 22 to 24B As shown, the compensation assembly (1500) further includes a first frame (1540), a second frame (1550), a first rotation axis (1542), a second rotation axis (1552), a first gear (1544), a second gear (1554), a first crank arm (1546), and a second crank arm (1556). Each frame (1540, 1550) defines a corresponding opening (1541, 1551). Each opening (1541, 1551) is configured to receive a corresponding compensation plate (e.g., compensation plates (842, 844, 942, 944, 1042, 1044) described above, etc.). The frame (1540, 1550), the housing element (1508, 1510) and the ring element (1512) are configured and arranged so that light can pass through the housing element (1508, 1510), the ring element (1512) and the compensation plate disposed in the opening (1541, 1551). In some versions, light enters the compensation assembly (1500) via the third side housing element (1508) and leaves the compensation assembly (1500) via the ring element (1512) and the fourth side housing element (1510). In some other versions, light enters the compensation assembly (1500) via the ring element (1512) and the fourth side housing element (1510) and leaves the compensation assembly (1500) via the third side housing element (1508).

[0168] The first frame (1540) is securely fixed to the first rotating shaft (1542) so that the first frame (1540) and the first rotating shaft (1542) rotate together as a whole. Similarly, the second frame (1550) is securely fixed to the second rotating shaft (1552) so that the second frame (1550) and the second rotating shaft (1552) rotate together as a whole. The rotating shafts (1542, 1552) pass through the base plate (1520) and are operable to rotate relative to the base plate (1520). The first rotating shaft (1542) is also securely fixed to the first gear (1544) and one end of the first crank arm (1546). The other end of the first crank arm (1546) is fixed to one end of the coil spring (1548). FIG. 23A to FIG. 24BThe coil spring (1548) is schematically shown. The other end of the coil spring (1548) is fixed to the fixed frame plate (1560). In this example, the coil spring (1548) can apply a resilient bias on the crank arm (1546), thereby applying a rotational resilient bias on the first rotating shaft (1542), the first gear (1544) and the first frame (1540) (e.g., FIG. 23A to FIG. 23B 1540). In some other versions, a torsion spring or other elastic element applies a rotational elastic bias to the first rotational shaft (1542), the first gear (1544), and the first frame (1540). In still other versions, a rotational elastic bias is not applied to the first rotational shaft (1542), the first gear (1544), and the first frame (1540).

[0169] The second rotating shaft (1552) is securely fixed to the second gear (1554) and one end of the second crank arm (1556). A roller bearing (1558) is fixed to the other end of the second crank arm (1556). The roller bearing (1558) is positioned to engage with a head (1536) at the end of the shaft (1534) of the actuator (1530). Therefore, when the actuator (1530) is activated to drive linear movement of the shaft (1534), the head (1536) abuts against the roller bearing (1558), so that the linear movement of the shaft (1534) provides rotational movement of the second gear (1554) via the crank arm (1556). The gears (1544, 1554) engage with each other via meshing teeth, so that rotation of the second gear (1554) in a first angular direction provides rotation of the first gear (1544) in a second angular direction. Fig.23A and Fig. 23B The movement is shown in the transition between .

[0170] As described above, the first frame (1540), the first rotating shaft (1542) and the first gear (1544) rotate together as a whole. Also as described above, the second frame (1550), the second rotating shaft (1552) and the second gear (1554) rotate together as a whole. Fig.23A and Fig. 23B The rotational movement described in the context of also provides for opposite angular movement of the frames (1540, 1550). Fig.24A and Fig. 24B This opposite angular movement of the frames (1540, 1550) is shown in the transition between. In the case where the compensating element is fixed in the opening (1541, 1551) of the frame (1540, 1550), this opposite angular movement of the frames (1540, 1550) will provide an opposite angular movement of the compensating element, as described above in FIG. 11A to FIG. 13 as described in the context of .

[0171] The resilient rotational bias provided by the coil spring (1548) to the first gear (1544) will be transmitted to the second gear (1554) via the meshing teeth of the gears (1544, 1554). Therefore, when the shaft (1534) is retracted toward the body (1532), the gears (1544, 1554), the shaft (1542, 1544) and the crank arms (1546, 1556) will move in the opposite direction from the corresponding angular positions (such as Fig. 23B and Fig. 24B angular positions shown) toward corresponding angular positions (such as Fig.23A and Fig.24A Furthermore, when the shaft (1534) is retracted toward the body (1532), the resilient rotational bias applied by the coil spring (1548) on the gears (1544, 1554) and crank arms (1546, 1556) will maintain contact between the head (1536) and the roller bearing (1558).

[0172] Although not in Figures 19 to 24B , but actuator (1530) may be coupled to a controller configured to control actuator (1530) to drive movement of frames (1540, 1550) (and, therefore, compensation elements secured within frames (1540, 1550)) in accordance with the teachings herein. Such a controller may be similar to the various controllers (114, 308, 520, 960, 1060) described above.

[0173] VII. Combined Examples

[0174] The following examples relate to various non-exhaustive ways in which the teachings of this article can be combined or applied. The following examples are not intended to limit the coverage of any claims that may be provided at any time in the present application or subsequent submissions of this application. It is not intended to make a disclaimer. The following examples are provided only for the purpose of illustration. It is conceivable that the various teachings of this article can be arranged and applied in a variety of other ways. It is also expected that some variations may omit certain features mentioned in the following examples. Therefore, any of the aspects or features mentioned below should not be considered decisive, unless otherwise, for example, by the inventor or the successor of the inventor concerned clearly indicates so at a later date. If any claim proposed in the present application or in the subsequent submissions related to this application includes additional features other than those mentioned below, these additional features should not be assumed to be added for any reason related to patentability.

[0175] Example 1

[0176] A device, the device comprising: a sample stage area; an optical component, the optical component comprising: an objective lens element, the objective lens element providing a field of view, at least a portion of the sample stage area is located within the field of view, the objective lens element having a variable astigmatism; a tube lens, the tube lens configured to receive light transmitted through the objective lens element and further transmit the light through an image space; a compensation component, the compensation component is located in the image space and is configured to cause a second astigmatism, the second astigmatism is configured to offset the variable astigmatism; and a camera component, the camera component configured to receive light transmitted from the compensation component.

[0177] Example 2

[0178] According to the device of embodiment 1, the compensation component is capable of operating to change the second astigmatism to dynamically cancel the variable astigmatism of the objective lens element.

[0179] Example 3

[0180] According to the device of embodiment 2, the device also includes a processor, which is capable of controlling the compensation component to change the second astigmatism.

[0181] Example 4

[0182] According to the apparatus of embodiment 3, the processor is operable to control the compensation component to change the second astigmatism based on a predetermined adjustment profile.

[0183] Example 5

[0184] According to the apparatus of embodiment 3, the processor is operable to determine an astigmatism value of the objective lens element.

[0185] Example 6

[0186] According to the apparatus of embodiment 5, the processor is operable to control the compensation component to change the second astigmatism based on the determined astigmatism value of the objective lens element.

[0187] Example 7

[0188] According to the device described in any one of embodiments 1 to 6, the compensation component includes a first light-transmitting plate and a second light-transmitting plate.

[0189] Example 8

[0190] According to the device described in embodiment 7, the first light-transmitting plate is inclined at a first angle around a first axis, and the second light-transmitting plate is inclined at a second angle around a second axis.

[0191] Example 9

[0192] According to the device described in embodiment 8, the first light-transmitting plate and the second light-transmitting plate are positioned along an image axis, the first axis is orthogonal to the image axis, and the second axis is parallel to the first axis.

[0193] Example 10

[0194] According to the device described in any one of Embodiments 8 to 9, the magnitude and direction of the first angle are respectively equal to and opposite to the magnitude and direction of the second angle.

[0195] Embodiment 11

[0196] According to the device of any one of embodiments 8 to 10, the compensation component also includes a first actuator, which is operable to drive one or both of the movement of the first light-transmitting plate around the first axis or the movement of the second light-transmitting plate around the second axis.

[0197] Example 12

[0198] According to the device described in Example 11, the compensation component also includes a linkage device, and the first actuator and the linkage device are configured to work together to drive the first light-transmitting plate to move around the first axis and concomitantly drive the second light-transmitting plate to move around the second axis.

[0199] Embodiment 13

[0200] According to the device described in Example 11, the compensation component also includes a second actuator, the first actuator is connected to the first light-transmitting plate to drive the first light-transmitting plate to move around the first axis, and the second actuator is connected to the second light-transmitting plate to drive the second light-transmitting plate to move around the second axis.

[0201] Embodiment 14

[0202] According to the apparatus of any of embodiments 11 to 13, the first actuator includes a motor.

[0203] Embodiment 15

[0204] According to the device described in any one of Examples 11 to 14, the compensation component further includes a first gear and a second gear, the first light-transmitting plate is used to rotate integrally with the first gear, and the second light-transmitting plate is used to rotate integrally with the second gear.

[0205] Example 16

[0206] In the apparatus of embodiment 15, the first gear is positioned to directly mesh with the second gear.

[0207] Embodiment 17

[0208] According to the device described in any one of Examples 15 to 16, the compensation assembly further comprises a crank arm connected to the first gear, the first actuator is used to drive the rotational movement of the crank arm, and the crank arm is used to drive the rotational movement of the first gear.

[0209] Embodiment 18

[0210] According to the device described in any one of embodiments 11 to 17, the compensation assembly further comprises a housing element, and the housing element forms a box around the first light-transmitting plate and the second light-transmitting plate.

[0211] Embodiment 19

[0212] According to the device described in any one of Examples 11 to 18, the compensation component also includes a first axis, a second axis and a base plate, the first axis and the second axis pass through the base plate, the first axis is used to drive the first light-transmitting plate to move around the first axis, and the second axis is used to drive the second light-transmitting plate to move around the second axis.

[0213] Embodiment 20

[0214] According to the device of any one of embodiments 1 to 6, the compensation component includes a first light-transmitting element and a reflective element.

[0215] Embodiment 21

[0216] According to the device of any one of embodiments 1 to 20, the compensation component includes a deformable element.

[0217] Embodiment 22

[0218] In the device of embodiment 21, the deformable element is light transmissive.

[0219] Embodiment 23

[0220] In the device of embodiment 21, the deformable element is reflective.

[0221] Embodiment 24

[0222] According to any one of embodiments 1 to 23, the device also includes a heating element, which is capable of operating to heat the objective lens element and thereby change the astigmatism of the objective lens element.

[0223] Embodiment 25

[0224] In the apparatus of embodiment 24, the heating element comprises a laser light source.

[0225] Embodiment 26

[0226] A device, the device comprising: a sample stage area; an optical assembly, the optical assembly comprising: an objective lens element, the objective lens element providing a field of view, at least a portion of the sample stage area is located within the field of view, the objective lens element having an astigmatism that can be changed based on the temperature of the objective lens element; a tube lens, the tube lens is configured to receive light transmitted through the objective lens element and further transmit the light through an image space; a first compensation element, the first compensation element is located in the image space and is configured to cause a second astigmatism; a second compensation element, the second compensation element is located in the image space and is configured to cause a third astigmatism; the second astigmatism and the third astigmatism are configured to work together to offset the variable astigmatism; and a camera assembly, the camera assembly is configured to receive light transmitted from the compensation assembly.

[0227] Embodiment 27

[0228] In the apparatus of embodiment 26, the first compensating element is inclined at a first angle and the second compensating element is inclined at a second angle, the second angle being equal to and opposite to the first angle.

[0229] Embodiment 28

[0230] According to the device described in any one of Embodiments 26 to 27, the first compensation element is movable relative to the objective lens element to adjust the second astigmatism, and the second compensation element is movable relative to the objective lens element to adjust the third astigmatism.

[0231] Embodiment 29

[0232] According to the device of embodiment 28, the device also includes a controller configured to drive the movement of the first compensation element and the second compensation element to track the thermally induced changes of the astigmatism of the objective lens element.

[0233] Embodiment 30

[0234] In accordance with the device of embodiment 29, the controller is also configured to track the thermally induced changes in the astigmatism of the objective lens element.

[0235] Embodiment 31

[0236] In accordance with the device of embodiment 30, the controller is configured to process images captured by the camera assembly, and the controller is further configured to determine and track the thermally induced changes in the astigmatism of the objective lens element based on the processed images.

[0237] Embodiment 32

[0238] According to the device of any one of embodiments 29 to 31, the controller is configured to drive the movement of the first compensation element and the second compensation element based on a predetermined adjustment profile.

[0239] Embodiment 33

[0240] According to the device of embodiment 32, the controller is configured to define the predetermined adjustment profile.

[0241] Embodiment 34

[0242] According to the device of embodiment 33, the controller is configured to perform a calibration routine and define the predetermined adjustment profile by means of the calibration routine.

[0243] Embodiment 35

[0244] According to any one of the apparatus of embodiments 26 to 34, the sample stage area is configured to receive a flow cell.

[0245] Embodiment 36

[0246] A method comprising: receiving light from a reaction site through an objective lens element, the objective lens element having astigmatism, the light further passing through a compensation component, the compensation component providing compensatory astigmatism, the compensatory astigmatism canceling out the astigmatism of the objective lens element; heating the objective lens element, the astigmatism of the objective lens element changing in response to the heating; and adjusting the compensation component to cause the compensatory astigmatism to change, thereby canceling out the changing astigmatism of the objective lens element.

[0247] Embodiment 37

[0248] According to the method described in Example 36, the method also includes irradiating the reaction site with excitation light.

[0249] Embodiment 38

[0250] According to the method described in Example 37, the excitation light passes through the objective lens element to reach the reaction site.

[0251] Embodiment 39

[0252] According to the method of embodiment 38, the excitation light causes the heating of the objective lens element.

[0253] Embodiment 40

[0254] According to the method of any one of Embodiments 37 to 39, the excitation light includes laser.

[0255] Embodiment 41

[0256] According to the method described in any one of Examples 36 to 40, the compensation assembly includes a first compensation element, and the action of adjusting the compensation assembly includes causing the first compensation element to pivot around a first pivot axis in a first angular direction through a first pivot motion range.

[0257] Embodiment 42

[0258] According to the method described in Example 41, the compensation assembly also includes a second compensation element, and the action of adjusting the compensation assembly also includes causing the second compensation element to pivot around a second pivot axis in a second angular direction through a second pivot motion range.

[0259] Embodiment 43

[0260] According to the method described in Example 42, the second angle direction is opposite to the first angle direction.

[0261] Embodiment 44

[0262] According to the method of any one of embodiments 42 to 43, the second pivot axis is parallel to the first pivot axis.

[0263] Embodiment 45

[0264] According to the method described in any one of embodiments 42 to 44, the second pivotal motion range is equal to the first pivotal motion range.

[0265] Embodiment 46

[0266] According to the method described in Example 41, in response to pivoting the first compensation element about a first pivot axis in a first angular direction through a first pivot motion range, the image axis of the light shifts, and the method also includes moving a camera based on the shift of the image axis of the light, wherein the camera captures at least some of the light.

[0267] Embodiment 47

[0268] According to the method of embodiment 41, in response to pivoting the first compensation element about a first pivot axis in a first angular direction through a first pivot motion range, the image axis of the light shifts, and the method also includes moving the reflective element based on the shift of the image axis of the light.

[0269] Embodiment 48

[0270] In the method according to Embodiment 47, the action of moving the reflective element includes pivoting the reflective element.

[0271] Embodiment 49

[0272] According to the method of any one of Embodiments 47 to 48, the action of moving the reflective element includes deforming the reflective element.

[0273] Embodiment 50

[0274] According to the method of any one of embodiments 47 to 49, the reflective element redirects the light toward the camera.

[0275] Embodiment 51

[0276] According to the method of embodiment 50, the camera maintains a fixed position during the movement of the reflective element.

[0277] Embodiment 52

[0278] According to the method described in any one of Examples 36 to 40, the compensation component includes a deformable compensation element, and the action of adjusting the compensation component includes deforming the compensation element.

[0279] Embodiment 53

[0280] According to the method of embodiment 52, the light is emitted along an image axis, and the act of deforming the compensation element includes deforming the compensation element along the image axis.

[0281] Embodiment 54

[0282] According to the method of any one of embodiments 36 to 53, the method also includes capturing the light using a camera, and the compensation component is interposed between the objective lens element and the camera.

[0283] Embodiment 55

[0284] According to any one of embodiments 36 to 53, the method also includes performing sequencing by synthesis.

[0285] VIII. Miscellaneous

[0286] Although the foregoing examples are provided in the context of a system (100) that can be used for a nucleotide sequencing process, the teachings herein can also be readily applied to other contexts, including systems that perform other processes (i.e., in addition to a nucleotide sequencing process). Therefore, the teachings herein are not necessarily limited to systems for performing a nucleotide sequencing process.

[0287] It should be understood that the subject matter described herein is not limited to the details of the construction and arrangement of the parts illustrated in the description of this article or in the drawings of this article in its application. The subject matter described herein can have other specific implementations and can be practiced or executed in various ways. In addition, it should be understood that the wording and terminology used herein are for the purpose of description and should not be considered as restrictive. As used herein, the elements or steps described in singular form and preceded by the words "one" or "a kind of" should be understood as not excluding a plurality of the elements or steps, unless such exclusion is explicitly indicated. In addition, the reference to "an example" is not intended to be interpreted as excluding the existence of additional examples that are also incorporated into the described features. "Including", "comprising" or "having" and its variations used herein are meant to cover the items listed thereafter and their equivalents and other items.

[0288] When used in the claims, the term "group" should be understood as one or more things that are grouped together. Similarly, when used in the claims, "based on" should be understood to indicate that one thing is at least partially determined by the thing designated as "based on." In the case where one thing needs to be exclusively determined by another thing, then that thing will be referred to as being "exclusively based on" the other thing by which it is determined.

[0289] Unless otherwise specified or limited, the terms "mounted," "connected," "supported," and "coupled," and variations thereof, are used broadly and cover both direct and indirect mounting, connection, support, and coupling. Furthermore, "connected" and "coupled" are not limited to physical or mechanical connections or physical or mechanical couplings. Furthermore, it should be understood that the words and terms used herein with reference to device or element orientations (such as, for example, terms like "above," "below," "front," "rear," "distal," "proximal," etc.) are used only to simplify the description of one or more examples described herein, and do not individually indicate or imply that the device or element referred to must have a particular orientation. Additionally, terms such as "external" and "internal" are used herein for descriptive purposes and are not intended to indicate or imply relative importance or significance.

[0290] It should be understood that the above description is intended to be illustrative rather than restrictive. For example, the above examples (and / or aspects thereof) can be used in combination with each other. In addition, without departing from the scope of the invention, many modifications can be made to adapt specific situations or materials to the teachings of the subject matter currently described. Although the sizes and types of materials and coatings described herein are intended to limit the parameters of the disclosed subject matter, they are by no means restrictive but illustrative. When viewing the above description, many other examples will be obvious to those skilled in the art. Therefore, the scope of the subject matter of the present disclosure should be determined with reference to the appended claims and the full range of equivalents granted by these claims. In the appended claims, the terms "including" and "wherein" are used as the plain English equivalents of the corresponding terms "including" and "wherein". In addition, in the following claims, the terms "first", "second" and "third" are used only as labels and are not intended to impose numerical requirements on their objects. In addition, the limitations of the following claims are not written in a means plus function format and are not intended to be interpreted based on the 35 U.S.C. § 112 (f) paragraph unless and until these claim limitations explicitly use the phrase "members for ..." followed by functional statements without other structures.

[0291] The following claims set forth certain exemplary aspects of the disclosed subject matter and are considered a part of the above disclosure. These aspects can be combined with each other.

Claims

1. A device, comprising: Sample stage area; An optical component, the optical component comprising: an objective lens element providing a field of view, wherein at least a portion of the sample stage area is located within the field of view, the objective lens element having a variable astigmatism, a tube lens configured to receive light transmitted through the objective lens element and further transmit the light through an image space, a compensating component located in the image space and configured to induce a second astigmatism configured to cancel the variable astigmatism; and A camera assembly is configured to receive light transmitted from the compensation assembly.

2. The apparatus of claim 1, wherein the compensating component is operable to vary the second astigmatism so as to dynamically cancel the variable astigmatism of the objective lens element.

3. The apparatus of claim 2, further comprising a processor operable to control the compensation component to change the second astigmatism.

4. The apparatus of claim 3, the processor being operable to control the compensation component to vary the second astigmatism based on a predetermined adjustment profile.

5. Apparatus according to claim 3, the processor being operable to determine an astigmatism value of the objective lens element.

6. Apparatus according to claim 5, the processor being operable to control the compensation component to vary the second astigmatism based on the determined astigmatism value of the objective lens element.

7. The device according to any one of claims 1 to 6, wherein the compensation assembly comprises a first light-transmitting plate and a second light-transmitting plate. 8 . The device according to claim 7 , wherein the first light-transmitting plate is inclined at a first angle around a first axis, and the second light-transmitting plate is inclined at a second angle around a second axis. 9 . The apparatus of claim 8 , wherein the first light-transmitting plate and the second light-transmitting plate are positioned along an image axis, the first axis is orthogonal to the image axis, and the second axis is parallel to the first axis.

10. The apparatus according to any one of claims 8 to 9, wherein the magnitude and direction of the first angle are respectively equal to and opposite to the magnitude and direction of the second angle.

11. The apparatus of any one of claims 8 to 10, the compensation assembly further comprising a first actuator operable to drive one or both of movement of the first light-transmitting plate about the first axis or movement of the second light-transmitting plate about the second axis.

12. The apparatus of claim 11, the compensation assembly further comprising a linkage, the first actuator and the linkage being configured to work in concert to drive movement of the first light-transmitting plate about the first axis and concomitantly drive movement of the second light-transmitting plate about the second axis.

13. The device according to claim 11, the compensation component also includes a second actuator, the first actuator is connected to the first light-transmitting plate to drive the first light-transmitting plate to move around the first axis, and the second actuator is connected to the second light-transmitting plate to drive the second light-transmitting plate to move around the second axis.

14. Apparatus according to any one of claims 11 to 13, the first actuator comprising a motor.

15. The device according to any one of claims 11 to 14, the compensation assembly further comprising a first gear and a second gear, the first light-transmitting plate being configured to rotate integrally with the first gear, and the second light-transmitting plate being configured to rotate integrally with the second gear.

16. The apparatus of claim 15, the first gear being positioned to directly mesh with the second gear.

17. The apparatus of any one of claims 15 to 16, the compensating assembly further comprising a crank arm coupled to the first gear, the first actuator being configured to drive rotational movement of the crank arm, the crank arm being configured to drive rotational movement of the first gear.

18. The device according to any one of claims 11 to 17, the compensation assembly further comprising a housing element, the housing element forming a box around the first light-transmitting plate and the second light-transmitting plate.

19. According to the device described in any one of claims 11 to 18, the compensation component also includes a first axis, a second axis and a base plate, the first axis and the second axis pass through the base plate, the first axis is used to drive the first light-transmitting plate to move around the first axis, and the second axis is used to drive the second light-transmitting plate to move around the second axis.

20. The apparatus of any one of claims 1 to 6, the compensating assembly comprising a first light transmissive element and a reflective element.

21. Apparatus according to any one of claims 1 to 20, the compensating component comprising a deformable element.

22. The device of claim 21, wherein the deformable element is light transmissive.

23. The device of claim 21, wherein the deformable element is reflective.

24. Apparatus according to any one of claims 1 to 23, further comprising a heating element operable to heat the objective lens element and thereby change the astigmatism of the objective lens element.

25. The apparatus of claim 24, the heating element comprising a laser light source.

26. A device, comprising: Sample stage area; An optical component, the optical component comprising: an objective lens element providing a field of view, wherein at least a portion of the sample stage area is located within the field of view, the objective lens element having an astigmatism that is variable based on a temperature of the objective lens element, a tube lens configured to receive light transmitted through the objective lens element and further transmit the light through an image space, a first compensating element located in the image space and configured to induce a second astigmatism; a second compensating element located in the image space and configured to induce a third astigmatism; the second astigmatism and the third astigmatism configured to cooperate to cancel the variable astigmatism; and A camera assembly is configured to receive light transmitted from the compensation assembly.

27. The apparatus of claim 26, the first compensating element being inclined at a first angle and the second compensating element being inclined at a second angle, the second angle being equal to and opposite to the first angle.

28. The apparatus of any one of claims 26 to 27, the first compensation element being movable relative to the objective lens element to adjust the second astigmatism, and the second compensation element being movable relative to the objective lens element to adjust the third astigmatism.

29. The apparatus of claim 28, further comprising a controller configured to drive movement of the first and second compensation elements to track thermally induced changes in the astigmatism of the objective lens element.

30. The apparatus of claim 29, the controller further configured to track the thermally induced changes in the astigmatism of the objective lens element.

31. The apparatus of claim 30, the controller being configured to process images captured by the camera assembly, the controller further configured to determine and track the thermally induced changes in the astigmatism of the objective lens element based on the processed images.

32. The apparatus of any one of claims 29 to 31, the controller being configured to drive movement of the first and second compensating elements based on a predetermined adjustment profile.

33. The apparatus of claim 32, the controller being configured to define the predetermined tuning profile.

34. The apparatus of claim 33, the controller being configured to perform a calibration routine and to define the predetermined adjustment profile by the calibration routine.

35. The apparatus of any one of claims 26 to 34, the sample stage area being configured to receive a flow cell.

36. A method comprising: receiving light from a reaction site through an objective lens element, the objective lens element having astigmatism, the light further passing through a compensating component, the compensating component providing compensatory astigmatism, the compensatory astigmatism canceling the astigmatism of the objective lens element; heating the objective lens element, the astigmatism of the objective lens element changing in response to the heating; as well as The compensating assembly is adjusted to vary the compensating astigmatism, thereby counteracting the varying astigmatism of the objective lens element.

37. The method of claim 36, further comprising irradiating the reaction sites with excitation light.

38. The method of claim 37, wherein the excitation light passes through the objective lens element to reach the reaction site.

39. The method of claim 38, wherein the excitation light causes the heating of the objective lens element.

40. The method of any one of claims 37 to 39, wherein the excitation light comprises laser light.

41. The method of any one of claims 36 to 40, wherein the compensation assembly includes a first compensation element, and the action of adjusting the compensation assembly includes pivoting the first compensation element about a first pivot axis in a first angular direction through a first range of pivotal motion.

42. The method of claim 41, wherein the compensating assembly further comprises a second compensating element, wherein the action of adjusting the compensating assembly further comprises pivoting the second compensating element about a second pivot axis in a second angular direction through a second range of pivotal motion.

43. The method of claim 42, wherein the second angular direction is opposite to the first angular direction.

44. The method of any one of claims 42 to 43, wherein the second pivot axis is parallel to the first pivot axis.

45. The method of any one of claims 42 to 44, wherein the second range of pivotal motion is equal to the first range of pivotal motion.

46. ​​The method of claim 41 , wherein in response to pivoting the first compensation element in a first angular direction about a first pivot axis through a first pivot motion range, the image axis of the light shifts, the method further comprising moving a camera based on the shift of the image axis of the light, the camera capturing at least some of the light.

47. The method of claim 41, wherein in response to pivoting the first compensation element in a first angular direction about a first pivot axis through a first range of pivotal motion, the image axis of the light shifts, the method further comprising moving a reflective element based on the shift of the image axis of the light.

48. The method of claim 47, the act of moving the reflective element comprising pivoting the reflective element.

49. The method of any one of claims 47 to 48, the act of moving the reflective element comprising deforming the reflective element.

50. A method as claimed in any one of claims 47 to 49, wherein the reflective element redirects the light towards a camera.

51. The method of claim 50, wherein the camera maintains a fixed position during movement of the reflective element.

52. The method of any one of claims 36 to 40, wherein the compensating assembly comprises a deformable compensating element, and wherein the act of adjusting the compensating assembly comprises deforming the compensating element.

53. The method of claim 52, the light being emitted along an image axis, the act of deforming the compensating element comprising deforming the compensating element along the image axis.

54. The method of any one of claims 36 to 53, further comprising capturing the light with a camera, the compensation component being interposed between the objective lens element and the camera.

55. The method of any one of claims 36 to 53, further comprising performing sequencing by synthesis.

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