Optical device for correcting thermally induced astigmatism in lenses

Abstract

The apparatus includes a sample stage area, an optical assembly, and a camera assembly. The optical assembly includes an objective element, an imaging lens, and a corrector element. The objective element provides a field of view, and at least a portion of the sample stage area is within the field of view. The objective element has variable astigmatism. The imaging lens is configured to receive light transmitted through the objective element and further transmit that light into image space. The corrector element is in image space. The corrector element is configured to induce a second astigmatism. The second astigmatism is configured to offset the variable astigmatism. The camera assembly is configured to receive light transmitted from the corrector assembly.

Description

Technical Field

[0004] ,

[0001] (Priority) This application claims the priority of U.S. Provisional Patent Application No. 63 / 463,601, filed on May 3, 2023, with the title "Optical Arrangement for Compensation of Thermally-Induced Astigmatism of Lens", the entire disclosure of which is incorporated herein by reference.

Background Art

[0002] Aspects of the present disclosure generally relate to devices, systems, and methods for providing biological or chemical analysis. Various protocols in biological or chemical research involve performing a number of controlled reactions on a local support surface or within a predetermined reaction chamber. Next, the specified reaction may be observed or detected, and subsequent analysis may be useful for identifying or elucidating the properties of the chemical substances involved in the reaction. For example, in some multiplex assays, an unknown analyte having an identifiable label (e.g., a fluorescent label) may be exposed to thousands of well-known probes under controlled conditions. Each well-known probe may be deposited in a corresponding well of a flow cell channel. Observing any chemical reaction that occurs between the well-known probe and the unknown analyte in the well may be useful for identifying or elucidating the properties of the analyte. Other examples of such protocols include well-known DNA sequencing processes such as Sequencing-By-Synthesis (SBS) or circular array sequencing.

[0003] Although various devices, systems, and methods have been made and used to perform biological or chemical analysis, prior to the present inventor(s), no one is believed to have made or used the devices and techniques described herein.

Brief Description of the Drawings

[0004] [Figure 1] A schematic diagram of one embodiment of a system that may be used to provide biological or chemical analysis is shown. [Figure 2] A schematic diagram of one embodiment of a set of components that can cooperate to provide a fluid path in the system shown in Figure 1 is depicted. [Figure 3] A schematic diagram of another embodiment of a system that may be used to provide biological or chemical analysis is depicted. [Figure 4] A cross-sectional view of one embodiment of a flow cell that may be used in the system shown in Figure 1 is depicted. [Figure 5] A cross-sectional view of another embodiment of a flow cell that may be used in the system shown in Figure 1 is depicted. [Figure 6] Figure 5 depicts a top view of the flow cell, with the upper wafer omitted to reveal the lower wafer. [Figure 7] A schematic diagram of another embodiment of a system that may be used to provide biological or chemical analysis is depicted. [Figure 8] A schematic diagram of one embodiment of an imaging component that can be integrated into the system shown in Figure 7 is depicted. [Figure 9] A schematic diagram of another embodiment of imaging components that can be integrated into the system shown in Figure 7 is depicted. [Figure 10] A schematic diagram of another embodiment of imaging components that can be integrated into the system shown in Figure 7 is depicted. [Figure 11A] A schematic diagram of one embodiment of an imaging component apparatus, including one embodiment of an astigmatism correction assembly in a first operating state, is shown. [Figure 11B] Figure 11A shows a schematic diagram of the imaging components of the apparatus in the second operating state of the astigmatism correction assembly. [Figure 12] A schematic diagram of an embodiment of an imaging component apparatus, including one embodiment of an astigmatism correction assembly and a first embodiment of an actuator, is shown. [Figure 13] A schematic diagram of an embodiment of an imaging component apparatus, including one embodiment of an astigmatism correction assembly and a second embodiment of an actuator, is shown. [Figure 14A] A schematic diagram is shown of one embodiment of an imaging component apparatus, including another embodiment of the astigmatism correction assembly in a first operating state. [Figure 14B] Figure 14A shows a schematic diagram of the imaging components of the apparatus when the astigmatism correction assembly is in the second operating state. [Figure 15A] A schematic diagram is shown of one embodiment of an imaging component apparatus, including another embodiment of the astigmatism correction assembly in a first operating state. [Figure 15B] Figure 15A shows a schematic diagram of the imaging components of the apparatus when the astigmatism correction assembly is in the second operating state. [Figure 16A] A schematic diagram is shown of one embodiment of an imaging component apparatus, including another embodiment of the astigmatism correction assembly in a first operating state. [Figure 16B] Figure 16A shows a schematic diagram of the imaging components of the apparatus when the astigmatism correction assembly is in the second operating state. [Figure 17] A schematic diagram of one embodiment of an imaging component apparatus, including another embodiment of an astigmatism correction assembly, is shown. [Figure 18] A graph is plotted showing one example of astigmatism induced by a glass plate as a function of the angle of incidence. [Figure 19] A perspective view of one embodiment of an astigmatism correction assembly is shown. [Figure 20] Another perspective view of the astigmatism correction assembly shown in Figure 19. [Figure 21] Figure 19 shows an exploded perspective view of the astigmatism correction assembly. [Figure 22] For clarity, another exploded perspective view of the astigmatism correction assembly in Figure 19 is depicted, with the housing components omitted. [Figure 23A] For clarity, Figure 19 shows a bottom view of the astigmatism correction assembly, with the housing components omitted and the astigmatism correction assembly in the first operating state. [Figure 23B]For clarity, Figure 19 shows a bottom view of the astigmatism correction assembly, with the housing components omitted and the astigmatism correction assembly in the second operating state. [Figure 24A] For clarity, Figure 19 shows a top view of the astigmatism correction assembly, with the housing components omitted and the astigmatism correction assembly in the first operating state. [Figure 24B] For clarity, Figure 19 shows a top view of the astigmatism correction assembly, with the housing components omitted and the astigmatism correction assembly in the second operating state. [Modes for carrying out the invention]

[0005] The following detailed descriptions of specific embodiments will be better understood when read in conjunction with the accompanying drawings. To the extent that the drawings show functional block diagrams of various embodiments, functional blocks do not necessarily represent divisions between hardware components. Therefore, for example, one or more functional blocks (e.g., processors or memory) may be implemented on a single piece of hardware (e.g., a general-purpose signal processor or random-access memory, a hard disk, etc.). Similarly, a program may be a standalone program, incorporated as a subroutine within an operating system, or a function within an installed software package, and so on. It should be understood that the various embodiments are not limited to the arrangements and means shown in the drawings.

[0006] I. Overview of Systems for Biological or Chemical Analysis The embodiments described herein may be used in various biological processes and systems or chemical processes and systems for academic analysis, commercial analysis, or other analysis. More specifically, the embodiments described herein may be used in various processes and systems where it is desirable to detect events, physical properties, qualities, or characteristics indicative of a specified reaction. A bioassay system as described herein may be configured to perform a plurality of specified reactions that can be detected individually or collectively. For example, a bioassay system may be used to sequence a high-density array of nucleic acid features through repeated cycles of enzyme manipulation and image acquisition. In some embodiments, nucleic acids may be attached to and amplified on a surface. Examples of such amplification are described in U.S. Patent No. 7,741,463, issued June 22, 2010, titled "Method of Preparing Libraries of Template Polynucleotides" (the entire disclosure of which is incorporated herein by reference), and / or U.S. Patent No. 7,270,981, issued September 18, 2007, titled "Recombinase Polymerase Amplification" (the entire disclosure of which is incorporated herein by reference).

[0007] Components used in a bioassay system may include one or more microfluidic channels that deliver reagents or other reaction components to a reaction site. The reaction sites may be randomly distributed across a substantially flat 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 indicative of photons emitted from the reaction site and detected by an imaging sensor may provide an illumination value. These illumination values may be combined with an image indicative of photons detected from the reaction site. These images may be further analyzed to identify the composition, reaction, conditions, etc. at each reaction site.

[0008] II. Examples of Fluidic Element Engineering Devices and Fluidic Flow Paths A. Example of a system with higher volume throughput FIG. 1 shows a schematic diagram of an embodiment of a system (100) that can be used to perform an analysis on one or more samples of interest. In some implementations, a sample may include one or more clusters of nucleotides (e.g., DNA) that are linearized to form single-stranded DNA (sstDNA). In the illustrated implementation, system (100) is configured to receive a flow cell cartridge assembly (102) that includes a flow cell assembly (103) and a sample cartridge (104). System (100) includes a flow cell receptacle (122) that receives the flow cell cartridge assembly (102), a vacuum chuck (124) that supports the flow cell assembly (103), and a flow cell interface (126) that is used to establish a fluid connection between system (100) and the flow cell assembly (103). The flow cell interface 126 may include one or more manifolds. System (100) further includes a sipper manifold assembly (106), a sample loading manifold assembly (108), and a pump manifold assembly (110). System 100 also includes a drive assembly 112, a controller 114, an imaging system 116, and a waste reservoir 118. Controller (114) is electrically and / or communicatively coupled to drive assembly (112) and imaging system (116), and is configured to cause drive assembly (112) and / or imaging system (116) to perform various functions as disclosed herein.

[0009] In this embodiment, the flow cell assembly (103) includes a flow cell (128) having a channel (130), fluid-coupled to the channel (130), and defining a plurality of first openings (132) located on a first side (134) of the channel (130). The flow cell (128) further includes a plurality of second openings (136) fluid-coupled to the channel (130) and located on a second side (138) of the channel (130). Thus, fluid may flow through the channel and through the flow cell (128). Although the flow cell (128) is shown to include one channel (130), the flow cell (128) may include two or more channels (130). The flow cell assembly (103) also includes a flow cell manifold assembly (140) connected to the flow cell (128) and having 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 containing multiple layers, as will be discussed in more detail below.

[0010] In the shown implementation, a first manifold fluid line (142) has a first fluid line opening (146) and is fluid-coupled to each of the first openings (132) of the flow cell (128), and a second manifold fluid line (144) has a second fluid line opening (148) and is fluid-coupled to each of the second openings (136). As shown, the flow cell assembly (103) is coupled to the flow cell manifold assembly (140) and includes a gasket (150) fluid-coupled to the fluid line openings (146, 148). In some implementations in which the flow cell (128) includes multiple channels (130), the flow cell manifold assembly (140) may include an additional fluid line (152) that connects the first fluid line opening (146) to a single manifold port (154). In this configuration, a single gasket (150) may be coupled to a flow cell manifold assembly (140) that surrounds a manifold port (154) and has fluid communication with multiple channels (130). During operation, the flow cell interface (126) engages with the corresponding gasket (150) to establish a fluid coupling between the system (100) and the flow cell (128). The engagement between the flow cell interface (126) and the gasket (150) reduces or eliminates fluid leakage between the flow cell interface (126) and the flow cell (128).

[0011] In the provided implementation, the first manifold fluid line (142) has a portion (156) substantially parallel to the longitudinal axis (158) of the channel (130), and the second manifold fluid line (144) has a portion (160) substantially parallel to the longitudinal axis (158) of the channel (130). 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). 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 to be preferable.

[0012] In the shown implementation, the system (100) includes a sample cartridge receptacle (166) that receives a sample cartridge (104) carrying one or more target samples (e.g., analytes). The system (100) also includes a sample cartridge interface (168) that establishes a fluid connection with the sample cartridge (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 pumps (172) may take any preferred form. The cache (176) may include a meandering cache, which may temporarily store one or more reaction components during bypass operation of the system (100). Although the cache (176) is shown to be contained within the pump manifold assembly (110), the cache (176) may alternatively be located elsewhere (for example, within the shipper manifold assembly (106) or in another manifold downstream of the bypass fluid line (178)).

[0013] The sample loading manifold assembly (108) and the pump manifold assembly (110) transport one or more samples of interest from the sample cartridge (104) to the flow cell cartridge assembly (102) through the fluid line (180). In some implementations, the sample loading manifold assembly (108) may load or handle each of the samples of interest individually into each channel (130) of the flow cell (128). The process of loading the samples of interest into the channels (130) may be performed automatically using a system (100). As shown in Figure 1, the sample cartridge (104) and the sample loading manifold assembly (108) are located downstream of the flow cell cartridge assembly (102). In the implementation shown, the sample loading manifold assembly (108) is coupled between the flow cell cartridge assembly (102) and the pump manifold assembly (110). To draw the target sample from the sample cartridge (104) toward the pump manifold assembly (110), the sample valve (170), the pump valve (174), and / or the pump (172) may be selectively actuated to bias the target sample toward the pump manifold assembly (110). The sample cartridge (104) may include multiple sample reservoirs that are selectively fluid-accessible via the corresponding sample valves (170). To individually flow the target sample toward the channels (130) of the flow cell 128 and away from the pump manifold assembly (110), the sample valves (170), the pump valves (174), and / or the pump (172) may be selectively actuated to bias the target sample toward each channel (130) of the flow cell (128) toward the flow cell cartridge assembly (102).

[0014] The drive assembly (112) interfaces with the sipper manifold assembly (106) and the pump manifold assembly (110) to flow one or more reagents that interact with the sample in the flow cell (128). In some scenarios, a reversible terminator is attached to the reagent to allow a single nucleotide to be incorporated onto the elongating DNA strand. In some such implementations, one or more of the nucleotides have a unique fluorescent label that emits a color when excited. The color (or lack thereof) is used to detect the corresponding nucleotide. In the implementation shown, the imaging system (116) excites one or more of the identifiable labels (e.g., fluorescent labels) and then acquires image data of the identifiable labels. The labels may be excited by incident light and / or laser, and the image data may include one or more colors emitted by each label in response to excitation. The image data (e.g., detection data) may be analyzed by the system (100). Examples of features and functions that may be incorporated into the imaging system (116) are described in more detail below.

[0015] After image data is obtained, the drive assembly (112) interfaces with the shipper manifold assembly (106) and the pump manifold assembly (110) to flow another reactant (e.g., a reagent) through the flow cell (128), which is then received by the waste reservoir (118) via the main waste line (182) and / or discharged by the system (100) in other ways. Some reactants may perform a flushing operation to chemically cleave a fluorescently labeled and reversible terminator from the sstDNA. The sstDNA may then be prepared for another cycle.

[0016] The main wastewater line (182) is connected between the pump manifold assembly (110) and the waste reservoir (118). In some implementations, the pump (172) and / or pump valve (174) of the pump manifold assembly (110) selectively deliver the reaction components from the flow cell cartridge assembly (102) through the fluid line (180) and the sample loading manifold assembly (108) to the main wastewater line (182). The flow cell cartridge assembly (102) is connected to the central valve (184) via the flow cell interface (126). The central valve (184) is connected to the flow cell interface (126) via the fluid line (185). The auxiliary wastewater line (186) is connected to the central valve (184) and the waste reservoir (118). In some implementations, the auxiliary waste line (186) receives excess fluid from the sample to be loaded back into the flow cell (128) via the central valve (184) when the sample to be loaded back into the flow cell (128), as described herein, and flows the excess fluid to the waste reservoir (118).

[0017] The shipper manifold assembly (106) includes a shared line valve (188) and a bypass valve (190). The shared line valve (188) may be referred to as a reagent selector valve. The central valve (184) and the valves (188, 190) of the shipper manifold assembly (106) may be selectively actuated to control the flow of fluid through the fluid lines (192, 194, 196). The shipper manifold assembly (106) may be coupled to a corresponding number of reagent reservoirs (198) via reagent shippers (200). The reagent reservoirs (198) may contain fluid (e.g., reagents and / or other reactive components). In some implementations, the shipper manifold assembly (106) includes multiple ports. Each port of the shipper manifold assembly (106) may accept one of the reagent shippers (200). The reagent shippers (200) may be referred to as fluid lines. Some forms of the reagent shipper (200) may include an array of shipper tubes extending downward along the z-dimension from a port in the body of the shipper manifold assembly (106). Reagent reservoirs (198) may be provided in a cartridge, and the tubes of the reagent shipper (200) may be configured to be inserted into the corresponding reagent reservoirs (198) in the reagent cartridge so that liquid reagents can be drawn from each reagent reservoir (198) into the shipper manifold assembly (106).

[0018] The shared line valve (188) of the sipper manifold assembly (106) is connected to the central valve (184) via the shared reagent fluid line (196). Different reagents may flow through the shared reagent fluid line (196) at different times. In some variations, when performing a flushing operation before changing one reagent with 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).

[0019] The bypass valve (190) of the sipper 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) may be associated with a single reagent. Fluids that may flow through the dedicated reagent fluid lines (194, 196) may be used during the sequencing operation and may include cutting reagents, integration reagents, scanning reagents, cutting wash solutions, and / or wash buffers.

[0020] The bypass valve (190) is also coupled to the cache (176) of the pump manifold assembly (110) via the bypass fluid line (178). One or more reagent priming, hydration, mixing, and / or transfer operations may be performed using the bypass fluid line (178). The priming, hydration, mixing, and / or transfer operations may be performed independently of the flow cell cartridge assembly (102). Thus, operations using the bypass fluid line (178) may be performed, for example, during the incubation of one or more target samples in the flow cell cartridge assembly (102). That is, the shared line valve (188) may be used independently of the bypass valve (190), so that while the shared line valve (188) and / or the central valve (184) are performing other operations simultaneously, substantially simultaneously, or in offset synchronization, the bypass valve (190) may use the bypass fluid line (178) and / or the cache (176) to perform one or more operations.

[0021] The drive assembly (112) includes a pump drive assembly (202) and a valve drive assembly (204). The pump drive assembly (202) may interface with one or more pumps (172) to pump fluid through a flow cell (128) and / or load one or more samples of interest into the flow cell (128). The valve drive assembly (204) may interface with one or more valves (170, 174, 184, 188, 190) to control the position of the corresponding valves (170, 174, 184, 188, 190).

[0022] Figure 2 shows an embodiment of a fluid device (220) that may be incorporated into a modified version of system (100). The fluid device (220) in this embodiment includes a pump manifold assembly (222) which can operate similarly to the pump manifold assembly (110) described above, a sample loading manifold assembly (228) which can operate similarly to the sample loading manifold assembly (108) described above, a flow cell interface (240) which can operate similarly to the flow cell interface (126) described above, a shipper manifold assembly (250) which can operate similarly to the shipper manifold assembly (106) described above, and a waste reservoir (270) which can operate similarly to the waste reservoir (118) described above. The pump manifold assembly (222) is connected to the port assembly (258) of the shipper manifold assembly (250) via a fluid line (224) which may be similar to the fluid line (178), and is connected to the sample loading manifold assembly (228) via a fluid line (226). The sample loading manifold assembly (228) is connected to a flow cell interface (240) via a fluid line (230) which may be similar to fluid line (180), and to a port assembly (258) via fluid lines (232, 234). The flow cell interface (240) is connected to a shipper manifold assembly (250) via a fluid line (242) which may be similar to fluid line (185). The shipper manifold assembly (250) includes a manifold body (252) and a common output port (256) which provides fluid communication via fluid line (185). A valve assembly (254) controls the flow of fluid through the common output port (256) and may operate similarly to a central valve (184). The port assembly (258) of the shipper manifold assembly (250) is connected to a waste reservoir (270) via a fluid line (272) which may be similar to fluid line (186).

[0023] Multiple reagent shippers (260) extend from the manifold body (252) and are fluid-coupled to a valve assembly (254) via their respective fluid channels (262) within the manifold body (252). The reagent shippers (260) may operate similarly to the reagent shipper (200). The valve assembly (254) can selectively connect the fluid channels (262) to a flow cell interface (240) via a common output port (256) and a fluid line (230), thereby enabling it to selectively supply different reagents to the flow cell interface (240). In other words, if each reagent shipper (260) is located within a different reagent (e.g., within each reagent reservoir (198)), a flow cell (e.g., a flow cell (128)) connected to the flow cell interface (240) may selectively accept these different reagents based on the control of the valve assembly (254).

[0024] The port assembly (258) may also provide a fluid interface between the pump manifold assembly (222) and the shipper manifold assembly (250), thereby enabling the shipper manifold assembly (250) to receive pressurized fluid from the pump manifold assembly (222). The port assembly (258) may also provide a fluid interface between the sample loading manifold assembly (228) and the shipper manifold assembly (250), thereby enabling the shipper manifold assembly (250) to receive sample fluid from the sample loading manifold assembly (228). The port assembly (258) may also provide a fluid interface between the waste reservoir (270) and the shipper manifold assembly (250), thereby enabling the shipper manifold assembly (250) to communicate waste liquid with the waste reservoir (270). Fluid communication through the port assembly (258) may be at least partially regulated by the valve assembly (254).

[0025] Referring back to Figure 1, the controller (114) of this embodiment includes a user interface (206), a communication interface (208), one or more processors (210), and a memory (212) that stores instructions executable by one or more processors (210) for performing various functions, including the disclosed implementation. The user interface (206), the communication interface (133), and the memory (212) are electrically and / or communicatively coupled to one or more processors (210). The user interface (206) may be adapted to receive input from a user and provide the user with information associated with the operation of the system (100) and / or analysis performed. The user interface (206) may include a touchscreen, a display, a keyboard, a speaker, a mouse, a trackball, and / or a voice recognition system.

[0026] 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 communication provided to the remote system may be associated with analysis results, imaging data, etc., generated or otherwise acquired by the system (100). Some of the communication provided to the system (100) may be associated with fluid analysis operations, patient records, and / or protocols performed by the system (100).

[0027] One or more processors (210) and / or systems (100) may include one or more processor-based systems or microprocessor-based systems. In some implementations, one or more processors (210) and / or systems (100) may include one or more programmable processors, programmable controllers, microprocessors, microcontrollers, graphics processing units (GPUs), digital signal processors (DSPs), reduced-instruction set computers (RISCs), application-specific integrated circuits (ASICs), field programmable gate arrays (FPGAs), field programmable logic devices (FPLDs), logic circuits, and / or other logic-based devices that perform various functions, including those described herein.

[0028] Memory (212) includes semiconductor memory, magnetically readable memory, optical memory, hard disk drives (HDDs), optical storage drives, solid-state storage devices, solid-state drives (SSDs), flash memory, read-only memory (ROMs), erasable programmable read-only memory (EPROMs), electrically erasable programmable read-only memory (EEPROMs), random-access memory (RAMs), non-volatile RAM (NVRAMs), compact discs (CDs), compact disc read-only memory (CD-ROMs), digital versatile discs (DVDs), Blu-ray discs, and redundant arrays of independent discs. This may include one or more of the following storage devices or storage disks: a disk, RAID system, a cache, and / or any other storage device or storage disk on which information is stored for any duration (e.g., permanently, temporarily, over a long period, for buffering, for caching).

[0029] B. Examples of systems with lower volume throughput Figure 3 shows a schematic diagram of another embodiment of system (300) that may be used to perform analysis on one or more target samples. Unless otherwise described below, system (300) in this embodiment may be configured and operable in the same way as system (100) described above with reference to Figure 1. In some embodiments, system (100) is used to provide a higher volume throughput, while system (300) is used to provide a lower volume throughput. Alternatively, systems (100, 300) may provide any other suitable volume or degree of throughput. System (300) in this embodiment receives a reagent cartridge (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 cartridge (302) may 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.

[0030] The reagent cartridge (302) in the shown configuration 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 periphery (328). The second wall (330) surrounds the first wall (318) and has a distal end (332). The distal end (332) may be referred to as the edge or outer edge. A cover (334) is connected to the distal end (324) of the first wall (318), covering the opening (326) along the opening periphery (328) at the connection portion (336), and is disconnected from the distal end (324) of the first wall (318) at the disconnected portion (338). The connection portion (336) may be referred to as a connection section or connection segment, and the disconnected portion (338) may be referred to as a disconnection section or disconnection segment. The first wall (318) has a height, and the second wall (330) has a height greater than the height of the first wall (318). Alternatively, the first well (318) and the second well (330) may be the same or similar height. An impermeable barrier (340) is connected to the distal end (332) of the second wall (330) and covers the well (320). The impermeable barrier (340) may be foil, plastic, or the like, and may prevent or block moisture from penetrating into the wells (320) of the reagent cartridge (302).

[0031] The unconnected portion (338) of the cover (334) forms a vent (342) that allows airflow from the well (320). The dry reagent (348) is contained within the well (320), and the vent (342) is sized to substantially hold the dry reagent (348) within the well (320). The body (316) may contain multiple wells (320), but Figure 3 shows one well (320). The liquid (346) may actually flow into the well (320) via the port (322) to rehydrate the dry reagent (348). The vent (342) may release gas from the well (320) as the liquid (346) flows into the well (320). The cover (334) prevents or prevents the reagent (348) and / or liquid (346) from leaking out of the well (320). In other words, the vent (342) holds the reagent (348) and / or liquid (346) within the well (320) and prevents or blocks the reagent (348) and / or liquid (346) from moving out of the well (320). The vent (342) and cover (334) prevent or block secondary contamination between reagents when the reagent cartridge (302) contains two or more wells (320). The liquid (346) and dry reagent (348) may flow into and out of the well (320) to mix the liquid (346) and dry reagent (348) from the liquid reservoir (362). The system (300) and / or reagent cartridge (302) may include a mixing chamber used for mixing the liquid (346) and dry reagent (348) in some implementations. The impermeable barrier (340) may be penetrated before the liquid (346) flows into the well (320).

[0032] A gas source (304) may be used to pressurize a liquid reservoir (362) to draw liquid (346) into a well (320), and / or a pump (350) may draw liquid (346) from the liquid reservoir (362) and flow liquid (346) into the well (320) to rehydrate the reagent (348). The gas source (304) may be provided by a system (300) and / or supported by a reagent cartridge (302). The gas source (304) may be omitted as an alternative. The pump (350) may be implemented by a syringe pump, a peristaltic pump, a diaphragm pump, etc. The pump (350) may be located downstream of the flow cell (368) as shown, the pump (350) may be located upstream of the flow cell (368), or may be omitted entirely.

[0033] The reagent cartridge (302) and / or system (300) includes a valve (352) which may be selectively actuated to control the flow of fluid through a fluid line (356). Such a valve (352) may be implemented by a valve manifold, rotary valve, switching valve, pinch valve, flat valve, solenoid valve, check valve, piezo valve, etc. A regulator (354) may be positioned between the gas source (304) and the valve (352) and regulate the pressure of the gas supplied to the valve (352). The regulator (354) may include a valve that controls the flow of gas from the gas source (304).

[0034] The body (316) of the well assembly (314) has a rim (364), and the impermeable barrier (340) may be hermetically connected to the body (316) along the rim (364). The impermeable barrier (340) may include foil, plastic, and / or any other suitable material. The system (300) may penetrate the impermeable barrier (340), the impermeable barrier (340) may be penetrated individually before use, or the impermeable barrier (340) may be penetrated by some other structure or method. The system (300) includes an actuator assembly (360) in the shown configuration that interfaces with the impermeable barrier (340) to penetrate the impermeable barrier (340). The system (300) may include projections such as struts having blunt or sharp ends that are movable by the actuator assembly (360) to penetrate the impermeable barrier (340). Alternatively, the impermeable barrier (340) may be punctured by an operator before the reagent cartridge (302) is positioned within the system (300). The system (300) also includes a liquid reservoir (362) containing liquid (346). Liquid (346) may include a rehydration solution, a washing buffer, and / or any other suitable type of liquid.

[0035] The system (300) further includes a flow cell receptacle (366) that receives a flow cell (368). The flow cell (368) may be configured and operable in the same way as the flow cell (128). In some modifications, the flow cell (368) is supported by and / or incorporated into a reagent cartridge (302). The flow cell 368 may support the sample of interest. A gas source (304) and / or a pump (350) may flow one or more liquid reagents through a reagent cartridge (302) that interacts with the sample, by flowing liquid (346) to rehydrate the dry reagent (348). The imaging system (310) may be configured and operable in the same way as the imaging system (116) so that the imaging system (310) can be used to acquire image data from the flow cell (368). After image data is obtained, the drive assembly (306) may interface with the reagent cartridge (302) to flow another reaction component (e.g., a reagent) through the flow cell (368), which is then received by the waste reservoir (312) and / or discharged by the reagent cartridge (302) in another manner. In this embodiment, 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) interfaces with the pump (350) to pump fluid through the reagent cartridge (302) and / or the flow cell (368), and the valve drive assembly (372) interfaces with the valve (352) to control the position of the valve (352).

[0036] The controller (308) in this embodiment includes a user interface (374), a communication interface (376), a processor (378), and memory (380). The user interface (374) may be configured and operable as the user interface (206) of the system (100). The communication interface (376) may be configured and operable as the communication interface (208) of the system (100). The processor (378) may be configured and operable as the processor (210) of the system (100). The memory (380) may be configured and operable as the memory (212) of the system (100).

[0037] Further examples and details of how the various features of each system (100, 300) can be configured and operated are described below. As merely a further example, various features of the system (100, 300) may be configured and operable in accordance with at least some of the teachings of International Publication No. 2023 / 055873, title of the invention "Flow Cells and Related Flow Cell Manifold Assemblies and Methods," published on April 6, 2023 (the entire disclosure of which is incorporated herein by reference), U.S. Patent No. 9,958,465, title of the invention "Detection Apparatus having a Microfluorometer, a Fluidic System, and a Flow Cell Latch Clamp Module," issued on May 1, 2018 (the entire disclosure of which is incorporated herein by reference), and / or U.S. Patent Application Publication No. 63 / 325,462, title of the invention "Well Assemblies and Related Systems and Methods," filed on March 30, 2022 (the entire disclosure of which is incorporated herein by reference).

[0038] III. Examples of Flow Cell Structures As described above, the system (100, 300) may carry out a reaction within a flow cell (128, 368) and / or perform analysis on one or more samples of a target within the flow cell (128, 368). The following describes examples of forms in which such a flow cell (128, 368) may take place, and it should be understood that the flow cell (128, 368) may take various other forms and may have various other features in addition to or instead of the features described below.

[0039] A. Examples of single-surface patterned flow cells Figure 4 shows an embodiment of a flow cell (400) comprising a patterned substrate (402) including recesses (404) separated by interstitial regions (406) and interfacial chemistry (410, 412) positioned within the recesses (404). The recesses (404) may be in the form of microwells or nanowells. The recesses (404) may contain nucleic acid chains or other oligonucleotides and thereby be configured to provide reaction sites for SBS and / or other types of processes. In some variants, each recess (404) has a cylindrical configuration with a generally circular cross-sectional profile. In some other variants, each recess (404) has a polygonal (e.g., hexagonal, octagonal, square, rectangular, elliptical, etc.) cross-sectional profile. Alternatively, the recesses (404) may have any other preferred configuration. It should also be understood that the recesses (404) may be arranged in any preferred pattern, including but not limited to a grid pattern.

[0040] The interfacial chemistry (410, 412) in this embodiment includes a functionalized coating layer (410) and a primer (412). Although not shown, the recess (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 region (406). In this embodiment, the hydrogel (440) is applied before the lid (420) is bonded to the substrate (402). The hydrogel (440) covers the interfacial chemistry (410, 412) in the recess (404) and at least a portion of the patterned substrate (402) (e.g., the gap region (406) which is not the bonding region (422)). As just one example, the hydrogel (440) may include PAZAM, crosslinked polyacrylamide, agarose gel, etc.

[0041] The flow cell (400) in this embodiment further includes a lid (420) bonded to a bonding region (422) of a patterned substrate (402). In the embodiment shown in Figure 4, the lid (420) includes a top (424) connected to several side walls (426), these components (424, 426) define a portion of each of the six channels (430A, 430B, 430C, 430D, 430E, 430F). Each side wall (426) isolates one channel (430A, 430B, 430C, 430D, 430E, 430F) from each adjacent channel (430A, 430B, 430C, 430D, 430E, 430F). Each flow path (430A, 430B, 430C, 430D, 430E, 430F) is selectively in fluid communication with each set of recesses (404).

[0042] The lid (420) may be bonded to the bonding region (422) of the substrate (402) using any preferred technique such as laser bonding, diffusion bonding, anodic bonding, eutectic bonding, plasma-activated bonding, glass frit bonding, or other methods well known in the art. In some variations, a spacer layer (428) may be used to bond the lid (420) to the bonding region (422). The spacer layer (428) may include any material that seals together at least a portion of the gap region (404) (e.g., the bonding region (422)) between the substrate (402) and the lid (420). Although not shown, the lid (420) or patterned substrate (402) may include inlet and outlet ports that fluidically engage with other ports (not shown), such as those of the sample cartridge interface (168), to direct fluid into each channel (430A, 430B, 430C, 430D, 430E, 430F) (e.g., from a reagent cartridge or other fluid storage system) and out of the channels (e.g., to a waste reservoir (118) or another waste removal system). The channels (430A, 430B, 430C, 430D, 430E, 430F) may function to selectively introduce reactants or reactants into the hydrogel (440) and the underlying interfacial chemistry (410, 412), for example, to initiate a specified reaction within / in a recess (404).

[0043] The flow cell (400) includes a pattern of recesses (404) for providing an array of reaction sites, but other modifications may provide reaction sites on or thereon on a variety of other types of structural features, including but not limited to continuously flat surfaces and / or protruding surfaces. As just a further example, the flow cell (400) may be constructed and operable in accordance with at least part of the teachings of U.S. Patent No. 10,919,033, issued February 16, 2021, titled “Flow Cells with Hydrogel Coating,” the entire disclosure of which is incorporated herein by reference.

[0044] B. Examples of dual-surface patterned flow cells Figure 4 shows an example of a flow cell (400) having a single surface patterned with reaction sites (i.e., recesses (404) formed in the substrate (402)). However, in some cases, it may be desirable to provide a variation of the flow cell (400) that provides two surfaces patterned with reaction sites. An example of a double-surface patterned flow cell (450) is shown in Figures 5-6. In this example, the flow cell (450) includes a pair of wafers (452, 454) joined together, with a spacer layer (456) inserted between the wafers (452, 454). Each wafer (452, 454) is patterned to provide a number of recesses (462, 464) such that when the flow cell (450) is assembled, the recesses (462) of wafer (452) align with the recesses (464) of 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 embodiment, the spacer layer (456) does not come into contact with the gap regions (466, 468).

[0045] The recesses (462, 464) of the flow cell (450) are configured and may be operable in the same manner as the recess (404) of the flow cell (400) described above. Each recess (462, 464) in this embodiment includes a grafted coating (470) which may be similar to the functionalized coating layer (410), and a primer (472) which may be similar to the primer (412) described above. Each recess (462, 464) may further include a hydrogel such as a hydrogel (440), and / or any other preferred features. As shown in Figures 5-6, the recesses (462, 464) are located within a plurality of channels (480A, 480B, 480C, 480D). The channels (480A, 480B, 480C, 480D) are separated from each other by walls (458) and ends (459) formed by a spacer layer (456). In the embodiment shown in Figure 6, the flow cell (450) provides four channels (480A, 480B, 480C, 480D), each channel (480A, 480B, 480C, 480D) containing several rows of recesses (462, 464). When the flow cell (450) is used in a system (100, 300), the channels (480A, 480B, 480C, 480D) may function to selectively introduce reactants or reactant interfacial chemistry (470, 472) to initiate a specified reaction in / at the recesses (462, 464), for example. In some cases, each wafer (452, 454) has its own set of recesses (462, 464) that provide corresponding reaction sites, so that the flow cell (450) can provide twice the reaction of a flow cell (400) of similar size over a given period of time.

[0046] The dashed lines in Figure 6 show how the flow cell (450) can be diced to effectively form smaller flow cells (450A, 450A), each having its own pair of channels (480A, 480B, 480C, 480D). However, in this embodiment, a single flow cell (450) has three or more channels (480A, 480B, 480C, 480D). The flow cell (450) includes a pattern of recesses (462, 464) for providing an array of reaction sites, but other modifications may provide reaction sites on or thereon on a variety of other types of structural features, including but not limited to continuously flat surfaces and / or protruding surfaces. As merely a further example, a flow cell (450) may be constructed and operational in accordance with at least part of the teachings of U.S. Patent No. 10,955,332, titled "Flow Cell Package and Method for Making the Same," issued March 23, 2021, the entire disclosure of which is incorporated herein by reference.

[0047] IV. Examples of Imaging System Features As described above, the system (100, 300) includes an imaging system (116, 310) that excites one or more identifiable labels (e.g., fluorescent labels) in a sample within a reaction site provided by recesses (404, 462, 464) of flow cells (128, 368, 400, 450), and subsequently acquires image data of the identifiable labels. This image data is used to identify nucleotides as part of a nucleic acid sequencing process. Alternatively, the image data may be used for various other purposes. The following description provides details on how several variations of the imaging system (116, 310) may be configured and operational.

[0048] Figure 7 shows a schematic diagram of another embodiment of system (500) that may be used to perform analysis on one or more target samples. Unless otherwise described below, system (500) in this embodiment may be configured and operable in the same way as systems (100, 300) described above. System (500) is configured to perform a number of parallel reactions within a flow cell (510). Flow cell (510) may be configured and operable in the same way as flow cells (400, 450) described above, or may have any other preferred configuration. Flow cell (510) may therefore include one or more channels that receive the solution from system (500) and direct the solution toward the reaction sites in flow cell (510).

[0049] The system (500) includes a system controller (520) capable of communicating with various components, assemblies, and subsystems of the system (500). The controller (520) may be configured and operable in the same manner 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 the reaction site on the flow cell (510). The light-emitting assembly (550) may 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 a light emitter output by one or more lasers or laser diodes. In some implementations, the light-emitting assembly (550) may include several different light sources (not shown), each emitting light in a different wavelength range. Some variations of the light emission assembly (550) may also include one or more collimating lenses (not shown), a light-structured optical assembly (not shown), a projection lens (not shown) that can be operated to adjust the structured beam shape and path, an epifluorescence microscope component, and / or other components. Although the system (500) is shown as having a single light emission assembly (550), some other implementations may include multiple light emission assemblies (550).

[0050] In this embodiment, light from the light-emitting assembly (550) is directed by the dichroic mirror assembly (546) through the objective lens assembly (542) onto the sample in the flow cell (510) positioned on the mobile stage (570). In fluorescence microscopy of the sample, the fluorescent element associated with the sample emits fluorescence in response to excitation light, and the resulting light is collected by the objective lens assembly (542) and directed to the imaging sensor of the camera system (540) to detect the emitted fluorescence. In some implementations, the imaging lens assembly may be positioned between the objective lens assembly (542) and the dichroic mirror assembly (546), or between the dichroic mirror (546) and the imaging sensor of the camera system (540). The movable lens element may be able to translate along the longitudinal axis of the imaging lens assembly, taking into account spherical aberration introduced by focusing onto the upper or lower inner surface of the flow cell (510) and / or by the movement of the objective lens assembly (542).

[0051] In this embodiment, a filter switching assembly (544) is inserted 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 allow emission wavelengths within a specific range to pass through and block (or reflect) emission wavelengths within other ranges. For example, emission filters may be used to direct different wavelength ranges of emitted light to different imaging sensors of the camera system (540) of the imaging assembly (522). For example, the emission filters may be implemented as dichroic mirrors that direct emitted light of different wavelengths from the flow cell (510) to different imaging sensors of the camera system (540). In some variations, a projection lens is inserted between the filter switching assembly (544) and the camera system (540). The filter switching assembly (544) may be omitted in some variations.

[0052] The system (500) further includes a fluid delivery assembly (590) capable of directing the flow of reagents (e.g., fluorescently labeled nucleotides, buffers, enzymes, dissection reagents, etc.) to a flow cell (510) and a waste valve (580) (and through the flow cell (510) and the waste valve (580)). The fluid delivery assembly (590) may be configured and operable as the various fluid delivery components described above in the context of Figures 1 to 3. The system (500) of this embodiment also includes a temperature station actuator (530) and a heater / cooler (532) capable of optionally adjusting the temperature conditions of the fluid in the flow cell (510). In some implementations, the heater / cooler (532) may be fixed to and / or integrated into the sample stage (570) on which the flow cell (510) is mounted.

[0053] The flow cell (510) may be detachably mounted on a sample stage (570) which can provide movement and alignment of the flow cell (510) relative to the objective lens assembly (542). The sample stage (570) may have one or more actuators to enable movement of the sample stage (570) in any of three dimensions. For example, actuators may be provided to enable the sample stage (570) to move in the x, y, and z directions relative to the objective lens assembly (542), to tilt relative to the objective lens assembly (542), and / or to move relative to the objective lens assembly (542). Movement of the sample stage (570) may enable one or more sample locations on the flow cell (510) to be optically aligned and positioned with respect to the objective lens assembly (542). Movement of the sample stage (570) relative to the objective lens assembly (542) may be achieved by moving the sample stage (570) itself, by moving the objective lens assembly (542), by moving some other components of the imaging assembly (522), by moving some other components of the system (500), or by any combination thereof. For example, in some implementations, the sample stage (570) may be operable in the x and y directions relative to the objective lens assembly (542), while the focal component (562) or z-stage may move the objective lens assembly (542) along the z-direction relative to the sample stage (570).

[0054] In some implementations, a focusing component (562) may be included to control the positioning of one or more elements of the objective lens assembly (542) relative to the flow cell (510) in the focal direction (e.g., along the z-axis or z-dimension). The focusing component (562) may include one or more actuators physically coupled to the objective lens assembly (542), an optical stage, a 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) and provide proper focusing for the imaging operation. In this embodiment, the focal component (562) is configured to detect the displacement of the objective lens assembly (542) relative to a portion of the flow cell (510) and output data indicating the focal position to the focal component (562) or to its components, or a focus tracking module (560) is used which can control the focal component (562), such as a controller (520), to move the objective lens assembly (542) and position the corresponding portion of the flow cell (510) at the focal point of the objective lens assembly (542).

[0055] In some implementations, actuators for the focal component (562) or sample stage (570) may be physically coupled to the objective lens assembly (542), optical stage, sample stage (570), or a combination thereof, for example, by direct or indirect mechanical, magnetic, fluid, or other mounting or contact to or with the stage or its components. The actuator for the focal component (562) may be configured to move the objective lens assembly (542) in the z-direction while keeping the sample stage (570) in the same plane (for example, while maintaining a level or horizontal orientation perpendicular to the optical axis). In some implementations, the sample stage (570) includes x-direction actuators and y-direction actuators to form an xy-stage. The sample stage (570) may also be configured to include one or more tilt or inclination actuators to tilt or incline the sample stage (570) and / or a portion thereof, taking into account the gradient of its surface.

[0056] The camera system (540) may include one or more imaging sensors for monitoring and tracking the imaging (e.g., array determination) of the flow cell (510). The camera system (540) may be implemented, for example, as a CCD or CMOS imaging sensor camera, but other imaging sensor technologies (e.g., active pixel sensors) may be used. As just further examples, the camera system (540) may include a dual-sensor time delay integration (TDI) camera, a single-sensor camera, a camera having one or more two-dimensional imaging sensors, and / or other types of camera technologies. The camera system (540) and associated optical components are shown in Figure 7 positioned above the flow cell (510), but one or more imaging sensors or other camera components may be incorporated into the system (500) in numerous other ways, as will be apparent to those skilled in the art by considering the teachings herein. For example, one or more imaging sensors may be positioned below the flow cell (510), such as within or below the sample stage (570), or they may be incorporated into the flow cell (510).

[0057] Figure 8 shows embodiments of various components that may be incorporated into the imaging assembly (522) of the system (500). In particular, the configuration shown in Figure 8 may represent a variation of the light emission assembly (550). The configuration shown in Figure 8 may be particularly useful in a scenario in which the camera system (540) includes a TDI camera. In the configuration shown in Figure 8, the Line Generation Module (LGM) (602) and the Emission Optics Module (EOM) (604) are mechanically coupled to and aligned with a precision mounting plate (610). The EOM (604) includes an objective lens assembly (606) aligned with an imaging lens (620) via a mirror (608), and the imaging lens 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 embodiments, the LGM(602) may include a first light source configured to emit red wavelength light and a second light source configured to emit green wavelength light. The LGM(602) may further include optical components such as focal planes, lenses, reflectors, or mirrors. The optical components may be located within the housing of the LGM(602) and may focus the light emitted from one or more light sources by directing it into adjacent module subassemblies. One or more of the optical components of the LGM(602) may also be configured to shape the 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, diffraction or scattering components). In some modifications, the LGM(602) may include one or more laser modules that can be individually removed from and replaced from the LGM(602).

[0058] The light beam generated by the LGM(602) passes through an interface baffle between the LGM(602) and the EOM(604), through the objective lens assembly(606), and strikes an optical target (e.g., a flow cell(510)). In some variations, the interface baffle includes an aperture shaped to allow light to pass through its center while obscuring interference from an external light source. The response light emission from the target can pass back through the objective lens assembly(606) and enter the imaging lens(622). The lens element(622), which may form part of the imaging lens(620), is configured to articulate along an axis (e.g., the z-axis) to correct spherical aberration artifacts introduced by the objective lens assembly(606) as it images through varying thicknesses of the flow cell(510) components. As shown in the figure, the lens element (622) may articulate to move closer to or further away from the objective lens assembly (606) to adjust the beam shape and path. The objective lens assembly (606) may emit excitation light toward an optical target (e.g., a flow cell (510)) and receive fluorescence emission from the optical target. The actuator may be configured to position the objective lens assembly (606) in a target region close to the optical target. Next, the processor of the controller (520) may execute program instructions to detect fluorescence emission from the optical target.

[0059] Figure 9 shows an embodiment of another configuration that may be provided within the imaging assembly (522). In particular, Figure 9 shows the imaging assembly (650) positioned relative to a flow cell (670). The flow cell (670) may represent any of the variations of the flow cells (128, 368, 400, 450, 510) described herein. The flow cell (670) has an upper layer (671) and a lower layer (673) separated by a fluid-filled channel (675). In the shown configuration, the upper layer (671) is optically transparent, and the imaging assembly (650) is focused on a region (676) on the inner surface (672) of the upper layer (671). In other variations, the imaging assembly (650) may be focused on the inner surface (674) of the lower layer (673). One or both of the surfaces (672, 674) may include array feature regions detected by the imaging assembly (650).

[0060] The imaging assembly (650) includes an objective lens assembly (666) configured to direct excitation radiation from the light-emitting assembly (652) to the flow cell (670), and radiation from the flow cell (670) to the detector (664). In the illustrated configuration, excitation radiation from the light-emitting assembly (652) passes through a lens (658), a beam splitter (660), and the objective lens assembly (666) to reach the flow cell (670). In this embodiment, the light-emitting assembly (652) includes two light-emitting diodes (LEDs) (656, 654) that produce radiation of different wavelengths. The radiation emitted from the flow cell (670) is captured by the objective lens assembly (666), reflected by the beam splitter (660), and passes through the tuner optical system (662) to the detector (664) (e.g., a CMOS sensor). The beam splitter (660) serves to direct the emitted radiation in a direction perpendicular to the path of the excitation radiation. The position of the objective lens assembly (666) may be moved in the z dimension to change the focus of the imaging assembly (650). The imaging assembly (650) may be moved back and forth in the y direction to capture images of several regions of at least one inner surface (672, 674) of the flow cell (670).

[0061] In this embodiment, a single imaging assembly (650) includes two LEDs (656, 654) that emit light at two different wavelengths, and a single detector (664) detects the light emitted from the fluorophore label in the flow cell (670) in response to irradiation at these two different wavelengths. In some other variations, there are two or more imaging assemblies (650), each imaging assembly (650) including a single LED (656, 654) and a single detector (664), and each imaging assembly (650) provides irradiation at only one single wavelength. In another variation, two or more detectors (664) may receive excitation radiation from a common emission assembly (652).

[0062] Figure 10 shows an embodiment of another configuration that may be provided within the imaging assembly (522). In particular, Figure 10 shows the imaging assembly (700) positioned relative to a flow cell (774). The flow cell (774) may represent any of the variations of the flow cells (128, 368, 400, 450, 510) described herein. The flow cell (770) has a translucent cover plate (772), a substrate (774), and a liquid layer (776) sandwiched between the cover plate (772) and the substrate (774). A biological sample may be placed on the inner surface of the cover plate (772) (above the liquid layer (776)) and / or on the inner surface of the substrate (774) (below the liquid layer (776)).

[0063] The imaging assembly (700) of this embodiment includes a LGM (710) with two light sources (712, 714) arranged inside. The light sources (712, 714) may include laser diodes, diode-pumped solid-state lasers, or other light sources known in the art that emit laser beams of different wavelengths (e.g., red or green light). The light beams emitted from the light sources (712, 714) are directed through one or more beam-shaping lenses (716). In some implementations, one or more photo-shaping lenses may be used to shape the light beams emitted from each or both light sources. The LGM (710) may use one or more Powell lenses to diffuse and / or shape the laser beams from single-mode or nearly single-mode laser sources. Other beam-shaping optical systems, such as active beam expanders, attenuators, a single relay lens, a cylindrical lens, an actuated mirror, a diffracting element, and scattering components, may be used to control uniformity and increase tolerances. The laser beams may intersect at the back focus of the objective lens to provide better tolerances on the surface of the flow cell (770).

[0064] The LGM(710) in this embodiment further includes mirrors (718, 720). A light beam generated by a light source (712) is reflected by mirror (718) and directed into the EOM(740) through a single interface port via an aperture or semi-reflective surface of mirror (720). Similarly, a light beam generated by a light source (714) is reflected by mirror (720) and directed into the EOM(740) through a single interface port. In some embodiments, an additional set of articulated mirrors may be incorporated adjacent to the mirrors (718, 720) to provide an additional adjustment surface. Both light beams may be combined using a dichroic mirror (720). Each of the mirrors (718, 720) may be configured to articulate using manual or automatic control to align the light beams from the light sources (712, 714). In this embodiment, the light beam also passes through a shutter element (722).

[0065] The EOM(740) includes an objective lens assembly(756) and a z-stage(758) for moving the objective lens assembly(756) longitudinally closer to or further away from the flow cell(770). The LGM(710) is configured to produce uniform line illumination through the objective lens assembly(756). The z-stage(758) may then move the objective lens assembly(756) to focus the light beam onto one of the inner surfaces of the flow cell(770) (for example, onto a biological sample). In some implementations, the objective lens assembly(756) may be configured to focus the light beam beyond the flow cell(770) to a focal point, for example, to increase the linewidth of the light beam on the surface of the flow cell(770).

[0066] The EOM (740) in this embodiment also includes a semi-reflective mirror (754) for directing light through the objective lens assembly (756) while allowing light returned from the flow cell (774) to pass through. The EOM (740) further includes an imaging lens (744) and a corrector lens (748). The corrector lens (748) may be articulated longitudinally by the z-stage (746) to move closer to or further away from the objective lens assembly (756) to ensure accurate imaging (e.g., to correct spherical aberration caused by moving the objective lens assembly (756) and / or from imaging through a thicker substrate). Light transmitted through the corrector lens (748) and the imaging lens (744) passes through a filter element (742) and enters the camera system (730). The camera system (730) includes one or more photosensors (732) for detecting light emitted from a biological sample in response to the incident light beam.

[0067] The EOM(740) in this embodiment further includes a semi-reflective mirror (752) that reflects the focus-tracking light beam emitted from the Focus Tracking Module (FTM)(760) to a flow cell (774), and then reflects the light returned from the flow cell (774) back to the FTM(760). The FTM(760) may include a focus-tracking light sensor that detects the characteristics of the returned focus-tracking light beam and generates a feedback signal for optimizing the focus of the objective lens assembly (756) on the flow cell (774).

[0068] The direction, size, and / or polarization of the laser beam may be adjusted by using lenses, mirrors, and / or polarizers. Optical lenses (e.g., cylindrical, spherical, or aspherical) may be used to actively adjust the illumination focus on the bifacial surface of the flow cell (770) target. The LGM(710) may also include multiple units, each designed for a specific / different wavelength and polarization. Stacking multiple units may be used to increase the laser power and wavelength options. Two or more laser wavelengths may be combined with dichroic and polarizers.

[0069] As just one example, other components of the focus tracking module (560) and / or imaging assembly (522) may be constructed and operable in accordance with at least some of the teachings of U.S. Patent No. 10,416,428, issued September 17, 2019, titled "Systems and Methods for Improved Focus Tracking Using a Light Source Configuration" (the entire disclosure of which is incorporated herein by reference), U.S. Patent Application Publication No. 63 / 300,531, filed January 18, 2022, titled "Dynamic Detilt Focus Tracking" (the entire disclosure of which is incorporated herein by reference), and U.S. Patent Application Publication No. 63 / 410,961, filed September 28, 2022, titled "Spot Error Handling for Focus Tracking" (the entire disclosure of which is incorporated herein by reference). As merely a further example, components of an imaging assembly (522) may be configured and operable in accordance with at least some of the teachings of U.S. Patent No. 10,774,371, entitled “Laser Line Illuminator for High Throughput Sequencing,” issued on 15 September 2020 (the entire disclosure of which is incorporated herein by reference), and U.S. Patent No. 9,958,465, entitled “Detection Apparatus having a Microfluorometer, a Fluidic System, and a Flow Cell Latch Clamp Module,” issued on 1 May 2018 (the entire disclosure of which is incorporated herein by reference).

[0070] V. Examples of optical devices for correcting thermally induced astigmatism in lenses During the operation of a system, such as any of the systems described herein (100, 300, 500), one or more components may tend to heat up, particularly during the initial stages of system use. In some such scenarios, the heated component may deform or undergo some other structural change, which 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 the operation of the system (100, 300, 500). Such heating of the objective lens element may be caused by heat generated from incident light from the light-emitting assemblies (550, 652), heat generated from incident light from the line generation modules (LGMs) (602, 710), and / or any other heat source.

[0071] Heating of the objective lens element during operation of a system such as any of the systems described herein (100, 300, 500) may tend to dynamically generate aberrations (e.g., astigmatism) in the objective lens element, or dynamically correct aberrations already present in the objective lens element. For example, heating of the objective lens element may induce changes in the refractive index gradient and / or thermal expansion coefficient of the objective lens element, and these physical changes may provide the corresponding generation or change of astigmatism in the objective lens element. In some cases, such thermal induction or aberration change may tend to occur during the initial heating phase of the objective lens element, and the generated / corrected aberration may then tend to remain substantially stable while the objective lens element maintains a substantially steady operating temperature.

[0072] As described above, the objective lens assemblies (542, 606, 666, 756) may provide images of reaction sites on the flow cells (128, 368, 400, 450, 510) during the operation of the system (100, 300, 500), and high image quality is desirable to obtain precise and accurate information about the real-time characteristics of small data points (e.g., nucleotides) at the reaction sites. In scenarios where the objective lens element has a dynamically changing aberration profile, the dynamically changing aberration profile can tend to dynamically negatively affect image quality unless some kind of dynamic correction is provided for the dynamically changing aberration profile. To the extent that it may be possible to provide some degree of dynamic correction for the thermally induced, dynamically changing aberration profile of the objective lens element through image processing techniques, it may be desirable to provide optical hardware-based solutions to provide dynamic correction for the thermally induced, dynamically changing aberration profile of the objective lens element. The following describes some embodiments of optical solutions that may be used to provide dynamic correction for the thermally induced, dynamically changing aberration profile of the objective lens element.

[0073] A. Example element of an optical device with dual pivot correction 1. Overview Figures 11A and 11B show an embodiment of a device (800) that can be integrated into an imaging system (116, 310) or an imaging assembly (522, 700). The device (800) in this embodiment includes a flow cell (810), an objective lens element (820), an imaging lens (830), a correction assembly (840), and a camera (850). The objective lens element (820) is positioned on the flow cell (810) and may be configured and operable as in any of the modifications of the flow cell (128, 368, 400, 450, 510) described herein. In this embodiment, a fluorescent label at a reaction site on the flow cell (810) emits light in response to excitation from one or more excitation light sources (not shown). The emitted beam is transmitted from the flow cell (810) through the objective lens element (820) to the imaging lens (830). In addition to the emission beam passing through the objective lens element (820), an excitation beam may also pass through the objective lens element (820) and reach the flow cell (820). This excitation beam may cause heating of the objective lens element (820), as described herein. As further described herein, this excitation beam may be emitted from the light emission assembly (550, 652), from the line generation module (LGM) (602, 710), or from any other light source.

[0074] The emitted beam from the flow cell (810) is generally emitted along the image axis (IA), and the objective lens element (820) is centered along the image axis (IA). In this embodiment, the image axis (IA) is parallel to the z-axis. The objective lens element (820) in this embodiment is configured to substantially collimate the emitted beam. Although only one objective lens element (820) is shown in this embodiment, such representations are intended to be schematic only. It should be understood that the objective lens element (820) may actually include a lens assembly formed by multiple lens elements and / or other optical features.

[0075] The imaging lens (830) is also centered along the imaging axis (IA) so that the collimated emitted beam from the objective lens element (820) passes through the imaging lens (830) into the converged image space. In this embodiment, only one lens element is shown to represent the imaging lens (830), but such representation is intended only as a schematic representation. It should be understood that the imaging lens (820) may actually include a lens assembly formed by multiple lens elements and / or other optical features.

[0076] The correction assembly (840) is positioned on the imaging axis (IA) in the converged image space between the imaging lens (830) and the camera (850). The correction assembly (840) in this embodiment includes a first correction plate (842) and a second correction plate (844). In this embodiment, each correction plate (842, 844) includes a flat plate formed of a light-transmitting material (e.g., glass), but other configurations may be used. The first correction plate (842) is positioned longitudinally along the imaging axis (IA) where a first vertical reference plane (R1) intersects the imaging axis (IA). The second correction plate (844) is positioned longitudinally along the imaging axis (IA) where a second vertical reference plane (R2) intersects the imaging axis (IA). Therefore, the first correction plate (842) is interposed longitudinally between the second correction plate (844) and the imaging lens (830). On the other hand, the second correction plate (844) is interposed longitudinally between the first correction plate (842) and the camera (850).

[0077] In this embodiment, the first correction plate (842) has the same structural configuration as the second correction plate (844) so ​​that the correction plates (842, 844) have the same material composition, thickness, etc. However, the correction plates (842, 844) are positioned at different angular orientations along the imaging axis (IA). In particular, in the operating state shown in Figure 11A, the first correction plate (842) is positioned along a first plate surface (P1) that is inclined at a first inclination angle (θ1) with respect to a first reference plane (R1) in a clockwise direction, centered on an inclination axis parallel to the x-axis. In the same operating state shown in Figure 11A, the second correction plate (844) is positioned along a second plate surface (P2) that is inclined at a first inclination angle (θ1) with respect to a second reference plane (R2) in a counterclockwise direction, centered on an inclination axis parallel to the x-axis. In other words, the correction plates (842, 844) are oriented at equal but opposite angles of inclination around their respective inclination axes parallel to the x-axis.

[0078] The correction assembly (840) is configured to correct any astigmatism that may be provided by the combination of the objective lens element (820) and the imaging lens (830). In particular, the first correction plate (842) may be configured to induce a first astigmatism that partially offsets the astigmatism provided by the combination of the objective lens element (820) and the imaging lens (830). On the other hand, the second correction plate (842) is configured to induce a second astigmatism that completes the offset of the astigmatism provided by the combination of the objective lens element (820) and the imaging lens (830). The first astigmatism induced by the first correction plate (842) may be a function of the thickness, refractive index, and angle of incidence (based on the inclination angle (θ)) of the first correction plate (842). The second astigmatism induced by the second correction plate (844) may be a function of the thickness, refractive index, and angle of incidence (based on the inclination angle (θ)) of the second correction plate (844).

[0079] After the emitted light passes through the first correction plate (842), the imaging axis (IA) may tend to shift slightly in the first direction along the y-dimension, and then, after passing through the second correction plate (844), it may tend to shift slightly again in the second direction along the y-dimension. This shift is not depicted in Figure 11A. In this embodiment, since the correction plates (842, 844) are oriented at equal and opposite inclination angles, the imaging shift caused by the second correction plate (844) is equal to and opposite to the imaging shift caused by the first correction plate (842). Thus, the imaging axis (IA) in the space between the second correction plate (844) and the camera (850) is aligned with the imaging axis (IA) in the space between the flow cell (810) and the first correction plate (842).

[0080] It should be understood from the foregoing that the correction plates (842, 844) cooperate to offset or correct any astigmatism that may be provided by the combination of the objective lens element (820) and the imaging lens (830). Meanwhile, an image is provided from the flow cell (810) to the camera (850) along the aligned imaging axis (IA). The camera (850) captures the image transmitted from the correction assembly (840). The camera (850) may be configured and operable as any of the camera systems (540, 730) described herein, and may include a CCD or CMOS imaging sensor camera, an active pixel sensor camera, a dual-sensor time-delay integral (TDI) camera, a single-sensor camera, a camera with one or more two-dimensional imaging sensors, and / or other types of camera technology. The image captured by the camera (850) may be analyzed to evaluate the characteristics of the reaction sites on the flow cell (810) as described herein.

[0081] As described above, the temperature of the objective lens element (820) may have a first value before the excitation light is activated and incident on the objective lens element (820). 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 rise and eventually stabilize at or near a second temperature value. Since the excitation light remains activated and incident on the objective lens element (820), the temperature of the objective lens element (820) may remain substantially constant at or near the second temperature value during continuous operation. Also as described above, when the temperature of the objective lens element (820) rises from the first temperature to the second temperature, the rise in temperature may generate or alter aberrations such as astigmatism in the objective lens element (820). In other words, the objective lens element (820) may have thermally induced dynamic aberrations during the initial heating period. In this embodiment, the temperature of the imaging lens (830) does not substantially change during operation, and therefore, any change in the aberration of the imaging lens (830) during operation can be considered negligible. In some other variations, temperature changes may induce or otherwise alter aberrations within the imaging lens (830) and / or within other optical components of the imaging system (116, 310) or imaging assembly (522, 700).

[0082] The correction assembly (840) is configured to offset or correct any astigmatism that may be provided by the combination of the objective lens element (820) and the imaging lens (830), so it may be necessary to dynamically adjust the correction assembly (840) to "keep up" with the thermally induced dynamic aberrations of the objective lens element (820) and / or other optical components during the initial heating period. In other words, it may be desirable to provide dynamic adjustment to the correction assembly (840) so as to dynamically offset or correct the thermally induced dynamic aberrations of the objective lens element (820) and / or other optical components during the initial heating period. Such adjustment may be performed by pivoting each correction plate (842, 844) around its respective pivot axis, since the offset astigmatism of each correction plate (842, 844) may be a function of the tilt angle (θ) of each correction plate (842, 844).

[0083] While the embodiments herein are provided in the context of dynamic aberrations of the objective lens element (820), the teachings herein may also be applied to scenarios in which one or more other optical components of the imaging system (116, 310) or imaging assembly (522, 700) provide dynamic aberrations (whether or not the objective lens element (820) also provides dynamic aberrations). In other words, the teachings herein do not necessarily depend on the objective lens element (820) as the source of the dynamic aberrations. Correction plates (842, 844) may be used to correct aberrations from any light source that could otherwise reach the camera (850).

[0084] Figures 11A and 11B both show examples of the pivotal movement of the correction plates (842, 844) to simultaneously adjust the inclination angle (θ) of each correction plate (842, 844). In Figure 11A, the first correction plate (842) is inclined clockwise with respect to the first reference plane (R1) at a first inclination angle (θ1) around its inclination axis, while the second correction plate (844) is inclined counterclockwise with respect to the second reference plane (R2) at a first inclination angle (θ1) around its own inclination axis. In Figure 11B, the first correction plate (842) is inclined clockwise with respect to the first reference plane (R1) at a second inclination angle (θ2) around its inclination axis. The second correction plate (844) is inclined counterclockwise with respect to the second reference plane (R2) at a second inclination angle (θ2) around its own inclination axis. Therefore, the correction plates (842, 844) are pivoted in opposite angular directions around their respective tilt axes to transition from a first tilt angle (θ1) to a second tilt angle (θ2). The astigmatism induced by each of the correction plates (842, 844) differs at the second tilt angle (θ2) compared to the astigmatism induced by each of the correction plates (842, 844) at the first tilt angle (θ1). This is due to the difference between the angle of incidence to the correction plates (842, 844) at the first tilt angle (θ1) and the angle of incidence to the correction plates (842, 844) at the second tilt angle (θ2), and the induced astigmatism is at least partially affected by the angle of incidence.

[0085] In some scenarios, the astigmatism induced by the corrector plates (842, 844) at a first tilt angle (θ1) offsets the astigmatism provided by the objective lens (830) combination at the initial lower temperature, and the astigmatism induced by the corrector plates (842, 844) at a second tilt angle (θ2) offsets the astigmatism provided by the objective lens element (820) and imaging lens (830) combination at the higher operating temperature. The speed at which the corrector plates (842, 844) pivot from the first tilt angle (θ1) to the second tilt angle (θ2) may be selected to track the rate at which the astigmatism provided by the objective lens element (820) and imaging lens (830) changes due to the temperature rise of the objective lens element (820). In other words, as the correction plates (842, 844) pivot from a first tilt angle (θ1) to a second tilt angle (θ2), the correction assembly (840) may dynamically correct the dynamic change in astigmatism provided by the combination of the objective lens element (820) and the imaging lens (830) while the objective lens element (820) is heating up. As long as the temperature of the objective lens element (820) remains substantially stable after it has heated up to its normal operating temperature, the correction plates (842, 844) may remain fixed at the second tilt angle (θ2) so that the correction assembly (840) maintains a fixed astigmatism offset.

[0086] It should be understood that when the correction plates (842, 844) pivot from a first tilt angle (θ1) to a second tilt angle (θ2), the imaging shift caused by the correction plates (842, 844) along the y-dimension can move along the y-dimension accordingly. However, since the correction plates (842, 844) rotate at the same speed in opposite directions about parallel axes, the light can remain centered along the aligned imaging axis (IA) in the space between the second correction plate (844) and the camera (850). In some variations, there may be scenarios in which the correction plates (842, 844) rotate simultaneously at the same speed in opposite directions about parallel axes, but one correction plate (842, 844) pivots independently of the other correction plate (842, 844). Such independent pivoting of a single correction plate (842, 844) (for example, while the other correction plate (842, 844) remains stationary) may be provided to adjust the beam position in the y-direction to maintain a desired alignment of the beam axis onto the imaging sensor of the camera (850).

[0087] It should also be understood that the correction assembly (840) may be positioned at any location along the imaging axis (IA) in the converged image space between the imaging lens (830) and the camera (850). Therefore, the correction assembly (840) may be positioned closer to the imaging lens (830) than shown in Figures 11A-11B, or closer to the camera (850) than shown in Figures 11A-11B. Furthermore, the correction plates (842, 844) may be positioned at any preferred distance from each other.

[0088] 2. Example of a method for operating a correction assembly Some variations of the apparatus (800) may provide real-time tracking of thermally induced or thermally altered astigmatism of the objective lens element (820) and dynamically adjust the tilt angle (θ) of the correction plates (842, 844) in real time via a feedback loop. In some such cases, real-time tracking of changes in thermally induced or thermally altered astigmatism of the objective lens element (820) may be achieved using image processing techniques. For example, an algorithm executed through a controller (114, 308, 520) may provide analysis of images captured by the camera (850) during the initial stage of operation while the objective lens element (820) is heated from its initial resting temperature to its normal stable operating temperature, thereby tracking the thermally induced or thermally altered astigmatism of the objective lens element (820) in real time. As just one example, the image analysis algorithm may evaluate the astigmatism of the objective lens element (820) by tracking the Full Width at Half Maximum (FWHM) value associated with the image captured along the x-dimension and the FWHM value associated with the image captured along the y-dimension. The same algorithm may further drive one or more actuators, etc., to provide the pivoting motion of the correction plates (842, 844) in real time through a feedback loop, based on the tracked astigmatism of the objective lens element (820). In some variants in which a real-time feedback loop is used to drive the pivoting motion of the correction plates (842, 844), such pivoting motion of the correction plates (842, 844) may vary each time the device (800) is used to the extent that the dynamically changing aberration profile of the objective lens element (820) may change between different uses of the device (800) (e.g., due to environmental factors, age of the equipment, different types of excitation light profiles being used, etc.).

[0089] As an alternative to using an ad hoc real-time feedback loop to drive the pivoting motion of the correction plates (842, 844) each time the device (800) is used, the pivoting motion of the correction plates (842, 844) may be provided based on a predetermined adjustment profile. In other words, the controllers (114, 308, 520) do not need to process the captured image to track changes in thermally induced or thermally altered astigmatism of the objective lens element (820) each time the device (800) is used. Instead, the controllers (114, 308, 520) may simply be programmed with a predetermined adjustment profile and simply consistently execute that predetermined adjustment profile each time the device (800) is used. The predetermined adjustment profile may be established through a calibration process, which can be performed at the facility where the device (800) is manufactured. Alternatively, the calibration process may be performed at the location where the device (800) will ultimately be used, such as during the initialization process when the device (800) is first used by the consumer.

[0090] Regardless of where the calibration process is performed, the calibration process may include a sequence of enabling the objective lens element (820) to heat from its initial resting temperature to its normal stable operating temperature, tracking the dynamic astigmatism of the objective lens element (820) in real time through the image processing techniques described above, and driving the pivoting motion of the correction plates (842, 844) based on the tracked dynamic astigmatism of the objective lens element (820). In some cases, after the first calibration run, the controllers (114, 308, 520) may stop the excitation light source, allowing the temperature of the objective lens element (820) to return to its initial resting temperature, and then repeat the process to perform a second calibration run. This can be repeated any number of times as desired. The controllers (114, 308, 520) may ultimately determine the best adjustment profile for the pivoting motion of the compensating plates (842, 844), thereby establishing that best adjustment profile as a predetermined adjustment profile for subsequent use of the device (800).

[0091] 3. Example of a correction assembly with dual actuators Figure 12 shows an embodiment of apparatus (900) in which dual actuators (970, 980) are used to drive a compensating assembly (940). Apparatus (900) is substantially identical to apparatus (800) unless otherwise described below. Apparatus (900) includes a flow cell (910), an objective lens element (920), an imaging lens (930), a compensating assembly (940), and a camera (950). The compensating assembly (940) includes a first compensating plate (942) and a second compensating plate (944). Apparatus (900) in this embodiment differs from apparatus (800) in that it is shown as including a controller (960), a first actuator (980), and a second actuator (970). The controller (960) may be configured and operable as any other controllers (114, 308, 520) described herein, such that the controller (960) is operable to process images captured by the camera (950), process other data, and control the operation of other components. To this end, the controller (960) is also operable to control the actuators (970, 980) by instigating the actuators (970, 980) to drive the movement of the correction plates (942, 944), as described herein.

[0092] The first actuator (980) is connected to the first compensator plate (942) so as to be operable to drive the pivotal motion of the first compensator plate (942). The second actuator (970) is connected to the second compensator plate (944) so ​​as to be operable to drive the pivotal motion of the second compensator plate (944). In some variations, each actuator (970, 980) is equipped with a motor, and activation of the actuators (970, 980) rotates the drive shaft of the motor, thereby driving the pivotal motion of the compensator plates (942, 944). In some other variations, each actuator (970, 980) is equipped with a solenoid or a voice coil. Alternatively, the actuators (970, 980) may take any other preferred form. In this embodiment, each correction plate (942, 944) has its own dedicated actuator (970, 980) so as to be theoretically possible to independently activate the actuators (970, 980) and thereby independently drive the pivoting motion of the correction plate (942, 944). For example, there may be a scenario in which one correction plate (942, 944) pivots independently of the other correction plate (942, 944). Such independent pivoting of a single correction plate (942, 944) (for example, while the other correction plate (942, 944) remains stationary) may be provided to adjust the beam position in the y-direction so as to maintain a desired alignment of the beam axis onto the imaging sensor of the camera (950). However, in this embodiment, the controller (960) is configured to activate the actuators (970, 980) synchronously with respect to each other.

[0093] 4. Embodiment of a Correction Assembly Having a Single Actuator and Link Mechanism Figure 13 shows an embodiment of apparatus (1000) in which a single dual actuator (1070) is used to drive a compensating assembly (1040). Apparatus (1000) is substantially identical to apparatus (800) unless otherwise described below. Apparatus (1000) includes a flow cell (1010), an objective lens element (1020), an imaging lens (1030), a compensating assembly (1040), and a camera (1050). The compensating assembly (1040) includes a first compensating plate (1042) and a second compensating plate (1044). Apparatus (1000) in this embodiment differs from apparatus (1000) in that it is shown as including a controller (1060), an actuator (1070), and a linkage mechanism (1080). The controller (1060) may be configured and operable as any other controllers (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) and driving the movement of the correction plates (1042, 1044), as described herein.

[0094] The link mechanism (1080) is connected to the actuator (1070) and both compensator plates (1042, 1044). The link mechanism (1080) in this embodiment comprises a mechanical assembly configured to drive the simultaneous synchronous pivotal motion of the compensator plates (1042, 1044) in opposite directions when the link mechanism (1080) is activated by the actuator (1070). In just one example, the link mechanism (1080) may include a plurality of rods, bars, or other links that are pivotally joined to one another. In just a further example, the link mechanism (1080) may include a plurality of gears that mesh with one another. In just a further example, the link mechanism (1080) may include a set of cams that provide a combination of engaged drive surfaces and bearing surfaces. Alternatively, the link mechanism (1080) may take any other preferred form. Similarly, the actuator (1070) may take any preferred form including, but not limited to, a motor, solenoid, voice coil, etc.

[0095] B. Example of an optical device with single pivot correction element In some scenarios, it may be desirable to provide variations of the compensator assemblies (840, 940, 1040) having only one compensator element. Figures 14A and 14B show an embodiment of such an apparatus (1100). The apparatus (1100) in this embodiment includes a flow cell (1110), an objective lens element (1120), an imaging lens (1130), a compensator assembly (1140), and a camera (1150). The flow cell (1110), objective lens element (1120), imaging lens (1130), and camera (1150) may be configured and operable in the same way as the flow cell (810), objective lens element (820), imaging lens (830), and camera (850) described above. The compensator assembly (1140) may be configured and operable in the same way as the compensator assembly (840), unless otherwise described below.

[0096] The correction assembly (1140) in this embodiment includes only one correction plate (1142). Similar to the correction plates (842, 844), the correction plate (1142) is configured to correct (by itself) any astigmatism that may be provided by the combination of the objective lens element (1120) and the imaging lens (1130). Similarly, the correction plate (1142) is rotatable about a pivot axis between different tilt angles (θ1, θ2) to adjust its own astigmatism, thereby dynamically correcting thermally induced changes in the astigmatism of the objective lens element (1120) as the objective lens element (1120) heats up from its initial resting temperature to its normal stable operating temperature. However, since the correction assembly (1140) has only one correction plate (1142), when the correction plate (1142) pivots around a pivot axis parallel to the z-axis, the imaging axis (IA) shifts along the y-dimension. This shift is shown in Figure 14B, where the imaging axis (IA2) in the space between the correction plate (1142) and the camera (1150) is shifted relative to the imaging axis (IA) in the space between the flow cell (1110) and the correction plate (1142). It should be understood that the shift shown in the transition from Figure 14A to Figure 14B may be exaggerated for illustrative purposes.

[0097] In the apparatus (1100) of this embodiment, the shift of the imaging axes (IA, IA2) is accounted for by the movement of the camera (1150) such that the camera (1150) moves with the imaging axes (IA, IA2) and remains centered along the imaging axis (IA2). This movement of the camera (1150) is shown in the transition from Figure 14A to Figure 14B. Such movement of the camera (1150) may be provided in various ways. As just one example, a dedicated actuator (not shown) may drive the movement of the camera (1150) along the y-dimension. Such an actuator may be configured and operable in the same way as any of the other actuators (970, 980, 1070) described herein. In another variation, a single actuator (not shown) may be connected to a linkage mechanism (not shown), which may be connected to both the compensating plate (1142) and the camera (1150). In another variation, the camera (1150) may be sized and configured to allow image movement resulting from the movement of the correction plate (1142). The combination of the actuator and the link mechanism may provide simultaneous synchronous motion of the correction plate (1142) and the camera (1150). The link mechanism may be configured and operable in the same way as the link mechanism (1080) described above. Alternatively, the pivoting motion of the correction plate (1142) may be provided in any other preferred manner, and the movement of the camera (1150) in the y-dimension may be provided in any other preferred manner.

[0098] Figures 15A–15B illustrate another embodiment of how to address imaging shift caused by the movement of a single correction plate. In particular, Figures 15A–15B show apparatus (1200), which includes a flow cell (1210), an objective lens element (1220), an imaging lens (1230), a correction assembly (1240), a camera (1250), and a reflecting element (1260). Apparatus (1200) is configured and operable substantially similarly to apparatus (1100). However, unlike the camera (1150) of apparatus (1100), the camera (1250) of apparatus (1200) is in a fixed position, and the reflecting element (1260) is inserted between the correction plate (1242) of the correction assembly (1240) and the camera (1250). The reflecting element (1260) reflects light from the correction plate (1242) toward the camera (1250). Although camera (1250) is shown facing along the y-dimension, this is merely an example, and camera (1250) may instead be oriented in any other suitable direction.

[0099] Similar to the correction plate (1142) of apparatus (1100), the correction plate (1242) of apparatus (1200) is configured to correct (by itself) any astigmatism that may be provided by the combination of the objective lens element (1220) and the imaging lens (1230). Similarly, the correction plate (1242) is rotatable around a pivot axis between different tilt angles (θ1, θ2) to adjust its own astigmatism, thereby dynamically correcting thermally induced changes in the astigmatism of the objective lens element (1220) as the objective lens element (1220) heats up from its initial resting temperature to its normal stable operating temperature. Also, similar to the correction plate (1142) of apparatus (1100), the correction plate (1242) of apparatus (1200) provides a shifted imaging axis (IA2) after the correction plate (1242) has been pivoted.

[0100] In the apparatus (1200) of this embodiment, the shift of the imaging axis lines (IA, IA2) is considered by the movement of the reflector element (1260) such that the reflector element (1260) pivots around an axis parallel to the x-axis, thereby redirecting the light from the correction plate (1242) to ensure that the light remains centered on the camera (1250). This pivotal movement of the reflector element (1260) is shown in the transition from Figure 15A to Figure 15B. Such movement of the reflector element (1260) may be provided in various ways. As just one example, a dedicated actuator (not shown) may drive the pivotal movement of the reflector element (1260). Such an actuator may be configured and operable in the same way as any of the other actuators (970, 980, 1070) described herein. In another variation, a single actuator (not shown) may be connected to a linkage mechanism (not shown), which may be connected to both the compensating plate (1242) and the reflecting element (1260). The combination of the actuator and the linkage mechanism may provide simultaneous synchronous motion of the compensating plate (1242) and the reflecting element (1260). The linkage mechanism may be configured and operable in the same manner as the linkage mechanism (1080) described above. Alternatively, the pivoting motion of the compensating plate (1242) may be provided in any other preferred manner, and the pivoting motion of the reflecting element (1260) may be provided in any other preferred manner. In some variations, the reflecting element (1260) is configured to deform rather than rotate to controllly redirect light toward the camera (1250).

[0101] In another variation, the reflector (1260) may be translated along a path parallel to the z-axis. Such movement of the reflector (1260) may move the image on the camera (1250)'s imaging sensor to compensate for the offset induced by the correction plate (1242).

[0102] C. Examples of optical devices with deformation correction element Figures 16A and 16B show another embodiment of a device (1300) that can be integrated into an imaging system (116, 310) or imaging assembly (522, 700). The device (1300) in this embodiment includes a flow cell (1310), an objective lens element (1320), an imaging lens (1330), a correction assembly (1340), and a camera (1350). The flow cell (1310), objective lens element (1320), imaging lens (1330), and camera (1350) may be configured and operable in the same way as the flow cell (810), objective lens element (820), imaging lens (830), and camera (850) described above. The correction assembly (1340) may be configured and operable in the same way as the correction assembly (840), unless otherwise described below.

[0103] The compensator assembly (1340) of this embodiment comprises a single compensator element (1342). The compensator element (1342) of this embodiment is configured to deform selectively in response to a control signal. For example, Figure 16A shows the compensator element (1342) in a substantially undeformed state, where the compensator element is substantially flat and positioned along a vertical reference plane (R1) intersecting the imaging axis (IA). Figure 16B shows the compensator element (1342) in a deformed state, where the compensator element is deformed relative to the reference plane (R1). In the illustrated embodiment, the compensator element (1342) deforms along the z dimension. In some deformation forms, the compensator element (1342) deforms along one or more other dimensions in addition to deforming along the z dimension. As just one example, the compensator element (1342) may include a film and a plurality of electrodes, the electrodes of which may be selectively activated to drive the deformation of the film in a controlled manner. Some such deformable forms may be configured similarly to the Delta 7 phase modulator by Phaseform GmbH (Freiburg, Germany). Some such deformable forms of the compensating element (1342) may further include a liquid or gel. Alternatively, the deformable compensating element (1342) may take any other suitable form.

[0104] When the corrector element (1342) is deformed, the astigmatism induced by the corrector element (1342) may change accordingly. The corrector element (1342) may therefore be deformable in a controllable manner, thereby dynamically changing the astigmatism induced by the corrector element (1342). This controlled deformation (and thus the changed astigmatism) may be provided to offset or correct the astigmatism induced by the combination of the objective lens element (1320) and the imaging lens (1342). Furthermore, since the astigmatism of the objective lens element (1320) changes dynamically as the objective lens element (1320) heats up from its initial resting temperature to its normal stable operating temperature, the deformation of the correction element (1342) may be adjusted accordingly to "follow" (i.e., dynamically correct) the thermally induced dynamic aberration of the objective lens element (1342) during the initial heating period.

[0105] It should be understood that controllers similar to controllers (114, 308, 520) may be used to drive the compensating element (1342) according to any of the control schemes described herein. In other words, the compensating element (1342) may be driven based on an ad-hoc real-time feedback loop, based on a predetermined adjustment profile, or based on any other preferred criterion.

[0106] In the embodiments shown in Figures 16A to 16B, deformation of the objective lens element (1342) does not cause any shift of the imaging axis (IA). In some other modifications, deformation of the corrector element (1342) may cause any shift of the imaging axis (IA). In such scenarios, the camera (1350) may be moved to track the shifting imaging axis (IA) in a manner similar to that described above with reference to Figures 14A to 14B. Alternatively, a movable reflector element may be inserted between the corrector element (1342) and the camera (1350), and the movable reflector element may be moved to track the shifting imaging axis (IA) in a manner similar to that described above with reference to Figures 15A to 15B. Or, any other suitable components and configurations may be used to account for the shift of the imaging axis (IA) caused by deformation of the objective lens element (1342).

[0107] D. Examples of optical devices with cylindrical correction. The embodiments described above include flat plates and deformable members as embodiments of the correcting elements (842, 844, 942, 944, 1042, 1044, 1142, 1242, 1342), but other types of components may be used. For example, Figure 17 shows an embodiment of a device (1400) including a flow cell (1410), an objective lens element (1420), an imaging lens (1430), a correcting assembly (1440), and a camera (1450). The flow cell (1410), objective lens element (1420), imaging lens (1430), and camera (1450) may be configured and operable in the same way as the flow cell (810), objective lens element (820), imaging lens (830), and camera (850) described above. The compensation assembly (1440) may be configured and operated in the same manner as the compensation assembly (840), unless otherwise specified below.

[0108] The correction assembly (1440) of this embodiment comprises a plurality of correction elements (1442). Each correction element (1442) of this embodiment is configured as a cylindrical lens element, with a convex surface (1444) facing the imaging lens (1430) and a flat surface (1446) facing the camera (1450). Each correction element (1442) may provide discrete degrees of astigmatism correction. Each correction element (1442) may also be selectively positioned within or away from the imaging axis (IA). Thus, although only one correction element (1442) positioned along the imaging axis (IA) is shown in Figure 17, in other scenarios, two or more correction elements (1442) positioned along the imaging axis (IA) may be provided simultaneously. In some variations, any correction element (1442) not positioned along the imaging axis (IA) may be positioned along a transverse axis (LA) that is laterally spaced away from the imaging axis (IA). Alternatively, any correction elements (1442) not positioned along the imaging axis (IA) may be positioned and arranged in any other preferred manner.

[0109] In this embodiment, since each corrector element (1442) provides discrete degrees of astigmatism correction, the corrector elements (1442) may be selectively aggregated along the imaging axis (IA) to provide varying aggregate degrees of astigmatism correction. For example, a first number of corrector elements (1442) may be positioned along the imaging axis (IA) when the combination of the objective lens element (1420) and the imaging lens (1430) is at an initial lower temperature. As the temperature of the objective lens element (1420) and the imaging lens (1430) rises during the initial stages of operation, and the thermally induced astigmatism of the objective lens element (1420) changes accordingly, the number of corrector elements (1442) along the imaging axis (IA) may be dynamically changed to track the changing astigmatism of the objective lens element (1420) until the combination of the objective lens element (1420) and the imaging lens (1430) reaches a steady-state operating temperature. In other words, the correction assembly (1440) may provide dynamically adjustable astigmatism correction by selectively changing the number of correction elements (1442) along the imaging axis (IA).

[0110] It should be understood that controllers similar to controllers (114, 308, 520) may be used to drive the movement of the compensator elements (1442) according to any of the control schemes described herein. In other words, the compensator elements (1442) may be driven based on an ad-hoc real-time feedback loop, based on a predetermined adjustment profile, or based on any other preferred criterion. It should also be understood that one or more actuators (not shown) may be used to drive such movement of the compensator elements (1442). Such actuators may include pneumatic actuators, solenoids, voice coils, electric rack and pinion assemblies, electric crankshaft assemblies, and / or any other preferred components and arrangements. Furthermore, the compensator elements (1442) may be driven independently of each other and thereby may be positioned within or away from the imaging axis (IA).

[0111] As another modification of the embodiment shown in Figure 17, different corrector elements (1442) corrector assemblies (1440) may have different radii of curvature on the curved surface (1444). Thus, each corrector element (1442) may provide a different degree of astigmatism correction than that provided by the other corrector elements (1442). In some such modifications, only one corrector element (1442) may be positioned on the imaging axis (IA) at a given time, and such corrector elements (1442) are selected based on a particular degree of astigmatism correction provided by that particular corrector element (1442). However, other scenarios may exist in which two or more corrector elements (1442) having different radii of curvature are selectively positioned simultaneously along the imaging axis (IA) to collectively provide a desired degree of astigmatism correction.

[0112] Figure 18 shows an example of how the astigmatism parameter can change as a function of the angle of incidence using a corrective element (e.g., a glass plate), such as various corrective elements described herein. In particular, Figure 18 shows a graph (1475) having a plot of the effective optical path length along the sagittal plane (1481), a plot of the effective optical path length along the tangent plane (1483), and a plot (1485) representing the difference between plots (1481, 1483). In the embodiment shown in Figure 18, the thickness of the corrective element is 1 mm and the refractive index (n) is 1.5. In the tangent plane, the transfer matrix can be defined as follows, where t is the thickness of the plate, n is the refractive index, and T is the angle of incidence.

[0113]

number

[0114] On the other hand, the sagittal plane transfer matrix may be defined as follows:

[0115]

number

[0116] VI. Embodiment of an Astigmatism Correction Assembly Having Housing Components and Operating Assembly Figures 19 to 21 show an embodiment of an astigmatism correction assembly (1500) that can be incorporated into any of the various devices described above (800, 900, 1000, 1100, 1200). For example, the correction assembly (1500) in this embodiment may represent a modification of the correction assembly (840), or more specifically, a modification of the correction assembly (1040). The correction assembly (1500) in this embodiment 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 base plate (1520). The upper housing element (1502) is fixed to the upper ends of the housing elements (1504, 1506, 1508, 1510). The lower ends of the housing elements (1504, 1506, 1508, 1510) are fixed to the base plate (1520). The housing elements (1502, 1504, 1506, 1508, 1510) and the base plate (1520) work together to form a box shape.

[0117] The ring element (1512) is connected to the fourth side housing element (1510). In some variations, the ring element (1512) structurally facilitates the physical coupling or integration of the compensating assembly (1500) with other components of the device (800, 900, 1000, 1100, 1200). The ring element (1512) may also be coupled to the fourth side housing element (1510) using a sliding seal ring to provide sealing from external light and contamination while allowing axial length adjustment to accommodate other system components.

[0118] As shown in Figures 22 to 24B, the compensating assembly (1500) further includes an actuator (1530) and a fixed frame plate (1560). The actuator (1530) comprises 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 motion of the shaft (1534) relative to the body (1532) and the fixed frame plate (1560), as shown in the transition between Figures 23A and 23B, and between Figures 24A and 24B. In some variations, the actuator (1530) includes a stepper motor coupled to a mechanical assembly (e.g., rack and pinion, screw gear and nut, etc.) which is operable to convert the rotation of the motor shaft into the linear motion of the shaft (1534). Alternatively, the actuator (1530) may take any other preferred form.

[0119] Furthermore, as shown in Figures 22 to 24B, the compensator assembly (1500) further includes a first frame (1540), a second frame (1550), a first rotating shaft (1542), a second rotating shaft (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 its respective opening (1541, 1551). Each opening (1541, 1551) is configured to receive its respective compensator plate (e.g., the compensator plates (842, 844, 942, 944, 1042, 1044) described above). The frames (1540, 1550), housing elements (1508, 1510), and ring element (1512) are configured and positioned so that light can pass through the housing elements (1508, 1510), the ring element (1512), and the compensating plate located within the openings (1541, 1551). In some variations, light enters the compensating assembly (1500) through the third side housing element (1508) and exits the compensating assembly (1500) through the ring element (1512) and the fourth side housing element (1510). In some other variations, light enters the compensating assembly (1500) through the ring element (1512) and the fourth side housing element (1510) and exits the third side housing element (1508) of the compensating assembly (1500).

[0120] The first frame (1540) is firmly fixed to the first rotating shaft (1542) so that the first frame (1540) and the first rotating shaft (1542) rotate together as a single unit. Similarly, the second frame (1550) is firmly fixed to the second rotating shaft (1552) so that the second frame (1550) and the second rotating shaft (1552) rotate together as a single unit. The rotating shafts (1542, 1552) are operable to pass through the base plate (1520) and rotate relative to the base plate (1520). The first rotating shaft (1542) is also firmly 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). A coil spring (1548) is schematically shown in Figures 23A to 24B. The other end of the coil spring (1548) is fixed to a fixed frame plate (1560). In this embodiment, the coil spring (1548) can impart elastic bias to the crank arm (1546), thereby imparting rotational elastic bias to the first rotating shaft (1542), the first gear (1544), and the first frame (1540) (for example, in a counterclockwise direction in the diagrams shown in Figures 23A to 23B). In some other variations, a torsion spring or other elastic element imparts rotational elastic bias to the first rotating shaft (1542), the first gear (1544), and the first frame (1540). Furthermore, in other modified forms, rotational elastic biasing is not applied to the first rotating shaft (1542), the first gear (1544), and the first frame (1540).

[0121] The second rotating shaft (1552) is firmly 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 the head (1536) at the end of the shaft (1534) of the actuator (1530). Thus, when the actuator (1530) is activated to drive the linear motion of the shaft (1534), the head (1536) contacts the roller bearing (1558) so that the linear motion of the shaft (1534) provides the rotational motion of the second gear (1554) via the crank arm (1556). The gears (1544, 1554) are engaged with each other via meshing teeth, such that rotation of the second gear (1554) in a first angular direction provides rotation of the first gear (1544) in a second angular direction. This movement is shown in the transition between Figure 23A and Figure 23B.

[0122] As described above, the first frame (1540), the first rotating shaft (1542), and the first gear (1544) rotate together as a single unit. Also as described above, the second frame (1550), the second rotating shaft (1552), and the second gear (1554) rotate together as a single unit. Therefore, the rotational motion described above in the context of Figures 23A and 23B also provides opposing angular motion of the frames (1540, 1550). This opposing angular motion of the frames (1540, 1550) is shown in the transition between Figures 24A and 24B. With the compensating element fixed within the openings (1541, 1551) of the frames (1540, 1550), this opposing angular motion of the frames (1540, 1550) provides opposing angular motion of the compensating element as described above in the context of Figures 11A to 13.

[0123] The elastic rotational bias provided to the first gear (1544) by the coil spring (1548) is transmitted to the second gear (1554) via the meshing teeth of the gears (1544, 1554). Thus, when the shaft (1534) retracts toward the body (1532), the gears (1544, 1554), the shafts (1542, 1544), and the crank arms (1546, 1556) return in opposite directions from their respective angular positions as shown in Figures 23B and 24B toward their respective angular positions as shown in Figures 23A and 24A. Furthermore, the coil spring (1548) provides elastic rotational bias to the gears (1544, 1554), and the crank arm (1546, 1556) maintains contact between the head (1536) and the roller bearing (1558) as the shaft (1534) retracts toward the main body (1532).

[0124] Although not shown in Figures 19 to 24B, the actuator (1530) may be coupled to a controller configured to control the actuator (1530) to drive the movement of the frames (1540, 1550) (and thus the compensating elements fixed within the frames (1540, 1550)) in accordance with the teachings herein. Such a controller may be similar to the various controllers described above (114, 308, 520, 960, 1060).

[0125] VII. Examples of Combinations The following examples illustrate various non-exclusive ways in which the teachings herein may be combined or applied. The following examples are not intended to limit the scope of any claims that may be presented at any point in this application or any subsequent application. No waiver is intended. The following examples are provided for illustrative purposes only. Various teachings herein are intended to be constructed and applied in numerous other ways. Some variations are also intended to omit certain features mentioned in the following examples. Accordingly, none of the embodiments or features mentioned below should be considered important unless explicitly indicated thereafter by the inventors or their successors. If any claim containing additional features beyond those mentioned below is presented in this application or any subsequent application relating to this application, those additional features should not be assumed to have been added for any reason relating to patentability. [Examples]

[0126] Apparatus comprising: an optical assembly including: a sample stage region; an optical assembly comprising: an objective lens element providing a field of view, wherein at least a portion of the sample stage region is within the field of view, and the objective lens element has variable astigmatism; an imaging lens configured to receive light transmitted through the objective lens element and to further transmit the light into image space; a correction assembly in image space configured to induce a second astigmatism, wherein the second astigmatism is configured to offset the variable astigmatism; and a camera assembly configured to receive light transmitted from the correction assembly. [Examples]

[0127] The apparatus according to Embodiment 1, wherein the correction assembly is operable to change the second astigmatism, thereby dynamically offsetting the variable astigmatism of the objective element. [Examples]

[0128] The apparatus according to Embodiment 2, further comprising a processor which controls the correction assembly and is operable to change the second astigmatism. [Examples]

[0129] The apparatus according to Embodiment 3, wherein the processor is capable of controlling the correction assembly and thereby operating to change the second astigmatism based on a predetermined adjustment profile. [Examples]

[0130] The apparatus according to Embodiment 3, wherein the processor is operable to determine the astigmatism value of the objective element. [Examples]

[0131] The apparatus according to Embodiment 5, wherein the processor is capable of controlling the correction assembly and thereby operating to change the second astigmatism based on the determined astigmatism value of the objective element. [Examples]

[0132] The correction assembly comprises a first light-transmitting plate and a second light-transmitting plate, as described in any of Examples 1 to 6. [Examples]

[0133] The apparatus according to Example 7, wherein the first light-transmitting plate is inclined at a first angle about a first axis, and the second light-transmitting plate is inclined at a second angle about a second axis. [Examples]

[0134] The apparatus according to Example 8, wherein the first light-transmitting plate and the second light-transmitting plate are positioned along the imaging axis, the first axis is perpendicular to the imaging axis, and the second axis is parallel to the first axis. [Examples]

[0135] The apparatus according to Example 8 or 9, wherein the first angle has an amplitude equal to the amplitude of the second angle and a direction opposite to the direction of the second angle. [Examples]

[0136] The apparatus according to any one of Examples 8 to 10, wherein the compensating assembly further comprises a first actuator, the first actuator being operable to drive the movement of one or both of the first light-transmitting plate about the first axis or the second light-transmitting plate about the second axis. [Examples]

[0137] The apparatus according to Embodiment 11, wherein the correction assembly further comprises a link mechanism, the first actuator and the link mechanism are configured to cooperate to simultaneously drive the movement of the first light-transmitting plate about the first axis and the movement of the second light-transmitting plate about the second axis. [Examples]

[0138] The apparatus according to Embodiment 11, wherein the correction assembly further comprises a second actuator, the first actuator being coupled to the first light-transmitting plate and thereby driving the movement of the first light-transmitting plate about the first axis, and the second actuator being coupled to the second light-transmitting plate and thereby driving the movement of the second light-transmitting plate about the second axis. [Examples]

[0139] The apparatus according to any one of Examples 11 to 13, wherein the first actuator comprises a motor. [Examples]

[0140] The apparatus according to any one of Examples 11 to 14, wherein the correction assembly further comprises a first gear and a second gear, the first light-transmitting plate rotating integrally with the first gear, and the second light-transmitting plate rotating integrally with the second gear. [Examples]

[0141] The apparatus according to Example 15, wherein the first gear is positioned to mesh directly with the second gear. [Examples]

[0142] The apparatus according to any one of Embodiments 15 to 16, wherein the correction assembly further comprises a crank arm coupled to the first gear, the first actuator drives the rotational motion of the crank arm, and the crank arm drives the rotational motion of the first gear. [Examples]

[0143] The apparatus according to any one of Examples 11 to 17, wherein the correction assembly further includes a housing element that forms a box around the first light-transmitting plate and the second light-transmitting plate. [Examples]

[0144] The corrective assembly further comprises a first shaft, a second shaft, and a base plate, wherein the first shaft and the second shaft penetrate the base plate, the first shaft drives the movement of a first light-transmitting plate about a first axis, and the second shaft drives the movement of a second light-transmitting plate about a second axis, as described in any of Embodiments 11 to 18. [Examples]

[0145] The correction assembly is the apparatus according to any one of Examples 1 to 6, comprising a first light-transmitting element and a reflective element. [Examples]

[0146] The apparatus according to any one of Examples 1 to 20, wherein the corrective assembly comprises a deformable element. [Examples]

[0147] The apparatus according to Example 21, wherein the deformable element is light-transmitting. [Examples]

[0148] The apparatus according to Example 21, wherein the deformable element is reflective. [Examples]

[0149] The apparatus according to any one of Examples 1 to 23, further comprising a heating element, the heating element being operable to heat the objective element and thereby change the astigmatism of the objective element. [Examples]

[0150] The apparatus according to Example 24, wherein the heating element includes a laser light source. [Examples]

[0151] Apparatus comprising: a sample stage region; an optical assembly comprising an objective element providing a field of view, wherein at least a portion of the sample stage region is within the field of view, and the objective element has astigmatism that is variable based on the temperature of the objective element; an imaging lens configured to receive light transmitted through the objective element and to transmit the light into image space; a first correction element in image space configured to induce a second astigmatism; a second correction element in image space configured to induce a third astigmatism, wherein the second astigmatism and the third astigmatism cooperate to offset the variable astigmatism; and a camera assembly configured to receive light transmitted from the correction assembly. [Examples]

[0152] The apparatus according to Embodiment 26, wherein the first corrective element is inclined at a first angle, and the second corrective element is inclined at a second angle equal to and opposite to the first angle. [Examples]

[0153] The apparatus according to any one of Examples 26 to 27, wherein the first correction element is movable relative to the objective element to adjust the second astigmatism, and the second correction element is movable relative to the objective element to adjust the third astigmatism. [Examples]

[0154] The apparatus according to Embodiment 28, further comprising a controller configured to drive the movement of the first and second correcting elements to track the thermally induced change in the astigmatism of the objective element. [Examples]

[0155] The apparatus according to Example 29, wherein the controller is further configured to track the thermally induced change in the astigmatism of the objective element. [Examples]

[0156] The apparatus according to Embodiment 30, wherein the controller is configured to process an image captured by the camera assembly, and the controller is further configured to determine and track the thermally induced change in the astigmatism of the objective element based on the processed image. [Examples]

[0157] The apparatus according to any one of Examples 29 to 31, wherein the controller is configured to drive the movement of the first corrective element and the second corrective element based on a predetermined adjustment profile. [Examples]

[0158] The apparatus according to Example 32, wherein the controller is configured to define the predetermined adjustment profile. [Examples]

[0159] The apparatus according to Embodiment 33, wherein the controller is configured to execute a calibration routine and define a predetermined adjustment profile through the calibration routine. [Examples]

[0160] The apparatus according to any one of Examples 26 to 34, wherein the sample stage region is configured to receive a flow cell. [Examples]

[0161] A method comprising: receiving light from a reaction site through an objective element, the objective element having astigmatism, the light further passing through a compensating assembly, the compensating assembly providing a corrected astigmatism, the corrected astigmatism offsetting the astigmatism of the objective element; heating the objective element, the astigmatism of the objective element changing in response to the heating; and adjusting the compensating assembly to thereby change the corrected astigmatism, thereby offsetting the changing astigmatism of the objective element. [Examples]

[0162] The method according to Example 36, further comprising irradiating the reaction site with excitation light. [Examples]

[0163] The method according to Example 37, wherein the excitation light passes through the objective element and reaches the reaction site. [Examples]

[0164] The method according to Example 38, wherein the excitation light causes the heating of the objective element. [Examples]

[0165] The excitation light is a laser beam, as described in any of Examples 37 to 39. [Examples]

[0166] The method according to any one of Examples 36 to 40, wherein the correction assembly comprises a first correction element, and the operation of adjusting the correction assembly includes pivoting the first correction element in a first angular direction over a first pivot range of motion about a first pivot axis. [Examples]

[0167] The method according to Embodiment 41, wherein the correction assembly further comprises a second correction element, and the operation of adjusting the correction assembly further includes pivoting the second correction element in a second angular direction over a second pivot range of motion about a second pivot axis. [Examples]

[0168] The method according to Example 42, wherein the second angular direction is opposite to the first angular direction. [Examples]

[0169] The method according to Example 42 or 43, wherein the second pivot axis is parallel to the first pivot axis. [Examples]

[0170] The method according to any one of Examples 42 to 44, wherein the second pivot range of motion is equal to the first pivot range of motion. [Examples]

[0171] The method according to Embodiment 41, wherein the imaging axis of the light shifts in response to pivoting the first correction element in a first angular direction over a first pivot range of motion about a first pivot axis, and the method further includes moving a camera based on the shift of the imaging axis of the light, the camera capturing at least a portion of the light. [Examples]

[0172] The method according to Embodiment 41, wherein the imaging axis of the light shifts in response to pivoting the first correction element in a first angular direction over a first pivot range of motion about a first pivot axis, and the method further includes moving a reflecting element based on the shift of the imaging axis of the light. [Examples]

[0173] The method according to Embodiment 47, wherein the operation to move the reflective element includes pivoting the reflective element. [Examples]

[0174] The method according to Example 47 or 48, wherein the operation of moving the reflective element includes deforming the reflective element. [Examples]

[0175] The reflective element redirects the light back towards the camera, as described in any of Examples 47 to 49. [Examples]

[0176] The camera maintains a fixed position while the reflective element moves, as described in Example 50. [Examples]

[0177] The method according to any one of Examples 36 to 40, wherein the correction assembly comprises a deformable correction element, and the operation of adjusting the correction assembly includes deforming the correction element. [Examples]

[0178] The method according to Example 52, wherein the light is emitted along the imaging axis, and the operation to deform the correcting element includes deforming the correcting element along the imaging axis. [Examples]

[0179] The method according to any one of Examples 36 to 53, further comprising capturing the light with a camera, wherein the correction assembly is inserted between the objective element and the camera. [Examples]

[0180] The method according to any one of Examples 36 to 53, further comprising performing sequencing-by-synthesis.

[0181] VIII. Others While the embodiments described herein are provided in the context of a system (100) that may be used in a nucleotide sequencing process, the teachings herein may also be readily applicable in other contexts, including systems that perform other processes (i.e., procedures other than nucleotide sequencing). Therefore, the teachings herein are not necessarily limited to systems used to perform a nucleotide sequencing process.

[0182] It should be understood that the subject matter described herein is not limited in its application to the configuration details and arrangement of components described herein or shown in the drawings herein. The subject matter described herein is capable of other implementations and can be carried out or performed in various ways. It should also be understood that the expressions and terms used herein are for illustrative purposes only and should not be considered limiting. When used herein, an element or process described in the singular and followed by the words "a" or "an" should be understood not to exclude multiple such elements or processes unless such exclusion is explicitly stated. Furthermore, references to "one example" are not intended to be interpreted as excluding the existence of additional examples that also incorporate the described features. The use of "including," "comprising," or "having" and their variations herein means that the items and their equivalents listed thereafter, as well as additional items, are included.

[0183] When used in patent claims, the term “set” should be understood as one or more things grouped together. Similarly, when used in patent claims, “based on” should be understood as indicating that one thing is at least partially determined by the thing it is designated as “based on.” When something needs to be exclusively determined by another, that thing is referred to as “exclusively based on” the thing on which it is determined.

[0184] Unless otherwise specified or limited, the terms “mounted,” “connected,” “supported,” and “coupled,” as well as their variations, are used broadly and encompass both direct and indirect mounting, connection, support, and coupling. Furthermore, “connected” and “coupled” are not limited to physical or mechanical connection or coupling. Also, please understand that the expressions and terms used herein with respect to the orientation of devices or elements (e.g., “above,” “below,” “front,” “rear,” “distal,” “proximal”) are used solely to simplify the description of one or more embodiments described herein and do not in themselves indicate or imply that the devices or elements mentioned must have a particular orientation. In addition, terms such as “outer” and “inner” are used herein for illustrative purposes only and are not intended to indicate or imply relative importance or significance.

[0185] It should be understood that the above description is illustrative and not restrictive. For example, the embodiments (and / or embodiments thereof) described above may be used in combination with each other. Furthermore, many modifications may be made to adapt specific circumstances or materials to the teachings of the subject matter described herein, without departing from its scope. The dimensions, material types, and coatings described herein are intended to define parameters of the disclosed subject matter, but they are not restrictive, but rather illustrative. Many further embodiments will be apparent to those skilled in the art upon consideration of the above description. Thus, the scope of the disclosed subject matter should be determined by reference to the appended claims, along with the entire scope of equivalents to which such claims are granted. In the appended claims, the terms “including” and “in which” are used as plain English equivalents to “comprising” and “wherein,” respectively. Furthermore, in the following claims, terms such as “first,” “second,” and “third” are used merely as designations and are not intended to impose numerical requirements on those objects. Moreover, the following limitations on the claims are not written in means-plus-function form, and such limitations on the claims are not intended to be interpreted under paragraph 112(f) of the U.S. Patent Act unless, and until, the phrase “means for” and a subsequent description of the function without further structure are explicitly used.

[0186] The following claims enumerate specific examples of the subject matter disclosed and are considered to be part of the above disclosure. These examples can be combined with one another.

[0187] [Implementation Method] (1) Sample stage area and An optical assembly, An objective element that provides a field of view, wherein at least a portion of the sample stage area is within the field of view, and the objective element has variable astigmatism. An imaging lens, configured to receive light that has passed through the objective element and to further transmit the light into the image space, An optical assembly comprising: a correction assembly in the image space, wherein the correction assembly is configured to induce a second astigmatism, and the second astigmatism is configured to offset the variable astigmatism; A device comprising: a camera assembly configured to receive light transmitted from the correction assembly. (2) The apparatus according to Embodiment 1, wherein the correction assembly is operable to change the second astigmatism, thereby dynamically offsetting the variable astigmatism of the objective element. (3) The apparatus according to Embodiment 2, further comprising a processor, the processor being operable to control the correction assembly and thereby change the second astigmatism. (4) The apparatus according to Embodiment 3, wherein the processor is operable to control the correction assembly and thereby change the second astigmatism based on a predetermined adjustment profile. (5) The apparatus according to Embodiment 3, wherein the processor is operable to determine the astigmatism value of the objective element.

[0188] (6) The apparatus according to Embodiment 5, wherein the processor is operable to control the correction assembly and thereby change the second astigmatism based on the determined astigmatism value of the objective element. (7) The apparatus according to any one of embodiments 1 to 6, wherein the correction assembly comprises a first light-transmitting plate and a second light-transmitting plate. (8) The apparatus according to Embodiment 7, wherein the first light-transmitting plate is inclined at a first angle about a first axis, and the second light-transmitting plate is inclined at a second angle about a second axis. (9) The apparatus according to Embodiment 8, wherein the first light-transmitting plate and the second light-transmitting plate are positioned along the imaging axis, the first axis is perpendicular to the imaging axis, and the second axis is parallel to the first axis. (10) The apparatus according to Embodiment 8 or 9, wherein the first angle has an amplitude equal to the amplitude of the second angle and a direction opposite to the direction of the second angle.

[0189] (11) The apparatus according to any one of embodiments 8 to 10, wherein the compensating assembly further comprises a first actuator, the first actuator being operable to drive the movement of one or both of the first light-transmitting plate about the first axis or the second light-transmitting plate about the second axis. (12) The apparatus according to embodiment 11, wherein the correction assembly further comprises a link mechanism, and the first actuator and the link mechanism are configured to cooperate to simultaneously drive the movement of the first light-transmitting plate about the first axis and the movement of the second light-transmitting plate about the second axis. (13) The apparatus according to embodiment 11, wherein the correction assembly further comprises a second actuator, the first actuator being coupled to the first light-transmitting plate and thereby driving the movement of the first light-transmitting plate about the first axis, and the second actuator being coupled to the second light-transmitting plate and thereby driving the movement of the second light-transmitting plate about the second axis. (14) The apparatus according to any one of embodiments 11 to 13, wherein the first actuator comprises a motor. (15) The apparatus according to any one of embodiments 11 to 14, wherein the correction assembly further comprises a first gear and a second gear, the first light-transmitting plate rotates integrally with the first gear, and the second light-transmitting plate rotates integrally with the second gear.

[0190] (16) The apparatus according to embodiment 15, wherein the first gear is positioned to mesh directly with the second gear. (17) The apparatus according to any one of embodiments 15 to 16, wherein the correction assembly further comprises a crank arm coupled to the first gear, the first actuator drives the rotational motion of the crank arm, and the crank arm drives the rotational motion of the first gear. (18) The apparatus according to any one of embodiments 11 to 17, wherein the correction assembly further includes a housing element that forms a box around the first light-transmitting plate and the second light-transmitting plate. (19) The apparatus according to any one of embodiments 11 to 18, wherein the correction assembly further comprises a first shaft, a second shaft, and a base plate, the first shaft and the second shaft passing through the base plate, the first shaft driving the movement of the first light-transmitting plate about the first axis, and the second shaft driving the movement of the second light-transmitting plate about the second axis. (20) The apparatus according to any one of embodiments 1 to 6, wherein the correction assembly comprises a first light-transmitting element and a reflective element.

[0191] (21) The apparatus according to any one of embodiments 1 to 20, wherein the correction assembly comprises a deformable element. (22) The apparatus according to embodiment 21, wherein the deformable element is light-transmitting. (23) The apparatus according to embodiment 21, wherein the deformable element is reflective. (24) The apparatus according to any one of embodiments 1 to 23, further comprising a heating element, wherein the heating element is operable to heat the objective element and thereby change the astigmatism of the objective element. (25) The apparatus according to embodiment 24, wherein the heating element includes a laser light source.

[0192] (26) Sample stage area and An optical assembly, An objective element that provides a field of view, wherein at least a portion of the sample stage area is within the field of view, and the objective element has astigmatism that is variable based on the temperature of the objective element. An imaging lens, configured to receive light that has passed through the objective element and to further transmit the light into the image space, An optical assembly comprising: a first correction element in the image space configured to induce a second astigmatism; and a second correction element in the image space configured to induce a third astigmatism, wherein the second astigmatism and the third astigmatism cooperate to offset the variable astigmatism; A device comprising: a camera assembly configured to receive light transmitted from the correction assembly. (27) The apparatus according to Embodiment 26, wherein the first correcting element is inclined at a first angle, and the second correcting element is inclined at a second angle equal to and opposite to the first angle. (28) The apparatus according to any one of embodiments 26 to 27, wherein the first corrector element is movable relative to the objective element to adjust the second astigmatism, and the second corrector element is movable relative to the objective element to adjust the third astigmatism. (29) The apparatus according to embodiment 28, further comprising a controller, the controller configured to drive the movement of the first and second correcting elements to track a thermally induced change in the astigmatism of the objective element. (30) The apparatus according to Embodiment 29, wherein the controller is further configured to track the thermally induced change in the astigmatism of the objective element.

[0193] (31) The apparatus according to Embodiment 30, wherein the controller is configured to process an image captured by the camera assembly, and the controller is further configured to determine and track the thermally induced change in the astigmatism of the objective element based on the processed image. (32) The apparatus according to any one of embodiments 29 to 31, wherein the controller is configured to drive the movement of the first correction element and the second correction element based on a predetermined adjustment profile. (33) The apparatus according to embodiment 32, wherein the controller is configured to define the predetermined adjustment profile. (34) The apparatus according to embodiment 33, wherein the controller is configured to execute a calibration routine and define the predetermined adjustment profile through the calibration routine. (35) The apparatus according to any one of embodiments 26 to 34, wherein the sample stage region is configured to receive a flow cell.

[0194] (36) Receiving light from a reaction site through an objective element, wherein the objective element has astigmatism, the light further passes through a correction assembly, the correction assembly provides corrected astigmatism, and the corrected astigmatism offsets the astigmatism of the objective element, Heating the objective element, wherein the astigmatism of the objective element changes in response to the heating, A method comprising adjusting the correction assembly to thereby change the corrected astigmatism and thereby offset the changing astigmatism of the objective element. (37) The method according to embodiment 36, further comprising irradiating the reaction site with excitation light. (38) The method according to embodiment 37, wherein the excitation light passes through the objective element and reaches the reaction site. (39) The method according to embodiment 38, wherein the excitation light causes the heating of the objective element. (40) The method according to any one of embodiments 37 to 39, wherein the excitation light includes laser light.

[0195] (41) The method according to any one of embodiments 36 to 40, wherein the correction assembly comprises a first correction element, and the operation of adjusting the correction assembly includes pivoting the first correction element in a first angular direction over a first pivot range of motion about a first pivot axis. (42) The method according to embodiment 41, wherein the correction assembly further comprises a second correction element, and the operation of adjusting the correction assembly further includes pivoting the second correction element in a second angular direction over a second pivot range of motion about a second pivot axis. (43) The method according to embodiment 42, wherein the second angular direction is opposite to the first angular direction. (44) The method according to embodiment 42 or 43, wherein the second pivot axis is parallel to the first pivot axis. (45) The method according to any one of embodiments 42 to 44, wherein the second pivot range of motion is equal to the first pivot range of motion.

[0196] (46) The method according to Embodiment 41, wherein the imaging axis of the light is shifted in response to pivoting the first correcting element in a first angular direction over a first pivot range of motion about a first pivot axis, and the method further includes moving a camera based on the shift of the imaging axis of the light, the camera capturing at least a portion of the light. (47) The method according to Embodiment 41, wherein the imaging axis of the light is shifted in response to pivoting the first correcting element over a first pivot range of motion about a first pivot axis in a first angular direction, and the method further includes moving a reflecting element based on the shift of the imaging axis of the light. (48) The method according to embodiment 47, wherein the operation for moving the reflective element includes pivoting the reflective element. (49) The method according to embodiment 47 or 48, wherein the operation for moving the reflective element includes deforming the reflective element. (50) The method according to any one of embodiments 47 to 49, wherein the reflecting element redirects the light back to the camera.

[0197] (51) The method according to embodiment 50, wherein the camera maintains a fixed position while the reflective element moves. (52) The method according to any one of embodiments 36 to 40, wherein the correction assembly comprises a deformable correction element, and the operation of adjusting the correction assembly includes deforming the correction element. (53) The method according to embodiment 52, wherein the light is emitted along the imaging axis, and the operation to deform the corrector element includes deforming the corrector element along the imaging axis. (54) The method according to any one of embodiments 36 to 53, further comprising capturing the light with a camera, wherein the correction assembly is inserted between the objective element and the camera. (55) The method according to any one of embodiments 36 to 53, further comprising performing sequencing-by-synthesis.

Claims

1. Sample stage area and An optical assembly, An objective element that provides a field of view, wherein at least a portion of the sample stage area is within the field of view, and the objective element has variable astigmatism. An imaging lens, configured to receive light that has passed through the objective element and to further transmit the light into the image space, An optical assembly comprising: a correction assembly in the image space, wherein the correction assembly is configured to induce a second astigmatism, and the second astigmatism is configured to offset the variable astigmatism; A device comprising: a camera assembly configured to receive light transmitted from the correction assembly.

2. The apparatus according to claim 1, wherein the correction assembly is operable to change the second astigmatism, thereby dynamically offsetting the variable astigmatism of the objective element.

3. The apparatus according to claim 2, further comprising a processor, the processor being operable to control the correction assembly and thereby change the second astigmatism.

4. The apparatus according to claim 3, wherein the processor is operable to control the correction assembly and thereby change the second astigmatism based on a predetermined adjustment profile.

5. The apparatus according to claim 3, wherein the processor is operable to determine the astigmatism value of the objective element.

6. The apparatus according to claim 5, wherein the processor is operable to control the correction assembly and thereby change the second astigmatism based on the determined astigmatism value of the objective element.

7. The apparatus according to claim 1, wherein the correction assembly comprises a first light-transmitting plate and a second light-transmitting plate.

8. The apparatus according to claim 7, wherein the first light-transmitting plate is inclined at a first angle about a first axis, and the second light-transmitting plate is inclined at a second angle about a second axis.

9. The apparatus according to claim 8, wherein the first light-transmitting plate and the second light-transmitting plate are positioned along the imaging axis, the first axis is perpendicular to the imaging axis, and the second axis is parallel to the first axis.

10. The apparatus according to claim 8, wherein the first angle has an amplitude equal to the amplitude of the second angle and a direction opposite to the direction of the second angle.

11. The apparatus according to claim 8, wherein the correction assembly further comprises a first actuator, the first actuator being operable to drive the movement of one or both of the first light-transmitting plate about the first axis or the second light-transmitting plate about the second axis.

12. The apparatus according to claim 11, wherein the correction assembly further comprises a link mechanism, and the first actuator and the link mechanism are configured to cooperate to simultaneously drive the movement of the first light-transmitting plate about the first axis and the movement of the second light-transmitting plate about the second axis.

13. The apparatus according to claim 11, wherein the correction assembly further comprises a second actuator, the first actuator being coupled to the first light-transmitting plate and thereby driving the movement of the first light-transmitting plate about the first axis, and the second actuator being coupled to the second light-transmitting plate and thereby driving the movement of the second light-transmitting plate about the second axis.

14. The apparatus according to claim 11, wherein the first actuator comprises a motor.

15. The apparatus according to claim 11, wherein the correction assembly further comprises a first gear and a second gear, the first light-transmitting plate rotates integrally with the first gear, and the second light-transmitting plate rotates integrally with the second gear.

16. The apparatus according to claim 15, wherein the first gear is positioned to mesh directly with the second gear.

17. The apparatus according to claim 15, wherein the correction assembly further comprises a crank arm coupled to the first gear, the first actuator drives the rotational motion of the crank arm, and the crank arm drives the rotational motion of the first gear.

18. The apparatus according to claim 11, wherein the correction assembly further includes a housing element that forms a box around the first light-transmitting plate and the second light-transmitting plate.

19. The apparatus according to claim 11, wherein the correction assembly further comprises a first shaft, a second shaft, and a base plate, the first shaft and the second shaft passing through the base plate, the first shaft driving the movement of the first light-transmitting plate about the first axis, and the second shaft driving the movement of the second light-transmitting plate about the second axis.

20. The apparatus according to claim 1, wherein the correction assembly comprises a first light-transmitting element and a reflective element.

21. The apparatus according to claim 1, wherein the correction assembly comprises a deformable element.

22. The apparatus according to claim 21, wherein the deformable element is light-transmitting.

23. The apparatus according to claim 21, wherein the deformable element is reflective.

24. The apparatus according to claim 1, further comprising a heating element, wherein the heating element is operable to heat the objective element and thereby change the astigmatism of the objective element.

25. The apparatus according to claim 24, wherein the heating element includes a laser light source.

26. Sample stage area and An optical assembly, An objective element that provides a field of view, wherein at least a portion of the sample stage area is within the field of view, and the objective element has astigmatism that is variable based on the temperature of the objective element. An imaging lens, configured to receive light that has passed through the objective element and to further transmit the light into the image space, An optical assembly comprising: a first correction element in the image space configured to induce a second astigmatism; and a second correction element in the image space configured to induce a third astigmatism, wherein the second astigmatism and the third astigmatism cooperate to offset the variable astigmatism; A device comprising: a camera assembly configured to receive light transmitted from the correction assembly.

27. The apparatus according to claim 26, wherein the first correcting element is inclined at a first angle, and the second correcting element is inclined at a second angle equal to and opposite to the first angle.

28. The apparatus according to claim 26, wherein the first correction element is movable relative to the objective element to adjust the second astigmatism, and the second correction element is movable relative to the objective element to adjust the third astigmatism.

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

30. The apparatus according to claim 29, wherein the controller is further configured to track the thermally induced change in the astigmatism of the objective element.

31. The apparatus according to claim 30, wherein the controller is configured to process an image captured by the camera assembly, and the controller is further configured to determine and track the thermally induced change in the astigmatism of the objective element based on the processed image.

32. The apparatus according to claim 29, wherein the controller is configured to drive the movement of the first correction element and the second correction element based on a predetermined adjustment profile.

33. The apparatus according to claim 32, wherein the controller is configured to define the predetermined adjustment profile.

34. The apparatus according to claim 33, wherein the controller is configured to execute a calibration routine and define the predetermined adjustment profile through the calibration routine.

35. The apparatus according to claim 26, wherein the sample stage region is configured to receive a flow cell.

36. Receiving light from a reaction site through an objective element, wherein the objective element has astigmatism, the light further passes through a correction assembly, the correction assembly provides corrected astigmatism, and the corrected astigmatism offsets the astigmatism of the objective element; Heating the objective element, wherein the astigmatism of the objective element changes in response to the heating, A method comprising adjusting the correction assembly to thereby change the corrected astigmatism and thereby offset the changing astigmatism of the objective element.

37. The method according to claim 36, further comprising irradiating the reaction site with excitation light.

38. The method according to claim 37, wherein the excitation light passes through the objective element and reaches the reaction site.

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

40. The method according to claim 37, wherein the excitation light includes laser light.

41. The method according to claim 36, wherein the correction assembly comprises a first correction element, and the operation of adjusting the correction assembly includes pivoting the first correction element in a first angular direction over a first pivot range of motion about a first pivot axis.

42. The method according to claim 41, wherein the correction assembly further comprises a second correction element, and the operation of adjusting the correction assembly further includes pivoting the second correction element in a second angular direction over a second pivot range of motion about a second pivot axis.

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

44. The method according to claim 42, wherein the second pivot axis is parallel to the first pivot axis.

45. The method according to claim 42, wherein the second pivot range of motion is equal to the first pivot range of motion.

46. The method according to claim 41, wherein the imaging axis of the light is shifted in response to pivoting the first correction element in a first angular direction over a first pivot range of motion about a first pivot axis, and the method further includes moving a camera based on the shift of the imaging axis of the light, the camera capturing at least a portion of the light.

47. The method according to claim 41, wherein the imaging axis of the light shifts in response to pivoting the first correction element over a first pivot range of motion about a first pivot axis in a first angular direction, and the method further includes moving a reflecting element based on the shift of the imaging axis of the light.

48. The method according to claim 47, wherein the operation for moving the reflective element includes pivoting the reflective element.

49. The method according to claim 47, wherein the operation of moving the reflective element includes deforming the reflective element.

50. The method according to claim 47, wherein the reflective element redirects the light back towards the camera.

51. The method according to claim 50, wherein the camera maintains a fixed position while the reflective element moves.

52. The method according to claim 36, wherein the correction assembly comprises a deformable correction element, and the operation of adjusting the correction assembly includes deforming the correction element.

53. The method according to claim 52, wherein the light is emitted along the imaging axis, and the operation to deform the correction element includes deforming the correction element along the imaging axis.

54. The method according to claim 36, further comprising capturing the light with a camera, wherein the correction assembly is inserted between the objective element and the camera.

55. The method according to claim 36, further comprising performing sequencing by synthesis.

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