Sequencer for transmitting light

Abstract

To provide a sequencer capable of establishing enhanced uniformity of illumination in the sequencer for transmitting light.SOLUTION: An image forming system of a sequencer includes: a fiber beam source; a collimator receiving an input beam from the fiber beam source and arranged at an input end located to generate a substantially-parallel beam; a microlens array for receiving the substantially-parallel beam and positioned to format the substantially-parallel beam into a shaped propagation beam having a substantially-rectangular cross-section in a far field; a convergence objective stage positioned to convert the shaped propagation beam into a sampling beam on a focal plane on a convergence objective stage for optically probing a flow cell sample or near there into a sampling beam having the substantially-rectangular cross-section; and a valve for controlling flow of fluid passing a fluid line from a reagent cartridge.SELECTED DRAWING: Figure 21

Description

[Technical Field]

[0001] (Related Applications) This application claims the benefit of and priority to U.S. Provisional Patent Application No. 63 / 200,754, filed March 25, 2021, and U.S. Provisional Patent Application No. 63 / 273,778, filed October 29, 2021, the contents of each of which are incorporated herein by reference in their entirety for all purposes. [Background technology]

[0002] Light formatting structures often need to be positioned at various focal lengths from the microscope objective lens they are paired with. If these light formatting structures perturb the light beam, resulting in divergence, the light beam can widen to the point where elements of the microscope objective lens are overfilled. As a result, the microscope objective lens clips the light beam it receives. This clipping can reduce the uniformity of the formatted beam and generate stray light that can be a source of noise or damage to the entire imaging system. Summary of the Invention [Problem to be solved by the invention]

[0003] Through the provision of an apparatus and method for transmitting light, the advantages of the prior art can be overcome and the benefits described below in this disclosure can be achieved. Various implementations of the apparatus and method are described below, and the apparatus and method, including and excluding the additional implementations listed below in any combination (provided that such combinations are not inconsistent), can overcome these disadvantages and achieve the benefits described herein. [Means for solving the problem]

[0004] According to a first implementation form, the apparatus comprises or includes: a collimator at an input end positioned to receive an input beam from a fiber beam source and generate a substantially parallel beam; a beam shaping group comprising or including one or more optical elements positioned to receive the substantially parallel beam from the collimator and format the substantially parallel beam into a shaped propagation beam that includes or has a substantially rectangular cross-section in the far field; and a focusing objective stage comprising or including an element aperture and an objective pupil for receiving the shaped propagation beam, the focusing objective stage positioned to convert the shaped propagation beam into a sampling beam of a substantially rectangular cross-section at or near a focal plane of the focusing objective stage for optically probing a sample.

[0005] According to a second implementation, a method for optically probing a sample encompasses or includes: generating a collimated beam from an input beam; using a beam shaping group to format the collimated beam into a shaped propagating beam that includes or has a substantially rectangular cross-section in the far field; providing the shaped propagating beam to an optical relay stage that generates the shaped propagating beam with respect to an objective pupil of a focusing objective stage; using the focusing objective stage to convert the shaped propagating beam into a sampling beam of substantially rectangular cross-section at a focal plane of the focusing objective stage; probing the sample at a first position in the focal plane; and at a second position in the focal plane, affecting optical compensation of the optical relay stage so that the focusing objective stage converts the shaped propagating beam into a sampling beam of substantially rectangular cross-section; and probing the sample at the second position.

[0006] According to a third implementation, a method comprises or includes receiving an input beam from a fiber beam source at a collimator, generating a substantially parallel beam from the input beam by the collimator, receiving the substantially parallel beam from the collimator at a beam shaping group comprising or including one or more optical elements, formatting the substantially parallel beam by the beam shaping group into a shaped propagating beam with or having a substantially rectangular cross-section in the far field, receiving the shaped propagating beam at a focusing objective stage comprising or including an objective pupil, converting the shaped propagating beam into a sampling beam of a substantially rectangular cross-section at or near a focal plane of the focusing objective stage, and optically probing a sample using the focusing objective stage.

[0007] Furthermore, in accordance with the first and / or second implementation forms described above, the apparatus and / or method may further include or comprise any one or more of the following: In one implementation, the apparatus further comprises or includes an optical relay stage positioned between the beam shaping group and the focusing objective stage for imaging the shaped propagating beam from the beam shaping group onto or near the objective pupil of the focusing objective stage.

[0008] In another implementation, the optical relay stage comprises or includes an input lens stage positioned to receive the shaped propagation beam from the beam shaping group and an output lens stage positioned to generate the shaped propagation beam for the objective pupil of the focusing objective stage.

[0009] In another implementation, the input lens stage and the output lens stage form a focusing element pair that defines an intermediate image plane within the optical relay stage. In another implementation, an optical relay stage comprising or having a beam affecting element at an intermediate image plane.

[0010] In another implementation, the beam-influencing element is an optical mask. In another implementation, the beam-influencing element is a despeckle element. In another implementation, the position of at least one of the input lens stage and the output lens stage is adjustable.

[0011] In another implementation, the apparatus further comprises or includes a Powell lens positioned before the optical relay stage. In another implementation, the apparatus further comprises or includes a Lineman lens positioned before the optical relay stage.

[0012] In another implementation, the optical relay stage is afocal. In another implementation, the optical relay stage is a fixed magnification relay. In another implementation, the optical relay stage is a variable magnification relay.

[0013] In another implementation, the beamforming group is an integrator. In another implementation, the integrator is an image-forming integrator formed from two microlens arrays positioned in series.

[0014] In another implementation, the integrator is an image-forming integrator formed from two cylindrical microlens arrays positioned in series. In another implementation, the integrator is a non-imaging integrator formed from a single microlens array.

[0015] In another implementation, the integrator is a non-imaging integrator formed from microlenses that are cylindrical lenses. In another implementation, the microlenses each include or have different focal lengths along the x and y directions.

[0016] In another implementation, the beam shaping group encompasses or includes an integrated diffractive feature. In another implementation, the beam shaping group encompasses or includes an integrated diffuser mechanism.

[0017] In another implementation, the integrator is an image-forming integrator formed with a microlens, the microlens being a cylindrical lens. In another implementation, the cylindrical lens is configured to provide divergence in one axial direction of the microlens and not in the orthogonal direction of the microlens.

[0018] In another implementation, the beam shaping group encompasses or includes one or more diffractive optical elements. In another implementation, the beam shaping group encompasses or includes a refractive optical element, a combination of a refractive optical element and a diffractive optical element, or a refractive optical element with an integrated diffractive or diffusing feature.

[0019] In another implementation, the beam shaping group transforms the parallel beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over an entire rectangle that encompasses or has an 8:1 ratio.

[0020] In another implementation, the beam shaping group transforms the collimated beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over a rectangle that encompasses or has a ratio of about 10:1 to about 20:1.

[0021] In another implementation, the beam shaping group transforms the parallel beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over an entire rectangle that encompasses or has a ratio of 24 to 1.

[0022] In another implementation, the beam shaping group transforms the collimated beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over a rectangle that encompasses or has ratios that substantially match the profile of a time delay and integration (TDI) line sensor.

[0023] In another implementation, the apparatus further comprises or includes a fiber beam source. In another implementation, the fiber beam source is a two-input beam source that generates input beams that include or have a first beam spanning a first wavelength range and a second beam spanning a second wavelength range that is different from the first wavelength range.

[0024] In another implementation, the fiber beam source comprises or includes two dedicated input fibers, each corresponding to one of the first beam and the second beam. In another implementation, each input fiber includes or has a substantially rectangular cross-section at the output face.

[0025] In another implementation, the fiber beam source is a light pipe. In another implementation, the apparatus comprises or includes an optical compensator positioned to receive the shaped propagating beam and encompassing or having two compensation positions: a first compensation position in which the focusing objective stage generates a sampling beam of substantially rectangular cross-section to probe the top surface of the sample, and a second compensation position in which the focusing objective stage generates a sampling beam of substantially rectangular cross-section to probe the bottom surface of the sample.

[0026] In another implementation, the optical compensator is electromechanically controllable between a first compensation position and a second compensation position. In another implementation, the optical compensator is electrically controllable between a first compensation position and a second compensation position.

[0027] In another implementation, an optical compensator can be inserted between the beam shaping group and the focusing objective stage. In another implementation, the apparatus comprises or includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising or including: an input lens stage positioned to receive the shaped propagation beam from the beam shaping group, and an output lens stage positioned to generate the shaped propagation beam with respect to an objective pupil of the focusing objective stage, and the optical compensator is positioned within the optical relay stage.

[0028] In another implementation, the optical compensator is an optical element that is electrically controllable to switch from a first optical state to a second optical state to affect the optical compensation. In another implementation, the apparatus comprises or includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising or including: an input lens stage positioned to receive the shaped propagation beam from the beam shaping group, and an output lens stage positioned to generate the shaped propagation beam with respect to an objective pupil of the focusing objective stage, and an optical compensator positioned before the optical relay stage.

[0029] In another implementation, the apparatus comprises or includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising or including: an input lens stage positioned to receive the shaped propagation beam from the beam shaping group, and an output lens stage positioned to generate the shaped propagation beam with respect to an objective pupil of the focusing objective stage, and the optical compensator positioned after the optical relay stage.

[0030] In another implementation, the apparatus comprises or includes an optical compensator and a positioner coupled to the optical compensator, the positioner being coupled to controllably (i) insert the optical compensator into the beam path to receive the shaped propagating beam and affect the shaped propagating beam path to probe one of the top or bottom surfaces of the sample, and (ii) remove the optical compensator from the beam path to affect the shaped propagating beam path to probe the other of the bottom or top surfaces of the sample.

[0031] In another implementation, the optical compensator is a plane-parallel plate of refractive material. In another implementation, the optical compensator is a lens. In another implementation, the optical compensator is inserted in the beam path before the optical relay stage.

[0032] In another implementation, the optical compensator is inserted into an optical relay stage in the beam path. In another implementation, the optical compensator is inserted in the beam after the optical relay stage.

[0033] In another implementation, the apparatus comprises or includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising: an input lens stage positioned to receive the shaped propagation beam from the beam shaping group; and an output lens stage positioned to generate the shaped propagation beam with respect to an objective pupil of the focusing objective stage. The input lens stage is movable between a first position where the focusing objective stage generates a sampling beam with a substantially rectangular cross-section to probe a top surface of a sample, and a second position where the focusing objective stage generates a sampling beam with a substantially rectangular cross-section to probe a bottom surface of a sample.

[0034] In another implementation, the apparatus comprises or includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising an input lens stage positioned to receive the shaped propagation beam from the beam shaping group and an output lens stage positioned to generate the shaped propagation beam for an objective pupil of the focusing objective stage, the output lens stage being movable between a first position in which the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe the top surface of the sample, and a second position in which the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe the bottom surface of the sample.

[0035] In another implementation, an apparatus comprises or includes a fiber beam source, the apparatus including or having a first separation distance between the collimator and the fiber beam source to generate a sampling beam of a substantially rectangular cross-section to probe a top surface of the sample, and the apparatus including or having a second separation distance between the collimator and the fiber beam source to generate a sampling beam of a substantially rectangular cross-section to probe a bottom surface of the sample.

[0036] In another implementation, influencing the optical compensation of the optical relay stage encompasses or includes adjusting the position or optical properties of an influencing element within the optical relay stage. In another implementation, the beam shaping group includes two microlens arrays.

[0037] In another implementation, the beam shaping group includes a diffractive optical element. In another implementation, the beam shaping group encompasses or includes a refractive optical element, a combination of a refractive optical element and a diffractive optical element, or a refractive optical element with an integrated diffractive feature.

[0038] In another implementation, the beam shaping group transforms the parallel beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over an entire rectangle that encompasses or has an 8:1 ratio.

[0039] In another implementation, the beam shaping group transforms the collimated beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over a rectangle that encompasses or has a ratio of about 10:1 to about 20:1.

[0040] In another implementation, the beam shaping group transforms the parallel beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over an entire rectangle that encompasses or has a ratio of 24 to 1.

[0041] In another implementation, generating the input beam includes or includes generating an input beam that includes or has a first beam over a first wavelength range and a second beam over a second wavelength range that is different from the first wavelength range.

[0042] In another implementation, generating the input beam encompasses or includes generating the input beam using two input beam sources. In another implementation, the fiber beam source comprises or includes two dedicated input fibers, each corresponding to one of the first beam and the second beam.

[0043] In another implementation, the output ends of two dedicated input fibers are presented to the collimator at a fixed spacing and with rotation about the fiber core and collimator axis. In another implementation, influencing the optical compensation of the optical relay stage encompasses or includes adjusting the position or optical properties of an influencing element within the optical relay stage.

[0044] In another implementation, the beam shaping group encompasses or includes two microlens arrays. In another implementation, the beam shaping group encompasses or includes a diffractive optical element.

[0045] In another implementation, the beam shaping group encompasses or includes a refractive optical element, a combination of a refractive optical element and a diffractive optical element, or a refractive optical element with an integrated diffractive feature. In another implementation, the beam shaping group transforms the parallel beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over an entire rectangle that encompasses or has an 8:1 ratio.

[0046] In another implementation, the beam shaping group transforms the collimated beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over a rectangle with a 10 to 1 ratio.

[0047] In another implementation, the beam shaping group transforms the parallel beam into a shaped propagating beam that encompasses or has uniform illumination in the far field over an entire rectangle that encompasses or has a ratio of 24 to 1.

[0048] In another implementation, the beam shaping group transforms the collimated beam into a shaped propagating beam with uniform illumination in the far field over a rectangle having a ratio of about 10:1 to about 20:1.

[0049] In another implementation, the beam shaping group transforms the collimated beam into a shaped propagating beam with uniform illumination in the far field over a rectangle with a ratio of approximately 1.

[0050] In another implementation, a method includes generating an input beam having a first beam spanning a first wavelength range and a second beam spanning a second wavelength range different from the first wavelength range.

[0051] In another implementation, a method includes generating an input beam using two input beam sources. It is understood that all combinations of the foregoing concepts and additional concepts, described in more detail below (provided such concepts are not mutually inconsistent), are considered to be part of the subject matter disclosed herein and / or can be combined to achieve particular benefits of particular embodiments. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are considered to be part of the subject matter disclosed herein. [Brief explanation of the drawings]

[0052] [Figure 1] 1 shows a schematic diagram of one implementation of an optical imaging device according to the teachings of the present disclosure, illustrating a beam shaping group and a collimator. [Figure 2] 1 shows a schematic diagram of another implementation of an optical imaging device according to the teachings of the present disclosure, illustrating a beam shaping group, a collimator, and an optical relay stage. [Figure 3] 1 shows a schematic diagram of another implementation of an optical imaging device according to the teachings of the present disclosure, showing a beam shaping group, a collimator, and an optical relay stage with internal beam shaping elements. [Figure 4] 1 shows a schematic diagram illustrating optical components for one implementation of an optical imaging device in accordance with the teachings of the present disclosure. [Figure 5] 1 shows a schematic diagram illustrating optical components for another implementation of an optical imaging device in accordance with the teachings of the present disclosure. [Figure 6] 1 shows a schematic diagram of one implementation of a beamforming group in accordance with the teachings of the present disclosure. [Figure 7] 10 is a plot of an illumination profile image of a substantially rectangular cross-sectional beam profile produced by a beam shaping group in accordance with the teachings of the present disclosure. [Figure 8] 1 illustrates one implementation of an input fiber beam source in accordance with the teachings of the present disclosure. [Figure 9] 1 illustrates a cross-sectional view of one implementation of an output surface of an integrated fiber bundle in accordance with the teachings of the present disclosure. [Figure 10] 1 illustrates a cross-sectional view of one implementation of an input face of an integrated fiber bundle in accordance with the teachings of the present disclosure. [Figure 11] 1 shows a cross-sectional view of the intensity profile of a substantially rectangular beam pair at a sample in accordance with the teachings of the present disclosure. [Figure 12] 1 illustrates optical components for another implementation of an optical imaging device in accordance with the teachings of the present disclosure. [Figure 13] 1 illustrates optical components for another implementation of an optical imaging device in accordance with the teachings of the present disclosure. [Figure 14] 1 illustrates one implementation of an optical imaging device having an optical compensator in accordance with the teachings of the present disclosure. [Figure 15] 1 shows the intensity profile of a substantially rectangular cross-section beam at the top area of ​​the sample in watts per square millimeter in accordance with the teachings of the present disclosure. [Figure 16] 1 shows the intensity profile of a substantially rectangular cross-section beam at the bottom area of ​​the sample in watts / square millimeter in accordance with the teachings of the present disclosure. [Figure 17A] 1 illustrates an optical imaging device with compensators in two different positions for one implementation according to the teachings of the present disclosure. [Figure 17B] 1 illustrates an optical imaging device with compensators in two different positions for one implementation according to the teachings of the present disclosure. [Figure 18A] 1 illustrates an optical imaging device with relay output lens groups at different locations for one implementation according to the teachings of the present disclosure. [Figure 18B] 1 illustrates an optical imaging device with relay output lens groups at different locations for one implementation according to the teachings of the present disclosure. [Figure 19A] 1A-1C show diagrams of an optical imaging device with relay input lens groups in different positions for one implementation according to the teachings of the present disclosure. [Figure 19B] 1A-1C show diagrams of an optical imaging device with relay input lens groups in different positions for one implementation according to the teachings of the present disclosure. [Figure 20]1 shows a schematic diagram of an optical imaging device having a dichroic configuration for one implementation according to the teachings of the present disclosure. [Figure 21] 1 shows a schematic diagram of one implementation of a system according to the teachings of the present disclosure. [Figure 22] 1 shows a flow diagram of an exemplary process that may be implemented by an apparatus, particularly an optical imaging apparatus, for analyzing one or more samples of interest. DETAILED DESCRIPTION OF THE INVENTION

[0053] Although the following text discloses detailed descriptions of implementations of methods, apparatus, and / or products, it should be understood that the legal scope of ownership is defined by the claims at the end of this patent. Accordingly, the following "Detailed Description" should be construed as exemplary only and does not describe every possible implementation, as describing every possible implementation would be impractical, if not impossible. Numerous alternative implementations may be implemented using either current technology or technology developed after the filing date of this patent. It is contemplated that such alternative implementations would still fall within the scope of the claims.

[0054] At least one aspect of the present disclosure is directed to an apparatus, particularly an optical imaging apparatus, for use with a system that can be used to perform an analysis on one or more samples of interest. The sample can include one or more DNA clusters, such as DNA clusters linearized to form single-stranded DNA (sstDNA). In various examples, the apparatus is designed to receive an input beam from a beam source and convert the input beam into a sampling beam of substantially rectangular cross-section for probing the sample. In this manner, the apparatus can probe the sample using uniform illumination across the sample, accounting for various types of photodetector geometries used in flow cell applications, such as time delay integration (TDI) line scanners. The TDI line scanner can have a footprint with an aspect ratio of about 10:1 to about 20:1. Alternatively, the TDI line scanner can have a footprint with an aspect ratio of approximately 1, about 4:3, and / or about 16:9. Other aspect ratios may also prove suitable. The TDI line scanner can use a cylindrical lens array and / or a spherical lens array. Furthermore, the power density for excitation illumination can be made more uniform across the illuminated area. Such an arrangement may advantageously reduce photobleaching or other photodamage to the sample of interest, one or more reagents used to perform chemical reactions, and / or a substrate used to support the sample of interest. Furthermore, such an arrangement may advantageously enable such optical systems to operate at high speeds, as substantially more uniform excitation illumination may result in edges of the area of ​​excitation illumination. While examples are described herein as generating a sampling beam of a substantially rectangular cross-section, the present technique may be used to form any number of elongated cross-sectional shapes in the far field, including ellipses, parallelograms, etc.

[0055] 1-3 show various schematic diagrams of exemplary implementations of the technology herein. Figure 1 shows, according to one example, an optical imaging apparatus 100 including a collimator stage 102 positioned to receive an input beam 104 generated by an input beam source 106. The collimator stage 102, which may be implemented as an optical collimator formed of a lens or group of lenses, generates a substantially parallel propagating beam 108 from the input beam 104.

[0056] The apparatus 100 further includes a beam shaping group 110, which includes one or more optical elements, positioned to receive the collimated beam 108 from the collimator stage 102. In various examples, the beam shaping group 110 is designed to format the collimated beam into a shaped propagating beam 112 having a substantially rectangular cross-section in the far field to enable probing of a sample 114 using a uniform intensity beam profile 116 that matches the profile of a line scanning sensor used in flow cell applications. A focusing objective stage 118 is provided between the beam shaping group 110 and the sample 114 to focus the shaped propagating beam onto the sample.

[0057] Although not shown, focusing objective stage 118 has an objective pupil and is positioned to receive propagating beam 112 that has been shaped so that the objective pupil is not overfilled, i.e., not clipped by the objective pupil or other apertures in objective stage 118. In various examples, the objective pupil is further illuminated uniformly. Focusing objective stage 118 converts beam 112 into a substantially rectangular cross-section sampling beam 120 having a substantially rectangular beam profile, such as profile 116, at the focal plane of the focusing objective stage.

[0058] 2 shows another exemplary optical imaging apparatus 200 having elements similar to those of apparatus 100. Apparatus 200 includes a collimator stage 202 positioned to receive an input beam 204 generated by an input beam source 206. Similar to collimator stage 102, collimator stage 202 generates a substantially parallel propagating beam 208 from input beam 204.

[0059] A beam shaping group 210 is also provided to receive the parallel beam 208 from the collimator stage 202 and to format the collimated beam into a shaped propagating beam 212 having a substantially rectangular cross-section in the far field to enable probing of a sample 214 using a uniform intensity beam profile 216 that matches the profile of a line scanning sensor used in flow cell applications. A focusing objective stage 218 is also provided, but unlike apparatus 100, apparatus 200 includes an optical relay stage 222 positioned between the beam shaping group 210 and the focusing objective stage 218. The optical relay stage 220 functions to relay the shaped propagating beam onto a pupil of the focusing objective stage or a plane proximal to it, and in various examples herein, the optical relay stage is formed with an input lens stage positioned to receive the propagating beam from the beam shaping group 210 and an output lens stage positioned to generate or provide the shaped propagating beam on or near the objective pupil. The optical relay stage may be afocal, in which case an object at infinity is focused at the focal plane of the objective lens. The optical relay stage may optionally not be fully afocal, in which case an object at infinity is not fully focused at the focal plane of the objective lens. In the implementation of FIG. 2, the beam shaping group 210 is external to the optical relay stage. In some examples, the beam shaping group may be partially or entirely within the optical relay stage.

[0060] 3 shows an example optical imaging apparatus 300 having similar elements and similar reference numbers to those of FIG. 2, but in which there is a beam shaping element 324 positioned within optical relay stage 322, e.g., between its input and output lens stages, in addition to beam shaping group 310 before optical relay stage 322. In some examples, a second beam shaping group different from group 310 may be positioned within optical relay stage 320.

[0061] Various types of beam-shaping groups can be deployed to generate a shaped propagating beam having a substantially rectangular cross-section in the far field. FIGS. 4 and 5 show two exemplary configurations of an optical imaging device, each having a beam-shaping group formed with an integrator. In some examples, including those shown in FIGS. 4 and 5, the integrators are imaging integrators formed from two cylindrical microlens arrays positioned in series. However, the microlenses may not be cylindrical in other implementations. In other examples, the integrators are non-imaging integrators formed from a single cylindrical microlens array. In still other examples, the beam-shaping group can be one or more diffractive optical elements or one or more refractive optical elements. In still other examples, the beam-shaping group can be a combination of refractive and diffractive optical elements, or a refractive optical element with an integrated diffractive feature (e.g., with an integrated diffuser). In some examples, the beam-shaping group is configured to receive an input beam from a beam source having a substantially rectangular shape, such as from one or more rectangular output surface optical fibers (as shown in FIGS. 8-10). The output face of the optical fiber can have a square cross-section, a round cross-section, or another cross-section. If the output face of the optical fiber has a square cross-section, then in some implementations, the beam shaping group 310 can be omitted. If the output face of the optical fiber has a round cross-section, then the beam shaping group 310 can be included in some implementations.

[0062] 4 shows an optical imaging device 400 having an input beam source in the form of an input fiber beam source 402 that produces an expanded beam output from its output face. The beam source herein may be a rigid fiber, light pipe, or other mode-confined based laser beam source. The input to the input fiber beam source 402 may be a laser, light emitting diode, or other illumination excitation source. A collimator 406 is positioned to receive the input beam, which is positioned to produce a generally parallel beam at its exit.

[0063] Adjacent to collimator 406 is beam shaping group 408, which in this example is a two-element imaging integrator that formats the collimated input beam into a shaped propagating beam having a substantially rectangular cross-section in the far field, for example as shown in Figure 7, where the imaging integrator was used to convert the output beam of a fiber containing a core with a 4:1 aspect ratio into a substantially rectangular (12:1 aspect ratio) cross-section as recorded in the laboratory. Beam shaping group 408 delivers the shaped propagating beam to focusing objective stage 412 to probe sample 414.

[0064] FIG. 6 shows a schematic diagram of an exemplary configuration of the beam shaping group 408. The collimated beam is received by a telescope including an input lens 452 and an output lens 454, and a rotating diffuser 450, which introduces time-dependent variations in the speckle pattern. Adjacent to the telescope, an image-forming integrator 455 is formed of two cylindrical microlens arrays 456 (LA1) and 458 (LA2), which, when focused using a focusing objective lens 462 (FL), generate a substantially rectangular cross-section beam at a far-field plane, FFP 460, which corresponds to the focal plane of the focusing objective lens. In the illustrated example, the microlenses are on opposite sides of each microlens array 456 and 458. In any case, in some examples, the beam shaping group 408 is formed solely from the two cylindrical microlens arrays 456 and 458.

[0065] 7 shows the intensity profile of a substantially rectangular cross-section beam as measured by a sensor positioned at the far-field plane FFP, along with a plot of intensity as a function of lateral distance of that beam profile. Although not shown, in some examples, the beam shaping group 408 may be a non-imaging integrator formed from a single one-sided cylindrical microlens array.

[0066] While FIG. 4 illustrates an optical imaging apparatus formed only with a collimator, a beam shaping group, and a focusing objective stage in a configuration similar to apparatus 100, FIG. 5 illustrates an optical imaging apparatus 500 with an optical relay stage in an exemplary configuration similar to apparatus 200. A fiber beam source 502 provides an input signal to a collimator 506, and a beam shaping group 508 is positioned adjacent to the collimator 506 to generate a shaped propagating beam from the incident parallel beam. In the illustrated example, the beam shaping group 508 is an image-forming integrator formed from two cylindrical microlens arrays, similar to beam shaping group 408 in FIG. 4 . That is, in some examples, the beam shaping group 408 may be formed only with two cylindrical microlens arrays 456 and 458. The optical relay stage 510 is formed from two lens groups 512 and 514. Input lens stage 512 receives the shaped propagation beam and generates an intermediate image of the entrance plane (i.e., the fiber exit plane) at intermediate image plane 516. Output lens stage 514 generates output from optical relay stage 510 and provides it to focusing objective lens 518 for probing sample 522. Optical relay stage 510 may be advantageous for manufacturing equipment that may have variations in manufacturing tolerances and / or may be paired with different components or configurations. That is, beam shaping group 508 may be designed or configured for a particular shaped propagation beam at a predetermined distance, and if the objective pupil of focusing objective stage 518 is not at that particular predetermined distance, optical relay stage 510 can be used to relay the shaped propagation beam to the actual location of the objective pupil of focusing objective stage 518. Additionally or alternatively, the optical relay stage 510 may further transform a particular shaped propagating beam such that the arrangement of the beam shaping groups can be used with different detection sensors by modifying how the optical relay stage 510 further transforms the particular propagating beam.

[0067] The beam shaping group 508, as with various other examples herein, is designed to format an incident collimated beam to have different sizes in the far field in orthogonal directions. Some beam shaping groups may include cylindrical microlens arrays. Other beam shaping groups may include anamorphic relays composed of cylindrical lenses. As a result, the beam profile in the far field where the sample is located (similar to the beam profile at the mid-plane of the optical relay configured in FIG. 5) will have a footprint in one plane (e.g., the XZ plane) and a different footprint in another orthogonal plane (e.g., the YZ plane). The pitch, focal length, and shape of the lenslets, as well as the location of the microlenses, such as whether they are on opposite sides of the optical system, can be selected to further control the beam profile at the focal plane.

[0068] In various examples, a beam-influencing element, such as an optical mask or despeckling element, can be positioned at the intermediate plane to establish greater uniformity of illumination across the substantially rectangular cross-section beam in the far field. As a mask, the beam-influencing element can be used to ensure, for example, that the illumination pattern substantially coincides with the field of view of the imager, so that only the region of the sample is illuminated while being imaged. As a despeckling element, a rotating diffuser disk or low-divergence beam-shaping element can be used and moved in one direction to influence the beam. In various examples, the beam-influencing element can be located elsewhere within the optical relay stage 510.

[0069] In various examples, the beam source is a fiber beam source, and more specifically, a two-input beam source that generates an input beam having a first beam spanning a first wavelength range and a second beam spanning a second wavelength range different from the first wavelength range.

[0070] FIG. 8 shows an exemplary fiber beam source 600 according to an exemplary configuration. The beam source 600 is formed by bundling two input fibers 602 and 604 together to form a bifurcated fiber bundle. In an example, either or both of the input fibers 602, 604 can receive an input beam at any suitable wavelength for flow cell probing applications, e.g., 455 nm, 488 nm, 532 nm, 660 nm, 780 nm, or 790 nm. In various implementations, the input beam may span any range of wavelengths from 200 to 2500 nm. An end view of the entrance face 610 of each fiber 602, 604 is shown in FIG. 10, which illustrates that for this example, the entrance faces are substantially rectangular. A Y-coupler 606 is provided to align and overlap the fibers to form a two-input beam source 608 having an exit face profile formed from two substantially rectangular faces 612, as shown in FIG. 9. As noted above, in some examples, the input beam originates from a substantially rectangular fiber face, but this need not be the case. Furthermore, the aspect ratio of the fiber face is not necessarily the same as desired in the far-field where the sample is probed. In any case, the beam shaping group is configured to generate a substantially rectangular beam. To illustrate the uniformity of the far-field illumination, an exemplary Zemax image of a generated sample beam formed from two input beam fibers is shown in FIG. 11 , demonstrating consistent illumination throughout the profile. This technique can be implemented with other fiber configurations and / or other fiber cross-sectional profiles. For example, other implementations can use more than two fibers and can be in other positions other than symmetrical about the centerline. For example, a hex pack of 3×1, 6×1, 2×2, or 3 fibers can be used.

[0071] 12 and 13 show other exemplary optical imaging device configurations with beam shaping groups composed of optical groups other than microlens arrays. FIG. 12 shows two views of device 700 coupled to an input fiber beam source 702 (the top view is looking down the XZ plane, and the bottom view is looking down the YZ plane). A collimator group 704 provides a collimated beam to a beam shaping group 706. The beam shaping group may be formed with cylindrical lenses. As shown in the different views, the propagation profiles in different planes, the XZ and YZ planes, are different, reflecting the different aspect ratios of the shaped propagating beams; in this example, the shaping of the propagating beams is affected by the cylindrical lenses. In the XZ (top) view, cylindrical lenses 708 and 710 have no magnification, and the collimated light passes through in the axial plane without any change in size. In the YZ (bottom) view, cylindrical lenses 708 and 710 have magnification such that the collimated beam size along Y after 710 is different from the collimated beam size along Y before 708. The presence of 706 results in anamorphic magnification of the image of 702 at 712.

[0072] Figure 13 shows an optical imaging apparatus 800 that uses a beam shaping group 806 of a type similar to that of group 706, and apparatus 800 includes an optical relay stage 816 between group 806 and a focusing objective stage 814, and a sample 812 positioned in the far field, where optical relay stage 816 may be formed in a manner similar to that of Figure 5 (e.g., optical relay stage 510).

[0073] Generally, in this technique, when a beam-shaping group with a given design divergence angle is imaged onto or near the objective pupil by a unit-conjugate optical relay stage, the divergence angle of the objective pupil is equal to the divergence angle from the beam-shaping group. In one example, the magnification of the optical relay stage can be selected to convert the divergence angle from the beam-shaping group to a different divergence angle in the objective pupil. This allows the divergence of a commercially available beam-shaping group to be converted to a target value. For example, the nominal divergence of Edmund Stock #86-844 is ±3.2°. When a ±3.2° fan is aimed at a focusing objective stage (e.g., a microscope objective) with an effective focal length (EFL) of 10 mm, a line is formed at the focus of the objective. The length of the line can be calculated by 2(10 mm) Tan [3.2°] (i.e., approximately 1.1 mm). If the target line length is 1.2 mm, such a commercially available part will shape the beam into a line 100 μm shorter than the desired 1.2 mm. However, if the magnification of the optical relay stage is selected to be 1 / 1.1, the objective pupil angle will be approximately 3.5°. The line length can be calculated by 2(10) mm Tan[3.5°] (i.e., approximately 1.2 mm). Therefore, the relay converts the output of the commercially available beam shaping group into an output adapted to meet different requirements.

[0074] Although a fixed-magnification optical relay stage can be used to convert a nominal commercially available fan into a nominal alternative fan, variations in the beam-shaping group will still result in variations in line length in the far field, i.e., variations in the substantially rectangular cross-section of the sampling beam. Variations in the focal length of the objective lens will also result in variations in line length. Therefore, in another example, the optical relay stage may include a lens stage whose focal length can be continuously changed by moving one or more of the stage's lens components along an axis, with one of the focal points of the zoom lens maintained in a fixed plane. With such an adjustable optical relay stage, afocality or deviation from afocality can be maintained while the relay magnification is adjusted. When such an optical relay stage is used to convert a commercially available fan into an alternative fan, the focal length of the zoom lens can be adjusted to compensate for variations in the beam-shaping means.

[0075] In various examples, the technology herein includes optical imaging devices and methods for formatting light at two different distances within a sample. That is, in various implementations, devices are provided that can generate a beam for probing a sample, the beam being characterized by a substantially rectangular cross-sectional beam profile at different depths within the sample, allowing for more accurate probing throughout the sample.

[0076] 14 shows an optical imaging apparatus 800 having an input beam source 802 that generates an input beam 804, a collimator stage 807 that generates a substantially parallel input beam 808, and a beam shaping group 810 that generates a shaped propagating beam 811. The apparatus 800 further includes an optical relay stage 814 that provides the shaped propagating beam to a focusing objective stage 816 for probing a sample 818. The optical imaging apparatus 800 further includes an optical compensator 820 that may be positioned within the apparatus 800 to control the sampling focal plane of the objective stage 816. In the implementation shown, the optical compensator 820 may be controllably provided in one of three different locations: before the optical relay stage 814, as shown as OC820A; after the optical relay stage 814, as shown as OC820B; or within the optical relay stage 814, as shown as OC820C. In other examples, the optical compensator may be positioned elsewhere within the apparatus.

[0077] In various examples, the optical compensator may be a plane-parallel plate formed of a refractive material. In various other examples, the optical compensator may be a lens. The optical compensator is designed to have a first compensation position or state such that the focusing objective stage can generate a substantially rectangular cross-section sampling beam 822 at the top surface or top region of the sample. Furthermore, the compensator is designed to have a second compensation position or state such that the focusing objective stage can generate a substantially rectangular cross-section sampling beam 824 to probe the bottom surface or bottom region of the sample. The optical compensator is designed and positioned within apparatus 800 to maintain a substantially uniform illumination profile of the probe beam at both the top and bottom portions of the sample. Figures 15 and 16 show exemplary Zemax images of the generated sample beam formed from two input beam fibers as beam sources, particularly showing the uniform, substantially rectangular cross-sections of the sample beam at the top surface (Figure 15) and the bottom surface (Figure 16), each achieved by controlling the change in the position or state of the optical compensator in the example embodiment.

[0078] The optical compensator may be mechanically controllable between a first compensation position and a second compensation position. The optical compensator may be electrically controllable between the first compensation position and the second compensation position. To that end, a position controller 826 ( FIG. 14 ) is provided in the illustrated implementation, and the positioner controller is coupled to the optical compensator. In some examples, the position controller 826 is designed to controllably (i) insert the optical compensator into the beam path to receive the shaped propagation beam and affect the shaped propagation beam path to probe one of the upper or lower surface of the sample, and (ii) remove the optical compensator from the beam path to affect the shaped propagation beam path to probe the other of the lower or upper surface of the sample. In some examples, the position controller 826 is designed to change the state of the optical compensator between a first state and a second state to select between them and generate a sampling beam of a substantially rectangular cross-section at the upper or lower surface of the sample. For example, the optical compensator may be an electro-optic refractive element that can change the optical path length in response to an applied voltage from the position controller 826 .

[0079] Although not shown, position controller 826 may include one or more processors and one or more computer-readable memories that store instructions that can be executed by the one or more processors to perform various functions, including the disclosed implementations. The position controller may include a user interface and a communication interface electrically and / or communicatively coupled to the one or more processors, as well as one or more memories.

[0080] In implementations, the user interface may be adapted to receive input from a user and provide the user with information associated with the operation of device 800. The user interface may include a touchscreen, a display, a keyboard, speaker(s), a mouse, a trackball, and / or a voice recognition system. The touchscreen and / or the display may display a graphical user interface (GUI).

[0081] In implementations, the communication interface is adapted to enable communication between device 800 and remote system(s) (e.g., a computer) over network(s). The network(s) may include the Internet, an intranet, a local-area network (LAN), a wide-area network (WAN), a coaxial cable network, a wireless network, a wired network, a satellite network, a digital subscriber line (DSL) network, a cellular network, a Bluetooth® connection, a near field communication (NFC) connection, etc. Some of the communications provided to the remote system may be associated with analysis results, imaging data, etc. generated or otherwise obtained by device 100.

[0082] The one or more processors of controller 826 may include one or more of a processor-based system(s) or a microprocessor-based system(s). In some implementations, the one or more processors include one or more of a programmable processor, a programmable controller, a microprocessor, a microcontroller, a graphics processing unit (GPU), a digital signal processor (DSP), a reduced-instruction set computer (RISC), an application specific integrated circuit (ASIC), a field programmable gate array (FPGA), a field programmable logic device (FPLD), a logic circuit, and / or another logic-based device that performs various functions, including those described herein.

[0083] The one or more memories may be semiconductor memory, magnetically readable memory, optical memory, hard disk drive (HDD), optical storage drive, solid-state storage device, solid-state drive (SSD), flash memory, read-only memory (ROM), erasable programmable read-only memory (EPROM), electrically erasable programmable read-only memory (EEPROM), random-access memory (RAM), non-volatile RAM (NVRAM) memory, compact disc (CD), compact disc read-only memory (CD-ROM), digital versatile disk (DVD), Blu-ray Disc, redundant array of independent disks, This may include one or more of: a storage device, a RAID (repeated array of independent disks, RAID) system, a cache, and / or any other storage device or disk on which information is stored for any duration (e.g., permanently, temporarily, long-term, for buffering, for caching).

[0084] 17A and 17B show another exemplary optical imaging apparatus 900 having a collimator 902 and a beam shaping group (BSG) 904, an optical relay stage 906 formed with a first lens group 1 (input lens stage 908) and a second lens group 2 (output lens stage 910), and an optical compensator 912 in two different positions / states: a first position / state ( FIG. 17B ) for probing the bottom of a sample 922 and a second position / state ( FIG. 17A ) for probing the top of the sample 922. In the illustrated example, the optical compensator 912 changes state between FIGS. 17A and 17B , the latter showing no or a small optical path length introduced to the beam within the optical relay stage 906, and the former showing a large optical path length introduced to the beam within the optical relay stage 906, for example, using an electro-optical compensator or any similar optical control means. Thus, the optical compensator may be an optical element, such as a liquid lens, that is electrically controllable to switch from a first optical state to a second optical state to affect optical compensation. In another example, the result of Figure 17A may be achieved by removing the optical compensator 912 from the optical path in the optical relay stage 906.

[0085] In different embodiments, right angle reflecting mirrors 920 and 918 may also be used as shown, as well as wavelength dependent reflectors 914 and 916 which may be used to filter unwanted wavelength components in the beam from propagating to sample 922 via final right angle reflector 924.

[0086] 18A and 18B show another exemplary optical imaging apparatus 930 having a collimator 932, a beam shaping group (BSG) 934, and an optical relay stage 936 formed of a first lens group 1 (input lens stage 938) and a second lens group 2 (output lens stage 940) that is movable between two different positions: a first position ( FIG. 18B ) that probes the bottom of a sample 950, and a second position ( FIG. 18A ) that probes the top of the sample 950. Varying the optical compensation in apparatus 930 is achieved by changing the positions of the lens groups of optical relay stage 936. Similar to optical stage 900, the illustrated example also employs right-angle reflecting mirrors 948 and 946, as shown, as well as wavelength-dependent reflectors 942, 944, which can be used to filter unwanted wavelength components in the beam from propagating to sample 950 via a final right-angle reflector 952.

[0087] 19A and 19B show another exemplary optical imaging apparatus 960 having a collimator 962, a beam shaping group (BSG) 964, and an optical relay stage 966 formed with a first lens group 1 (input lens stage 968) and a second lens group 2 (output lens stage 970), where the relay input lens group 968 is movable between two different positions: a first position ( FIG. 19B ) that probes the bottom of a sample 972, and a second position ( FIG. 19A ) that probes the top of the sample. Similar to the optical stage 900, in the illustrated example, right-angle reflecting mirrors 980 and 978 may also be used as shown, as well as one or more wavelength-dependent reflectors 974, 976 that may be used to filter unwanted wavelength components in the beam from propagating to the sample 972 via the final right-angle reflector 982.

[0088] FIG. 20 shows another exemplary optical imaging device 1100 having a dichroic arrangement that can be used to direct two input beams 1101 of different wavelengths arriving at the same input fiber beam source to different locations within a sample 1103. A collimator 1102 receives the two-wavelength input beam and generates a parallel output beam having both wavelengths. As with other examples described herein, a beam shaping group (BSG) 1104 formats the parallel beam into a shaped propagating beam having a substantially rectangular cross-section in the far field for each wavelength. An optical relay stage 1106 is formed by a first lens group 1 (input lens stage 1108) and a second lens group 2 (output lens stage 1110). In the illustrated example, the second relay input lens group 1110 is movable between two different positions to probe across the sample 1103, for example, from the bottom to the top of the sample 1103. Dichroic right-angle reflecting mirrors 1112 and 1114 are each provided to reflect different wavelengths in input beam(s) 1101 and transmit other wavelengths. Two different mirrors 1116 and 1118 are provided to reflect the incident light. For example, BSG 1104 can format the beam, while mirror 1112 reflects the blue wavelength component and transmits the green wavelength component, mirror 1118 reflects the blue wavelength component, mirror 1116 reflects the green wavelength component, and mirror 1114 reflects the green wavelength component and transmits the blue wavelength component. The angles of mirrors 1116 and 1118 are set to generate specific angles between the blue and green wavelength beam components after exiting mirror 1114. The different angles reach an objective lens (optionally through a relay), and the position of the shaped beam at the focal point of the objective lens is determined by the angle of the beam relative to the axis of the objective lens.

[0089] Any of the above examples shown in Figures 17A-17B, 18A-18B, 19A-19B, and / or 20 may be implemented using any of the implementations described above with reference to Figures 1-14.

[0090] 21 shows a schematic diagram of one implementation of a system 1000 according to the teachings of the present disclosure. The system 1000 can be used to perform analyses on one or more samples of interest. The samples may include one or more DNA clusters that have been linearized to form single-stranded DNA (sstDNA). In the implementation shown, the system 1000 receives a reagent cartridge 1002 and includes, in part, a drive assembly 1004 and a controller 1006. The system 1000 also includes an imaging system 1012 and a waste reservoir 1014. In other implementations, the waste reservoir 1014 may be included with the reagent cartridge 1002. The imaging system 1012 includes any one or more of the optical imaging devices 100, 200, 300, 400, 800, and 900 disclosed herein. The controller 1006 is electrically and / or communicatively coupled to the drive assembly 1004 and the imaging system 1012 and causes the drive assembly 1004 and / or the imaging system 1012 to perform various functions as disclosed herein.

[0091] A reagent cartridge 1002 holds a sample of interest that can be loaded into a channel of a flow cell 1020. A drive assembly 1004 interfaces with the reagent cartridge 1002 to flow one or more reagents (e.g., A, T, G, C nucleotides) that interact with the sample through the flow cell 1020.

[0092] In implementations, a reversible terminator is attached to the reagent to allow incorporation of a single nucleotide onto the growing 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 illustrated implementation, the imaging system 1012 excites one or more of the distinguishable labels (e.g., fluorescent labels) and then acquires image data of the distinguishable labels. The labels can be excited by incident light and / or a laser, and the image data can include one or more colors emitted by each label in response to excitation. The image data (e.g., detection data) can be analyzed by the system 1000. The imaging system 1012 can be a fluorescence spectrophotometer including an objective lens and / or a solid-state imaging device. The solid-state imaging device can include a charge coupled device (CCD) and / or a complementary metal oxide semiconductor (CMOS).

[0093] After the image data is acquired, the drive assembly 1004 interfaces with the reagent cartridge 1002 to flush another reaction component (e.g., a reagent) through the reagent cartridge 1002, which is then received by a waste reservoir 1014 and / or otherwise expelled by the reagent cartridge 1002. The reaction components perform a flushing action that chemically cleaves the fluorescent label and reversible terminator from the sstDNA. The sstDNA is then ready for another cycle.

[0094] Referring now to the drive assembly 1004, in the illustrated implementation, the drive assembly 1024 includes a pump drive assembly 1022, a valve drive assembly 1024, and an actuator assembly 192. The pump drive assembly 1022 interfaces with a pump 1026 to pump fluid through the reagent cartridge 1002 and / or flow cell 1020, and the valve drive assembly 1024 interfaces with a valve 1028 to control the position of the valve 1028. Interaction between the valve 1028 and the valve drive assembly 1024 selectively actuates the valve 1028 to control fluid flow through fluid lines 1030 of the reagent cartridge 1002. One or more of the fluid lines 1030 fluidly couple one or more reagent reservoirs 1032 and the flow cell 1020. One or more of the valves 1028 may be realized by a valve manifold, a rotary valve, a pinch valve, a flat valve, a solenoid valve, a reed valve, a check valve, a piezo valve, or the like.

[0095] Referring to the controller 1006, in the illustrated implementation, the controller 1006 includes a user interface 1034, a communication interface 1036, one or more processors 1038, and a memory 1040 that stores instructions executable by the one or more processors 1038 to perform various functions, including the disclosed implementations. The user interface 1034, the communication interface 1036, and the memory 1040 are electrically and / or communicatively coupled to the one or more processors 1038.

[0096] In implementations, the user interface 1034 receives input from a user and provides the user with information associated with the operation of the system 1000 and / or the analyses performed. The user interface 1034 may include a touchscreen, a display, a keyboard, speaker(s), a mouse, a trackball, and / or a voice recognition system. The touchscreen and / or display may display a graphical user interface (GUI).

[0097] In implementations, communication interface 1036 enables communication between system 1000 and remote system(s) (e.g., computers) over a network. The network(s) may include an intranet, a local area network (LAN), a wide area network (WAN), an intranet, etc. Some of the communications provided to the remote systems may be related to analysis results, imaging data, etc. generated or otherwise obtained by system 1000. Some of the communications provided to system 1000 may be related to fluid analysis operations, patient records, and / or protocol(s) performed by system 1000.

[0098] The one or more processors 1038 and / or system 1000 may include one or more of a processor-based system(s) or a microprocessor-based system(s). In some implementations, the one or more processors 1038 and / or system 1000 include reduced instruction set computer(s) (RISC), application specific integrated circuit(s) (ASIC), field programmable gate array(s) (FPGA), field programmable logic device(s) (FPLD), logic circuit(s), and / or another logic-based device that performs various functions, including those described herein.

[0099] The memory 1040 may include one or more of a hard disk drive, flash memory, read-only memory (ROM), erasable programmable read-only memory (EPROM), electrically erasable programmable read-only memory (EEPROM), random access memory (RAM), non-volatile RAM (NVRAM) memory, compact disc (CD), digital versatile disc (DVD), cache, and / or any other storage device or storage disk on which information is stored for any period of time (e.g., permanently, temporarily, long-term, buffering, caching).

[0100] FIG. 22 shows a flow diagram of an exemplary process 1200 that may be implemented by an apparatus, particularly an optical imaging apparatus, for analyzing one or more samples of interest. The sample may include one or more DNA clusters, such as DNA clusters linearized to form single-stranded DNA (sstDNA). In block 1202, the apparatus receives an input beam and generates a collimated output beam using a front-end collimator. In block 1204, the output of the collimated beam is provided to a beam shaping group, which formats the collimated beam into a shaped propagation beam having a substantially rectangular cross-section in the far field. For example, the beam shaping group may be an image integrator formed from two different elements, each a cylindrical microlens array. In block 1206, the shaped propagation beam is provided to an optical relay stage, which generates a shaped propagation beam relative to the objective pupil of a focusing objective stage. In block 1208, the shaped propagation beam is converted into a sampling beam of substantially rectangular cross-section at the focal plane of the focusing objective stage. The optical relay stage may alternatively be omitted. In block 1210, the apparatus optically probes a sample at a first location using a sampling beam of substantially rectangular cross-section. Further, optionally, in block 1212, optical compensation is performed to adjust the sampling position of the substantially rectangular cross-section sampling beam to optically probe the sample at a second location different from the first location. The process of block 1212 may be performed at different locations, sequentially across different locations, or multiple times at one location before process 1200 ends with the sample being optically probed at least once with the substantially rectangular cross-section sampling beam. Block 1212 may be implemented using any number of compensation techniques herein, including introducing an optical compensator into an optical relay stage, or before or after such a stage. Compensation may be achieved by changing the position of a lens group in the optical relay stage.

[0101] Another process begins with an input beam having a first beam spanning a first wavelength range and a second beam spanning a second wavelength range different from the first wavelength range. The input beams may additionally or alternatively be generated using two input beam sources. A collimator receives the input beam from a fiber beam source, and the collimator generates a substantially parallel beam from the input beam. The substantially parallel beam is received from the collimator by a beam shaping group including one or more optical elements, and the substantially parallel beam is formatted by the beam shaping group into a shaped propagation beam having a substantially rectangular cross-section in the far field, and the shaped propagation beam is received by a focusing objective stage including an objective pupil. The shaped propagation beam is converted into a sampling beam of substantially rectangular cross-section at or near the focal plane of the focusing objective stage, and a sample is optically probed using the focusing objective stage.

[0102] 1. An apparatus comprising: a collimator at an input end positioned to receive an input beam from a fiber beam source and generate a substantially parallel beam; a beam shaping group including one or more optical elements positioned to receive the substantially parallel beam from the collimator and format the substantially parallel beam into a shaped propagation beam having a substantially rectangular cross-section in a far field; and a focusing objective stage including an objective pupil for receiving the shaped propagation beam, the focusing objective stage positioned to convert the shaped propagation beam into a sampling beam of a substantially rectangular cross-section at or near a focal plane of the focusing objective stage for optically probing a sample.

[0103] In one example, the apparatus further includes an optical relay stage positioned between the beam shaping group and the focusing objective stage for imaging the shaped propagating beam from the beam shaping group onto the objective pupil of the focusing objective stage.

[0104] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical relay stage comprises an input lens stage positioned to receive the shaped propagation beam from the beam shaping group, and an output lens stage positioned to generate the shaped propagation beam to an objective pupil of the focusing objective stage.

[0105] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the input lens stage and the output lens stage form a focusing element pair that defines an intermediate image plane within the optical relay stage.

[0106] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical relay stage has a beam influencing element at an intermediate image plane. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam influencing element is an optical mask.

[0107] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam influencing element is a despeckle element. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the position of at least one of the input lens stage and the output lens stage is adjustable.

[0108] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus further includes a Powell lens positioned before the optical relay stage.

[0109] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus further includes a Lineman lens positioned in front of the optical relay stage.

[0110] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical relay stage is afocal. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical relay stage is a fixed magnification relay.

[0111] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical relay stage is a variable magnification relay. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group is an integrator.

[0112] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the integrator is an image-forming integrator formed from two cylindrical microlens arrays positioned in series.

[0113] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the microlenses are cylindrical lenses. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the microlenses each have different focal lengths along the x and y directions.

[0114] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the integrator is a non-imaging integrator formed from a microlens array.

[0115] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group includes an integrated diffractive feature. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group includes an integrated diffuser mechanism.

[0116] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the integrator is an image-forming integrator formed from microlenses, and the microlenses are cylindrical lenses.

[0117] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the cylindrical lens is configured to provide divergence in one axial direction of the microlens and not in an orthogonal direction of the microlens.

[0118] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group comprises a diffractive optical element. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group includes a refractive optical element, a combination of a refractive optical element and a diffractive optical element, or a refractive optical element with an integrated diffractive or diffractive feature.

[0119] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the collimated beam into a shaped propagating beam having uniform illumination in the far field across a rectangle having an 8:1 ratio.

[0120] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the collimated beam into a shaped propagating beam having uniform illumination in the far field across a rectangle having a ratio of 10 to 1.

[0121] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the parallel beam into a shaped propagating beam having uniform illumination in the far field across a rectangle having a ratio of 24 to 1.

[0122] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the collimated beam into a shaped propagating beam with uniform illumination in the far field across a rectangle having ratios that match the profile of a time delay integration (TDI) line sensor.

[0123] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus further comprises a fiber beam source. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the fiber beam source is a two-input beam source generating an input beam having a first beam over a first wavelength range and a second beam over a second wavelength range different from the first wavelength range.

[0124] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the fiber beam source comprises two dedicated input fibers, each corresponding to one of the first beam and the second beam.

[0125] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the output ends of two dedicated input fibers are presented to the collimator at a fixed interval and with rotation about the fiber core and collimator axis.

[0126] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein each input fiber has a substantially rectangular cross-section at the output face. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the fiber beam source is a light pipe.

[0127] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes an optical compensator positioned to receive the shaped propagating beam and having two compensation positions: a first compensation position in which the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe a top surface of the sample, and a second compensation position in which the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe a bottom surface of the sample.

[0128] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is electromechanically controllable between a first compensation position and a second compensation position.

[0129] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is electrically controllable between a first compensation position and a second compensation position.

[0130] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein an optical compensator is insertable between the beam shaping group and the focusing objective stage.

[0131] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising an input lens stage positioned to receive the shaped propagation beam from the beam shaping group and an output lens stage positioned to generate the shaped propagation beam for an objective pupil of the focusing objective stage, and wherein the optical compensator is positioned within the optical relay stage.

[0132] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is an optical element electrically controllable to switch from a first optical state to a second optical state to affect optical compensation.

[0133] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising an input lens stage positioned to receive the shaped propagation beam from the beam shaping group and an output lens stage positioned to generate the shaped propagation beam for an objective pupil of the focusing objective stage, and wherein an optical compensator is positioned before the optical relay stage.

[0134] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising an input lens stage positioned to receive the shaped propagation beam from the beam shaping group and an output lens stage positioned to generate the shaped propagation beam for an objective pupil of the focusing objective stage, and wherein the optical compensator is positioned after the optical relay stage.

[0135] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes an optical compensator and a positioner coupled to the optical compensator, the positioner being coupled to controllably (i) insert the optical compensator into the beam path to receive the shaped propagating beam and affect the shaped propagating beam path to probe one of the top or bottom surfaces of the sample, and (ii) remove the optical compensator from the beam path to affect the shaped propagating beam path to probe the other of the bottom or top surfaces of the sample.

[0136] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is a plane-parallel plate of refractive material. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is a lens.

[0137] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is inserted before the optical relay stage in the beam path.

[0138] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is inserted within an optical relay stage in the beam path.

[0139] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the optical compensator is inserted after the optical relay stage in the beam. The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising an input lens stage positioned to receive the shaped propagation beam from the beam shaping group and an output lens stage positioned to generate the shaped propagation beam with respect to an objective pupil of the focusing objective stage, the input lens stage being movable between a first position where the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe a top surface of the sample, and a second position where the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe a bottom surface of the sample.

[0140] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes an optical relay stage positioned between the beam shaping group and the focusing objective stage, the optical relay stage comprising an input lens stage positioned to receive the shaped propagation beam from the beam shaping group and an output lens stage positioned to generate the shaped propagation beam with respect to an objective pupil of the focusing objective stage, the output lens stage being movable between a first position such that the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe a top surface of the sample, and a second position such that the focusing objective stage generates a sampling beam of a substantially rectangular cross-section to probe a bottom surface of the sample.

[0141] The apparatus of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the apparatus includes a fiber beam source, and wherein the apparatus has a first separation distance between the collimator and the fiber beam source to generate a sampling beam of a substantially rectangular cross-section to probe a top surface of the sample, and a second separation distance between the collimator and the fiber beam source to generate a sampling beam of a substantially rectangular cross-section to probe a bottom surface of the sample.

[0142] 1. A method for optically probing a sample, the method comprising: generating a collimated beam from an input beam; formatting the collimated beam using a beam shaping group into a shaped propagating beam having a substantially rectangular cross-section in a far field; providing the shaped propagating beam to an optical relay stage that outputs the shaped propagating beam to an objective pupil of a focusing objective stage; converting the shaped propagating beam using the focusing objective stage into a sampling beam of substantially rectangular cross-section at a focal plane of the focusing objective stage; probing the sample at a first location in the focal plane; and at a second location in the focal plane, affecting optical compensation of the optical relay stage such that the focusing objective stage converts the shaped propagating beam into a sampling beam of substantially rectangular cross-section; and probing the sample at the second location. The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein influencing the optical compensation of the optical relay stage comprises adjusting the position or optical properties of an influencing element within the optical relay stage.

[0143] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein affecting the optical compensation of the optical relay stage comprises adjusting a position of an input lens stage of the optical relay stage or a position of an output lens stage of the optical relay stage.

[0144] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group includes two cylindrical microlens arrays.

[0145] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group comprises a diffractive optical element. The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group comprises a refractive optical element, a combination of a refractive optical element and a diffractive optical element, or a refractive optical element with an integrated diffractive feature.

[0146] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the parallel beam into a shaped propagating beam having uniform illumination in the far field over an entire rectangle having an 8 to 1 ratio.

[0147] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the parallel beam into a shaped propagating beam having uniform illumination in the far field over an entire rectangle having a ratio of 10 to 1.

[0148] A method according to any one or more of the preceding examples and / or any one or more of the examples disclosed below; The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the parallel beam into a shaped propagating beam having uniform illumination in the far field across a rectangle having a ratio of 24 to 1.

[0149] 1. A method comprising: receiving an input beam from a fiber beam source with a collimator; generating a substantially parallel beam from the input beam by the collimator; receiving the substantially parallel beam from the collimator with a beam shaping group including one or more optical elements; formatting the substantially parallel beam into a shaped propagating beam having a substantially rectangular cross-section in a far field by the beam shaping group; receiving the shaped propagating beam with a focusing objective stage including an objective pupil; converting the shaped propagating beam into a sampling beam of substantially rectangular cross-section at or near a focal plane of the focusing objective stage; and optically probing a sample using the focusing objective stage.

[0150] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, further comprising generating an input beam having a first beam over a first wavelength range and a second beam over a second wavelength range different from the first wavelength range.

[0151] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, further comprising generating the input beam using two input beam sources.

[0152] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the fiber beam source comprises two dedicated input fibers, each corresponding to one of the first beam and the second beam.

[0153] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the output ends of two dedicated input fibers are presented to the collimator at a fixed interval and with rotation about the fiber core and collimator axis.

[0154] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein influencing the optical compensation of the optical relay stage comprises adjusting the position or optical properties of an influencing element within the optical relay stage.

[0155] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group includes two microlens arrays. The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group comprises a diffractive optical element.

[0156] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group comprises a refractive optical element, a combination of a refractive optical element and a diffractive optical element, or a refractive optical element with an integrated diffractive feature.

[0157] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the parallel beam into a shaped propagating beam having uniform illumination in the far field over an entire rectangle having an 8 to 1 ratio.

[0158] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the parallel beam into a shaped propagating beam having uniform illumination in the far field over an entire rectangle having a ratio of 10 to 1.

[0159] The method of any one or more of the preceding examples and / or any one or more of the examples disclosed below, wherein the beam shaping group transforms the parallel beam into a shaped propagating beam having uniform illumination in the far field across a rectangle having a ratio of 24 to 1.

[0160] The foregoing description is provided to enable one skilled in the art to practice the various configurations described herein. While the subject technology has been particularly described with reference to various diagrams and configurations, it should be understood that these are for illustrative purposes only and should not be construed as limiting the scope of the subject technology.

[0161] As used herein, elements or steps described in the singular and followed by the word "a" or "an" should be understood as not excluding a plurality of those elements or steps, unless such exclusion is expressly stated. Furthermore, references to "one implementation" are not intended to be interpreted as excluding the existence of additional implementations that also incorporate the recited features. Furthermore, unless expressly stated to the contrary, implementations that "comprising," "including," or "having" an element or elements having a particular characteristic may include additional elements whether or not they have that characteristic. Furthermore, the terms "comprising," "including," "having," etc. are used interchangeably herein.

[0162] As used throughout this specification, the terms "substantially," "approximately," and "about" are used to describe and take into account small variations due to processing variations, etc. For example, small variations can refer to ±5% or less, such as ±2% or less, such as ±1% or less, such as ±0.5% or less, such as ±0.2% or less, such as ±0.1% or less, such as ±0.05% or less.

[0163] There may be many other ways to implement the subject technology. The various functions and elements described herein may be divided differently than shown without departing from the scope of the subject technology. Various modifications to these implementations may be readily apparent to those skilled in the art, and the general principles defined herein may be applied to other implementations. Accordingly, many changes and modifications may be made to the subject technology by those skilled in the art without departing from the scope of the subject technology. For example, a different number of given modules or units may be used, different types or multiple types of given modules or units may be used, given modules or units may be added, or given modules or units may be omitted.

[0164] Underlined and / or italicized headings and subheadings are used for convenience only, do not limit the subject technology, and are not referred to in connection with interpreting the description of the subject technology. All structural and functional equivalents to the elements of the various implementations described throughout this disclosure that are known or later become known to those skilled in the art are expressly incorporated herein by reference and are intended to be encompassed by the subject technology. Furthermore, nothing disclosed herein is intended to be publicly exclusive, regardless of whether such disclosure is explicitly set forth in the description above.

[0165] It is understood that all combinations of the foregoing concepts and additional concepts described in more detail below (provided such concepts are not mutually inconsistent) are considered to be part of the subject matter disclosed herein. In particular, all combinations of claimed subject matter appearing at the end of this disclosure are considered to be part of the subject matter disclosed herein.

Claims

1. A sequencer, an image forming system, a fiber beam source including one or more input fibers and configured to provide one or more input beams via the one or more input fibers; a collimator at the input end positioned to receive an input beam from the fiber beam source and produce a substantially parallel beam; a microlens array positioned to receive the substantially parallel beam from the collimator and to format the substantially parallel beam into a shaped propagating beam having a substantially rectangular cross-section in the far field; a focusing objective stage having an objective pupil for receiving the shaped propagation beam, the focusing objective stage positioned to convert the shaped propagation beam into a sampling beam of substantially rectangular cross-section at or near a focal plane of the focusing objective stage for optically probing a sample in the flow cell; a valve for controlling the flow of fluid through the fluid line from the reagent cartridge; A sequencer comprising:

2. 10. The sequencer of claim 1, further comprising an optical relay stage positioned between the microlens array and the focusing objective stage for imaging the shaped propagation beam from the microlens array near an objective pupil of the focusing objective stage.

3. 3. The sequencer of claim 2, wherein the optical relay stage comprises an input lens stage positioned to receive the shaped propagation beam from the microlens array, and an output lens stage positioned to generate the shaped propagation beam for the objective pupil of the focusing objective stage.

4. 4. The sequencer of claim 3, wherein the input lens stage and the output lens stage form a focusing element pair that defines an intermediate image plane within the optical relay stage.

5. The sequencer of claim 4 , wherein the microlens array comprises two cylindrical microlens arrays.

6. The sequencer of claim 4 , wherein the microlens array comprises a single optic with microlens arrays disposed on two sides.

7. The sequencer of claim 4 , wherein the microlens array comprises two one-sided microlens arrays mounted in series.

8. The sequencer of claim 5 , wherein an output face of the one or more input fibers has a rectangular cross section.

9. further comprising an optical compensator; 2. The sequencer of claim 1, wherein the optical compensator is configured to move between a first position for controlling a sampling focal plane of a focusing objective stage at a first sampling focal plane and a second position for controlling a sampling focal plane of a focusing objective stage at a second sampling focal plane.

10. The sequencer of claim 9 , wherein the optical compensator comprises a lens that is movable.

11. The sequencer of claim 9 , wherein the optical compensator is a plane-parallel plate.

12. the first sampling focal plane corresponds to a first surface of the flow cell; 10. The sequencer of claim 9, wherein the second sampling focal plane corresponds to a second surface of the flow cell.

13. 2. The sequencer of claim 1, wherein the fiber beam source is a dual-input beam source that generates the input beam having a first beam spanning a first wavelength range and a second beam spanning a second wavelength range different from the first wavelength range.

14. 14. The sequencer of claim 13, wherein the fiber beam source includes two dedicated input fibers each corresponding to one of the first beam and the second beam.

15. The sequencer of claim 1 , wherein the fiber beam source includes one or more light emitting diodes.

16. The sequencer of claim 1 , wherein the fiber beam source includes one or more lasers.

17. A sequencer, an image forming system, an input fiber beam source including one or more light emitting diodes; a fiber beam source including one or more input fibers optically connected to the input fiber beam source and configured to provide one or more input beams via the one or more input fibers; a collimator at the input end positioned to receive an input beam from the fiber beam source and produce a substantially parallel beam; a microlens array assembly positioned to receive the substantially collimated beam from the collimator and to format the substantially collimated beam into a shaped propagating beam having a substantially rectangular cross-section in the far field; a focusing objective stage having an objective pupil for receiving the shaped propagation beam, the focusing objective stage positioned to convert the shaped propagation beam into a sampling beam of substantially rectangular cross-section at or near a focal plane of the focusing objective stage for optically probing a sample in the flow cell; an optical compensator configured to move between a first position for controlling the sampling focal plane of the focusing objective stage at the first sampling focal plane and a second position for controlling the sampling focal plane of the focusing objective stage at the second sampling focal plane; a valve for controlling the flow of fluid through the fluid line from the reagent cartridge; Equipped with the first sampling focal plane corresponds to a bottom surface of the flow cell; The second sampling focal plane corresponds to a top surface of the flow cell.

18. 20. The sequencer of claim 17, wherein the microlens array assembly includes two one-sided cylindrical microlens arrays positioned in series.

19. 20. The sequencer of claim 17, wherein the microlens array assembly includes a single optic with a first microlens array disposed on a first surface and a second microlens array disposed on a second surface.

20. 20. The sequencer of claim 17, wherein an output face of the one or more input fibers has a rectangular cross section.

21. 20. The sequencer of claim 17, wherein the optical compensator comprises a lens that is movable.

22. 18. The sequencer of claim 17, wherein the input fiber beam source is a dual input beam source that generates a first beam spanning a first wavelength range and a second beam spanning a second wavelength range different from the first wavelength range.

23. A sequencer, an image forming system, an input fiber beam source including one or more light emitting diodes; a fiber beam source including one or more input fibers optically connected to the input fiber beam source and configured to provide one or more input beams via the one or more input fibers; a collimator at the input end positioned to receive an input beam from the fiber beam source and produce a substantially parallel beam; a microlens array assembly including two cylindrical microlens arrays positioned to receive the substantially parallel beam from the collimator and format the substantially parallel beam into a shaped propagating beam having a substantially rectangular cross-section in the far field; a focusing objective stage having an objective pupil for receiving the shaped propagation beam, the focusing objective stage positioned to convert the shaped propagation beam into a sampling beam of substantially rectangular cross-section at or near a focal plane of the focusing objective stage for optically probing a sample in the flow cell; an optical compensator including a movable lens configured to move between a first position for controlling the sampling focal plane of the focusing objective stage at the first sampling focal plane and a second position for controlling the sampling focal plane of the focusing objective stage at the second sampling focal plane; a valve for controlling the flow of fluid through the fluid line from the reagent cartridge; Equipped with a first sampling focal plane corresponding to the bottom surface of the flow cell; A second sampling focal plane corresponds to the top surface of the flow cell.

24. 24. The sequencer of claim 23, wherein the input fiber beam source is a dual input beam source that generates a first beam spanning a first wavelength range and a second beam spanning a second wavelength range different from the first wavelength range.

Images