Auto-focus function in optical sample analysis

Abstract

The method includes: directing a first autofocus light toward a sensor using an objective lens and a first reflective surface, where the first autofocus light is reflected from a first surface of a substrate; preventing a second autofocus light from reaching the sensor, where the second autofocus light is reflected from a second surface of the substrate; and directing an emission light toward the sensor using the objective lens and a second reflective surface, where the emission light originates from a sample of the substrate.

Description

Technical Field

[0001] (Cross - Reference to Related Applications) This application claims priority to U.S. Provisional Patent Application No. 62 / 959,681, filed on January 10, 2020, entitled "AUTOFOCUS FUNCTIONALITY IN OPTICAL SAMPLE ANALYSIS". This application also claims priority to U.S. Provisional Patent Application No. 62 / 956,083, filed on December 31, 2019, entitled "AUTOFOCUS FUNCTIONALITY IN OPTICAL SAMPLE ANALYSIS". The content of both of the above applications is incorporated herein by reference.

Background Art

[0002] Samples of different materials can be analyzed using one or more types of optical systems. The optical system may include an autofocus function to assist in adjusting the optical components in order to improve the quality of the measurement and the sample analysis thereby obtained. The autofocus system is typically integrated with the optical system but operates, in a sense, independently of the function of the optical system. For example, the autofocus components may use a dedicated light source, one or more optical components (e.g., lenses), and / or a photodetector. That is, these components can be used only for the purpose of autofocus. Having dedicated parts for the autofocus system can add to the manufacturing cost of the optical system. As another example, a large number of mounted components increases the likelihood of requiring repairs.

Summary of the Invention

[0003] In a first aspect, the method is to direct a first autofocus light towards a sensor using an objective lens and a first reflective surface, wherein the first autofocus light is reflected from a first surface of the substrate, and to prevent a second autofocus light from reaching the sensor, wherein the second autofocus light is reflected from a second surface of the substrate, and to direct emitted light towards the sensor using the objective lens and a second reflective surface, wherein the emitted light is generated from a sample on the substrate.

[0004] The implementation form can include any or all of the following features. The method further includes directing a first autofocus light towards a second reflective surface, the second reflective surface being transmissive to the first autofocus light, and the first reflective surface being positioned behind the second reflective surface with respect to the traveling direction of the first autofocus light. The method further includes directing a second autofocus light towards the second reflective surface, the second reflective surface being transmissive to the second autofocus light, and the first reflective surface being transmissive to the second autofocus light so as to prevent the second autofocus light from reaching the sensor. The first reflective surface is positioned on a first reflective component, the second reflective surface is positioned on a second reflective component, the first reflective component is separated from the second reflective component, and the method further includes orienting the first reflective component independently of the orientation of the second reflective component. Orienting the first reflective component includes guiding the first autofocus light on the sensor independently of the position of the emitted light on the sensor. The method further includes using a lateral displacement prism to form a left autofocus light and a right autofocus light that diverge from each other at a predetermined angle, the first autofocus light including a first left autofocus light from the reflection of the left autofocus light from the first surface of the substrate, the first autofocus light further including a first right autofocus light from the reflection of the right autofocus light from the first surface of the substrate, the second autofocus light including a second left autofocus light from the reflection of the left autofocus light from the second surface of the substrate, the second autofocus light further including a second right autofocus light from the reflection of the right autofocus light from the second surface of the substrate, directing the first autofocus light towards the sensor includes using an objective lens and the first reflective surface to direct the first left autofocus light and the first right autofocus light towards the sensor, and preventing the second autofocus light from reaching the sensor includes preventing the second left autofocus light and the second right autofocus light from reaching the sensor.The substrate further includes a third surface. The left autofocus light forms third left autofocus light upon reflection from the third surface, and the right autofocus light forms third right autofocus light upon reflection from the third surface. The method further includes using the objective lens and the first reflective surface to direct the third left autofocus light and the third right autofocus light towards the sensor. The method further includes adjusting the distance between the objective lens and the substrate based on the first autofocus light.

[0005] In a second aspect, the system includes a substrate for holding a sample for analysis, a sensor, an objective lens, a first reflective surface for directing first autofocus light towards the sensor, where the first autofocus light is reflected from a first surface of the substrate and transmitted by the objective lens, a second reflective surface for directing emitted light towards the sensor, where the emitted light is generated from the sample and transmitted by the objective lens, and a structure for preventing second autofocus light from reaching the sensor, where the second autofocus light is reflected from a second surface of the substrate and transmitted by the objective lens.

[0006] The implementation form can include any or all of the following features. The first reflective surface is positioned behind the second reflective surface with respect to the traveling direction of the first autofocus light, and the second reflective surface is transparent to the first autofocus light. The first reflective surface is positioned on the first reflective component, the second reflective surface is positioned on the second reflective component, and the first reflective component is separated from the second reflective component. The second reflective surface is positioned on the front surface of the reflective component with respect to the traveling direction of the first autofocus light, the first reflective surface covers the first part of the back surface of the reflective component with respect to the traveling direction of the first autofocus light, and the structure covers the second part of the back surface of the reflective component. The system further includes a lateral displacement prism, the lateral displacement prism forms left autofocus light and right autofocus light that diverge from each other at a predetermined angle, the first autofocus light includes the first left autofocus light from the reflection of the left autofocus light from the first surface of the substrate, the first autofocus light further includes the first right autofocus light from the reflection of the right autofocus light from the first surface of the substrate, the second autofocus light includes the second left autofocus light from the reflection of the left autofocus light from the second surface of the substrate, and the second autofocus light further includes the second right autofocus light from the reflection of the right autofocus light from the second surface of the substrate. The lateral displacement prism includes exit surfaces having a non-zero angle with respect to each other. The lateral displacement prism includes a first surface, a second surface parallel to the first surface, a third surface, a fourth surface, and a fifth surface having a boundary with the fourth surface, wherein each of the fourth surface and the fifth surface forms a common angle with the third surface, and a partially reflective layer extending between the fifth surface, the third surface, the boundary between the fourth surface and the fifth surface. The first surface has a boundary with the third surface, the fourth surface, and the fifth surface, and the second surface has a boundary with the third surface, the fourth surface, and the fifth surface. The third surface is an entrance surface, the fourth surface is an exit surface of the left autofocus light, and the fifth surface is an exit surface of the right autofocus light.The lateral displacement prism includes a first prism having a first wedge profile, the first wedge profile including a first side forming a non-zero angle with respect to a first exit side; a second prism having a second wedge profile, the second wedge profile including a second side forming a non-zero angle with respect to a second exit side; and a third prism having a parallelogram profile, the parallelogram profile including a third side parallel to a fourth side and a fifth side parallel to a sixth side, wherein the third side of the parallelogram profile is part of an entrance surface of the lateral displacement prism. Each of the first side of the first prism and the second side of the second prism faces toward the fourth side of the third prism. The system is configured for the analysis of nucleic acid materials on a substrate.

[0007] In a third aspect, the method includes forming left autofocus light and right autofocus light that diverge from each other at a predetermined angle; directing the left autofocus light and the right autofocus light through an objective lens toward a first surface of a substrate; and after reflection from the first surface, directing at least a first portion of the left autofocus light and at least a first portion of the right autofocus light toward a sensor, wherein a predefined separation between the first portion of the left autofocus light and the first portion of the right autofocus light at the sensor indicates that the substrate is at the focus of the objective lens.

[0008] The implementation form can include any or all of the following features. The substrate further includes a second surface. The reflection of the left autofocus light from the first surface forms the first left autofocus light, and the reflection of the left autofocus light from the second surface forms the second left autofocus light. In the sensor, the first portion of the left autofocus light includes the first left autofocus light and the second left autofocus light. The reflection of the right autofocus light from the first substrate forms the first right autofocus light, and the reflection of the right autofocus light from the second surface forms the second right autofocus light. In the sensor, the first portion of the right autofocus light includes the first right autofocus light and the second right autofocus light. The first predefined separation between the first left autofocus light and the first right autofocus light in the sensor indicates that the first surface of the substrate is at the focus of the objective lens. The second predefined separation between the second left autofocus light and the second right autofocus light in the sensor indicates that the second surface of the substrate is at the focus of the objective lens. Directing the first portion of the left autofocus light and the first portion of the right autofocus light towards the sensor includes using the first reflective surface to direct the first portion of the left autofocus light and the first portion of the right autofocus light towards the sensor. The method is to direct the emitted light towards the sensor using the objective lens and the second reflective surface, and further includes directing the emitted light generated from the sample on the substrate. The method further includes directing the first portion of the left autofocus light and the first portion of the right autofocus light towards the second reflective surface, where the second reflective surface is transmissive to the first portion of the left autofocus light and the first portion of the right autofocus light, and the first reflective surface is positioned behind the second reflective surface with respect to the traveling direction of the first portion of the left autofocus light and the first portion of the right autofocus light.The substrate further includes a second surface, a second portion of the left autofocus light is formed upon reflection of the left autofocus light from the second surface, a second portion of the right autofocus light is formed upon reflection of the right autofocus light from the second surface, the method further includes directing the second portion of the left autofocus light and the second portion of the right autofocus light toward a second reflective surface, the second reflective surface is also transparent to the second portion of the left autofocus light and the second portion of the right autofocus light, and the first reflective surface is transparent to the second portion of the left autofocus light and the second portion of the right autofocus light to prevent the second portion of the left autofocus light and the second portion of the right autofocus light from reaching the sensor. The first reflective surface is positioned on a first reflective component, the second reflective surface is positioned on a second reflective component, the first reflective component is separated from the second reflective component, and the method further includes orienting the first reflective component independently of the orientation of the second reflective component. Orienting the first reflective component causes the induction of a first portion of the left autofocus light and a first portion of the right autofocus light on the sensor independent of the position of the emitted light on the sensor. The method further includes adjusting the distance between the objective lens and the substrate based on the first portion of the left autofocus light and the first portion of the right autofocus light.

[0009] In a fourth aspect, the system comprises a beam splitter for forming left and right autofocus light diverging from each other at a predetermined angle, an objective lens for transmitting the left and right autofocus light toward a first surface of a substrate, and a sensor for receiving at least a first portion of the left autofocus light and at least a first portion of the right autofocus light after reflection from the first surface, wherein a predefined separation between the first portion of the left autofocus light and the first portion of the right autofocus light at the sensor indicates that the substrate is at the focus of the objective lens.

[0010] The implementation form can include any or all of the following features. The beam splitter is part of a lateral displacement prism. The lateral displacement prism includes exit surfaces having a non-zero angle with respect to each other. The lateral displacement prism includes a first surface, a second surface parallel to the first surface, a third surface, a fourth surface, and a fifth surface having a boundary with the fourth surface, wherein each of the fourth surface and the fifth surface forms a common angle with the third surface, and a partially reflective layer extending between the fifth surface, the third surface, and the boundary between the fourth surface and the fifth surface. The first surface has a boundary with the third surface, the fourth surface, and the fifth surface, and the second surface has a boundary with the third surface, the fourth surface, and the fifth surface. The third surface is an entrance surface, the fourth surface is an exit surface for the left autofocus light, and the fifth surface is an exit surface for the right autofocus light. The lateral displacement prism includes a first prism having a first wedge profile, the first wedge profile including a first side forming a non-zero angle with respect to the first exit side, a second prism having a second wedge profile, the second wedge profile including a second side forming a non-zero angle with respect to the second exit side, and a third prism having a parallelogram profile, the parallelogram profile including a third side parallel to a fourth side and a fifth side parallel to a sixth side, and the third side of the parallelogram profile being part of the entrance surface of the lateral displacement prism, and each of the first side of the first prism and the second side of the second prism faces toward the fourth side of the third prism. The beam splitter includes a first reflective surface on which the initial autofocus light is incident, a partially reflective layer on which the initial autofocus light is incident after being reflected from the first reflective surface, the partially reflective layer forming the left autofocus light and the right autofocus light, and a second reflective surface on which one of the left autofocus light or the right autofocus light is incident after being formed on the partially reflective layer. The system further includes a first reflective surface for directing a first portion of the left autofocus light and a first portion of the right autofocus light toward the sensor.The system further comprises a second reflective surface for directing the emitted light towards the sensor, the emitted light being generated from the sample at the substrate and transmitted by the objective lens. The substrate further includes a second surface, a second portion of the left autofocus light being formed upon reflection of the left autofocus light from the second surface of the substrate, and a second portion of the right autofocus light being formed upon reflection of the right autofocus light from the second surface of the substrate, the system further including a structure for preventing the second portion of the left autofocus light and the second portion of the right autofocus light from reaching the sensor. The first reflective surface is positioned behind the second reflective surface with respect to the traveling directions of the first portion of the left autofocus light, the second portion of the left autofocus light, the first portion of the right autofocus light, and the second portion of the right autofocus light, and the second reflective surface is transmissive with respect to the first portion of the left autofocus light, the second portion of the left autofocus light, the first portion of the right autofocus light, and the second portion of the right autofocus light. The first reflective surface is positioned on the first reflective component, the second reflective surface is positioned on the second reflective component, and the first reflective component is separated from the second reflective component. The second reflective surface is positioned on the front surface of the second reflective component with respect to the traveling directions of the first portion of the left autofocus light, the second portion of the left autofocus light, the first portion of the right autofocus light, and the second portion of the right autofocus light, the first reflective surface covering a first portion of the back surface of the second reflective component with respect to the traveling directions of the first portion of the left autofocus light, the second portion of the left autofocus light, the first portion of the right autofocus light, and the second portion of the right autofocus light, and the structure covering a second portion of the back surface of the second reflective component. The system is configured for the analysis of nucleic acid materials at the substrate.

[0011] In a fifth aspect, the autofocus assembly is a prism having a first surface, a second surface parallel to the first surface, a third surface, a fourth surface, and a fifth surface having a boundary with the fourth surface, wherein each of the fourth surface and the fifth surface forms a common angle with the third surface, and a partially reflective layer extending between the third surface and the boundary between the fourth surface and the fifth surface; a prism; and a light source for directing light in the prism, wherein the prism forms a first autofocus light and a second autofocus light from the light, and the first autofocus light and the second autofocus light diverge from each other at a predetermined angle.

[0012] The implementation form can include any or all of the following features. The fourth surface and the fifth surface form an exit surface having a non-zero angle with respect to each other. The first surface has a boundary with the third surface, the fourth surface, and the fifth surface, and the second surface has a boundary with the third surface, the fourth surface, and the fifth surface. The third surface is an entrance surface. The prism includes a first prism having a first wedge outer shape, the first prism forming the fourth surface, and the first wedge outer shape including a first side forming a non-zero angle with respect to the fourth surface; a second prism having a second wedge outer shape, the second prism forming the fifth surface, and the second wedge outer shape including a second side forming a non-zero angle with respect to the fifth surface; and a third prism having a parallelogram outer shape, the parallelogram outer shape including a third side parallel to a fourth side, the third side defining the third surface, and a fifth side parallel to a sixth side, wherein each of the first side of the first prism and the second side of the second prism faces toward the fourth side of the third prism.

[0013] It should be understood that all combinations of the foregoing concepts and additional concepts, to be considered in more detail below, are intended to be part of the subject matter of the invention disclosed herein (provided such concepts are not mutually inconsistent). Specifically, all combinations of the claimed subject matter appearing at the end of this disclosure are intended to be part of the subject matter of the invention disclosed herein.

Brief Description of the Drawings

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BRIEF DESCRIPTION OF THE DRAWINGS

[0058] The present disclosure describes systems, techniques, and / or manufactured articles related to various improvements related to autofocus functionality. When a focus tracking system or other autofocus system is used, stray light reflections may appear in the detector, and stray light reflections arising from multiple optical interfaces (e.g., layers or other surfaces) can interfere with the focus tracking algorithm. In some implementations, additional beam guiding optics can be used to direct reflections related to autofocus towards the image sensor and prevent unrelated reflections from reaching the sensor. Such an approach can provide that the target focus tracking reflection can be selectively directed to a predefined area of the detector that is free from interference from stray reflections. This can enhance the focus tracking ability of the system. One or more implementations described herein can facilitate integrating a focus tracking system, such as an autofocus module, into an optical system for imaging a sample. For example, the optical system can be configured to collect fluorescence generated by the sample.

[0059] In some implementations, the optical system can include a filter having a coating that reflects emitted light towards the sensor, and the filter transmits related and unrelated reflections. The beam guiding optics can be positioned behind the filter and can include a reflective material (e.g., a mirror) positioned within the path of the related reflection and outside the path of the unrelated reflection. Absorbent material can be placed in the path of the unrelated reflection. The reflective material can be movable to direct related reflections towards the sensor (e.g., to direct them away from the emitted light). In another implementation, the reflective material can include a coating on the back surface of the filter, and a high transmittance coating can be used to allow unrelated reflections to exit the filter.

[0060] In some implementations, the beam of autofocus light can be formed to diverge from each other after being split. For example, a diverging autofocus beam can be provided using an angled exit surface in a beam splitting component, such as using a custom prism or a commercially available prism with an additional wedge prism. As another example, a diverging autofocus beam can be provided using a mirror arrangement, a 50% reflective filter, and a glass plate that forms an angled exit surface. Each of the diverging AFM beams forms a respective spot on a sensor offset on the opposite side of the center of the field of view. The angled exit surface of the beam splitting component is configured to induce a predetermined distance between spots reflected from the same surface such that a measure of the difference between the measured distance between spots and the predetermined distance is used to calculate the z - separation between the objective lens and the flow cell. The predetermined distance corresponds to the best focus that is more easily measurable without affecting the alignment of the emission optics.

[0061] The embodiments described herein refer to the analysis of one or more samples. As used herein, the term "sample" includes various items of interest for which an imaging session is conducted in which an optical signal from the sample is observed. In certain embodiments, the sample may include a biological substance of interest and / or a chemical substance of interest. Optionally, the sample may include an optical substrate or a support structure that supports the biological or chemical substance. Thus, the sample may or may not include an optical substrate or a support structure. As used herein, the term "biological substance" or "chemical substance" may include various biological or chemical substances suitable for imaging or inspection with the optical systems described herein. For example, the biological or chemical substance may include one or more biomolecules such as nucleosides, nucleic acids, polynucleotides, oligonucleotides, proteins, enzymes, polypeptides, antibodies, antigens, ligands, receptors, polysaccharides, carbohydrates, polyphosphoric acids, nanopores, organelles, lipid bilayers, cells, tissues, organisms, and biologically active chemical compounds such as analogs or mimetics of the foregoing species. Other chemical substances include labels that can be used for identification, examples of which include fluorescent labels. The analysis of the sample can include, but is not limited to, gene sequencing (e.g., determining the structure of genetic material), genotyping (e.g., determining differences in an individual's genetic makeup), gene expression (e.g., synthesizing gene products using genetic information), proteomics (e.g., large-scale studies of proteins), or combinations thereof.

[0062] Examples herein refer to a substrate. The substrate can refer to any material that provides at least a substantially rigid structure, or a structure that holds its shape rather than taking the shape of a container in which it is placed in contact. The material can have a surface to which another material can be attached, including, for example, a smooth support (such as the surfaces of metals, glass, plastics, silicon, and ceramics), as well as textured and / or porous materials. Possible substrates include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylic, polystyrene, and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethane, Teflon™, etc.), polysaccharides, nylon or nitrocellulose, resins, silica-based materials including silica or silicon and modified silicon, carbon, metals, inorganic glass, plastics, optical fiber bundles, and various other polymers. Generally, the substrate enables optical detection and does not fluoresce in a perceptible manner itself.

[0063] The examples described in this specification refer to a flow cell. The flow cell can be regarded as a substrate that can be used to prepare, contain, or carry one or more samples at at least one stage of an analysis process. The flow cell is made of a material compatible with both the sample material (e.g., genetic material), illumination, and the chemical reactions it is exposed to. The substrate can have one or more channels on which the sample material can be deposited. A substance (e.g., a liquid) can be flowed through the channel where the sample genetic material is present to trigger one or more chemical reactions and / or remove unwanted materials. The flow cell can enable imaging by applying illumination light to the sample in the flow cell channel and facilitating the detection of the fluorescence reaction from the sample. Some implementations of the system can be designed to be used with at least one flow cell, but may not include the flow cell during some stages, such as during shipping or when delivered to the customer. The flow cell can have one or more surfaces configured to contain a sample, such as, but not limited to, a sample of nucleic acid material. In some implementations, the surface is coated with one or more polymers. For example, the polymer can include poly(N-(5-azidoacetamidopentyl)acrylamide-co-acrylamide), which may also be referred to as Pazam.

[0064] The embodiments described herein refer to autofocus light. The autofocus light can be used by an autofocus module within a sample analysis system to facilitate relative adjustment between an optical component (e.g., an objective lens) and a substrate (e.g., holding a sample to be analyzed). The autofocus module can optically measure the distance between two or more objects (e.g., an optical component and a substrate) using the autofocus light. In some implementations, the autofocus module performs triangulation with respect to two or more objects using the autofocus light. For example, a source of autofocus light (e.g., a laser diode) can generate a light beam that impinges on and is reflected from at least one surface of the substrate. A photodetector (e.g., a photosensitive sensor) can align the reflection of the light beam from the at least one surface. The position of the reflection (e.g., a light spot) on the photodetector is an indicator of the distance to the substrate. The autofocus light can have any suitable wavelength considering the type of material in the sample (i.e., so that the autofocus light does not substantially degrade the sample or otherwise change its chemical properties) and / or considering the photodetector (i.e., so that the photodetector can detect the autofocus light). In some implementations, the autofocus light can have one or more wavelengths in the range of about 770 nanometers (nm) to about 880 nm.

[0065] The embodiments described herein refer to emitted light. One or more types of emitted light can be caused to be emitted from a sample as part of performing an analysis regarding one or more characteristics or preparing the sample therefor. In some implementations, the emitted light includes fluorescent light (sometimes referred to as fluorescence) emitted by one or more fluorescent markers or tags in the material of the sample. For example, the emission of fluorescent light can be triggered or otherwise stimulated by subjecting the sample to excitation light, including (but not limited to) directing laser light at the sample.

[0066] The examples described in this specification refer to a surface as being reflective or a reflective surface. The surface can be reflective for at least substantially all wavelengths of light, or can be reflective for only one or more pre-defined wavelengths (e.g., one or more bands of wavelengths). The surface can exhibit specular reflection, which means that an image embodied in the incident light is preserved in at least substantially the reflected light. The reflectivity does not necessarily involve the reflection of all incident light, or all incident light of a pre-defined wavelength. Rather, if the surface reflects some amount (e.g., more than zero) of the reflected light, or light having a pre-defined wavelength, the surface can be considered transmissive. The reflective surface can be formed on any type of substrate, and the surface can include any of a plurality of reflective materials. The reflective surface can be formed by applying one or more layers to the substrate. In some implementations, the reflective surface operates based on thin-film interference including the upper surface of the layer and the upper surface of the substrate.

[0067] The reflective surface can be referred to as a filter within an optical system. For example, the reflective surface can include a dichroic filter. As used herein, the term filter within an optical system is intended to mean a device for selectively permitting or rejecting the passage of radiation in a wavelength-, polarization- or frequency-dependent manner. This term can include interference filters in which multiple layers of dielectric material pass or reflect radiation according to constructive or destructive interference between reflections from the various layers. Interference filters are also sometimes referred to in the art as dichroic filters or dielectric filters. This term can include absorption filters that prevent the passage of radiation having a selectively wavelength or wavelength range by absorption. Absorption filters include, for example, colored glass or liquids.

[0068] The embodiments described herein refer to a surface as being transmissive or having a transmissive surface. The surface can be transmissive for at least substantially all wavelengths of light, or can be transmissive for only one or more pre-defined wavelengths (e.g., to one or more bands of wavelengths). Transmissivity does not necessarily involve the transmission of all incident light, or all incident light of pre-defined wavelengths. Rather, a surface can be considered transmissive if it transmits incident light, or light having a pre-defined wavelength, to some extent (e.g., more than zero). A transmissive surface can be formed on any type of substrate, and the surface can include any of a plurality of transmissive materials. A transmissive surface can be formed by applying one or more anti-reflection materials to the substrate. Examples of suitable anti-reflection materials that can be used include, but are not limited to, any transmissive material having a refractive index equal to the square root of the refractive index of the substrate and the surrounding medium. Some examples of anti-reflection materials include magnesium fluoride (MgF2), fluoropolymers, mesoporous silica nanoparticles, alternating stacks of silica and high refractive index materials, or other anti-reflection materials that exhibit desirable anti-reflection characteristics within the desired emission band / wavelength being used.

[0069] The embodiments described herein refer to one or more structures that prevent the transmission of light to a pre-defined component or in a pre-defined direction (e.g., autofocus light). In some implementations, the structure can prevent transmission to a pre-defined component or in a pre-defined direction by absorbing the light. For example, the structure can include an absorptive material for capturing at least substantially all of the energy of the light impinging on the structure. In some implementations, the structure can prevent transmission to a pre-defined component or in a pre-defined direction by not reflecting light towards the pre-defined component or in the pre-defined direction. For example, the structure can include a material that is transmissive to wavelengths for which it is desired that the structure be prevented from reaching a pre-defined component or being transmitted in a pre-defined direction.

[0070] The embodiments described in this specification refer to a portion of light using modifiers such as "left" or "right". The terms left and right are used in this specification for illustrative purposes only and do not necessarily reflect the spatial arrangement of any component or the relative position of any portion of light. In some implementations, the alternatives to the left and right modifiers can be the first and second terms, respectively. For example, the left autofocus light and the right autofocus light can, in some situations, be referred to instead as the first autofocus light and the second autofocus light, respectively.

[0071] The embodiments described in this specification refer to a portion of light using modifiers such as "upper" or "bottom". The terms upper and lower are used in this specification for illustrative purposes only and do not necessarily reflect the spatial arrangement of any component. In some implementations, the alternatives to the upper and bottom modifiers can be the first and second terms, respectively. For example, the upper surface and the bottom surface can, in some situations, be referred to as the first surface and the second surface, respectively.

[0072] The embodiments described in this specification refer to a component as being "behind" or "in front of" another component, or as being "in front of" or "behind" another component. The terms behind, in front of, and behind are used in this specification for illustrative purposes only and do not necessarily reflect only one of the multiple spatial arrangements of any component or only one of the possible spatial arrangements. In some implementations, the terms behind, in front of, and behind are used in a relative sense with respect to one or more specified reference items. For example, a first item can be characterized as being behind a second item with respect to the direction of light propagation, which means that the light reaches the second item before reaching the first item. As another example, a first item can be characterized as being in front of a second item with respect to the direction of light propagation, which means that the light reaches the first item before reaching the second item. As another example, the surface of a component can be referred to as the front surface with respect to the direction of light propagation, which means that the light reaches the front surface before reaching other aspects of the component. As another example, the surface of a component can be referred to as the rear surface with respect to the direction of light propagation, which means that the light reaches other aspects of the component before reaching the front surface.

[0073] The embodiments described herein refer to detectors of light. In some implementations, the detector of light can be sensitive to one or more forms of electromagnetic radiation. The detector can include a device or apparatus having several elements that convert the energy of the incident photons into an electrical response. Such elements can be referred to as sensors, or an array of elements can be collectively referred to as a sensor. The sensor can include a charge coupled device (CCD), which is a photosensitive charge collection portion that accumulates charge in response to incident photons. The sensor can include a complementary metal oxide semiconductor (CMOS) detector array, a photodiode array, an avalanche photodiode (APD) detector array, and / or a Geiger mode photon counter detector array. The elements of the sensor can have any of a variety of arrangements. For example, a rectangular sensor array can have elements in a two-dimensional orthogonal arrangement where a first dimension, referred to as the “horizontal” dimension, is longer than a second dimension, referred to as the “vertical” dimension. A square sensor array can have elements in a two-dimensional orthogonal arrangement where the first and second dimensions of the arrangement are of the same length. The sensor can detect light and generate corresponding outputs from one or more pixels. In some implementations, the separation between two or more portions of light in the sensor can be determined (e.g., as part of an autofocus operation). For example, the separation can be measured using the distance within a pixel or using a suitable linear distance unit.

[0074] The embodiments described herein refer to an objective lens. The objective lens is part of an optical system and can include one or more optical components. As used herein, the term optical component includes, but is not limited to, various elements that affect the propagation of an optical signal. For example, an optical component can be at least one of redirecting, filtering, shaping, magnifying, or focusing an optical signal. Optical signals that can be affected include an optical signal upstream from a sample and an optical signal downstream from the sample. In a fluorescence detection system, upstream components include those that directly direct excitation radiation towards the sample, and downstream components include those that direct emitted radiation away from the sample. Optical components can be, for example, reflectors, dichroic filters, dichroic mirrors, beam splitters, collimators, lenses, filters, wedges, prisms, mirrors, and detectors, among others. Optical components can include bandpass filters, optical wedges, and optical devices similar to those described herein. In some implementations, the optical system can include a projection lens. The term projection lens can include an optical element configured to transfer an image of an object to a detector. For example, a lens can be arranged to transfer an image emitted from the objective lens to a detector array. The objective lens can support depth of field control (DFC). In some implementations, DFC can facilitate selection among different depths of field. For example, DFC controls the distance between the nearest and farthest objects in focus.

[0075] The embodiments described herein refer to components that are in focus of the objective lens. Due to the inherent limitations of physical optical systems (as opposed to an ideal system), there may not be an exact point of focus compared to the components and the objective lens. Rather, there may be a range of best focus applicable to the components and the objective lens, which may also be referred to as the component that is at the best focus of the objective lens. As used herein, being in focus or out of focus (e.g., being at the best focus or not at the best focus) includes the process of adjusting the detection system to obtain desired characteristics for the representation of the detected object. For example, the optical detection system can be adjusted to increase the sharpness, contrast, or modulation transfer function (MTF) of the image of the detected test sample. As a further example, the optical detection system can be adjusted to obtain an image having a desired uniformity, and in certain embodiments, the image can have both the desired uniformity and an MTF that exceeds a defined minimum value. The MTF of the image can vary at different locations of the detected sample. For example, the MTF can be different at two separate locations of the sample, and it can be possible for the image to have one or more other characteristics that are similar or within a desired range at each location.

[0076] The embodiments described herein refer to a beam splitter. A beam splitter means an optical element that passes a first portion of a radiation beam and reflects a second portion of the beam. In some implementations, the beam splitter can be configured to selectively pass radiation within a first wavelength range and reflect radiation within a second, different radiation range. For example, the beam splitter can split autofocus light into two separate (e.g., at least substantially equivalent to each other) light beams. The beam splitter can include a partially reflective layer. The partially reflective layer can include any material having optical properties (e.g., refractive index and / or thickness) such that it reflects a portion of the light and transmits another portion of the light by irregular total internal reflection. In some implementations, the partially reflective layer can have a reflectivity of about 45 - 55%. The reflectivity can be applied to a pre-defined wavelength or wavelength range. For example, the reflectivity can be measured for one or more wavelengths from about 77 nm to about 880 nm. The reflectivity can be applied to one or more angles of incidence. For example, the reflectivity can be applied at one or more angles of incidence from about 45 degrees to about 55 degrees.

[0077] The embodiments herein refer to a prism. A prism is an optical element that is flat and smooth and has surfaces that form an angle with each other, and the prism is transmissive to light of at least one wavelength. Two adjacent surfaces of the prism that form an angle with each other are separated by a boundary. For example, the boundary can be an edge defined by one of the planes of the surface that intersects the plane of the other surface at the boundary. The prism can include one or more optically effective components. In some implementations, the prism includes a partially reflective layer.

[0078] The prism can be referred to as having a predefined outer shape, which means at least a part of the geometric structure of the prism as manifested by at least some of the boundaries of the prism. In some implementations, the outer shape of the prism corresponds to the shape of the prism (i.e., at least some of the shapes of the visible boundaries) when viewed from at least one direction. In some implementations, the prism can have a wedge outer shape. A prism having a wedge outer shape can have a first side of the wedge outer shape that forms a non-zero angle with respect to a second side of the wedge outer shape, and the first side and the second side can share a common boundary or not share a common boundary. In some implementations, the prism can have a parallelogram outer shape. A prism having a parallelogram outer shape can have a first side of the parallelogram outer shape and a second side of the parallelogram outer shape that are parallel to each other, and a third side of the parallelogram outer shape and a fourth side of the parallelogram outer shape that are parallel to each other.

[0079] A prism intended to form each light beam can be referred to as a lateral displacement prism due to the lateral displacement of one or more light beams with respect to at least one other light beam. The lateral displacement prism can include a beam splitter, including but not limited to, partial reflective layers. In some implementations, the prism can be made of any material that is transmissive to one or more wavelengths of light. For example, the prism can be made of one or more of glass (e.g., optical borosilicate crown glass), plastic, or fluorophore. The surface of the prism can be polished to have a predefined flatness and smoothness.

[0080] The embodiments of this specification refer to structured illumination microscopy (SIM). SIM imaging is based on spatially structured light. For example, the structure can consist of, or can include, a pattern of illumination light that helps increase the resolution of the acquired image. In some embodiments, the structure can include a pattern of stripes. The stripes of light can be generated by colliding a light beam onto a diffraction grating (referred to as a diffraction grating for simplicity) such that reflective or transmissive diffraction occurs. The structured light can be collided onto the sample and illuminate the sample according to each stripe that can occur according to some periodicity. For example, an image of the sample can be acquired at different phases of the stripes in the structured light, which may be referred to as respective pattern phases of the image. This can enable various locations on the sample to be exposed to light of a number of illumination light intensities. The pattern of the structured light can be rotated with respect to the sample, and the aforementioned images can be captured by adding to each of the rotation angles.

[0081] Examples of this specification refer to the blue channel of the emitted light (e.g., detected by a blue sensor assembly) and / or the green channel of the emitted light (e.g., detected by a green sensor assembly). The emitted illumination light is identified using wavelength bands, each of which can be classified into respective color channels. For example, the wavelength bands of the emitted illumination can correspond to blue (e.g., 450 nm to 525 nm) and / or green (e.g., 525 nm to 570 nm). In some implementations, the wavelength bands can be defined based on two or more light wavelengths present during simultaneous illumination. For example, if only the colors blue and green are analyzed, the wavelength bands corresponding to blue and green can be defined as wavelength bands different from the aforementioned ranges. For example, the blue wavelength band can be set as emitted light of about 450 nm to 510 nm (e.g., 486 nm to 506 nm). In some cases, the blue wavelength band can have only an upper limit (e.g., about 500 nm to 510 nm, or about 506 nm). Similarly, the green wavelength band can be set as emitted light of about 525 nm to 650 nm (e.g., 584 nm to 637 nm). Although the aforementioned green wavelength band may extend into the colors yellow and red, when analyzing the emitted light expected to be only within the color ranges of blue and green, the upper and / or lower ends of the wavelength band can extend to capture additional emitted light that is emitted above or below the wavelength of that color. In some cases, the green wavelength band can have only a lower limit (e.g., about 550 nm to 600 nm, or about 584 nm).

[0082] FIG. 1 shows an embodiment of a system 100 that can be used for analyzing a sample. System 100 can include or be used in conjunction with one or more other embodiments described elsewhere in this specification. In some implementations, system 100 can include or be used in conjunction with system 4200 of FIG. 42. In some implementations, system 100 can include or be used in conjunction with at least some components of computing device 4300 of FIG. 43. In some implementations, system 100 can include or be used in conjunction with optical system 200 of FIG. 2. In some implementations, system 100 can include or be used in conjunction with optical system 500 of FIG. 5. In some implementations, system 100 can include or be used in conjunction with optical system 800 of FIG. 8A. In some implementations, system 100 can include or be used in conjunction with optical system 820 of FIG. 8B. In some implementations, system 100 can include or be used in conjunction with lateral displacement prism 1000 of FIGS. 10A - 10C. In some implementations, system 100 can include or be used in conjunction with optical system 1100 of FIG. 11. In some implementations, system 100 can include or be used in conjunction with optical system 1200 of FIG. 12. In some implementations, system 100 can include or be used in conjunction with optical system 1300 of FIG. 13. In some implementations, system 100 can include or be used in conjunction with optical system 1400 of FIG. 14. In some implementations, system 100 can include or be used in conjunction with lateral displacement prism 1600 of FIGS. 16A - 16B. In some implementations, system 100 can include or be used in conjunction with beam splitter 1700 of FIG. 17.In some implementations, system 100 can include, or be used in conjunction with, the imaging module 1800 of FIGS. 18 and 19A-19B. In some implementations, system 100 can include, or be used in conjunction with, the SIM assembly 2000 of FIG. 20. In some implementations, system 100 can include, or be used in conjunction with, the imaging module 2100 of FIG. 21. In some implementations, system 100 can include, or be used in conjunction with, the imaging module 2200 of FIG. 22. In some implementations, system 100 can include, or be used in conjunction with, the imaging module 2400 of FIG. 24. In some implementations, system 100 can include, or be used in conjunction with, the optical system 2500 of FIG. 25. In some implementations, system 100 can include, or be used in conjunction with, the optical system 2600 of FIG. 26. In some implementations, system 100 can include, or be used in conjunction with, the reflective component 2700 of FIG. 27. In some implementations, system 100 can include, or be used in conjunction with, the reflective component 2800 of FIG. 28. In some implementations, system 100 can generate the autofocus light 2900 of FIG. 29. In some implementations, system 100 can generate the autofocus light 3000 of FIG. 30. In some implementations, system 100 can generate the autofocus light 3100 of FIGS. 31A-31C. In some implementations, system 100 can include, or be used in conjunction with, the laser engine heat sink 3200 of FIGS. 32A-32C. In some implementations, system 100 can include, or be used in conjunction with, the laser engine heat sink 3300 of FIGS. 33A-33C. In some implementations, system 100 can include, or be used in conjunction with, the SIM assembly 3400 of FIG. 34.In some implementations, system 100 can include or be used with the RIGS 3500 of FIG. 35. In some implementations, system 100 can include or be used with the RIGS 3600 of FIG. 36. In some implementations, system 100 can include or be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, system 100 can include or be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, system 100 can include or be used with the projection lens 3900 of FIG. 39. In some implementations, system 100 can include or be used with the projection lens 4000 of FIG. 40. In some implementations, system 100 can generate the field of view 4100 of FIG. 41.

[0083] System 100 can be used to analyze one or more types of sample materials and can be referred to as a sample analysis system. In some implementations, system 100 can be configured for the analysis of nucleic acid materials on a substrate. System 100 includes an autofocus module 102 and a fluorescence collection optical system 104. The autofocus module 102 can perform one or more autofocus functions with respect to imaging performed using the fluorescence collection optical system 104. In some implementations, the fluorescence collection optical system 104 collects fluorescence (sometimes referred to as emitted light) generated in a sample for the purpose of performing the same analysis. For example, the autofocus module 102 can automatically determine the best focus applied by the fluorescence collection optical system 104 to the sample being analyzed, and in response, the fluorescence collection optical system 104 can apply the best focus.

[0084] The autofocus module 102 includes one or more autofocus components 106. In some implementations, the autofocus component 106 includes a source of autofocus light (e.g., a laser diode). In some implementations, the autofocus component 106 includes a beam splitter (e.g., as part of a lateral displacement prism). In some implementations, the autofocus component 106 includes an aspherical lens (e.g., for collimating light from the light source). One or more other components used by the autofocus module 102 can be shared with, for example, the fluorescence collection optical system 104 as described below.

[0085] The fluorescence collection optical system 104 includes one or more fluorescence components 108. The fluorescence component 108 is involved in the collection of fluorescence in one or more ways. In some implementations, the fluorescence component 108 can trigger the emission of fluorescence. For example, the fluorescence component 108 can include one or more excitation lasers that generate excitation light of a wavelength and energy that activates one or more fluorescent tags in the sample material, and the activation causes the fluorescent tags to emit fluorescent light. In some implementations, the fluorescence component 108 can control the sample for imaging and / or during imaging. For example, the fluorescence component 108 can condition the sample (e.g., by heat treatment and / or by using chemicals) for analysis and / or can position the substrate that holds the sample for imaging. In some implementations, the fluorescence component 108 can analyze the fluorescence collected from the sample. For example, the collected fluorescence can be analyzed to identify the fluorescent tags of the sample, thereby determining one or more characteristics of the sample.

[0086] System 100 can include one or more shared components 110. The shared components 110 can be used by the autofocus module 102, or by the fluorescence collection optical system 104, or by both the autofocus module 102 and the fluorescence collection optical system 104. The use can be simultaneous or can occur at different times. For example, the autofocus module 102 can use the shared components 110 during an autofocus process that is performed prior to an analysis process (e.g., involving imaging of a sample) performed by the fluorescence collection optical system 104.

[0087] The shared components 110 can include one or more objective lenses 112. For example, the objective lens 112 can be used to direct autofocus light on a substrate and to transmit the reflected autofocus light from the substrate for performing an autofocus procedure. For example, the objective lens 112 can be used to direct excitation light on a sample and to transmit the emitted fluorescence from the sample for collection.

[0088] The shared components 110 can include one or more reflective / transmissive components 114. The reflective / transmissive components 114 can include one or more components that are reflective (e.g., a mirror), and / or transmissive (e.g., a filter), and / or both reflective and transmissive (e.g., a partially reflective layer), and / or refractive components (e.g., a lens). In some implementations, the reflective / transmissive components 114 can be used to direct one or more types of light from one or more other types of light. For example, the reflective / transmissive components 114 can include at least one filter 116. Such direction by the reflective / transmissive components 114 can serve to distinguish currently relevant light from currently irrelevant light, thereby improving the detection of autofocus light by the autofocus module 102.

[0089] The shared component 110 can include one or more detectors 118. The detector 118 can be used to align the autofocus light reflected from the sample for the purpose of the autofocus process. The detector 118 can be used to align the emitted light (e.g., fluorescence) of the analysis process. The detector 118 can include one or more sensors 120. For example, the sensor 120 includes photosensitive elements arranged in a rectangular array.

[0090] FIG. 2 shows an embodiment of the optical system 200. The optical system 200 can include, or be used in conjunction with, one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 200 can include, or be used in conjunction with, the optical system 500 of FIG. 5. In some implementations, the optical system 200 can be included within the system 100 of FIG. 1. In some implementations, the optical system 200 can include, or be used in conjunction with, the optical system 800 of FIG. 8A. In some implementations, the optical system 200 can include, or be used in conjunction with, the optical system 820 of FIG. 8B. In some implementations, the optical system 200 can include, or be used in conjunction with, the lateral displacement prism 1000 of FIGS. 10A - 10C. In some implementations, the optical system 200 can include, or be used in conjunction with, the optical system 1100 of FIG. 11. In some implementations, the optical system 200 can include, or be used in conjunction with, the optical system 1200 of FIG. 12. In some implementations, the optical system 200 can include, or be used in conjunction with, the optical system 1300 of FIG. 13. In some implementations, the optical system 200 can include, or be used in conjunction with, the optical system 1400 of FIG. 14. In some implementations, the optical system 200 can include, or be used in conjunction with, the lateral displacement prism 1600 of FIGS. 16A - 16B. In some implementations, the optical system 200 can include, or be used in conjunction with, the beam splitter 1700 of FIG. 17. In some implementations, the optical system 200 can include, or be used in conjunction with, the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the optical system 200 can include, or be used in conjunction with, the SIM assembly 2000 of FIG. 20.In some implementations, the optical system 200 can include, or be used with, the imaging module 2100 of FIG. 21. In some implementations, the optical system 200 can include, or be used with, the imaging module 2200 of FIG. 22. In some implementations, the optical system 200 can include, or be used with, the imaging module 2400 of FIG. 24. In some implementations, the optical system 200 can include, or be used with, the optical system 2500 of FIG. 25. In some implementations, the optical system 200 can include, or be used with, the optical system 2600 of FIG. 26. In some implementations, the optical system 200 can include, or be used with, the reflective component 2700 of FIG. 27. In some implementations, the optical system 200 can include, or be used with, the reflective component 2800 of FIG. 28. In some implementations, the optical system 200 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 200 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 200 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the optical system 200 can include, or be used with, the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the optical system 200 can include, or be used with, the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the optical system 200 can include, or be used with, the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 200 can include, or be used with, the RIGS 3500 of FIG. 35. In some implementations, the optical system 200 can include, or be used with, the RIGS 3600 of FIG. 36.In some implementations, the optical system 200 can include, or be used in conjunction with, the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the optical system 200 can include, or be used in conjunction with, the piezoelectric phase shifter 3800 of FIG. 3E. In some implementations, the optical system 200 can include, or be used in conjunction with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 200 can include, or be used in conjunction with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 200 can generate the field of view 4100 of FIG. 41.

[0091] The optical system 200 includes a substrate 202. The substrate can be used to hold one or more samples to be analyzed. In some implementations, the sample on the substrate 202 can include a nucleic acid material. For example, the substrate 202 can include a flow cell for imaging a nucleic acid material.

[0092] The optical system 200 includes an objective lens 204. The objective lens 204 can be a component immediately upstream of the substrate 202. For example, the objective lens 204 can be used to direct autofocus light at the substrate 202 and transmit the reflected autofocus light from the substrate 202 to perform an autofocus procedure. For example, the objective lens 204 can be used to direct excitation light at a sample on the substrate 202 and transmit the emitted fluorescence from the sample for collection.

[0093] The optical system 200 includes a filter 206. The filter 206 can be a component immediately upstream of the objective lens 204. The filter 206 can be a dichroic filter. The filter 206 can allow one or more types of light to enter the beam. For example, excitation light from an excitation light source (not shown) can be added through the filter 206 and thereby transmitted toward the substrate 202.

[0094] The optical system 200 includes a filter 208. The filter 208 can be a component directly upstream of the filter 206. The filter 206 can be a dichroic filter. In some implementations, the filter 208 can reflect the autofocus light reflected from the substrate 202 and the emission light generated in the sample, thereby facilitating the transmission of the autofocus light and the emission light to further aspects of the optical system 200. The filter 208 can allow one or more types of light to enter the stream. For example, autofocus light can be added through the filter 208 and thereby transmitted towards the substrate 202.

[0095] The optical system 200 includes a structure 210. The structure 210 can be a component directly upstream of the filter 208. Since it is transmitted to a further aspect of the system 100, the structure 210 can function to block one or more beams arriving from the filter 208. In some implementations, the structure 210 can block one or more aspects of the autofocus light reflected from the substrate 202. For example, the structure 210 can block the autofocus light reflected from the upper surface of the flow cell.

[0096] The optical system 200 includes a filter 212. The filter 212 can be a component directly upstream of the structure 210. The filter 212 can be a dichroic filter. In some implementations, the filter 212 can transmit the autofocus light reflected by the substrate 202 and the emission light generated by the sample, thereby facilitating the transmission of the autofocus light and the emission light to further aspects of the optical system 200. The filter 212 can split the emission light from the substrate 202 between two or more paths. In some implementations, each path can be associated with a respective color channel. For example, a component upstream of the filter 212 can be associated with one color channel (e.g., a blue or green channel), and other components (not shown) can be associated with another color channel.

[0097] The optical system 200 includes at least one tube lens 214. The tube lens 214 can be a component directly upstream of the filter 212. In some implementations, the tube lens 214 can serve to focus the incident light in preparation for its detection. For example, the tube lens 214 can focus the autofocus light for detection as part of an autofocus process. As another example, the tube lens 214 can focus the emission light for detection as part of an analysis process.

[0098] The optical system 200 includes a filter 216. The filter 216 can be a component directly upstream of the tube lens 214. The filter 216 can be a dichroic filter. The filter 216 can facilitate the guiding of one or more types of light, either alone or in conjunction with at least one other component. In some implementations, the filter 216 can reflect the emitted light and transmit the autofocus light. For example, the filter 216 can have an antireflection coating that prevents reflection of the autofocus light (i.e., facilitates transmission of the autofocus light) and reflects the emitted light. In other implementations, the filter 216 can be configured to prevent reflection of the emitted light (i.e., facilitate transmission) and reflect the autofocus light.

[0099] The optical system 200 includes a filter 218. The filter 218 can be a component directly upstream of the filter 216. The filter 218 can be a dichroic filter. In some implementations, the filter 218 can adjust the light at one or more points for detection preparation. For example, the filter 218 can provide bandpass filtering based on the wavelengths of the reflected autofocus light and the emitted light to eliminate noise.

[0100] The optical system 200 includes a sensor 220. The sensor 220 can be a component directly upstream of the filter 218. The sensor 220 can detect the autofocus light reflected during the autofocus procedure and / or detect the emitted light during the analysis procedure. For example, the sensor 220 includes a rectangular array of photosensitive elements that can detect the respective positions of one or more portions of the light incident on the sensor 220.

[0101] The optical system 200 includes one or more sources of autofocus light (not shown). The connector 222 can represent the point of entry into the optical system 200 for the laser light that functions as autofocus light. In some implementations, the laser light can be provided via an optical fiber cable by a superluminescent diode that provides autofocus light based on superluminescence (e.g., spontaneously emitted light amplified by stimulated emission). For example, the autofocus light can be collimated by passing through an aspherical lens.

[0102] The initial autofocus light can be split (or laterally displaced) into two or more portions of the autofocus light. The optical system 200 includes a lateral displacement prism 224. The lateral displacement prism 224 can be positioned proximate to the filter 208. For example, the lateral displacement prism 224 is positioned on the side of the filter 208 opposite the side that reflects the autofocus light and the emitted light generated at the sample. The side portion of the filter 208 facing the lateral displacement prism 224 can be transmissive to the autofocus light from the lateral displacement prism 224 in order to enable transmission of the autofocus light toward the substrate 202. The lateral displacement prism 224 can form respective portions that diverge the autofocus light from each other, as described below for example.

[0103] The optical system 200 includes one or more reflective components 226. The reflective component 226 can include one or more reflective surfaces and can be positioned behind the filter 216 in the direction of travel of the light arriving from the tube lens 214. In some implementations, the reflective component 226 reflects the light transmitted through the filter 216, and the reflection directs the light towards the sensor 220. For example, the reflective component 226 can reflect a portion (but not all) of the autofocus light reflected at the substrate 202. The reflective component 226 can have optical properties based on the type of autofocus light used. In some implementations, the reflective component 226 is reflective at least in part in the near-infrared wavelength range (e.g., any reflection from about 750 nm to about 1400 nm).

[0104] The optical system 200 includes one or more structures 228. The structure 228 can be positioned behind the filter 216 in the direction of travel of the light arriving from the tube lens 214. In some implementations, the structure 228 absorbs the light transmitted through the filter 216, and the absorption prevents the light from reaching the sensor 220 or another region of the optical system 200. For example, the structure 228 can absorb some (but not all) of the autofocus light reflected at the substrate 202.

[0105] In the operation of the optical system 200, the autofocus light 230A and the autofocus light 230B can be formed by the lateral displacement prism 224. The autofocus light 230A and the autofocus light 230B diverge at a predetermined angle from each other. Each of the autofocus light 230A and the autofocus light 230B can be transmitted through the filter 208, through the objective lens 204, and collide with the substrate 202. In some implementations, the reflections of the autofocus light 230A and the autofocus light 230B on the substrate 202 can form the autofocus light 232A, the autofocus light 232B, the autofocus light 234A, and the autofocus light 234B. For example, the autofocus light 232A to 232B may respectively result from the reflections of the autofocus light 230A to 230B on the first layer or other surface of the substrate 202. Thus, the optical system 200 can direct the autofocus light 232A to 232B toward the filter 216. As another example, the autofocus light 234A to 234B may respectively result from the reflections of the autofocus light 230A to 230B on the second layer or other surface of the substrate 202. Thus, the optical system 200 can direct the autofocus light 234A to 234B toward the filter 216.

[0106] The autofocus lights 232A to 232B and the autofocus lights 234A to 234B can pass through the filter 216. For example, the autofocus lights 232A to 232B and the autofocus lights 234A to 234B can have wavelengths outside the wavelength range for which the filter 216 is reflective. The reflective component 226 can be positioned in a spatial location such that one or more (but not all) of the autofocus lights 232A to 232B and the autofocus lights 234A to 234B are incident on the reflective component 226. For example, the autofocus lights 232A and 232B can be incident on the reflective component 226. Accordingly, the reflective component 226 can direct the autofocus lights 232A and 232B toward the sensor 220. On the other hand, the autofocus lights 234A and 234B may not be incident on the reflective component 226. Rather, the autofocus lights 234A and 234B can be incident on the structure 228. In some implementations, the structure 228 absorbs the autofocus lights 234A and 234B. For example, this can prevent the autofocus lights 234A and 234B from reaching the sensor 220.

[0107] The autofocus process can be performed based on one or more portions of the autofocus light detected by the sensor 220. In some implementations, the distance between the autofocus light 232A and the autofocus light 232B at the sensor 220 can indicate the distance between the objective lens 204 (e.g., its lens) and the substrate 202. For example, a predefined distance on the sensor 220 corresponding to the substrate 202 being at the focus of the objective lens can be specified. Accordingly, the optical system 200 can automatically adjust the distance between the objective lens 204 and the substrate 202 based on the detected distance between the autofocus light 232A and the autofocus light 232B at the sensor 220.

[0108] Optical system 200 shows an example of a method that includes using an objective lens and a first reflective surface to direct a first autofocus light towards a sensor. For example, optical system 200 uses the reflective surface of objective lens 204 and reflective component 226 to direct autofocus light 232A and autofocus light 232B towards sensor 220. The first autofocus light is reflected from a first surface of the substrate. This method includes preventing a second autofocus light from reaching the sensor, and the second autofocus light is reflected from a second surface of the substrate. For example, optical system 200 includes a structure 210 that can block some of the autofocus light reflected at substrate 202. As another example, optical system 200 includes a structure 228 that can prevent autofocus light 234A and autofocus light 234B from reaching sensor 220.

[0109] Optical system 200 shows an example of a system that includes a substrate for holding a sample for analysis, a sensor, and an objective lens. For example, optical system 200 includes substrate 202, sensor 220, and objective lens 204. The system includes a first reflective surface for directing a first autofocus light toward the sensor, and the first autofocus light is reflected from a first surface of the substrate and transmitted by the objective lens. For example, optical system 200 includes a reflective surface in reflective component 226. The system includes a second reflective surface for directing emitted light toward the sensor, and the emitted light is generated from the sample and transmitted by the objective lens. For example, optical system 200 includes filter 216 that can direct emitted light (not shown) toward sensor 220. The system includes a structure that prevents a second autofocus light from reaching the sensor, and the second autofocus light is reflected from a second surface of the substrate and transmitted by the objective lens. For example, optical system 200 includes structure 210 that can block some of the autofocus light reflected at substrate 202. As another example, optical system 200 includes structure 228 that can prevent autofocus light 234A and autofocus light 234B from reaching sensor 220.

[0110] Optical system 200 includes a beam splitter and shows an example of a system that forms left autofocus light and right autofocus light that diverge at a predetermined angle from each other. For example, optical system 200 includes a beam splitter within lateral displacement prism 224 to form autofocus light 230A and autofocus light 230B that diverge at a predetermined angle from each other. The system includes an objective lens for transmitting the left autofocus light and the right autofocus light toward the first surface of the substrate. For example, optical system 200 includes objective lens 204 for transmitting autofocus light 230A-230B toward substrate 202. The system includes a sensor for receiving at least a first portion of the left autofocus light and at least a first portion of the right autofocus light after reflection from the first surface. For example, optical system 200 includes sensor 220. A predefined separation between the first portion of the left autofocus light and the first portion of the right autofocus light at the sensor indicates that the substrate is at the focus of the objective lens. For example, optical system 200 can determine the distance between autofocus lights 230A-230B at sensor 220.

[0111] Figure 3 is a diagram showing an example of desired reflections and unwanted reflections 300 from multiple surfaces of a multilayer sample substrate in some embodiments. The reflections 300 can be created by one or more of the embodiments described herein. In some implementations, the reflections 300 can be created using the system 100 of FIG. 1. In some implementations, the reflections 300 can be created using the optical system 200 of FIG. 2. In some implementations, the reflections 300 can be created using the optical system 500 of FIG. 5. In some implementations, the reflections 300 can be created using the optical system 800 of FIG. 8A. In some implementations, the reflections 300 can be created using the optical system 820 of FIG. 8B. In some implementations, the reflections 300 can be created using the optical system 1100 of FIG. 11. In some implementations, the reflections 300 can be created using the optical system 1200 of FIG. 12. In some implementations, the reflections 300 can be created using the optical system 1300 of FIG. 13. In some implementations, the reflections 300 can be created using the optical system 1400 of FIG. 14. In some implementations, the reflections 300 can be created using the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the reflections 300 can be created using the SIM assembly 2000 of FIG. 20. In some implementations, the reflections 300 can be created using the imaging module 2100 of FIG. 21. In some implementations, the reflections 300 can be created using the imaging module 2200 of FIG. 22. In some implementations, the reflections 300 can be created using the imaging module 2400 of FIG. 24. In some implementations, the reflections 300 can be created using the optical system 2500 of FIG. 25. In some implementations, the reflections 300 can be created using the optical system 2600 of FIG. 26. In some implementations, the reflections 300 can be created using the reflective component 2700 of FIG. 27. In some implementations, the reflections 300 can be created using the reflective component 2800 of FIG. 28.In some implementations, reflection 300 can be created using the SIM assembly 3400 of FIG. 34. In some implementations, reflection 300 can be created using the RIGS 3500 of FIG. 35. In some implementations, reflection 300 can be created using the RIGS 3600 of FIG. 36. In some implementations, reflection 300 can be created using the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, reflection 300 can be created using the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, reflection 300 can be created using the projection lens 3900 of FIG. 39. In some implementations, reflection 300 can be created using the projection lens 4000 of FIG. 40. In some implementations, reflection 300 can be created using the field of view 4100 of FIG. 41.

[0112] Reflection 300 is created such that light 302 is transmitted from the objective lens 304 towards the flow cell 306, with the objective lens 304 and the flow cell 306 shown schematically for simplicity. In some implementations, light 302 is autofocus light. For example, light 302 can be one of a pair of beams of autofocus light (e.g., the left beam), where the other beam can be, for example, the right beam, and light 302 is formed to diverge at a predetermined angle from another beam (not shown).

[0113] In some implementations, the flow cell 306 includes a substrate 308 (e.g., a cladding of a transmissive material), a substrate 310 (e.g., a cladding of a transmissive material), and a channel 312 (e.g., a fluid channel) formed between the substrates 308 and 310. For example, a sample (e.g., of nucleic acid material) and / or one or more chemical substances (e.g., sequencing reagents) can be located within and / or flow through the channel 312. One or more additional layers or other surfaces can be associated with the flow cell 306. Here, the layer 314 is positioned on one side of the substrate 310 opposite the channel 312. In some implementations, the layer 314 joins the flow cell 306 to another structure. For example, the layer 314 can include a pressure-sensitive adhesive that joins the flow cell 306 to a carrier plate.

[0114] The flow cell 306 includes a plurality of layers or other surfaces. Here, the surface S1 can be characterized as the upper surface of the substrate 308. The surface S2 can be referred to as the bottom surface of the substrate 308, or the upper surface of the channel 312, or both. The surface S3 can be referred to as the bottom surface of the channel 312, or the upper surface of the substrate 310, or both. The surface S4 can be characterized as the bottom surface of the substrate 310. The surface S5 can be characterized as the bottom surface of the layer 314.

[0115] When the light 302 is incident on the flow cell 306, the light 302 can be reflected by one or more of the surfaces S1 - S5, and that reflection produces a corresponding reflection of the reflection 300. In some implementations, the reflection 300A is formed by the reflection of the light 302 from the surface S1. In some implementations, the reflection 300B is formed by the reflection of the light 302 from the surface S2. In some implementations, the reflection 300C is formed by the reflection of the light 302 from the surface S3. In some implementations, the reflection 300D is formed by the reflection of the light 302 from the surface S4. In some implementations, the reflection 300E is formed by the reflection of the light 302 from the surface S5.

[0116] One or more reflected portions of the autofocus light can be considered more relevant than other portions. In some implementations, the autofocus light reflected from the surface where the sample material is located, or is intended to be located, can be relatively more relevant than the surface where the sample material should not be located. For example, reflections 300B - 300C (i.e., from surfaces S2 and S3) can here be considered relatively more relevant than reflection 300A (i.e., from S1), reflection 300D (i.e., from S4), or reflection 300E (i.e., from S5).

[0117] The autofocus process can be more difficult to execute and / or result in less satisfactory results when the relevant autofocus light appears at the sensor together with less relevant autofocus light. FIGS. 4A - 4C show the autofocus light aligned with the sensor. The detection of the light is shown using graphs 400, 402, and 404. Here, graph 400 corresponds to the adjustment of an out-of-focus optical system, and the z - distance between the objective lens and the substrate is 25 micrometers (μm) greater than optimal. Graph 402 corresponds to the adjustment of an optical system at best focus, and the z - distance between the objective lens and the substrate is optimal. Graph 404 corresponds to the adjustment of an out-of-focus optical system, and the z - distance between the objective lens and the substrate is 25 μm less than optimal.

[0118] However, the above focus situation (i.e., whether the objective lens is at -25 μm from the best focus, or at the best focus, or at +25 μm from the best focus) may not be known during the autofocus process. Rather, the autofocus process attempts to identify when the optical system is at the best focus or not. The optical systems for which graphs 400, 402, and 404 were generated did not have the advantages of some aspects of the present subject matter. For example, the optical system was not equipped to direct the relevant autofocus light away from less relevant autofocus light. In each of graphs 400, 402, and 404, the spots of reflection from surfaces S4 - S5 (FIG. 3) overlap the spots of reflection from surfaces S2 - S3 (FIG. 3). For example, each spot in spot cluster 400A is generated from the same autofocus light beam (e.g., the right beam), but the spots are spatially dispersed and difficult to distinguish from one another. As another example, each spot in spot cluster 400B is generated from the same autofocus light beam (e.g., the left beam), but the spots are spatially dispersed and difficult to distinguish from one another. Due to the overlap, the autofocus module may have difficulty determining when relevant aspects of spot clusters 400A - 400B, such as spots due to reflection from surfaces S2 - S3, are separated by a predefined distance. This can impair the autofocus or other focus tracking processes.

[0119] In some implementations, the associated autofocus light can be directed away from where there is less of the less relevant autofocus light. FIG. 5 shows an embodiment of an optical system 500. The optical system 500 can include or be used with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 500 can be included within the system 100 of FIG. 1. In some implementations, the optical system 500 can include or be used with the optical system 200 of FIG. 2. In some implementations, the optical system 500 can include or be used with the optical system 800 of FIG. 8A. In some implementations, the optical system 500 can include or be used with the optical system 820 of FIG. 8B. In some implementations, the optical system 500 can include or be used with the lateral displacement prism 1000 of FIGS. 10A-10C. In some implementations, the optical system 500 can include or be used with the optical system 1100 of FIG. 11. In some implementations, the optical system 500 can include or be used with the optical system 1200 of FIG. 12. In some implementations, the optical system 500 can include or be used with the optical system 1300 of FIG. 13. In some implementations, the optical system 500 can include or be used with the optical system 1400 of FIG. 14. In some implementations, the optical system 500 can include or be used with the lateral displacement prism 1600 of FIGS. 16A-16B. In some implementations, the optical system 500 can include or be used with the beam splitter 1700 of FIG. 17. In some implementations, the optical system 500 can include or be used with the imaging module 1800 of FIGS. 18 and 19A-19B.In some implementations, the optical system 500 can include or be used with the SIM assembly 2000 of FIG. 20. In some implementations, the optical system 500 can include or be used with the imaging module 2100 of FIG. 21. In some implementations, the optical system 500 can include or be used with the imaging module 2200 of FIG. 22. In some implementations, the optical system 500 can include or be used with the imaging module 2400 of FIG. 24. In some implementations, the optical system 500 can include or be used with the optical system 2500 of FIG. 25. In some implementations, the optical system 500 can include or be used with the optical system 2600 of FIG. 26. In some implementations, the optical system 500 can include or be used with the reflective component 2700 of FIG. 27. In some implementations, the optical system 500 can include or be used with the reflective component 2800 of FIG. 28. In some implementations, the optical system 500 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 500 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 500 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the optical system 500 can include or be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the optical system 500 can include or be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the optical system 500 can include or be used with the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 500 can include or be used with the RIGS 3500 of FIG. 35.In some implementations, the optical system 500 can include, or be used with, the RIG S3600 of FIG. 36. In some implementations, the optical system 500 can include, or be used with, the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the optical system 500 can include, or be used with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 500 can include, or be used with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 500 can include, or be used with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 500 can generate the field of view 4100 of FIG. 41.

[0120] The optical system 500 includes an optical component 502. The optical component 502 can include a substrate (not shown). The substrate can be used to hold one or more samples to be analyzed. In some implementations, the sample on the substrate can include nucleic acid material. For example, the substrate can include a flow cell for imaging nucleic acids.

[0121] The optical component 502 includes an objective lens (not shown). For example, the objective lens can be used to direct autofocus light on the substrate and transmit the reflected autofocus light from the substrate to perform an autofocus procedure. For example, the objective lens can be used to direct excitation light on a sample on the substrate and transmit the emitted fluorescence from the sample for collection.

[0122] The optical component 502 can include one or more filters (not shown). The filter can be a dichroic filter. In some implementations, the filter can be used to remove one or more unrelated portions from the light transmitted toward and / or away from the substrate. For example, the filter can help remove the excitation light reflected at the substrate. As another example, the filter can reflect the autofocus light reflected at the substrate and the emission light generated at the sample, thereby facilitating the transmission of the autofocus light and the emission light to further aspects of the optical system 500. The filter can allow one or more types of light to enter the stream. For example, additional autofocus light can be passed through the filter and thereby transmitted toward the substrate.

[0123] The optical system 500 includes a structure 504. The structure 504 can be a component directly upstream of the optical component 502. The structure 504 can function to block one or more beams reaching it from being transmitted from the optical component 502 to further aspects of the optical system 500. In some implementations, the structure 504 can block one or more aspects of the autofocus light reflected by the substrate. For example, the structure 504 can block the autofocus light reflected from the upper surface of the flow cell (e.g., surface S1 of FIG. 3).

[0124] Optical system 500 includes filter 506. Filter 506 can be a component directly upstream of structure 504. Filter 506 can be a dichroic filter. In some implementations, filter 506 can transmit autofocus light reflected from the substrate and emission light generated by the sample, thereby facilitating the transmission of the autofocus light and the emission light to further aspects of optical system 500. Filter 506 can split the emission light from the substrate between two or more paths. In some implementations, each path can be associated with a respective color channel. For example, a component upstream of filter 506 can be associated with one color channel (e.g., a blue or green channel), and another component (not shown) can be associated with a different color channel.

[0125] Optical system 500 includes at least one tube lens 508. Tube lens 508 can be a component directly upstream of filter 506. In some implementations, tube lens 508 can serve to focus incident light in preparation for its detection. For example, tube lens 508 can focus autofocus light for detection as part of an autofocus process. As another example, tube lens 508 can focus emission light for detection as part of an analysis process.

[0126] The optical system 200 includes a filter 510. The filter 510 can be a component directly upstream of the tube lens 508. The filter 510 can be a dichroic filter. The filter 510 can facilitate the guidance of one or more types of light, either alone or together with at least one other component. In some implementations, the filter 510 can reflect the emitted light and transmit the autofocus light. For example, the filter 510 can have an antireflection coating that prevents reflection of the autofocus light (i.e., facilitates transmission of the autofocus light) and reflects the emitted light. In other implementations, the filter 510 can be configured to prevent reflection of the emitted light (i.e., facilitate transmission) and reflect the autofocus light.

[0127] The optical system 500 includes a filter 512. The filter 512 can be a component directly upstream of the filter 510. The filter 512 can be a dichroic filter. In some implementations, the filter 512 can adjust the light at one or more points for detection preparation. For example, the filter 512 can provide band - pass filtering based on the wavelengths of the reflected autofocus light and the emitted light to remove noise.

[0128] The optical system 500 includes a sensor 514. The sensor 514 can be a component directly upstream of the filter 512. The sensor 514 can detect the autofocus light reflected during the autofocus procedure and / or detect the emitted light during the analysis procedure. For example, the sensor 514 includes a rectangular array of photosensitive elements that can detect the respective positions of one or more portions of the light incident on the sensor 514.

[0129] The optical system 500 includes one or more sources of autofocus light (not shown). In some implementations, the laser light can be provided via an optical fiber cable by a superluminescent diode that provides autofocus light based on superluminescence (e.g., spontaneously emitted light amplified by stimulated emission). For example, the autofocus light can be collimated by passing through an aspherical lens.

[0130] The initial autofocus light can be split (or laterally displaced) into two or more portions of the autofocus light. The optical system 500 includes a beam splitter (not shown). The beam splitter can be included in a lateral displacement prism. The beam splitter can be positioned proximate to the optical component 502 to inject the autofocus light so as to transmit it toward the substrate. The beam splitter can form respective portions that diverge the autofocus light from each other, for example, as described below.

[0131] The optical system 200 includes one or more reflective components 516. The reflective component 516 can include one or more reflective surfaces and can be positioned behind the filter 510 in the direction of travel of the light reaching from the tube lens 508. In some implementations, the reflective component 516 reflects the light transmitted through the filter 510, and the reflection directs the light toward the sensor 514. For example, the reflective component 516 can reflect a portion (but not all) of the autofocus light reflected at the substrate. The reflective component 516 can have optical properties based on the type of autofocus light used. In some implementations, the reflective component 516 is reflective at least in a portion of the near-infrared wavelength range (e.g., any reflection from about 750 nm to about 1400 nm).

[0132] Optical system 500 includes one or more structures 518. The structure 518 can be positioned behind the filter 510 in the traveling direction of the light reaching from the tube lens 508. In some implementations, the structure 518 absorbs the light transmitted through the filter 510, and the absorption prevents the light from reaching the sensor 514 or another area of the optical system 500. For example, the structure 518 can absorb some (but not all) of the autofocus light reflected by the substrate.

[0133] In the operation of the optical system 500, the left autofocus light and the right autofocus light can be formed by a beam splitter. The left autofocus light and the right autofocus light diverge from each other at a predetermined angle. Each of the left autofocus light and the right autofocus light can be transmitted through the optical component 502 and collide with the substrate. In some implementations, the reflections of the left autofocus light and the right autofocus light on the substrate can form the autofocus light 520A, the autofocus light 520B, the autofocus light 522A, and the autofocus light 522B. For example, the autofocus lights 520A - 520B can respectively result from the reflections of the left autofocus light and the right autofocus light on the first layer or other surfaces (e.g., the S2 surface and / or the S3 surface in FIG. 3) on the substrate. Therefore, the optical system 500 can direct the autofocus lights 520A - 520B toward the filter 510. As another example, the autofocus lights 522A - 522B can respectively result from the reflections of the left autofocus light and the right autofocus light on the second layer or other surfaces (e.g., the S4 surface and / or the S5 surface in FIG. 3) on the substrate. Therefore, the optical system 500 can direct the autofocus lights 522A - 522B toward the filter 510.

[0134] The autofocus lights 520A - 520B and the autofocus lights 522A - 522B can pass through the filter 510. For example, the autofocus lights 520A - 520B and the autofocus lights 522A - 522B can have wavelengths outside the wavelength range for which the filter 510 is reflective. The reflective component 516 can be positioned in a spatial location such that one or more (but not all) of the autofocus lights 520A - 520B and the autofocus lights 522A - 522B are incident on the reflective component 516. For example, the autofocus lights 520A and 520B can be incident on the reflective component 516. Thus, the reflective component 516 can direct the autofocus lights 520A and 520B towards the sensor 514. On the other hand, the autofocus lights 522A and 522B do not necessarily have to be incident on the reflective component 516. Rather, the autofocus lights 522A and 522B can be incident on the structure 518. In some implementations, the structure 518 absorbs the autofocus lights 522A and 522B. For example, this can prevent the autofocus lights 522A and 522B from reaching the sensor 514.

[0135] The autofocus process can be performed based on one or more portions of the autofocus light detected by the sensor 514. In some implementations, the distance between the autofocus light 520A and the autofocus light 520B at the sensor 514 can indicate the distance between the objective lens of the optical component 502 and the substrate. For example, a predefined distance on the sensor 514 corresponding to the substrate being at the focus of the objective lens can be specified. Thus, the optical system 500 can automatically adjust the distance between the objective lens and the substrate based on the detected distance between the autofocus light 520A and the autofocus light 520B at the sensor 514.

[0136] Figures 6A - 6C show autofocus light aligned in the sensor. The alignment of the autofocus light is shown using graphs 600, 602, and 604. Graphs 600, 602, and 604 can be created using one or more embodiments described herein. In some implementations, graphs 600, 602, and 604 can be created using the system 100 of FIG. 1. In some implementations, graphs 600, 602, and 604 can be created using the optical system 200 of FIG. 2. In some implementations, graphs 600, 602, and 604 can be created using the optical system 500 of FIG. 5. In some implementations, graphs 600, 602, and 604 can be created using the optical system 800 of FIG. 8A. In some implementations, graphs 600, 602, and 604 can be created using the optical system 820 of FIG. 8B. In some implementations, graphs 600, 602, and 604 can be created using the optical system 1100 of FIG. 11. In some implementations, graphs 600, 602, and 604 can be created using the optical system 1200 of FIG. 12. In some implementations, graphs 600, 602, and 604 can be created using the optical system 1300 of FIG. 13. In some implementations, graphs 600, 602, and 604 can be created using the optical system 1400 of FIG. 14. In some implementations, graphs 600, 602, and 604 can be created using the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, graphs 600, 602, and 604 can be created using the SIM assembly 2000 of FIG. 20. In some implementations, graphs 600, 602, and 604 can be created using the imaging module 2100 of FIG. 21. In some implementations, graphs 600, 602, and 604 can be created using the imaging module 2200 of FIG. 22. In some implementations, graphs 600, 602, and 604 can be created using the imaging module 2400 of FIG. 24.In some implementations, graphs 600, 602, and 604 can be created using the optical system 2500 of FIG. 25. In some implementations, graphs 600, 602, and 604 can be created using the optical system 2600 of FIG. 26. In some implementations, graphs 600, 602, and 604 can be created using the reflective component 2700 of FIG. 27. In some implementations, graphs 600, 602, and 604 can be created using the reflective component 2800 of FIG. 28. In some implementations, graphs 600, 602, and 604 can be created using the SIM assembly 3400 of FIG. 34. In some implementations, graphs 600, 602, and 604 can be created using the RIGS 3500 of FIG. 35. In some implementations, graphs 600, 602, and 604 can be created using the RIGS 3600 of FIG. 36. In some implementations, graphs 600, 602, and 604 can be created using the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, graphs 600, 602, and 604 can be created using the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, graphs 600, 602, and 604 can be created using the projection lens 3900 of FIG. 39. In some implementations, graphs 600, 602, and 604 can be created using the projection lens 4000 of FIG. 40. In some implementations, graphs 600, 602, and 604 can be created using the field of view 4100 of FIG. 41.

[0137] In graphs 600, 602, and 604, spot 606A corresponds to the reflection of one autofocus light beam (e.g., the left autofocus light) from one substrate surface (e.g., the S2 surface in FIG. 3), and spot 606B corresponds to the reflection of another autofocus light beam (e.g., the right autofocus light) from the substrate surface (e.g., the S2 surface in FIG. 3). In graphs 600, 602, and 604, spot 608A corresponds to the reflection of one autofocus light beam (e.g., the left autofocus light) from another substrate surface (e.g., the S3 surface in FIG. 3), and spot 608B corresponds to the reflection of another autofocus light beam (e.g., the right autofocus light) from the substrate surface (e.g., the S3 surface in FIG. 3).

[0138] Here, graphs 600, 602, and 604 are labeled according to whether the S2 surface (FIG. 3) is currently in focus. That is, it depends on whether the distance between spots 606A - 606B in graphs 600, 602, and 604 is equal to a predefined separation 610 associated with the optical system. In graph 600, the distance between spots 606A - 606B is greater than the predefined separation 610. That is, graph 600 corresponds to the adjustment of an out-of-focus optical system, and the z - distance between the objective lens and the substrate is 25 micrometers (μm) less than optimal. In graph 602, the distance between spots 606A - 606B is equal to the predefined separation 610. That is, graph 602 corresponds to the adjustment of an optical system at the best focus, and the z - distance between the objective lens and the substrate is optimal. In graph 604, the distance between spots 606A - 606B is shorter than the predefined separation 610. That is, graph 604 corresponds to the adjustment of an out-of-focus optical system, and the z - distance between the objective lens and the substrate is 25 μm greater than optimal.

[0139] However, the above focus situation (i.e., whether the objective lens is at -25 μm from the best focus, or at the best focus, or at +25 μm from the best focus) may not be known during the autofocus process. Rather, the autofocus process attempts to identify when the optical system is at the best focus or when it is not. The optical system in which graphs 600, 602, and 604 are generated has the advantages of at least some aspects of the present subject matter. For example, the optical system is equipped to direct the relevant autofocus light away from less relevant autofocus light. In each of graphs 600, 602, and 604, the spots of reflection from surfaces S4 - S5 (FIG. 3) are not visible and thus do not overlap with the spots of reflection from surfaces S2 - S3 (FIG. 3). Accordingly, the autofocus module can more accurately determine when the distance between spots 606A - 606B is equal to a predefined separation 610. This can improve the autofocus or other focus tracking process.

[0140] Figures 7A - 7C show autofocus light aligned with the sensor. The alignment of the autofocus light is shown using graphs 700, 702, and 704. Graphs 700, 702, and 704 can be created using one or more embodiments described herein. In some implementations, graphs 700, 702, and 704 can be created using the system 100 of FIG. 1. In some implementations, graphs 700, 702, and 704 can be created using the optical system 200 of FIG. 2. In some implementations, graphs 700, 702, and 704 can be created using the optical system 500 of FIG. 5. In some implementations, graphs 700, 702, and 704 can be created using the optical system 800 of FIG. 8A. In some implementations, graphs 700, 702, and 704 can be created using the optical system 820 of FIG. 8B. In some implementations, graphs 700, 702, and 704 can be created using the optical system 1100 of FIG. 11. In some implementations, graphs 700, 702, and 704 can be created using the optical system 1200 of FIG. 12. In some implementations, graphs 700, 702, and 704 can be created using the optical system 1300 of FIG. 13. In some implementations, graphs 700, 702, and 704 can be created using the optical system 1400 of FIG. 14. In some implementations, graphs 700, 702, and 704 can be created using the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, graphs 700, 702, and 704 can be created using the SIM assembly 2000 of FIG. 20. In some implementations, graphs 700, 702, and 704 can be created using the imaging module 2100 of FIG. 21. In some implementations, graphs 700, 702, and 704 can be created using the imaging module 2200 of FIG. 22. In some implementations, graphs 700, 702, and 704 can be created using the imaging module 2400 of FIG. 24.In some implementations, graphs 700, 702, and 704 can be created using the optical system 2500 of FIG. 25. In some implementations, graphs 700, 702, and 704 can be created using the optical system 2600 of FIG. 26. In some implementations, graphs 700, 702, and 704 can be created using the reflective component 2700 of FIG. 27. In some implementations, graphs 700, 702, and 704 can be created using the reflective component 2800 of FIG. 28. In some implementations, graphs 700, 702, and 704 can be created using the SIM assembly 3400 of FIG. 34. In some implementations, graphs 700, 702, and 704 can be created using the RIGS 3500 of FIG. 35. In some implementations, graphs 700, 702, and 704 can be created using the RIGS 3600 of FIG. 36. In some implementations, graphs 700, 702, and 704 can be created using the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, graphs 700, 702, and 704 can be created using the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, graphs 700, 702, and 704 can be created using the projection lens 3900 of FIG. 39. In some implementations, graphs 700, 702, and 704 can be created using the projection lens 4000 of FIG. 40. In some implementations, graphs 700, 702, and 704 can be created using the field of view 4100 of FIG. 41.

[0141] In graphs 700, 702, and 704, spot 706A corresponds to the reflection of one autofocus light beam (e.g., the left autofocus light) from one substrate surface (e.g., the S2 surface in FIG. 3), and spot 706B corresponds to the reflection of another autofocus light beam (e.g., the right autofocus light) from the substrate surface (e.g., the S2 surface in FIG. 3). In graphs 700, 702, and 704, spot 708A corresponds to the reflection of one autofocus light beam (e.g., the left autofocus light) from another substrate surface (e.g., the S3 surface in FIG. 3), and spot 708B corresponds to the reflection of another autofocus light beam (e.g., the right autofocus light) from the substrate surface (e.g., the S3 surface in FIG. 3).

[0142] Here, graphs 700, 702, and 704 are labeled according to whether the S3 surface (FIG. 3) is currently in focus. That is, it depends on whether the distance between spots 708A - 708B in graphs 700, 702, and 704 is equal to a predefined separation 710 associated with the optical system. In graph 700, the distance between spots 708A - 708B is greater than the predefined separation 710. That is, graph 700 corresponds to the adjustment of an out-of-focus optical system, and the z - distance between the objective lens and the substrate is 25 micrometers (μm) less than the optimum. In graph 702, the distance between spots 708A - 708B is equal to the predefined separation 710. That is, graph 702 corresponds to the adjustment of an optical system at the best focus, and the z - distance between the objective lens and the substrate is optimum. In graph 704, the distance between spots 708A - 708B is shorter than the predefined separation 710. That is, graph 704 corresponds to the adjustment of an out-of-focus optical system, and the z - distance between the objective lens and the substrate is 25 μm greater than the optimum.

[0143] However, the above focus situation (i.e., whether the objective lens is at -25 μm from the best focus, or at the best focus, or at +25 μm from the best focus) may not be known during the autofocus process. Rather, the autofocus process attempts to identify when the optical system is at the best focus or when it is not. The optical system in which graphs 700, 702, and 704 are generated has the advantages of at least some aspects of the present subject matter. For example, the optical system is equipped to direct the relevant autofocus light away from less relevant autofocus light. In each of graphs 700, 702, and 704, the spots of reflection from surfaces S4 - S5 (FIG. 3) are not visible and thus do not overlap with the spots of reflection from surfaces S2 - S3 (FIG. 3). Accordingly, the autofocus module can more accurately determine when the distance between spots 708A - 708B is equal to a predefined separation 710. This can improve the autofocus or other focus tracking process.

[0144] FIG. 8A shows an embodiment of an optical system 800. The optical system 800 can include or be used in conjunction with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 800 can be included within the system 100 of FIG. 1. In some implementations, the optical system 800 can include or be used in conjunction with the optical system 200 of FIG. 2. In some implementations, the optical system 800 can include or be used in conjunction with the optical system 500 of FIG. 5. In some implementations, the optical system 800 can include or be used in conjunction with the optical system 820 of FIG. 8B. In some implementations, the optical system 800 can include or be used in conjunction with the lateral displacement prism 1000 of FIGS. 10A - 10C. In some implementations, the optical system 800 can include or be used in conjunction with the optical system 1100 of FIG. 11. In some implementations, the optical system 800 can include or be used in conjunction with the optical system 1200 of FIG. 12. In some implementations, the optical system 800 can include or be used in conjunction with the optical system 1300 of FIG. 13. In some implementations, the optical system 800 can include or be used in conjunction with the optical system 1400 of FIG. 14. In some implementations, the optical system 800 can include or be used in conjunction with the lateral displacement prism 1600 of FIGS. 16A - 16B. In some implementations, the optical system 800 can include or be used in conjunction with the beam splitter 1700 of FIG. 17. In some implementations, the optical system 800 can include or be used in conjunction with the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the optical system 800 can include or be used in conjunction with the SIM assembly 2000 of FIG. 20.In some implementations, the optical system 800 can include, or be used with, the imaging module 2100 of FIG. 21. In some implementations, the optical system 800 can include, or be used with, the imaging module 2200 of FIG. 22. In some implementations, the optical system 800 can include, or be used with, the imaging module 2400 of FIG. 24. In some implementations, the optical system 800 can include, or be used with, the optical system 2500 of FIG. 25. In some implementations, the optical system 800 can include, or be used with, the optical system 2600 of FIG. 26. In some implementations, the optical system 800 can include, or be used with, the reflective component 2700 of FIG. 27. In some implementations, the optical system 800 can include, or be used with, the reflective component 2800 of FIG. 28. In some implementations, the optical system 800 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 800 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 800 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the optical system 800 can include, or be used with, the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the optical system 800 can include, or be used with, the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the optical system 800 can include, or be used with, the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 800 can include, or be used with, the RIGS 3500 of FIG. 35. In some implementations, the optical system 800 can include, or be used with, the RIGS 3600 of FIG. 36.In some implementations, the optical system 800 can include, or can be used with, the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the optical system 800 can include, or can be used with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 800 can include, or can be used with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 800 can include, or can be used with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 800 can generate the field of view 4100 of FIG. 41.

[0145] For clarity, only a portion of the optical system 800 is shown. The optical system 800 includes at least one tube lens 802. In some implementations, the tube lens 802 can serve to prepare the incident light for its detection. For example, the tube lens 802 can focus the autofocus light for detection as part of an autofocus process. As another example, the tube lens 802 can focus the emitted light for detection as part of an analysis process.

[0146] The optical system 800 includes a filter 804. The filter 804 can be a component directly upstream of the tube lens 802. The filter 804 can be a dichroic filter. The filter 804 can facilitate the guiding of one or more types of light, alone or in conjunction with at least one other component. In some implementations, the filter 804 can reflect the emitted light and transmit the autofocus light. For example, the filter 804 can have an antireflection coating that prevents reflection of the autofocus light (i.e., facilitates transmission of the autofocus light) and reflects the emitted light. In other implementations, the filter 804 can be configured to prevent reflection of the emitted light (i.e., facilitate transmission) and reflect the autofocus light.

[0147] The optical system 800 includes a filter 806. The filter 806 can be a component directly upstream of the filter 804. The filter 806 can be a dichroic filter. In some implementations, the filter 806 can adjust light at one or more points in preparation for detection. For example, the filter 806 can provide bandpass filtering based on the wavelength of the reflected autofocus light and the wavelength of the emitted light to eliminate noise.

[0148] The optical system 800 includes a sensor 808. The sensor 808 can be a component directly upstream of the filter 806. The sensor 808 can detect the autofocus light reflected during the autofocus procedure and / or the emitted light during the analysis procedure. For example, the sensor 808 includes a rectangular array of photosensitive elements that can detect the respective positions of one or more portions of the light incident on the sensor 808.

[0149] The optical system 800 can include a substrate (not shown). The substrate can be used to hold one or more samples to be analyzed. In some implementations, the sample on the substrate can include nucleic acid material. For example, the substrate can include a flow cell for imaging nucleic acid material. The optical system 800 can include one or more other optical components (not shown). The other optical components can include, but are not limited to, one or more of an objective lens, a filter, a structure that blocks one or more beams, a source of autofocus light, or a beam splitter.

[0150] The optical system 800 includes one or more reflective components. Here, the optical system 800 includes a reflective component 810A and a reflective component 810B. Each of the reflective components 810A - 810B can include one or more reflective surfaces and can be positioned behind the filter 804 in the direction of travel of the light reaching from the tube lens 802. In some implementations, either or both of the reflective components 810A - 810B reflect the light transmitted through the filter 804, and the reflection directs the light towards the sensor 808. For example, either or both of the reflective components 810A - 810B can reflect a portion (but not all) of the autofocus light reflected on the substrate. Each of the reflective components 810A - 810B can have optical properties based on the type of autofocus light used. In some implementations, each of the reflective components 810A - 810B is reflective at least in part in the near - infrared wavelength range (e.g., any reflection between about 750 nm and about 1400 nm).

[0151] One or more of the reflective components 810A - 810B can be movable. The mobility can include one or more of translation or rotation of at least one of the reflective components 810A - 810B. The reflective component 810A may be separated from the filter 804. In some implementations, the reflective component 810A can be oriented independently of the orientation of the filter 804. For example, the reflective component 810A can be coupled to a motor or actuator that controls the orientation of the reflective component 810A without affecting the orientation of the filter 804. The reflective component 810B may be separated from the filter 804. The reflective component 810B may be separated from the reflective component 810A. In some implementations, the reflective component 810B can be oriented independently of the orientation of the filter 804. For example, the reflective component 810B can be coupled to a motor or actuator that controls the orientation of the reflective component 810B without affecting the orientation of the filter 804.

[0152] Optical system 800 includes one or more structures 812. The structure 812 can be positioned behind the filter 804 in the direction of travel of the light reaching from the tube lens 802. In some implementations, the structure 812 absorbs the light transmitted through the filter 804, and the absorption prevents the light from reaching the sensor 808 or another area of the optical system 800. For example, the structure 812 can absorb a part (but not all) of the autofocus light reflected on the substrate.

[0153] In the operation of the optical system 800, the left autofocus light and the right autofocus light can be formed by a beam splitter. The left autofocus light and the right autofocus light diverge from each other at a predetermined angle. Each of the left autofocus light and the right autofocus light can be transmitted through one or more optical components and can collide with the substrate. In some implementations, the reflections of the left autofocus light and the right autofocus light on the substrate can form the autofocus light 814A, the autofocus light 814B, the autofocus light 816A, and the autofocus light 816B. For example, the autofocus lights 814A to 814B can respectively result from the reflections of the left autofocus light and the right autofocus light on the first layer or another surface of the substrate (e.g., the S2 surface and / or the S3 surface in FIG. 3). Therefore, the optical system 800 can direct the autofocus lights 814A to 814B towards the filter 804. As another example, the autofocus lights 816A to 816B can respectively result from the reflections of the left autofocus light and the right autofocus light on the second layer or another surface of the substrate (e.g., the S4 surface and / or the S5 surface in FIG. 3). Therefore, the optical system 800 can direct the autofocus lights 816A to 816B towards the filter 804.

[0154] The autofocus lights 814A - 814B and the autofocus lights 816A - 816B can pass through the filter 804. For example, the autofocus lights 814A - 814B and the autofocus lights 816A - 816B can have wavelengths outside the wavelength range for which the filter 804 is reflective. The reflective component 810A can be positioned in a spatial position such that the autofocus light 814A, rather than the autofocus light 814B or the autofocus lights 816A - 816B, is incident on the reflective component 810A. Thus, the reflective component 810A can direct the autofocus light 814A towards the sensor 808. For example, the movement (e.g., rotation) of the reflective component 810A can direct the autofocus light 814A at the sensor 808. The reflective component 810B can be positioned in a spatial position such that the autofocus light 814B, rather than the autofocus light 814A or the autofocus lights 816A - 816B, is incident on the reflective component 810B. Thus, the reflective component 810B can direct the autofocus light 814B towards the sensor 808. For example, the movement (e.g., rotation) of the reflective component 810B can direct the autofocus light 814B at the sensor 808. The autofocus lights 816A and 816B can be incident on the structure 812. In some implementations, the structure 812 absorbs the autofocus lights 816A and 816B. For example, this can prevent the autofocus lights 816A and 816B from reaching the sensor 808.

[0155] The autofocus process can be performed based on one or more portions of the autofocus light detected by sensor 808. In some implementations, the distance between autofocus light 814A and autofocus light 814B in sensor 808 can indicate the distance between the objective lens of the optical system 800 and the substrate. For example, a predefined distance on sensor 808 corresponding to the substrate being at the focus of the objective lens can be specified. Thus, the optical system 800 can automatically adjust the distance between the objective lens and the substrate based on the detected distance between autofocus light 814A and autofocus light 814B in sensor 808.

[0156] FIG. 8B shows an embodiment of an optical system 820. The optical system 820 can be used with or incorporated into one or more other embodiments described herein. In some implementations, the optical system 820 can be included within the system 100 of FIG. 1. In some implementations, the optical system 820 can be used with or incorporated into the optical system 200 of FIG. 2. In some implementations, the optical system 820 can be used with or incorporated into the optical system 500 of FIG. 5. In some implementations, the optical system 820 can be used with or incorporated into the optical system 820 of FIG. 8B. In some implementations, the optical system 820 can be used with or incorporated into the optical system 1100 of FIG. 11. In some implementations, the optical system 820 can be used with or incorporated into the optical system 1200 of FIG. 12. In some implementations, the optical system 820 can be used with or incorporated into the optical system 1300 of FIG. 13. In some implementations, the optical system 820 can be used with or incorporated into the optical system 1400 of FIG. 14. In some implementations, the optical system 820 can be used with or incorporated into the imaging module 1800 of FIGS. 18 and 19A-19B. In some implementations, the optical system 820 can be used with or incorporated into the imaging module 2100 of FIG. 21. In some implementations, the optical system 820 can be used with or incorporated into the imaging module 2200 of FIG. 22. In some implementations, the optical system 820 can be used with or incorporated into the imaging module 2400 of FIG. 24. In some implementations, the optical system 820 can be used with or incorporated into the optical system 2500 of FIG. 25.In some implementations, the optical system 820 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, the optical system 820 can include or be used with the reflective component 2700 of FIG. 27. In some implementations, the optical system 820 can include or be used with the reflective component 2800 of FIG. 28. In some implementations, the optical system 820 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 820 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 820 can generate the autofocus light 3100 of FIGS. 31A-31C. In some implementations, the optical system 820 can be used with the laser engine heat sink 3200 of FIGS. 32A-32C. In some implementations, the optical system 820 can be used with the laser engine heat sink 3300 of FIGS. 33A-33C. In some implementations, the optical system 820 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 820 can be used with the RIGS 3500 of FIG. 35. In some implementations, the optical system 820 can be used with the RIGS 3600 of FIG. 36. In some implementations, the optical system 820 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the optical system 820 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 820 can be used with the projection lens 3900 of FIG. 39. In some implementations, the optical system 820 can be used with the projection lens 4000 of FIG. 40. In some implementations, the optical system 820 can generate the field of view 4100 of FIG. 41.

[0157] For clarity, only a portion of the optical system 820 is shown. The optical system 820 includes a filter 822. The filter 822 can be a dichroic filter. The filter 822 can facilitate the guiding of one or more types of light, either alone or in conjunction with at least one other component. In some implementations, the filter 822 can have an anti-reflection coating 824 that prevents the reflection of autofocus light (i.e., facilitates the transmission of autofocus light) and reflects the emitted light. For example, the anti-reflection coating 824 can be positioned on the front surface of the filter 822 in the direction of travel of the light reaching the filter 822. In other implementations, the anti-reflection coating 824 can be configured to prevent the reflection of the emitted light (i.e., facilitate transmission) and reflect the autofocus light.

[0158] The optical system 820 includes one or more reflective components. Here, the optical system 820 includes a reflective component 826A and a reflective component 826B. Each of the reflective components 826A-826B can include one or more reflective surfaces and can be positioned on the surface of the filter 822. For example, the reflective components 826A-826B can be positioned on the rear surface of the filter 822 in the direction of travel of the light reaching the filter 822. In some implementations, either or both of the reflective components 826A-826B reflect the light transmitted through the filter 822, and that reflection directs the light towards another part of the optical system 820 (e.g., towards a sensor). For example, the reflective component 826A can reflect the autofocus light 828A. Each of the reflective components 826A-826B can have optical properties based on the type of autofocus light used. In some implementations, each of the reflective components 826A-826B is reflective at least in part in the near-infrared wavelength range (e.g., any reflection between about 750 nm and about 1400 nm).

[0159] The optical system 820 includes one or more structures 830. The structure 830 can be positioned on the rear surface of the filter 822 in the traveling direction of the autofocus light 828A. In some implementations, the structure 830 absorbs the light transmitted through the filter 822, and the absorption prevents the light from reaching a sensor or another area of the optical system 820. For example, the structure 830 can absorb some (but not all) of the autofocus light 828B. As another example, the structure 830 can transmit the autofocus light 828B, as schematically indicated by the autofocus light 828B'. In some implementations, the structure 830 can be omitted from the optical system 820.

[0160] That is, in the operation of the optical system 820, the reflective component 826A can reflect the autofocus light 828A, thereby enabling the induction of the autofocus light 828A in the sensor of the optical system 820. As another example, the reflective component 826B can reflect other autofocus light (not shown), thereby enabling the induction of the other autofocus light in the sensor of the optical system 820. Simultaneously with and / or at another time point of the aforementioned reflection, the antireflection coating 824 can reflect the emitted light 832 towards another part of the optical system 820 (e.g., towards the sensor). For example, the emitted light 832 can include fluorescence generated by the sample for the purpose of imaging the sample for analysis.

[0161] Figures 9A - 9B are diagrams showing examples of creating desired reflections 900 and unwanted reflections 900' from multiple surfaces of a sample substrate in some embodiments. Reflections 900 and 900' can be created by one or more of the embodiments described herein. In some implementations, reflections 900 and 900' can be created using the system 100 of FIG. 1. In some implementations, reflections 900 and 900' can be created using the optical system 200 of FIG. 2. In some implementations, reflections 900 and 900' can be created using the optical system 500 of FIG. 5. In some implementations, reflections 900 and 900' can be created using the optical system 800 of FIG. 8A. In some implementations, reflections 900 and 900' can be created using the optical system 820 of FIG. 8B. In some implementations, reflections 900 and 900' can be created using the optical system 1100 of FIG. 11. In some implementations, reflections 900 and 900' can be created using the optical system 1200 of FIG. 12. In some implementations, reflections 900 and 900' can be created using the optical system 1300 of FIG. 13. In some implementations, reflections 900 and 900' can be created using the optical system 1400 of FIG. 14. In some implementations, reflections 900 and 900' can be created using the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, reflections 900 and 900' can be created using the SIM assembly 2000 of FIG. 20. In some implementations, reflections 900 and 900' can be created using the imaging module 2100 of FIG. 21. In some implementations, reflections 900 and 900' can be created using the imaging module 2200 of FIG. 22. In some implementations, reflections 900 and 900' can be created using the imaging module 2400 of FIG. 24. In some implementations, reflections 900 and 900' can be created using the optical system 2500 of FIG. 25. In some implementations, reflections 900 and 900' can be created using the optical system 2600 of FIG. 26.In some implementations, reflections 900 and 900' can be created using the reflective component 2700 of FIG. 27. In some implementations, reflections 900 and 900' can be created using the reflective component 2800 of FIG. 28. In some implementations, reflections 900 and 900' can be created using the SIM assembly 3400 of FIG. 34. In some implementations, reflections 900 and 900' can be created using the RIGS 3500 of FIG. 35. In some implementations, reflections 900 and 900' can be created using the RIGS 3600 of FIG. 36. In some implementations, reflections 900 and 900' can be created using the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, reflections 900 and 900' can be created using the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, reflections 900 and 900' can be created using the projection lens 3900 of FIG. 39. In some implementations, reflections 900 and 900' can be created using the projection lens 4000 of FIG. 40. In some implementations, reflections 900 and 900' can be created using the field of view 4100 of FIG. 41.

[0162] In some implementations, reflections 900 and 900' can be generated by respective portions of the autofocus light incident on the substrate. For example, reflection 900 is created as a result of light 902 being transmitted from the objective lens 904 towards the flow cell 906, and light 902 is the left autofocus light (e.g., a portion of the output from the beam splitter). For example, reflection 900' is created as a result of light 902' being transmitted from the objective lens 904 towards the flow cell 906, and light 902' is the right autofocus light (e.g., another portion of the output from the beam splitter). Lights 902 and 902' can diverge from each other by a predetermined angle. The objective lens 904 and the flow cell 906 are shown schematically for simplicity.

[0163] In some implementations, the flow cell 906 includes a substrate 908 (e.g., a cladding of a transmissive material), a substrate 910 (e.g., a cladding of a transmissive material), and a channel 912 (e.g., a fluid channel) formed between the substrates 908 and 910. For example, a sample (e.g., of nucleic acid material) and / or one or more chemical substances (e.g., sequencing reagents) can be located within and / or flow through the channel 912. One or more additional layers or other surfaces can be associated with the flow cell 906. Here, the layer 914 is positioned on one side of the substrate 910 opposite the channel 912. In some implementations, the layer 914 joins the flow cell 906 to another structure. For example, the layer 914 can include a pressure-sensitive adhesive that joins the flow cell 906 to a carrier plate.

[0164] The flow cell 906 includes a plurality of layers or other surfaces. Here, surface S1 can be characterized as the upper surface of the substrate 908. Surface S2 can be referred to as the bottom surface of the substrate 908, or the upper surface of the channel 912, or both. Surface S3 can be referred to as the bottom surface of the channel 912, or the upper surface of the substrate 910, or both. Surface S4 can be characterized as the bottom surface of the substrate 910. Surface S5 can be characterized as the bottom surface of the layer 914.

[0165] When light 902 is incident on the flow cell 906, the light 902 can be reflected by one or more of the surfaces S1 - S5, and that reflection produces a corresponding reflection of the reflection 900. In some implementations, the reflection 900A is formed by the reflection of the light 902 from the surface S1. In some implementations, the reflection 900B is formed by the reflection of the light 902 from the surface S2. In some implementations, the reflection 900C is formed by the reflection of the light 902 from the surface S3. In some implementations, the reflection 900D is formed by the reflection of the light 902 from the surface S4. In some implementations, the reflection 900E is formed by the reflection of the light 902 from the surface S5.

[0166] One or more reflected portions of the autofocus light can be considered to be more relevant than other portions. In some implementations, the autofocus light reflected from the surface where the sample material is located, or is intended to be located, can be relatively more relevant than the surfaces where the sample material should not be located. For example, reflections 900B - 900C (i.e., from surfaces S2 and S3) can here be considered to be relatively more relevant than reflection 900A (i.e., from S1), reflection 900D (i.e., from S4), or reflection 900E (i.e., from S5).

[0167] When light 902' is incident on flow cell 906, light 902' can be reflected by one or more of surfaces S1 - S5, and that reflection results in a corresponding reflection of reflection 900'. In some implementations, reflection 900A' is formed by the reflection of light 902' from surface S1. In some implementations, reflection 900B' is formed by the reflection of light 902' from surface S2. In some implementations, reflection 900C' is formed by the reflection of light 902' from surface S3. In some implementations, reflection 900D' is formed by the reflection of light 902' from surface S4. In some implementations, reflection 900E' is formed by the reflection of light 902' from surface S5.

[0168] One or more reflected portions of the autofocus light can be considered to be more relevant than other portions. In some implementations, the autofocus light reflected from the surface where the sample material is located, or is intended to be located, can be relatively more relevant than the surfaces where the sample material should not be located. For example, reflections 900B' - 900C' (i.e., from surfaces S2 and S3) can here be considered to be relatively more relevant than reflection 900A (i.e., from S1), reflection 900D (i.e., from S4), or reflection 900E (i.e., from S5).

[0169] Figures 10A - 10C illustrate an embodiment of the lateral displacement prism 1000. The lateral displacement prism 1000 can be used with or incorporated into one or more other embodiments described herein. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the system 100 of FIG. 1. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 200 of FIG. 2. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 500 of FIG. 5. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 800 of FIG. 8A. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 820 of FIG. 8B. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 1100 of FIG. 11. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 1200 of FIG. 12. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 1300 of FIG. 13. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the optical system 1400 of FIG. 14. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the imaging module 2100 of FIG. 21. In some implementations, the lateral displacement prism 1000 can be used with or incorporated into the imaging module 2200 of FIG. 22.In some implementations, the lateral displacement prism 1000 can be used with or included in the imaging module 2400 of FIG. 24. In some implementations, the lateral displacement prism 1000 can be used with or included in the optical system 2500 of FIG. 25. In some implementations, the lateral displacement prism 1000 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, the lateral displacement prism 1000 can be used with the reflective component 2700 of FIG. 27. In some implementations, the lateral displacement prism 1000 can be used with the reflective component 2800 of FIG. 28. In some implementations, the lateral displacement prism 1000 can generate the autofocus light 2900 of FIG. 29. In some implementations, the lateral displacement prism 1000 can generate the autofocus light 3000 of FIG. 30. In some implementations, the lateral displacement prism 1000 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the lateral displacement prism 1000 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the lateral displacement prism 1000 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the lateral displacement prism 1000 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the lateral displacement prism 1000 can be used with the RIGS 3500 of FIG. 35. In some implementations, the lateral displacement prism 1000 can be used with the RIGS 3600 of FIG. 36. In some implementations, the lateral displacement prism 1000 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the lateral displacement prism 1000 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the lateral displacement prism 1000 can be used with the projection lens 3900 of FIG. 39.In some implementations, the lateral displacement prism 1000 can be used with the projection lens 4000 of FIG. 40.

[0170] The lateral displacement prism 1000 includes a surface 1002. In some implementations, the surface 1002 can be regarded as the upper surface of the lateral displacement prism 1000. The lateral displacement prism 1000 includes a surface 1004 parallel to the surface 1002. In some implementations, the surface 1004 can be regarded as the bottom surface of the lateral displacement prism 1000. The lateral displacement prism 1000 includes a surface 1006. In some implementations, the surface 1006 can be regarded as the side surface of the lateral displacement prism 1000. For example, the surface 1006 can be the entrance surface of the lateral displacement prism 1000. The lateral displacement prism 1000 includes a surface 1008A. In some implementations, the surface 1008A can be regarded as the exit surface of the lateral displacement prism 1000. The lateral displacement prism 1000 includes a surface 1008B. In some implementations, the surface 1008B can be regarded as the exit surface of the lateral displacement prism 1000. Each of the surfaces 1008A-1008B forms a common angle with the surface 1006. In some implementations, the surfaces 1008A-1008B can have a non-zero angle with respect to each other. The lateral displacement prism 1000 includes a partially reflective layer 1010. In some implementations, the lateral displacement prism 1000 can be manufactured by assembling two prism pieces that are at least substantially identical to each other, and the partially reflective layer 1010 is positioned at the junction between the two prism pieces. The surface 1002 can have a boundary with at least the surfaces 1006, 1008A, and 1008B. The surface 1004 can have a boundary with at least the surfaces 1006, 1008A, and 1008B.

[0171] Light 1012 can enter the lateral displacement prism 1000 through the surface 1006. For example, the light 1012 is autofocus light generated by a light source (such as a laser diode). After at least one reflection within the lateral displacement prism 1000 or after no reflection within the lateral displacement prism 1000, the light 1012 can be incident on the partially reflective layer 1010. As a result, the light 1012A reflected by the partially reflective layer 1010 can exit the lateral displacement prism 1000 through the surface 1008A. Also, the light 1012B transmitted through the partially reflective layer 1010 can exit the lateral displacement prism 1000 through the surface 1008B after at least one reflection within the lateral displacement prism 1000 or after no reflection within the lateral displacement prism 1000. The light 1012A and the light 1012B diverge from each other at a predetermined angle. In some implementations, each of the lights 1012A - 1012B diverges at an angle of about 1 degree to about 3 degrees from the normal of the surface 1006. For example, each of the lights 1012A - 1012B can diverge at an angle of about 1.4 degrees (such as about 1.464 degrees) from the normal of the surface 1006. Thus, the lights 1012A - 1012B can diverge from each other at an angle of about 2 degrees to about 6 degrees. For example, the lights 1012A - 1012B can diverge from each other at an angle of about 2.9 degrees (such as about 2.928 degrees). The surfaces 1008A - 1008B can have a boundary 1014 with each other. In some implementations, the partially reflective layer 1010 can extend between the surface 1006 and the boundary 1014. For example, the partially reflective layer 1010 can divide the surface 1006 into two parts of at least substantially equal size. As another example, the surfaces 1008A - 1008B can be at least substantially equal in size to each other.

[0172] The lateral displacement prism 1000 can be included in the autofocus assembly. In some implementations, the autofocus assembly includes at least the lateral displacement prism 1000 and a light source that directs light (e.g., light 1012) in the lateral displacement prism 1000. For example, the light source can be part of the autofocus component 106 (FIG. 1). In such an autofocus assembly, the lateral displacement prism 1000 can form a first autofocus light (e.g., light 1012A) and a second autofocus light (e.g., light 1012B) from the light such that the first autofocus light and the second autofocus light diverge from each other at a predetermined angle.

[0173] FIG. 11 schematically shows an optical system 1100 having a lateral displacement prism 1102. The optical system 1100 can include or be used with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 1100 can be included within the system 100 of FIG. 1. In some implementations, the optical system 1100 can include or be used with the optical system 200 of FIG. 2. In some implementations, the optical system 1100 can include or be used with the optical system 500 of FIG. 5. In some implementations, the optical system 1100 can include or be used with the optical system 800 of FIG. 8A. In some implementations, the optical system 1100 can include or be used with the optical system 820 of FIG. 8B. In some implementations, the optical system 1100 can include or be used with the lateral displacement prism 1000 of FIGS. 10A-10C. In some implementations, the optical system 1100 can include or be used with the optical system 1200 of FIG. 12. In some implementations, the optical system 1100 can include or be used with the optical system 1300 of FIG. 13. In some implementations, the optical system 1100 can include or be used with the optical system 1400 of FIG. 14. In some implementations, the optical system 1100 can include or be used with the lateral displacement prism 1600 of FIGS. 16A-16B. In some implementations, the optical system 1100 can include or be used with the beam splitter 1700 of FIG. 17. In some implementations, the optical system 1100 can be included within the imaging module 1800 of FIGS. 18 and 19A-19B. In some implementations, the optical system 1100 can be used with the SIM assembly 2000 of FIG. 20.In some implementations, the optical system 1100 may be included within the imaging module 2100 of FIG. 21. In some implementations, the optical system 1100 may be included within the imaging module 2200 of FIG. 22. In some implementations, the optical system 1100 may be included within the imaging module 2400 of FIG. 24. In some implementations, the optical system 1100 may be included within the system 2500 of FIG. 25. In some implementations, the optical system 1100 may be included within the system 2600 of FIG. 26. In some implementations, the optical system 1100 may include or be used with the reflective component 2700 of FIG. 27. In some implementations, the optical system 1100 may include or be used with the reflective component 2800 of FIG. 28. In some implementations, the optical system 1100 may generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 1100 may generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 1100 may generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the optical system 1100 may include or be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the optical system 1100 may include or be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the optical system 1100 may include or be used with the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 1100 may include or be used with the RIGS 3500 of FIG. 35. In some implementations, the optical system 1100 may include or be used with the RIGS 3600 of FIG. 36. In some implementations, the optical system 1100 may include or be used with the piezoelectric phase shifter 3700 of FIG. 37.In some implementations, the optical system 1100 can include, or can be used in conjunction with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 1100 can include, or can be used in conjunction with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 1100 can include, or can be used in conjunction with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 1100 can generate the field of view 4100 of FIG. 41.

[0174] Light 1104 can enter the lateral displacement prism 1102 through the entrance surface. For example, light 1104 is autofocus light generated by a light source (e.g., a laser diode). Light 1104A can exit the lateral displacement prism 1102 through the exit surface. Light 1104B can exit the lateral displacement prism 1102 through another exit surface. Light 1104A and light 1104B diverge from each other at a predetermined angle.

[0175] The optical system 1100 includes a substrate 1106. The substrate 1106 can be used to hold one or more samples to be analyzed. In some implementations, the sample on the substrate 1106 can include nucleic acid material. For example, the substrate 1106 can include a flow cell for imaging nucleic acid material. Reflection of light 1104A on the surface of the substrate 1106 can form light 1108A. Reflection of light 1104B on the surface of the substrate 1106 can form light 1108B.

[0176] Lights 1108A-1108B can be transmitted and / or reflected and / or refracted by at least one other component (not shown) within the optical system 1100. Here, line 1110 schematically shows additional components of the optical system 1100 and the processing of lights 1108A-1108B performed by the additional components.

[0177] Optical system 1100 includes a sensor 1112. The sensor 1112 can detect autofocus light reflected during an autofocus procedure and / or emitted light during an analysis procedure. In some implementations, the sensor 1112 includes a rectangular array of photosensitive elements that can detect the respective positions of one or more portions of the light incident on the sensor 1112. For example, lights 1108A-1108B can be incident on the sensor 1112.

[0178] The sensor 1112 can be used to determine one or more characteristics of lights 1108A-1108B. In some implementations, the distance 1114 between lights 1108A-1108B at the sensor 1112 can indicate the distance between the objective lens of the optical system 1100 and the substrate 1106. For example, a predefined distance on the sensor 1112 corresponding to the substrate 1106 being at the focus of the objective lens can be specified.

[0179] Optical system 1100 shows an example of executing a method that includes forming left autofocus light (e.g., light 1104A) and right autofocus light (e.g., light 1104B) that diverge at a predetermined angle from each other (e.g., by the lateral displacement prism 1102). The method includes directing the left autofocus light and the right autofocus light through the objective lens toward a first surface of a substrate (e.g., substrate 1106). The method includes directing at least a first portion of the left autofocus light and at least a first portion of the right autofocus light toward a sensor (e.g., sensor 1112) after reflection from the first surface. A predefined separation between the first portion of the left autofocus light and the first portion of the right autofocus light at the sensor indicates that the substrate is at the focus of the objective lens. For example, the distance 1114 may or may not currently be equal to the predefined separation.

[0180] FIG. 12 schematically shows an optical system 1200 having a lateral displacement prism 1202. The optical system 1200 can include or be used with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 1200 can be included within the system 100 of FIG. 1. In some implementations, the optical system 1200 can include or be used with the optical system 200 of FIG. 2. In some implementations, the optical system 1200 can include or be used with the optical system 500 of FIG. 5. In some implementations, the optical system 1200 can include or be used with the optical system 800 of FIG. 8A. In some implementations, the optical system 1200 can include or be used with the optical system 820 of FIG. 8B. In some implementations, the optical system 1200 can include or be used with the lateral displacement prism 1000 of FIGS. 10A - 10C. In some implementations, the optical system 1200 can include or be used with the optical system 1100 of FIG. 11. In some implementations, the optical system 1200 can include or be used with the optical system 1300 of FIG. 13. In some implementations, the optical system 1200 can include or be used with the optical system 1400 of FIG. 14. In some implementations, the optical system 1200 can include or be used with the lateral displacement prism 1600 of FIGS. 16A - 16B. In some implementations, the optical system 1200 can include or be used with the beam splitter 1700 of FIG. 17. In some implementations, the optical system 1200 can be included within the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the optical system 1200 can be used with the SIM assembly 2000 of FIG. 20.In some implementations, the optical system 1200 may be included within the imaging module 2100 of FIG. 21. In some implementations, the optical system 1200 may be included within the imaging module 2200 of FIG. 22. In some implementations, the optical system 1200 may be included within the imaging module 2400 of FIG. 24. In some implementations, the optical system 1200 may be included within the system 2500 of FIG. 25. In some implementations, the optical system 1200 may be included within the system 2600 of FIG. 26. In some implementations, the optical system 1200 may be able to include or be used with the reflective component 2700 of FIG. 27. In some implementations, the optical system 1200 may be able to include or be used with the reflective component 2800 of FIG. 28. In some implementations, the optical system 1200 may be able to generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 1200 may be able to generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 1200 may be able to generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the optical system 1200 may be able to include or be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the optical system 1200 may be able to include or be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the optical system 1200 may be able to include or be used with the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 1200 may be able to include or be used with the RIGS 3500 of FIG. 35. In some implementations, the optical system 1200 may be able to include or be used with the RIGS 3600 of FIG. 36. In some implementations, the optical system 1200 may be able to include or be used with the piezoelectric phase shifter 3700 of FIG. 37.In some implementations, the optical system 1200 can include, or can be used with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 1200 can include, or can be used with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 1200 can include, or can be used with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 1200 can generate the field of view 4100 of FIG. 41.

[0181] Light 1204 can enter the lateral displacement prism 1202 through the entrance surface. For example, the light 1204 can be autofocus light generated by a light source (e.g., a laser diode). Light 1204A can exit the lateral displacement prism 1202 through the exit surface. Light 1204B can exit the lateral displacement prism 1202 through another exit surface. The light 1204A and the light 1204B diverge from each other at a predetermined angle.

[0182] The optical system 1200 includes a substrate 1206. The substrate 1206 can be used to hold one or more samples to be analyzed. In some implementations, the sample on the substrate 1206 can include nucleic acid material. For example, the substrate 1206 can include a flow cell for imaging nucleic acid material. The substrate 1206 can include at least a surface 1206A and a surface 1206B. The reflection of the light 1204A on the surface 1206A can form the light 1208A. The reflection of the light 1204A on the surface 1206B can form the light 1210A. The reflection of the light 1204B on the surface 1206A can form the light 1208B. The reflection of the light 1204B on the surface 1206B can form the light 1210B.

[0183] Lights 1208A - 1208B and 1210A - 1210B can be transmitted and / or reflected and / or refracted by at least one other component (not shown) within the optical system 1200. Here, line 1212 schematically shows additional components of the optical system 1200 and the processing of lights 1208A - 1208B and 1210A - 1210B performed in the additional components.

[0184] The optical system 1200 includes a sensor 1214. The sensor 1214 can detect autofocus light reflected during an autofocus procedure and / or detect emitted light during an analysis procedure. In some implementations, the sensor 1214 includes a rectangular array of photosensitive elements that can detect the respective positions of one or more portions of the light incident on the sensor 1214. For example, lights 1208A - 1208B and 1210A - 1210B can be incident on the sensor 1214.

[0185] The sensor 1214 can be used to determine one or more characteristics of lights 1208A - 1208B and 1210A - 1210B. In some implementations, a predefined separation 1216 corresponding to the substrate 1206 being at the focal point of the objective lens of the optical system 1200 can be specified. For example, the optical system 1200 can determine whether the distance between lights 1208A - 1208B at the sensor 1214 is at least substantially equal to the predefined separation 1216 (indicating that surface 1206A is currently at the focal point). As another example, the optical system 1200 can determine whether the distance between lights 1210A - 1210B at the sensor 1214 is at least substantially equal to the predefined separation 1216 (indicating that surface 1206B is currently at the focal point).

[0186] FIG. 13 schematically shows an optical system 1300 having a lateral displacement prism 1302. The optical system 1300 can include or be used with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 1300 can be included within the system 100 of FIG. 1. In some implementations, the optical system 1300 can include or be used with the optical system 200 of FIG. 2. In some implementations, the optical system 1300 can include or be used with the optical system 500 of FIG. 5. In some implementations, the optical system 1300 can include or be used with the optical system 800 of FIG. 8A. In some implementations, the optical system 1300 can include or be used with the optical system 820 of FIG. 8B. In some implementations, the optical system 1300 can include or be used with the lateral displacement prism 1000 of FIGS. 10A - 10C. In some implementations, the optical system 1300 can include or be used with the optical system 1100 of FIG. 11. In some implementations, the optical system 1300 can include or be used with the optical system 1200 of FIG. 12. In some implementations, the optical system 1300 can include or be used with the optical system 1400 of FIG. 14. In some implementations, the optical system 1300 can include or be used with the lateral displacement prism 1600 of FIGS. 16A - 16B. In some implementations, the optical system 1300 can include or be used with the beam splitter 1700 of FIG. 17. In some implementations, the optical system 1300 can be included within the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the optical system 1300 can be used with the SIM assembly 2000 of FIG. 20.In some implementations, the optical system 1300 may be included within the imaging module 2100 of FIG. 21. In some implementations, the optical system 1300 may be included within the imaging module 2200 of FIG. 22. In some implementations, the optical system 1300 may be included within the imaging module 2400 of FIG. 24. In some implementations, the optical system 1300 may be included within the system 2500 of FIG. 25. In some implementations, the optical system 1300 may be included within the system 2600 of FIG. 26. In some implementations, the optical system 1300 can include or can be used with the reflective component 2700 of FIG. 27. In some implementations, the optical system 1300 can include or can be used with the reflective component 2800 of FIG. 28. In some implementations, the optical system 1300 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 1300 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 1300 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the optical system 1300 can include or can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the optical system 1300 can include or can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the optical system 1300 can include or can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 1300 can include or can be used with the RIGS 3500 of FIG. 35. In some implementations, the optical system 1300 can include or can be used with the RIGS 3600 of FIG. 36. In some implementations, the optical system 1300 can include or can be used with the piezoelectric phase shifter 3700 of FIG. 37.In some implementations, the optical system 1300 can include, or be used with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 1300 can include, or be used with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 1300 can include, or be used with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 1300 can generate the field of view 4100 of FIG. 41.

[0187] Light 1304 can enter the lateral displacement prism 1302 through the entrance surface. For example, the light 1304 is autofocus light generated by a light source (e.g., a laser diode). Light 1304A can exit the lateral displacement prism 1302 through the exit surface. Light 1304B can exit the lateral displacement prism 1302 through another exit surface. The light 1304A and the light 1304B diverge from each other at a predetermined angle.

[0188] The optical system 1300 includes a substrate 1306. The substrate 1306 can be used to hold one or more samples to be analyzed. In some implementations, the sample on the substrate 1306 can include a nucleic acid material. For example, the substrate 1306 can include a flow cell for imaging a nucleic acid material. The substrate 1306 can include at least a surface 1306A and a surface 1306B. The reflection of the light 1304A on the surface 1306A can form the light 1308A. The reflection of the light 1304A on the surface 1306B can form the light 1310A. The reflection of the light 1304B on the surface 1306A can form the light 1308B. The reflection of the light 1304B on the surface 1306B can form the light 1310B.

[0189] Lights 1308A - 1308B and 1310A - 1310B can be transmitted and / or reflected and / or refracted by at least one other component (not shown) within the optical system 1300. Here, line 1312 schematically shows additional components of the optical system 1300 and the processing of lights 1308A - 1308B and 1310A - 1310B performed in the additional components.

[0190] The optical system 1300 includes a sensor 1314. The sensor 1314 can detect the autofocus light reflected during an autofocus procedure and / or detect the emitted light during an analysis procedure. In some implementations, the sensor 1314 includes a rectangular array of photosensitive elements that can detect the respective positions of one or more portions of the light incident on the sensor 1314. For example, lights 1310A - 1310B can be incident on the sensor 1214.

[0191] The optical system 1300 can include one or more structures. Here, the optical system 1300 includes a structure 1316A and a structure 1316B. The structure 1316A can function to block one or more beams from being transmitted to the sensor 1314. In some implementations, the structure 1316A can block one or more aspects of the autofocus light reflected from the substrate 1306. For example, the structure 1316A can block the light 1308A. The structure 1316B can function to block one or more beams from being transmitted to the sensor 1314. In some implementations, the structure 1316B can block one or more aspects of the autofocus light reflected from the substrate 1306. For example, the structure 1316B can block the light 1308B.

[0192] Sensor 1314 can be used to determine one or more characteristics of lights 1310A to 1310B. In some implementations, a predefined separation 1318 corresponding to the substrate 1306 being at the focal point of the objective lens of the optical system 1300 can be specified. For example, the optical system 1300 can determine whether the distance between lights 1310A to 1310B in the sensor 1314 is at least substantially equal to the predefined separation 1216 (indicating that the surface 1306B is currently at the focal point).

[0193] FIG. 14 schematically shows an optical system 1400 having a lateral displacement prism 1402. The optical system 1400 can include or be used with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 1400 can be included within the system 100 of FIG. 1. In some implementations, the optical system 1400 can include or be used with the optical system 200 of FIG. 2. In some implementations, the optical system 1400 can include or be used with the optical system 500 of FIG. 5. In some implementations, the optical system 1400 can include or be used with the optical system 800 of FIG. 8A. In some implementations, the optical system 1400 can include or be used with the optical system 820 of FIG. 8B. In some implementations, the optical system 1400 can include or be used with the lateral displacement prism 1000 of FIGS. 10A - 10C. In some implementations, the optical system 1400 can include or be used with the optical system 1100 of FIG. 11. In some implementations, the optical system 1400 can include or be used with the optical system 1200 of FIG. 12. In some implementations, the optical system 1400 can include or be used with the optical system 1300 of FIG. 13. In some implementations, the optical system 1400 can include or be used with the lateral displacement prism 1600 of FIGS. 16A - 16B. In some implementations, the optical system 1400 can include or be used with the beam splitter 1700 of FIG. 17. In some implementations, the optical system 1400 can be included within the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the optical system 1400 can be used with the SIM assembly 2000 of FIG. 20.In some implementations, the optical system 1400 may be included within the imaging module 2100 of FIG. 21. In some implementations, the optical system 1400 may be included within the imaging module 2200 of FIG. 22. In some implementations, the optical system 1400 may be included within the imaging module 2400 of FIG. 24. In some implementations, the optical system 1400 may be included within the system 2500 of FIG. 25. In some implementations, the optical system 1400 may be included within the system 2600 of FIG. 26. In some implementations, the optical system 1400 can include or can be used with the reflective component 2700 of FIG. 27. In some implementations, the optical system 1400 can include or can be used with the reflective component 2800 of FIG. 28. In some implementations, the optical system 1400 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 1400 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 1400 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the optical system 1400 can include or can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the optical system 1400 can include or can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the optical system 1400 can include or can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 1400 can include or can be used with the RIGS 3500 of FIG. 35. In some implementations, the optical system 1400 can include or can be used with the RIGS 3600 of FIG. 36. In some implementations, the optical system 1400 can include or can be used with the piezoelectric phase shifter 3700 of FIG. 37.In some implementations, the optical system 1400 can include, or be used with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 1400 can include, or be used with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 1400 can include, or be used with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 1400 can generate the field of view 4100 of FIG. 41.

[0194] Light 1404 can enter the lateral displacement prism 1402 through the entrance surface. For example, light 1404 is autofocus light generated by a light source (e.g., a laser diode). Light 1404A can exit the lateral displacement prism 1402 through the exit surface. Light 1404B can exit the lateral displacement prism 1402 through another exit surface. Light 1404A and light 1404B diverge from each other at a predetermined angle.

[0195] The optical system 1400 includes a substrate 1406. The substrate 1406 can be used to hold one or more samples to be analyzed. In some implementations, the sample on the substrate 1406 can include nucleic acid material. For example, the substrate 1406 can include a flow cell for imaging nucleic acid material. The substrate 1406 can include at least a surface 1406A, a surface 1406B, and a surface 1406C. The reflection of light 1404A at the surface 1406A can form light 1408A. The reflection of light 1404A at the surface 1406B can form light 1410A. The reflection of light 1404A at the surface 1406C can form light 1412A. The reflection of light 1404B at the surface 1406A can form light 1408B. The reflection of light 1404B at the surface 1406B can form light 1410B. The reflection of light 1404B at the surface 1406C can form light 1412B.

[0196] Lights 1408A - 1408B, 1410A - 1410B, and 1412A - 1412B can be transmitted and / or reflected and / or refracted by at least one other component (not shown) within the optical system 1400. Here, line 1414 schematically shows additional components of the optical system 1400 and the processing of lights 1408A - 1408B, 1410A - 1410B, and 1412A - 1412B performed by the additional components.

[0197] The optical system 1400 includes a sensor 1416. The sensor 1416 can detect autofocus light reflected during an autofocus procedure and / or emitted light during an analysis procedure. In some implementations, the sensor 1416 includes a rectangular array of photosensitive elements that can detect the respective positions of one or more portions of the light incident on the sensor 1416. For example, lights 1408A - 1408B and 1410A - 1410B can be incident on the sensor 1416.

[0198] The optical system 1400 can include one or more structures. Here, the optical system 1400 includes a structure 1418A and a structure 1418B. The structure 1418A can function to block one or more beams from being transmitted to the sensor 1416. In some implementations, the structure 1418A can block one or more aspects of the autofocus light reflected at the substrate 1406. For example, the structure 1418A can block the light 1412A. The structure 1418B can function to block one or more beams from being transmitted to the sensor 1416. In some implementations, the structure 1418B can block one or more aspects of the autofocus light reflected at the substrate 1406. For example, the structure 1418B can block the light 1412B.

[0199] Sensor 1416 can be used to determine one or more characteristics of lights 1408A - 1408B and 1410A - 1410B. In some implementations, a predefined separation 1420 corresponding to the substrate 1406 being at the focal point of the objective lens of the optical system 1400 can be specified. For example, the optical system 1400 can determine whether the distance between lights 1408A - 1408B at the sensor 1416 is at least substantially equal to the predefined separation 1420 (indicating that surface 1406A is currently at the focal point). As another example, the optical system 1400 can determine whether the distance between lights 1410A - 1410B at the sensor 1416 is at least substantially equal to the predefined separation 1420 (indicating that surface 1406B is currently in focus).

[0200] FIG. 15 shows an embodiment of autofocus light in sensor 1500. Sensor 1500 can be used with or incorporated into one or more other embodiments described herein. In some implementations, sensor 1500 can be included within system 100 of FIG. 1. In some implementations, sensor 1500 can be used with or incorporated into optical system 200 of FIG. 2. In some implementations, sensor 1500 can be used with or incorporated into optical system 500 of FIG. 5. In some implementations, sensor 1500 can be used with or incorporated into optical system 800 of FIG. 8A. In some implementations, sensor 1500 can be used with or incorporated into optical system 820 of FIG. 8B. In some implementations, sensor 1500 can be used with or incorporated into optical system 1100 of FIG. 11. In some implementations, sensor 1500 can be used with or incorporated into optical system 1200 of FIG. 12. In some implementations, sensor 1500 can be used with or incorporated into optical system 1300 of FIG. 13. In some implementations, sensor 1500 can be used with or incorporated into optical system 1400 of FIG. 14. In some implementations, sensor 1500 can be used with or incorporated into imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, sensor 1500 can be used with or incorporated into imaging module 2100 of FIG. 21. In some implementations, sensor 1500 can be used with or incorporated into imaging module 2200 of FIG. 22. In some implementations, sensor 1500 can be used with or incorporated into imaging module 2400 of FIG. 24.In some implementations, sensor 1500 can be used with or included in the optical system 2500 of FIG. 25. In some implementations, sensor 1500 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, sensor 1500 can be used with the reflective component 2700 of FIG. 27. In some implementations, sensor 1500 can be used with the reflective component 2800 of FIG. 28. In some implementations, sensor 1500 can receive the autofocus light 2900 of FIG. 29. In some implementations, sensor 1500 can receive the autofocus light 3000 of FIG. 30. In some implementations, sensor 1500 can receive the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, sensor 1500 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, sensor 1500 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, sensor 1500 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, sensor 1500 can be used with the RIGS 3500 of FIG. 35. In some implementations, sensor 1500 can be used with the RIGS 3600 of FIG. 36. In some implementations, sensor 1500 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, sensor 1500 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, sensor 1500 can be used with the projection lens 3900 of FIG. 39. In some implementations, sensor 1500 can be used with the projection lens 4000 of FIG. 40. In some implementations, sensor 1500 can capture the field of view 4100 of FIG. 41.

[0201] Sensor 1500 shows a light spot corresponding to the alignment of the incident light by sensor 1500. In some implementations, the light spot corresponds to a portion of the autofocus light reflected from each surface of the substrate. For example, the spot labeled "S2" may be reflected from the upper surface of the fluid channel in the flow cell. As another example, the spot labeled "S3" may be reflected from the bottom surface of the fluid channel in the flow cell. The separation between two S2 spots tracks the distance between the S2 surface and the objective lens of the optical system. The separation between two S3 spots tracks the distance between the S3 surface and the objective lens of the optical system. Sensor 1500 can form a divergence between the beams of the autofocus light (e.g., using a lateral displacement prism) and / or indicate at least one of the desired autofocus reflections or unwanted autofocus reflections, and provide a clear image that facilitates efficient and accurate tracking of the focus in the optical system.

[0202] Figures 16A - 16B illustrate an embodiment of a lateral displacement prism 1600. The lateral displacement prism 1600 can be used with or incorporated into one or more other embodiments described herein. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the system 100 of FIG. 1. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 200 of FIG. 2. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 500 of FIG. 5. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 800 of FIG. 8A. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 820 of FIG. 8B. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 1100 of FIG. 11. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 1200 of FIG. 12. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 1300 of FIG. 13. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the optical system 1400 of FIG. 14. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the imaging module 2100 of FIG. 21. In some implementations, the lateral displacement prism 1600 can be used with or incorporated into the imaging module 2200 of FIG. 22.In some implementations, the lateral displacement prism 1600 can be used with or included in the imaging module 2400 of FIG. 24. In some implementations, the lateral displacement prism 1600 can be used with or included in the optical system 2500 of FIG. 25. In some implementations, the lateral displacement prism 1600 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, the lateral displacement prism 1600 can be used with the reflective component 2700 of FIG. 27. In some implementations, the lateral displacement prism 1600 can be used with the reflective component 2800 of FIG. 28. In some implementations, the lateral displacement prism 1600 can generate the autofocus light 2900 of FIG. 29. In some implementations, the lateral displacement prism 1600 can generate the autofocus light 3000 of FIG. 30. In some implementations, the lateral displacement prism 1600 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the lateral displacement prism 1600 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the lateral displacement prism 1600 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the lateral displacement prism 1600 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the lateral displacement prism 1600 can be used with the RIGS 3500 of FIG. 35. In some implementations, the lateral displacement prism 1600 can be used with the RIGS 3600 of FIG. 36. In some implementations, the lateral displacement prism 1600 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the lateral displacement prism 1600 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the lateral displacement prism 1600 can be used with the projection lens 3900 of FIG. 39.In some implementations, the lateral displacement prism 1600 can be used with the projection lens 4000 of FIG. 40.

[0203] The lateral displacement prism 1600 includes a partially reflective layer 1602. In some implementations, the lateral displacement prism 1600 can be manufactured by assembling prism pieces 1604A and prism piece 1604B with the partially reflective layer 1602 positioned at the junction between the two prism pieces, and the prism pieces 1604A to 1604B are at least substantially identical to each other. Each of the prism pieces 1604A to 1604B has a parallelogram outer shape as seen in the current figure. In some implementations, the prism piece 1604A is a quadrilateral having sides 1606A and 1606B that are parallel to each other, and sides 1606C and 1606D that are parallel to each other. In some implementations, the prism piece 1604B is a quadrilateral having sides 1608A and 1608B that are parallel to each other, and sides 1608C and 1608D that are parallel to each other. The assembly of the prism pieces 1604A to 1604B having the partially reflective layer 1602 also has a parallelogram outer shape as seen in the current figure.

[0204] The lateral displacement prism 1600 includes a prism 1610 and a prism 1612. Each of the prisms 1610 - 1612 can have a wedge outer shape. For example, the wedge outer shape can include a triangular shape. In some implementations, the prism 1610 has a side portion 1610A that can be regarded as the exit side of the prism 1610. For example, the side portion 1610B can be on the opposite side of the side portion 1610A within the prism 1610, and the side portions 1610A - 1610B can form a non - zero angle with respect to each other. In some implementations, the prism 1612 has a side portion 1612A that can be regarded as the exit side of the prism 1612. For example, the side portion 1612B can be opposite to the side portion 1612A within the prism 1612, and the side portions 1612A - 1612B can form a non - zero angle with respect to each other. The lateral displacement prism 1600 can be assembled by disposing the side portion 1610B of the prism 1610 against the side portion 1606B of the prism piece 1604A and disposing the side portion 1612B of the prism 1612 against the side portion 1608B of the prism piece 1604B. In some implementations, this facilitates the side portions 1610A and 1612A to function as the exit surfaces of the lateral displacement prism 1600. For example, this arrangement can provide a lateral displacement prism 1600 having exit surfaces with non - zero angles with respect to each other.

[0205] The lateral displacement prism 1600 can also or alternatively include, for example, as shown in FIG. 16B, a prism 1610' and a prism 1612'. Each of the prisms 1610' and 1612' can have a wedge outer shape. For example, the wedge outer shape can include a truncated triangular shape. In some implementations, the prism 1610' has a side portion 1610A' that can be regarded as the exit side of the prism 1610'. For example, the side portion 1610B' can be on the opposite side of the side portion 1610A' within the prism 1610', and the side portions 1610A' and 1610B' can form a non-zero angle with respect to each other. In some implementations, the prism 1612' has a side portion 1612A' that can be regarded as the exit side of the prism 1612'. For example, the side portion 1612B' can be on the opposite side of the side portion 1612A' within the prism 1612', and the side portions 1612A' and 1612B' can form a non-zero angle with respect to each other. The lateral displacement prism 1600 can be assembled by disposing the side portion 1610B of the prism 1610 against the side portion 1606B of the prism piece 1604A and disposing the side portion 1612B of the prism 1612 against the side portion 1608B of the prism piece 1604B. In some implementations, this facilitates the side portions 1610A and 1612A to function as the exit surface of the lateral displacement prism 1600. For example, this arrangement can provide a lateral displacement prism 1600 having an exit surface with a non-zero angle with respect to each other.

[0206] FIG. 17 shows an embodiment of a beam splitter 1700. The beam splitter 1700 can be used with or incorporated into one or more other embodiments described herein. In some implementations, the beam splitter 1700 can be used with or incorporated into the system 100 of FIG. 1. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 200 of FIG. 2. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 500 of FIG. 5. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 800 of FIG. 8A. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 820 of FIG. 8B. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 1100 of FIG. 11. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 1200 of FIG. 12. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 1300 of FIG. 13. In some implementations, the beam splitter 1700 can be used with or incorporated into the optical system 1400 of FIG. 14. In some implementations, the beam splitter 1700 can be used with or incorporated into the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the beam splitter 1700 can be used with or incorporated into the imaging module 2100 of FIG. 21. In some implementations, the beam splitter 1700 can be used with or incorporated into the imaging module 2200 of FIG. 22.In some implementations, the beam splitter 1700 can be used with or included in the imaging module 2400 of FIG. 24. In some implementations, the beam splitter 1700 can be used with or included in the optical system 2500 of FIG. 25. In some implementations, the beam splitter 1700 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, the beam splitter 1700 can be used with the reflective component 2700 of FIG. 27. In some implementations, the beam splitter 1700 can be used with the reflective component 2800 of FIG. 28. In some implementations, the beam splitter 1700 can generate the autofocus light 2900 of FIG. 29. In some implementations, the beam splitter 1700 can generate the autofocus light 3000 of FIG. 30. In some implementations, the beam splitter 1700 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the beam splitter 1700 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the beam splitter 1700 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the beam splitter 1700 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the beam splitter 1700 can be used with the RIGS 3500 of FIG. 35. In some implementations, the beam splitter 1700 can be used with the RIGS 3600 of FIG. 36. In some implementations, the beam splitter 1700 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the beam splitter 1700 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the beam splitter 1700 can be used with the projection lens 3900 of FIG. 39.In some implementations, beam splitter 1700 can be used with projection lens 4000 of FIG. 40.

[0207] Beam splitter 1700 includes a partially reflective layer 1702. Beam splitter 1700 includes a reflective surface 1704 and a reflective surface 1706. Light 1708 can enter beam splitter 1700. For example, light 1708 is autofocus light generated by a light source (e.g., a laser diode). After reflection at reflective surface 1704, light 1708 can be incident on partially reflective layer 1702. As a result, light 1708A reflected at partially reflective layer 1702 can be formed by beam splitter 1700. Also, light 1708B can be transmitted through partially reflective layer 1702 and reflected at reflective surface 1706. Light 1708A and light 1708B diverge from each other at a predetermined angle.

[0208] FIG. 18 shows an embodiment of the imaging module 1800. The imaging module 1800 can include or can be used with one or more other embodiments described herein. In some implementations, the imaging module 1800 can include or can be used with the system 4200 of FIG. 42. In some implementations, the imaging module 1800 can include or can be used with at least some components of the computing device 4300 of FIG. 43. In some implementations, the imaging module 1800 can be included within the system 100 of FIG. 1. In some implementations, the imaging module 1800 can include or can be used with the optical system 200 of FIG. 2. In some implementations, the imaging module 1800 can include or can be used with the optical system 500 of FIG. 5. In some implementations, the imaging module 1800 can include or can be used with the optical system 800 of FIG. 8A. In some implementations, the imaging module 1800 can include or can be used with the optical system 820 of FIG. 8B. In some implementations, the imaging module 1800 can include or can be used with the lateral displacement prism 1000 of FIGS. 10A-10C. In some implementations, the imaging module 1800 can include or can be used with the optical system 1100 of FIG. 11. In some implementations, the imaging module 1800 can include or can be used with the optical system 1200 of FIG. 12. In some implementations, the imaging module 1800 can include or can be used with the optical system 1300 of FIG. 13. In some implementations, the imaging module 1800 can include or can be used with the optical system 1400 of FIG. 14. In some implementations, the imaging module 1800 can include or can be used with the lateral displacement prism 1600 of FIGS. 16A-16B.In some implementations, the imaging module 1800 can include, or be used in conjunction with, the beam splitter 1700 of FIG. 17. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the SIM assembly 2000 of FIG. 20. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the imaging module 2100 of FIG. 21. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the imaging module 2200 of FIG. 22. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the imaging module 2400 of FIG. 24. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the optical system 2500 of FIG. 25. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the optical system 2600 of FIG. 26. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the reflective component 2700 of FIG. 27. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the reflective component 2800 of FIG. 28. In some implementations, the imaging module 1800 can generate the autofocus light 2900 of FIG. 29. In some implementations, the imaging module 1800 can generate the autofocus light 3000 of FIG. 30. In some implementations, the imaging module 1800 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the laser engine heat sink 3200 of FIGS. 32A - 32C.In some implementations, the imaging module 1800 can include, or be used in conjunction with, the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the SIM assembly 3400 of FIG. 34. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the RIGS 3500 of FIG. 35. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the RIG S 3600 of FIG. 36. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the projection lens 3900 of FIG. 39. In some implementations, the imaging module 1800 can include, or be used in conjunction with, the projection lens 4000 of FIG. 40. In some implementations, the imaging module 1800 can generate the field of view 4100 of FIG. 41.

[0209] The imaging module 1800 includes a plurality of components and / or devices that can be integrated to operate coherently as a system to perform one or more tasks. In some implementations, the imaging module 1800 performs imaging as part of analyzing a sample. For example, the imaging module 1800 can detect fluorescence emitted from a sample of genetic material. The imaging module 1800 includes a SIM assembly 1802 that is only partially visible in this figure. For example, the SIM assembly can generate spatially structured light for illuminating the sample material. The imaging module 1800 includes an objective lens 1804. In some implementations, the objective lens 1804 can transmit SIM light from the SIM assembly 1802 and apply the SIM light to a substrate (not shown) that holds the sample. The imaging module 1800 includes a z-stage 1806. In some implementations, the z-stage 1806 can change (e.g., increase or decrease) the distance (herein referred to as the z-distance) between the objective lens 1804 and the substrate that holds the sample.

[0210] The imaging module 1800 can include one or more portions of a housing. In some implementations, the housing can substantially surround the components of the imaging module 1800. For example, the housing 1808 can at least partially surround the SIM assembly 1802. As another example, the housing 1810 can at least partially surround the emission optics of the imaging module 1800 (e.g., one or more tube lenses and / or sensors). As another example, the housing 1812 can at least partially surround the SIM assembly 1802 and / or at least partially surround the detection optics.

[0211] One or more of the housings may not be present in the imaging module 1800, whereby some of the components may be visible. This may occur, for example, during the assembly process and / or during maintenance or repair. FIGS. 19A-19B show an embodiment of the imaging module 1800 of FIG. 18. The imaging module 1800 is shown in a partially unassembled or disassembled state. For example, the housings 1808 and 1810 (FIG. 18) are currently not present in the imaging module 1800. Visible at least partially in this figure are the SIM assembly 1802, the autofocus module 1814, the compensator 1816, and the emission optical system 1818. The SIM assembly 1802, the autofocus module 1814, the compensator 1816, and the emission optical system 1818, as well as the objective lens 1804, can be used when the imaging module 1800 (in the operating state) performs imaging of the substrate 1820 shown for illustrative purposes. For example, the autofocus module 1814 can perform one or more autofocus functions described elsewhere in this specification.

[0212] In some implementations, the emission optical system 1818 includes a filter assembly 1822. The filter assembly 1822 can include at least one filter. For example, the filter assembly 1822 can include one or more of the filter 212 of FIG. 2 or the filter 506 of FIG. 5. In some implementations, the emission optical system 1818 includes a tube lens 1824. For example, the tube lens 1824 can be one or more of the tube lens 214 of FIG. 2, the tube lens 508 of FIG. 5, or the tube lens 802 of FIG. 8A. The tube lens 1824 can be assigned to a blue detector channel. In some implementations, the emission optical system 1818 includes a tube lens 1826. The tube lens 1826 can be assigned to a green detector channel. For example, the tube lens 1826 can be one or more of the tube lens 214 of FIG. 2, the tube lens 508 of FIG. 5, or the tube lens 802 of FIG. 8A. In some implementations, the emission optical system 1818 includes a filter assembly 1828. For example, the filter assembly 1828 can include one or more of the filter 216, the reflective component 226, or the structure 228 of FIG. 2. As another example, the filter assembly 1828 can include one or more of the filter 510, the reflective component 516, or the structure 518 of FIG. 5. As another example, the filter assembly 1828 can include one or more of the filter 804, the reflective components 810A - 810B, or the structure 812 of FIG. 8A.

[0213] In some implementations, the emission optical system 1818 includes a sensor assembly 1830. The sensor assembly 1830 can be assigned to a blue detector channel. The sensor assembly 1830 can include one or more sensors for the emitted light and / or autofocus light. For example, the sensor assembly 1830 can include one or more of the sensors 120 of FIG. 1, the sensors 220 of FIG. 2, the sensor 514 of FIG. 5, the sensor 808 of FIG. 5, the sensor 1112 of FIG. 11, the sensor 1214 of FIG. 12, the sensor 1314 of FIG. 13, or the sensor 1416 of FIG. 14. In some implementations, the emission optical system 1818 includes a sensor assembly 1832. The sensor assembly 1832 can be assigned to a green detector channel. The sensor assembly 1832 can include one or more sensors for the emitted light and / or autofocus light. For example, the sensor assembly 1832 can include one or more of the sensors 120 of FIG. 1, the sensors 220 of FIG. 2, the sensor 514 of FIG. 5, the sensor 808 of FIG. 5, the sensor 1112 of FIG. 11, the sensor 1214 of FIG. 12, the sensor 1314 of FIG. 13, or the sensor 1416 of FIG. 14.

[0214] FIG. 20 shows one embodiment of a SIM assembly 2000. The SIM assembly 2000 can be used with or incorporated into one or more other embodiments described herein. In some implementations, the SIM assembly 2000 can be used with or incorporated into the system 100 of FIG. 1. In some implementations, the SIM assembly 2000 can be used with or incorporated into the optical system 200 of FIG. 2. In some implementations, the SIM assembly 2000 can be used with or incorporated into the optical system 500 of FIG. 5. In some implementations, the SIM assembly 2000 can be used with or incorporated into the optical system 820 of FIG. 8B. In some implementations, the SIM assembly 2000 can be used with or incorporated into the optical system 1100 of FIG. 11. In some implementations, the SIM assembly 2000 can be used with or incorporated into the optical system 1200 of FIG. 12. In some implementations, the SIM assembly 2000 can be used with or incorporated into the optical system 1300 of FIG. 13. In some implementations, the SIM assembly 2000 can be used with or incorporated into the optical system 1400 of FIG. 14. In some implementations, the SIM assembly 2000 can be used with or incorporated into the imaging module 1800 of FIGS. 18 or 19A-19B. In some implementations, the SIM assembly 2000 can be used with or incorporated into the imaging module 2100 of FIG. 21. In some implementations, the SIM assembly 2000 can be used with or incorporated into the imaging module 2200 of FIG. 22. In some implementations, the SIM assembly 2000 can include or be used with the imaging module 2400 of FIG. 24.In some implementations, the SIM assembly 2000 can include, or be used with, the optical system 2500 of FIG. 25. In some implementations, the SIM assembly 2000 can include, or be used with, the optical system 2600 of FIG. 26. In some implementations, the SIM assembly 2000 can include, or be used with, the reflective component 2700 of FIG. 27. In some implementations, the SIM assembly 2000 can include, or be used with, the reflective component 2800 of FIG. 28. In some implementations, the SIM assembly 2000 can generate the autofocus light 2900 of FIG. 29. In some implementations, the SIM assembly 2000 can generate the autofocus light 3000 of FIG. 30. In some implementations, the SIM assembly 2000 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the SIM assembly 2000 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the SIM assembly 2000 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the SIM assembly 2000 can include, or be used with, the SIM assembly 3400 of FIG. 34. In some implementations, the SIM assembly 2000 can include, or be used with, the RIGS 3500 of FIG. 35. In some implementations, the SIM assembly 2000 can include, or be used with, the RIGS 3600 of FIG. 36. In some implementations, the SIM assembly 2000 can include, or be used with, the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the SIM assembly 2000 can include, or be used with, the piezoelectric phase shifter 3800 of FIG. 38.In some implementations, the SIM assembly 2000 can include or be used with the projection lens 3900 of FIG. 39. In some implementations, the SIM assembly 2000 can include or be used with the projection lens 4000 of FIG. 40. In some implementations, the SIM assembly 2000 can generate the field of view 4100 of FIG. 41.

[0215] The SIM assembly 2000 includes a rotatable mirror 2002. The SIM assembly 2000 includes a light source 2004. In some implementations, the light source 2004 provides light that it receives through at least one optical fiber cable 2006. For example, the light source 2004 and the optical fiber cable 2006 can be collectively regarded as a fiber activation module. The SIM assembly 2000 includes a grating 2008 and a grating 2010. In some implementations, the grating 2008 and / or 2010 can function as a diffraction component with respect to the light from the light source 2004. For example, the grating 2008 and / or 2010 can comprise a substrate having a periodic structure, and the substrate is combined with a prism. The gratings 2008 and 2010 can be positioned relative to each other according to one or more arrangements. Here, the gratings 2008 and 2010 face each other within the SIM assembly 2000. The gratings 2008 and 2010 can be substantially identical to each other or can have one or more differences. The size, periodicity, or other spatial aspect of one of the gratings 2008 and 2010 may be different from that of the other(s). The grating orientation of one of the gratings 2008 and 2010 (i.e., the spatial orientation of the periodic structure) may be different from that of the other(s). In some implementations, the respective grating orientations of the gratings 2008 and 2010 can be substantially perpendicular to each other or at any other angle with respect to each other although the gratings themselves face each other. In some implementations, the gratings 2008 and 2010 can be in an offset position with respect to the rotatable mirror 2002. In some implementations, the grating 2008 and / or 2010 can be in a fixed position with respect to the light source 2004.

[0216] The SIM assembly 2000 can include one or more components (e.g., as a phase selector) to facilitate phase selection for light to be applied to a sample. Here, the SIM assembly 2000 includes a phase shifter 2012. In some implementations, the phase shifter 2012 includes a piezoelectric fringe shifter. For example, the phase shifter 2012 can receive light from gratings 2008 and / or 2010 and perform phase selection on some or all of that light. For example, the phase shifter 2012 can be used to control the phase of a structured light pattern for which a particular image is to be captured. The phase shifter 2012 can include a piezoelectric actuator. For example, a piezoelectric piston system can be used to achieve phase selection. Other approaches can be used. For example, a tilted optical plate can be used for phase selection. For example, the SIM assembly 2000 is here implemented on a board 2014, and one or more regions of the board 2014 can be tilted to achieve phase selection. As another example, one or more of the gratings 2008 and 2010 can be moved (e.g., translated) for phase selection, such as by a piezoelectric actuator. The light emitted from the phase shifter 2012 may be referred to as phase-selected light to indicate that the light has been adjusted according to a particular phase selection. In some implementations, the gratings 2008 and / or 2010 can be in a fixed position relative to the light source 2004.

[0217] The SIM assembly 2000 includes a projection lens 2016 that can include one or more optical components (e.g., lenses) for conditioning the light received from the phase shifter 2012. For example, the projection lens 2016 can control the characteristics of the light before the light enters an objective lens (e.g., the objective lens 204 of FIG. 2).

[0218] The rotatable mirror 2002 can be used to redirect at least one light beam toward and / or to reach one or more of the gratings 2008 or 2010. The rotatable mirror 2002 can include one or more materials so as to sufficiently reflect the electromagnetic wave by which the sample is illuminated. In some implementations, the light from the light source 2004 includes a laser beam of one or more wavelengths. For example, a metal-coated mirror and / or a dielectric mirror can be used. The rotatable mirror 2002 can be double-sided. For example, the rotatable mirror 2002 can be regarded as double-sided if it can perform reflection on at least a part of both of its sides (for example, being reflective at the first end for the first beam path and being reflective at the second end opposite to the first end for the second beam path).

[0219] The rotatable mirror 2002 can include an elongated member. The rotatable mirror 2002 can have any of various form factors or other shape characteristics. The rotatable mirror 2002 can have a substantially flat configuration. The rotatable mirror 2002 can have a substantially square or other rectangular shape. The rotatable mirror 2002 can have rounded corners. The rotatable mirror 2002 can have a substantially constant thickness. The reflective surface of the rotatable mirror 2002 can be substantially planar.

[0220] The rotatable mirror 2002 can be supported by the axis 2018 of the SIM assembly 2000. The axis 2018 can enable the rotatable mirror 2002 to rotate about the axis 2018 in either or both directions. The axis 2018 can be made of a material having sufficient rigidity to hold and manipulate the rotatable mirror 2002, and such materials include, but are not limited to, metals. The axis 2018 can be coupled substantially at the center of the rotatable mirror 2002. For example, the rotatable mirror 2002 can have an opening at the center or a notch from one side reaching the center to facilitate coupling with the axis 2018. The axis 2018 can extend at least substantially to one side of the rotatable mirror 2002. As another example, the axis 2018 can include separate axis portions coupled to respective faces of the rotatable mirror 2002 without requiring any openings within the rotatable mirror 2002. The axis 2018 can have at least one suspension with respect to the substrate 2014. The suspension can be positioned at the ends of the axis 2018 on both sides of the rotatable mirror 2002. The suspension can include bearings or other features that facilitate low-friction operation.

[0221] The rotatable mirror 2002 can be actuated to assume one or more positions. Any form of motor or other actuator can be used to control the rotatable mirror 2002. In some implementations, a stepper motor 2020 is used. The stepper motor 2020 can be coupled to the axis 2018 and used to rotate the axis 2018, and thereby the rotatable mirror 2002, to assume a desired position. In some implementations, the rotatable mirror 2002 rotates in the same direction (e.g., always clockwise or always counterclockwise about the axis of rotation of the axis 2018) towards a new position. In some implementations, the rotatable mirror 2002 reciprocates between two or more positions (e.g., alternately clockwise or counterclockwise about the axis of rotation of the axis 2018).

[0222] In some implementations, the light source 2004 can generate light that first propagates towards the mirror 2024. After reflection at the mirror 2024, the light propagates towards the grating 2010. The rotatable mirror 2002 can now be positioned (e.g., oriented about the axis of rotation of the axis 2018) such that the first end 2022 of the rotatable mirror 2002 does not block the light. Currently, the first end 2022 can be positioned closer to the viewer than the light that can propagate within the plane of the drawing. That is, the reflective surface of the rotatable mirror 2002 facing towards the light source 2004 does not currently block the light because the first end 2022 does not block the light path. Thus, the light propagates (through air, vacuum, or another fluid) until it reaches the grating 2010.

[0223] The light interacts with the grating 2010 in one or more ways. In some implementations, the light undergoes diffraction based on the grating 2010. Here, the light emitted from the grating 2010 can be structured light (e.g., light having one or more pattern fringes) based on the interaction with the light. The light emitted from the grating 2010 initially propagates substantially in a direction generally towards the projection lens 2016. However, the position of the rotatable mirror 2002 is such that the second end 2026 of the rotatable mirror 2002 blocks the light. The second end 2026 can be on the opposite side of the first end 2022. In some implementations, the first end 2022 and the second end 2026 can be positioned at any angle relative to each other, such as any angle from 0 degrees to 180 degrees. Currently, the second end 2026 can be positioned as close to the viewer as the light. That is, the reflective surface of the rotatable mirror 2002 facing towards the grating 2010 blocks the light emitted from the grating 2010 because the second end 2026 blocks the light path. Thus, the rotatable mirror 2002 directs the light towards the phase shifter 2012.

[0224] The phase shifter 2012 performs phase selection of light. For example, the phase shifter 2012 selects the pattern phase that the sample should receive in the current illumination (e.g., for the purpose of capturing one or more specific images). The light is emitted from the phase shifter 2012, propagates towards the projection lens 2016, and enters the projection lens 2016. The light corresponds to the specific phase selection performed using the phase shifter 2012. Thus, the light can be characterized as phase-selected light. Then, the light can continue to propagate through the system, for example, to illuminate the sample.

[0225] Here, the characteristics of the phase-selected electromagnetic wave of the light entering the projection lens 2016 correspond to the fact that the light is diffracted by the grating 2010 and the fact that the phase selection is performed by the phase shifter 2012. Further, the involvement of the grating 2010 here is the result of positioning the rotatable mirror 2002 such that the second end 2026 of the rotatable mirror 2002 blocks the light, while the first end 2022 does not block the light.

[0226] Here, assume that the rotatable mirror 2002 is instead placed at a different position. Here, the light source 2004 first generates light that is reflected by the mirror 2024 and then propagates towards the grating 2010. The rotatable mirror 2002 is currently positioned such that the first end 2022 of the rotatable mirror 2002 blocks the light (e.g., oriented about the axis of rotation of the axis 2018). The first end 2022 can be positioned as close to the viewer as the light. That is, the reflective surface of the rotatable mirror 2002 facing the light source 2004 blocks the light because the first end 2022 blocks the path of the light. Thus, the light propagates (through air, vacuum, or another fluid) until it reaches the grating 2008.

[0227] Light interacts with grating 2008 in one or more ways. In some implementations, light undergoes diffraction based on grating 2008. Here, the light has structured light (e.g., stripes of one or more patterns) emitted from grating 2008 based on the interaction with the light. The light propagates in a direction substantially towards phase shifter 2012. The position of rotatable mirror 2002 is such that the second end 2026 of rotatable mirror 2002 does not block the light. Currently, the second end 2026 can be positioned closer to the viewer than the light. That is, since the second end 2026 does not block the path of the light, currently none of the reflective surfaces of rotatable mirror 2002 block the light. Thus, the light propagates until it reaches phase shifter 2012.

[0228] Phase shifter 2012 performs phase selection of the light. For example, phase shifter 2012 selects the pattern phase that the sample should receive in the current illumination (e.g., for the purpose of capturing one or more specific images). The light is emitted from phase shifter 2012 and propagates towards projection lens 2016 and enters projection lens 2016. The light corresponds to the specific phase selection performed using phase shifter 2012. Thus, the light can be characterized as phase - selected light. Then, the light can continue to propagate through the system, for example, to illuminate a sample.

[0229] Here, the characteristics of the phase - selected electromagnetic wave of the light correspond to the fact that the light is diffracted by grating 2008 and the fact that phase selection is performed by phase shifter 2012. Further, the involvement of grating 2008 is here the result of positioning rotatable mirror 2002 such that the second end 2022 of rotatable mirror 2002 blocks the light while the first end 2026 does not. Rotatable mirror 2002 can repeatedly assume different positions by various rotations. For example, rotatable mirror 2002 can reciprocate between positions. As another example, rotatable mirror 2002 can rotate in the same direction (e.g., clockwise or counter - clockwise from the perspective of stepper motor 2020) to repeatedly assume positions.

[0230] The SIM assembly 2000 can include one or more anamorphic prisms 2028. When a single anamorphic prism is used, light can exit the prism at a certain angle. A pair of anamorphic prisms can be arranged so that the exiting light is parallel to the incoming light. In some implementations, the anamorphic prism 2028 can transform light from the light source 2004 with respect to one or more points. The light from the light source 2004 (e.g., the exit surface of the optical fiber cable 2006) can have a specific shape (e.g., a square shape), and this light will enter the flow cell and then be imaged by the sensors of the system. Further, the sensors can have a shape different from the light from the light source 2004 (e.g., a rectangular shape), and the anamorphic prism can change the shape of the light based on the sensor shape. For example, the anamorphic prism 2028 can stretch a square fiber surface into a rectangle. As another example, the anamorphic prism 2028 can convert an elliptical beam into a circular light beam and / or convert an annular light beam into an elliptical beam. Due to the problem of using a square multimode laser fiber for the excitation light source to generate a rectangular illumination footprint, insufficient irradiance on the sample plane may occur. Such technical problems may cause a reduction in sequencing performance due to a decrease in the signal reaching the sensor from the DNA clusters. This is solved by expanding the square fiber of one axis through the use of at least one anamorphic prism, including but not limited to one or more pairs of anamorphic prisms. In some examples, a custom rectangular laser fiber can be implemented, but a square fiber may be preferred due to manufacturability and / or maintainability. That is, the problem of custom fibers can be due to tolerance issues. Matching the required numerical aperture is difficult and / or may be unreliable at the preform stage of the fiber preform. In addition, custom rectangular fibers may also be difficult to form the core dimensions required to generate the required illumination footprint.Finally, the fiber bending radius with respect to both axes of the custom rectangular fiber may be less well known than that of square fibers.

[0231] The rectangular illumination footprint ensures that all laser power reaches the sample, taking into account that all transmission losses pass through the excitation path. The laser illumination footprint using the A.P.P for this project converts the square to a rectangle. The square footprint did not match the sample plane tile dimensions. Reaching the sensor with a full square illumination caused unnecessary illumination of adjacent tiles, which could prematurely reduce the intensity in the process. During the initial prototype stage, baffles were included in the excitation path to clip the upper and bottom portions of the square illumination footprint, which resulted in a reduction in the irradiance of the square fiber. Instead, an anamorphic prism pair set is included within the SIM beam path. The 0.9 mm × 1.2 mm sample tile dimensions mean that they match the aspect ratio of the sensor of the integrated imaging module. The introduction of the anamorphic prism pair expands the square fiber output and shapes it into a rectangle. This means that this means can optimize the amount of laser power exciting the sample. This is demonstrated by comparing the rectangular FOV to the square FOV with respect to the imaging tile area. This is to determine how much more laser power the rectangular footprint can provide over the square footprint. Overlap of torso to rectangle [%] = (area_torso) / (area_rectangle) = 0.968 / 1.08 = 0.896 = 89.6% Overlap of torso to square [%] = (area_torso) / (area_square) = 0.968 / 1.44 = 0.672 = 67.2%.

[0232] That is, by using an anamorphic prism pair to reshape the square fiber output, the power increase rate is (rectangular pair barrel overlap%) / (square pair barrel overlap%) = 89.6 / 67.2 = 1.3333%. As a result of implementing the anamorphic prism pair, it is not necessary to clip the upper and lower sections of the laser, and the irradiance on the sample plane is also increased by 33%.

[0233] The stepper motor 2020 can be referred to as a Rotating In-Plane Grating Switch (RIGS). In some implementations, the stepper motor 2020 actuates an axis 2018 that rotates a rotatable mirror 2002 (i.e., the "rotating" of the RIGS). The rotatable mirror 2002 rotates within the plane (i.e., the "in-plane" of the RIGS). By rotating the rotatable mirror 2002, either grating 2008 or grating 2010 is used (i.e., the "grating switch" of the RIGS).

[0234] FIG. 21 shows an embodiment of the imaging module 2100. The imaging module 2100 can be used with or incorporated into one or more other embodiments described herein. In some implementations, the imaging module 2100 can include or be used with the system 4200 of FIG. 42. In some implementations, the imaging module 2100 can include or be used with at least some components of the computing device 4300 of FIG. 43. In some implementations, the imaging module 2100 can be used with or incorporated into the system 100 of FIG. 1. In some implementations, the imaging module 2100 can be used with or incorporated into the optical system 200 of FIG. 2. In some implementations, the imaging module 2100 can be used with or incorporated into the optical system 500 of FIG. 5. In some implementations, the imaging module 2100 can be used with or incorporated into the optical system 820 of FIG. 8B. In some implementations, the imaging module 2100 can be used with or incorporated into the optical system 1100 of FIG. 11. In some implementations, the imaging module 2100 can be used with or incorporated into the optical system 1200 of FIG. 12. In some implementations, the imaging module 2100 can be used with or incorporated into the optical system 1300 of FIG. 13. In some implementations, the imaging module 2100 can be used with or incorporated into the optical system 1400 of FIG. 14. In some implementations, the imaging module 2100 can be used with or incorporated into the imaging module 1800 of FIG. 18 or FIGS. 19A-19B. In some implementations, the imaging module 2100 can be used with the SIM assembly 2000 of FIG. 20. In some implementations, the imaging module 2100 can be used with the imaging module 2200 of FIG. 22.In some implementations, the imaging module 2100 can include, or be used with, the imaging module 2400 of FIG. 24. In some implementations, the imaging module 2100 can include, or be used with, the optical system 2500 of FIG. 25. In some implementations, the imaging module 2100 can include, or be used with, the optical system 2600 of FIG. 26. In some implementations, the imaging module 2100 can include, or be used with, the reflective component 2700 of FIG. 27. In some implementations, the imaging module 2100 can include, or be used with, the reflective component 2800 of FIG. 28. In some implementations, the imaging module 2100 can generate the autofocus light 2900 of FIG. 29. In some implementations, the imaging module 2100 can generate the autofocus light 3000 of FIG. 30. In some implementations, the imaging module 2100 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the imaging module 2100 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the imaging module 2100 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the imaging module 2100 can include, or be used with, the SIM assembly 3400 of FIG. 34. In some implementations, the imaging module 2100 can include, or be used with, the RIGS 3500 of FIG. 35. In some implementations, the imaging module 2100 can include, or be used with, the RIGS 3600 of FIG. 36. In some implementations, the imaging module 2100 can include, or be used with, the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the imaging module 2100 can include, or be used with, the piezoelectric phase shifter 3800 of FIG. 38.In some implementations, the imaging module 2100 can include, or be used with, the projection lens 3900 of FIG. 39. In some implementations, the imaging module 2100 can include, or be used with, the projection lens 4000 of FIG. 40. In some implementations, the imaging module 2100 can generate the field of view 4100 of FIG. 41.

[0235] The imaging module 2100 includes a plurality of components and / or devices that can be integrated to operate coherently as a system to perform one or more tasks. In some implementations, the imaging module 2100 performs imaging as part of analyzing a sample. For example, the imaging module 2100 can detect fluorescence emitted from a sample of genetic material. The imaging module 2100 includes a SIM assembly 2102 that is only partially visible in this figure. For example, the SIM assembly 2102 can generate spatially structured light for illuminating a sample material. The imaging module 2100 includes an objective lens 2104. In some implementations, the objective lens 2104 can transmit SIM light from the SIM assembly 2102 and apply the SIM light to a substrate 2114 that holds the sample. The imaging module 2100 includes a z-stage 2106. In some implementations, the z-stage 2106 can change (e.g., increase or decrease) the distance (herein referred to as the z-distance) between the objective lens 2104 and the substrate that holds the sample.

[0236] The imaging module 2100 can include one or more portions of the housing. In some implementations, the housing can substantially surround the components of the imaging module 2100. For example, the housing 2108 can at least partially surround the SIM assembly 2102. As another example, the housing 2110 can at least partially surround the emission optical system of the imaging module 2100 (e.g., one or more tube lenses and / or sensors). As another example, the housing 2112 can at least partially surround the SIM assembly 2102 and / or at least partially surround the detection optical system.

[0237] One or more of the housings may not be present in the imaging module 2100, whereby some of the components may be visible. This may occur, for example, during the assembly process and / or during maintenance or repair.

[0238] In some implementations, one or more of the housings 2108, 211, or 2112 of the imaging module 2100 can include aluminum. For example, the housing 2108, 2110, or 2112 can include two welded aluminum pieces that can be assembled using side fasteners. The tolerance can be defined with respect to the mounting holes, and the assembly can include a suitable match drill. The implementation can be designed to reduce or eliminate the absolute camera tilt that would otherwise result in the force applied to the main base plate of the imaging module 2100.

[0239] FIG. 22 shows an embodiment of the imaging module 2200. The imaging module 2200 can be used with or incorporated in one or more other embodiments described herein. In some implementations, the imaging module 2200 can include or be used with the system 4200 of FIG. 42. In some implementations, the imaging module 2200 can include or be used with at least some components of the computing device 4300 of FIG. 43. In some implementations, the imaging module 2200 can be used with or incorporated in the system 100 of FIG. 1. In some implementations, the imaging module 2200 can be used with or incorporated in the optical system 200 of FIG. 2. In some implementations, the imaging module 2200 can be used with or incorporated in the optical system 500 of FIG. 5. In some implementations, the imaging module 2200 can be used with or incorporated in the optical system 820 of FIG. 8B. In some implementations, the imaging module 2200 can be used with or incorporated in the optical system 1100 of FIG. 11. In some implementations, the imaging module 2200 can be used with or incorporated in the optical system 1200 of FIG. 12. In some implementations, the imaging module 2200 can be used with or incorporated in the optical system 1300 of FIG. 13. In some implementations, the imaging module 2200 can be used with or incorporated in the optical system 1400 of FIG. 14. In some implementations, the imaging module 2200 can be used with or incorporated in the imaging module 1800 of FIG. 18 or FIGS. 19A - 19B. In some implementations, the imaging module 2200 can be used with or incorporated in the SIM assembly 2000 of FIG. 20.In some implementations, the imaging module 2200 can be used with or included in the imaging module 2100 of FIG. 21. In some implementations, the imaging module 2200 can include or be used with the imaging module 2400 of FIG. 24. In some implementations, the imaging module 2200 can include or be used with the optical system 2500 of FIG. 25. In some implementations, the imaging module 2200 can include or be used with the optical system 2600 of FIG. 26. In some implementations, the imaging module 2200 can include or be used with the reflective component 2700 of FIG. 27. In some implementations, the imaging module 2200 can include or be used with the reflective component 2800 of FIG. 28. In some implementations, the imaging module 2200 can generate the autofocus light 2900 of FIG. 29. In some implementations, the imaging module 2200 can generate the autofocus light 3000 of FIG. 30. In some implementations, the imaging module 2200 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the imaging module 2200 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the imaging module 2200 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the imaging module 2200 can include or be used with the SIM assembly 3400 of FIG. 34. In some implementations, the imaging module 2200 can include or be used with the RIGS 3500 of FIG. 35. In some implementations, the imaging module 2200 can include or be used with the RIGS 3600 of FIG. 36. In some implementations, the imaging module 2200 can include or be used with the piezoelectric phase shifter 3700 of FIG. 37.In some implementations, the imaging module 2200 can include, or can be used with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the imaging module 2200 can include, or can be used with, the projection lens 3900 of FIG. 39. In some implementations, the imaging module 2200 can include, or can be used with, the projection lens 4000 of FIG. 40. In some implementations, the imaging module 2200 can generate the field of view 4100 of FIG. 41.

[0240] The imaging module 2200 includes a plurality of components and / or devices that can be integrated to operate coherently as a system to perform one or more tasks. In some implementations, the imaging module 2200 performs imaging as part of analyzing a sample. For example, the imaging module 2200 can detect fluorescence emitted from a sample of genetic material. The imaging module 2200 includes a SIM assembly 2202 that is only partially visible in this figure. For example, the SIM assembly 2202 can generate spatially structured light to illuminate the sample material. The imaging module 2200 includes an objective lens 2204. In some implementations, the objective lens 2204 can transmit SIM light from the SIM assembly 2202 and apply the SIM light to a substrate (not shown) that holds the sample. The imaging module 2200 includes a z-stage 2206. In some implementations, the z-stage 2206 can change (e.g., increase or decrease) the distance (herein referred to as the z-distance) between the objective lens 2204 and the substrate that holds the sample.

[0241] The imaging module 2200 can include one or more portions of the housing. In some implementations, the housing can substantially surround the components of the imaging module 2200. For example, the housing 2208 can at least partially surround the SIM assembly 2202. As another example, the housing 2210 can at least partially surround the emission optical system of the imaging module 2200 (e.g., one or more tube lenses and / or sensors). As another example, the housing 2212 can at least partially surround the SIM assembly 2202 and / or at least partially surround the detection optical system.

[0242] One or more of the housings may not be present in the imaging module 2200, whereby some of the components may be visible. This may occur, for example, during the assembly process and / or during maintenance or repair.

[0243] In some implementations, one or more of the housings 2208, 2210, or 2212 of the imaging module 2200 can include aluminum. The housings 2208, 2210, or 2212 can include aluminum components that are assembled without welding (e.g., bolted together). For example, such an approach can increase the tolerance for component variability. In some implementations, a seal can be provided against light ingress and / or egress, and / or particulate ingress and / or egress. For example, an adhesive tape can be used for the seal.

[0244] FIG. 23 shows a chart 2300 of error rates. The error rate (measured as a positive number, for example) is shown against the vertical axis, which here has a scaling in the range 0-10. The number of cycles is shown against the horizontal axis, which here has a scaling in the range 0-110. In some implementations, the effects of vibrations of optical components caused by the movement of the RIGS (e.g., the stepper motor 2020 of FIG. 20) can be reduced or eliminated. For example, such vibrations would otherwise affect stability and thereby the quality of imaging. The RIGS can operate according to an S-curve movement profile. For example, this can prevent sudden acceleration or deceleration of the RIGS. In some implementations, the S-curve movement profile can be optimized to minimize the generation of vibrations. In some implementations, the order in which the RIGS takes its states can be specified to reduce the effects of vibrations. For example, in one state of the RIGS, a reflective component that is subject to vibrations can be downstream (e.g., behind) of the applicable grating of the light flow, but in another state of the RIGS, the reflective component corresponding to the vibrations (or another reflective component) can be upstream (e.g., in front) of the grating. The upstream position can be more sensitive to vibrations of the reflective component than the downstream position. In some implementations, the effects of vibrations can be eliminated or reduced by designing the timing and / or order in which the RIGS takes its respective states. For example, the upstream position can be processed before the downstream position in the operation of the RIGS, or vice versa. As another example, a delay can be implemented after the RIGS movement or RIGS reset sequence. In some implementations, one or more approaches regarding the RIGS can reduce or eliminate the effects of vibrations on the imaging process. For example, the error rate can be reduced.

[0245] FIG. 24 shows an embodiment of the imaging module 2400. The imaging module 2400 can be used with or incorporated in one or more other embodiments described herein. In some implementations, the imaging module 2400 can include or be used with the system 4200 of FIG. 42. In some implementations, the imaging module 2400 can include or be used with at least some components of the computing device 4300 of FIG. 43. In some implementations, the imaging module 2400 can be used with or incorporated in the system 100 of FIG. 1. In some implementations, the imaging module 2400 can be used with or incorporated in the optical system 200 of FIG. 2. In some implementations, the imaging module 2400 can be used with or incorporated in the optical system 500 of FIG. 5. In some implementations, the imaging module 2400 can be used with or incorporated in the optical system 820 of FIG. 8B. In some implementations, the imaging module 2400 can be used with or incorporated in the optical system 1100 of FIG. 11. In some implementations, the imaging module 2400 can be used with or incorporated in the optical system 1200 of FIG. 12. In some implementations, the imaging module 2400 can be used with or incorporated in the optical system 1300 of FIG. 13. In some implementations, the imaging module 2400 can be used with or incorporated in the optical system 1400 of FIG. 14. In some implementations, the imaging module 2400 can be used with or incorporated in the imaging module 1800 of FIG. 18 or FIGS. 19A - 19B. In some implementations, the imaging module 2400 can be used with the SIM assembly 2000 of FIG. 20.In some implementations, the imaging module 2400 can include, or be used with, the imaging module 2100 of FIG. 21. In some implementations, the imaging module 2400 can be used with the imaging module 2200 of FIG. 22. In some implementations, the imaging module 2400 can include, or be used with, the optical system 2500 of FIG. 25. In some implementations, the imaging module 2400 can include, or be used with, the optical system 2600 of FIG. 26. In some implementations, the imaging module 2400 can include, or be used with, the reflective component 2700 of FIG. 27. In some implementations, the imaging module 2400 can include, or be used with, the reflective component 2800 of FIG. 28. In some implementations, the imaging module 2400 can generate the autofocus light 2900 of FIG. 29. In some implementations, the imaging module 2400 can generate the autofocus light 3000 of FIG. 30. In some implementations, the imaging module 2400 can generate the autofocus light 3100 of FIGS. 31A-31C. In some implementations, the imaging module 2400 can be used with the laser engine heat sink 3200 of FIGS. 32A-32C. In some implementations, the imaging module 2400 can be used with the laser engine heat sink 3300 of FIGS. 33A-33C. In some implementations, the imaging module 2400 can include, or be used with, the SIM assembly 3400 of FIG. 34. In some implementations, the imaging module 2400 can include, or be used with, the RIGS 3500 of FIG. 35. In some implementations, the imaging module 2400 can include, or be used with, the RIGS 3600 of FIG. 36. In some implementations, the imaging module 2400 can include, or be used with, the piezoelectric phase shifter 3700 of FIG. 37.In some implementations, the imaging module 2400 can include, or be used in conjunction with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the imaging module 2400 can include, or be used in conjunction with, the projection lens 3900 of FIG. 39. In some implementations, the imaging module 2400 can include, or be used in conjunction with, the projection lens 4000 of FIG. 40. In some implementations, the imaging module 2400 can generate the field of view 4100 of FIG. 41.

[0246] The imaging module 2400 includes a plurality of components and / or devices that can be integrated to operate coherently as a system to perform one or more tasks. In some implementations, the imaging module 2400 performs imaging as part of analyzing a sample. For example, the imaging module 2400 can detect fluorescence emitted from a sample of genetic material. The imaging module 2400 includes a SIM assembly 2402 that is only partially visible in this figure. In some implementations, the SIM assembly 2402 can generate spatially structured light to illuminate the sample material. For example, the SIM assembly 2402 can include RIGS. The imaging module 2400 includes an objective lens 2404. In some implementations, the objective lens 2404 can transmit SIM light from the SIM assembly 2402 and apply the SIM light to a substrate 2406 that holds the sample. The imaging module 2400 can include a z-stage. In some implementations, the z-stage can change (e.g., increase or decrease) the distance (herein referred to as the z-distance) between the objective lens 2404 and the substrate 2406.

[0247] The imaging module 2400 can include one or more portions of the housing. In some implementations, the housing can substantially surround the components of the imaging module 2400. For example, the housing 2408 can at least partially surround the SIM assembly 2402. One or more of the housings may not be present in the imaging module 2400, whereby some of the components may be visible. This may occur, for example, during the assembly process and / or during maintenance or repair.

[0248] The imaging module 2400 can include an emission optical system 2410. In some implementations, the emission optical system 2410 includes a filter assembly 2412. The filter assembly 2412 can include at least one filter. For example, the filter assembly 2412 can include one or more of the filter 212 in FIG. 2 or the filter 506 in FIG. 5. In some implementations, the emission optical system 2410 includes a tube lens 2414. For example, the tube lens 2414 can be one or more of the tube lens 214 in FIG. 2, the tube lens 508 in FIG. 5, or the tube lens 802 in FIG. 8A. The tube lens 2414 can be assigned to the blue detector channel. In some implementations, the emission optical system 2410 includes a tube lens 2416. The tube lens 2416 can be assigned to the green detector channel. For example, the tube lens 2416 can be one or more of the tube lens 214 in FIG. 2, the tube lens 508 in FIG. 5, or the tube lens 802 in FIG. 8A. In some implementations, the emission optical system 2410 includes a filter assembly 2418. For example, the filter assembly 2418 can include one or more of the filter 216, the reflective component 226, or the structure 228 in FIG. 2. As another example, the filter assembly 2418 can include one or more of the filter 510, the reflective component 516, or the structure 518 in FIG. 5. As another example, the filter assembly 2418 can include one or more of the filter 804, the reflective components 810A - 810B, or the structure 812 in FIG. 8A.

[0249] In some implementations, the emission optical system 2410 includes a sensor assembly 2420. The sensor assembly 2420 can be assigned to the blue detector channel. The sensor assembly 2420 can include one or more sensors for the emitted light and / or autofocus light. For example, the sensor assembly 2420 can include one or more of the sensor 120 of FIG. 1, the sensor 220 of FIG. 2, the sensor 514 of FIG. 5, the sensor 808 of FIG. 5, the sensor 1112 of FIG. 11, the sensor 1214 of FIG. 12, the sensor 1314 of FIG. 13, or the sensor 1416 of FIG. 14. In some implementations, the emission optical system 2410 includes a sensor assembly 2422. The sensor assembly 2422 can be assigned to the green detector channel. The sensor assembly 2422 can include one or more sensors for the emitted light and / or autofocus light. For example, the sensor assembly 2422 can include one or more of the sensor 120 of FIG. 1, the sensor 220 of FIG. 2, the sensor 514 of FIG. 5, the sensor 808 of FIG. 5, the sensor 1112 of FIG. 11, the sensor 1214 of FIG. 12, the sensor 1314 of FIG. 13, or the sensor 1416 of FIG. 14.

[0250] FIG. 25 shows an embodiment of an optical system 2500. The optical system 2500 can include or be used with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 2500 can include or be used with the system 4200 of FIG. 42. In some implementations, the optical system 2500 can include or be used with at least some components of the computing device 4300 of FIG. 43. In some implementations, the optical system 2500 can be used with or included in the system 100 of FIG. 1. In some implementations, the optical system 2500 can include or be used with the optical system 200 of FIG. 2. In some implementations, the optical system 2500 can include or be used with the optical system 500 of FIG. 5. In some implementations, the optical system 2500 can include or be used with the optical system 800 of FIG. 8A. In some implementations, the optical system 2500 can include or be used with the optical system 820 of FIG. 8B. In some implementations, the optical system 2500 can include or be used with the lateral displacement prism 1000 of FIGS. 10A-10C. In some implementations, the optical system 2500 can include or be used with the optical system 1100 of FIG. 11. In some implementations, the optical system 2500 can include or be used with the optical system 1200 of FIG. 12. In some implementations, the optical system 2500 can include or be used with the optical system 1300 of FIG. 13. In some implementations, the optical system 2500 can include or be used with the optical system 1400 of FIG. 14.In some implementations, the optical system 2500 can include, or can be used with, the lateral displacement prism 1600 of FIGS. 16A-16B. In some implementations, the optical system 2500 can include, or can be used with, the beam splitter 1700 of FIG. 17. In some implementations, the optical system 2500 can be used with, or can be included in, the imaging module 1800 of FIG. 18 or FIGS. 19A-19B. In some implementations, the optical system 2500 can be used with the SIM assembly 2000 of FIG. 20. In some implementations, the optical system 2500 can include, or can be used with, the imaging module 2100 of FIG. 21. In some implementations, the optical system 2500 can be used with the imaging module 2200 of FIG. 22. In some implementations, the optical system 2500 can include, or can be used with, the imaging module 2400 of FIG. 24. In some implementations, the optical system 2500 can include, or can be used with, the optical system 2600 of FIG. 26. In some implementations, the optical system 2500 can include, or can be used with, the reflective component 2700 of FIG. 27. In some implementations, the optical system 2500 can include, or can be used with, the reflective component 2800 of FIG. 28. In some implementations, the optical system 2500 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 2500 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 2500 can generate the autofocus light 3100 of FIGS. 31A-31C. In some implementations, the optical system 2500 can be used with the laser engine heat sink 3200 of FIGS. 32A-32C. In some implementations, the optical system 2500 can be used with the laser engine heat sink 3300 of FIGS. 33A-33C.In some implementations, the optical system 2500 can include, or be used with, the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 2500 can include, or be used with, the RIGS 3500 of FIG. 35. In some implementations, the optical system 2500 can include, or be used with, the RIGS 3600 of FIG. 36. In some implementations, the optical system 2500 can include, or be used with, the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the optical system 2500 can include, or be used with, the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 2500 can include, or be used with, the projection lens 3900 of FIG. 39. In some implementations, the optical system 2500 can include, or be used with, the projection lens 4000 of FIG. 40. In some implementations, the optical system 2500 can generate the field of view 4100 of FIG. 41.

[0251] The optical system 2500 includes an objective lens 2502. In some implementations, the objective lens 2502 can be used to direct excitation light towards a sample on a substrate and receive the emitted light from the sample. The optical system 2500 includes a filter 2504. In some implementations, the filter 2504 can be used to add one or more types of light to the transmitted light and / or remove one or more types of light from the transmitted light. For example, the filter 2504 can enable excitation light (e.g., from the SIM assembly 2402 of FIG. 24) to be introduced and transmitted towards the objective lens 2502. The optical system 2500 includes a filter 2506. The filter 2506 can redirect light to another level of the optical system 2500. For example, the filter 2506 can redirect the emitted light in a horizontal direction. The optical system 2500 includes a filter 2508. The filter 2508 can redirect light to another level of the optical system 2500. In some implementations, the filter 2508 can redirect the emitted light in a vertical direction. For example, the filter 2508 can branch the light from the green channel to the blue channel, or vice versa. The optical system 2500 includes a filter 2510. The filter 2510 can redirect light in a horizontal direction. The optical system 2500 includes a tube lens 2512. For example, the tube lens 2512 can adjust the light for detection. The optical system 2500 includes a sensor 2514. In some implementations, the sensor 2514 can be used to receive the emitted light and / or autofocus light. The optical system 2500 includes a filter 2516. The filter 2516 can redirect light in a horizontal direction. The optical system 2500 includes a tube lens 2518. For example, the tube lens 2518 can adjust the light for detection. The optical system 2500 includes a sensor 2520. In some implementations, the sensor 2520 can be used to receive the emitted light and / or autofocus light.In some implementations, the optical system 2500 corresponds to the system layout of the imaging module 2400 of FIG. 24.

[0252] FIG. 26 shows an embodiment of an optical system 2600. The optical system 2600 can include or be used in conjunction with one or more other embodiments described elsewhere in this specification. In some implementations, the optical system 2600 can include or be used in conjunction with the system 4200 of FIG. 42. In some implementations, the optical system 2600 can include or be used in conjunction with at least some components of the computing device 4300 of FIG. 43. In some implementations, the optical system 2600 can be used in conjunction with or included within the system 100 of FIG. 1. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 200 of FIG. 2. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 500 of FIG. 5. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 800 of FIG. 8A. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 820 of FIG. 8B. In some implementations, the optical system 2600 can include or be used in conjunction with the lateral displacement prism 1000 of FIGS. 10A-10C. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 1100 of FIG. 11. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 1200 of FIG. 12. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 1300 of FIG. 13. In some implementations, the optical system 2600 can include or be used in conjunction with the optical system 1400 of FIG. 14.In some implementations, the optical system 2600 can include, or can be used with, the lateral displacement prism 1600 of FIGS. 16A-16B. In some implementations, the optical system 2600 can include, or can be used with, the beam splitter 1700 of FIG. 17. In some implementations, the optical system 2600 can be used with, or can be included in, the imaging module 1800 of FIG. 18 or FIGS. 19A-19B. In some implementations, the optical system 2600 can be used with the SIM assembly 2000 of FIG. 20. In some implementations, the optical system 2600 can include, or can be used with, the imaging module 2100 of FIG. 21. In some implementations, the optical system 2600 can be used with the imaging module 2200 of FIG. 22. In some implementations, the optical system 2600 can include, or can be used with, the imaging module 2400 of FIG. 24. In some implementations, the optical system 2600 can include, or can be used with, the optical system 2500 of FIG. 25. In some implementations, the optical system 2600 can include, or can be used with, the reflective component 2700 of FIG. 27. In some implementations, the optical system 2600 can include, or can be used with, the reflective component 2800 of FIG. 28. In some implementations, the optical system 2600 can generate the autofocus light 2900 of FIG. 29. In some implementations, the optical system 2600 can generate the autofocus light 3000 of FIG. 30. In some implementations, the optical system 2600 can generate the autofocus light 3100 of FIGS. 31A-31C. In some implementations, the optical system 2600 can be used with the laser engine heat sink 3200 of FIGS. 32A-32C. In some implementations, the optical system 2600 can be used with the laser engine heat sink 3300 of FIGS. 33A-33C.In some implementations, the optical system 2600 can include or be used with the SIM assembly 3400 of FIG. 34. In some implementations, the optical system 2600 can include or be used with the RIGS 3500 of FIG. 35. In some implementations, the optical system 2600 can include or be used with the RIGS 3600 of FIG. 36. In some implementations, the optical system 2600 can include or be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the optical system 2600 can include or be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the optical system 2600 can include or be used with the projection lens 3900 of FIG. 39. In some implementations, the optical system 2600 can include or be used with the projection lens 4000 of FIG. 40. In some implementations, the optical system 2600 can generate the field of view 4100 of FIG. 41.

[0253] The optical system 2600 includes an objective lens 2602. In some implementations, the objective lens 2602 can be used to direct excitation light toward a sample on a substrate and receive the emitted light from the sample. The optical system 2600 includes a filter 2604. In some implementations, the filter 2604 can be used to add one or more types of light to the transmitted light and / or remove one or more types of light from the transmitted light. For example, the filter 2604 can enable excitation light (e.g., from the SIM assembly 2402 of FIG. 24) to be introduced and transmitted toward the objective lens 2602. The optical system 2600 includes a filter 2606. The filter 2606 can redirect light to another level of the optical system 2600. For example, the filter 2606 can redirect the emitted light in the horizontal direction. The optical system 2600 includes a filter 2608. The filter 2608 can redirect light to another level of the optical system 2600. In some implementations, the filter 2608 can redirect the emitted light in the horizontal direction. For example, the filter 2608 can branch the light of the green channel from the light of the blue channel, or vice versa. The optical system 2500 includes a tube lens 2610. For example, the tube lens 2610 can adjust the light for detection. The optical system 2600 includes a sensor 2612. In some implementations, the sensor 2612 can be used to receive the emitted light and / or autofocus light. The optical system 2600 includes a tube lens 2614. For example, the tube lens 2614 can adjust the light for detection. The optical system 2600 includes a filter 2616. The filter 2616 can redirect light in the horizontal direction. The optical system 2600 includes a sensor 2618. In some implementations, the sensor 2618 can be used to receive the emitted light and / or autofocus light. In some implementations, the optical system 2600 corresponds to the system layout of the imaging module 1800 of FIGS. 18 and 19A-19B.

[0254] The optical performance between two or more systems can be compared. The comparison may include one or more simulated measurements. The following table shows values for three systems labeled A, B, and C, respectively. In some implementations, System A can correspond to an implementation that includes the imaging module 1800 of FIGS. 18 and 19A - 19B, the SIM assembly 2000 of FIG. 20, and the optical system 2600 of FIG. 26. In some implementations, System B can correspond to a reference system. For example, the reference system can include an objective lens that supports DFC. In some implementations, System C can correspond to an implementation that includes the imaging module 2400 of FIG. 24 and the optical system 2500 of FIG. 25.

Table 1

[0255] Figure 27 shows one embodiment 2700 of a reflective component. The reflective component 2700 can be used with or included in one or more other embodiments described herein. In some implementations, the reflective component 2700 can be used with or included in the system 100 of FIG. 1. In some implementations, the reflective component 2700 can be used with or included in the optical system 200 of FIG. 2. In some implementations, the reflective component 2700 can be used with or included in the optical system 500 of FIG. 5. In some implementations, the reflective component 2700 can be used with or included in the optical system 800 of FIG. 8A. In some implementations, the reflective component 2700 can be used with or included in the optical system 820 of FIG. 8B. In some implementations, the reflective component 2700 can be used with or included in the optical system 1100 of FIG. 11. In some implementations, the reflective component 2700 can be used with or included in the optical system 1200 of FIG. 12. In some implementations, the reflective component 2700 can be used with or included in the optical system 1300 of FIG. 13. In some implementations, the reflective component 2700 can be used with or included in the optical system 1400 of FIG. 14. In some implementations, the reflective component 2700 can be used with or included in the imaging module 1800 of FIGS. 18 and 19A-19B. In some implementations, the reflective component 2700 can be used with or included in the imaging module 2100 of FIG. 21. In some implementations, the reflective component 2700 can be used with or included in the imaging module 2200 of FIG. 22.In some implementations, the reflective component 2700 can be used with or included in the imaging module 2400 of FIG. 24. In some implementations, the reflective component 2700 can be used with or included in the optical system 2500 of FIG. 25. In some implementations, the reflective component 2700 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, the reflective component 2700 can include or be used with the reflective component 2800 of FIG. 28. In some implementations, the reflective component 2700 can generate the autofocus light 2900 of FIG. 29. In some implementations, the reflective component 2700 can generate the autofocus light 3000 of FIG. 30. In some implementations, the reflective component 2700 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the reflective component 2700 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the reflective component 2700 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the reflective component 2700 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the reflective component 2700 can be used with the RIGS 3500 of FIG. 35. In some implementations, the reflective component 2700 can be used with the RIGS 3600 of FIG. 36. In some implementations, the reflective component 2700 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the reflective component 2700 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the reflective component 2700 can be used with the projection lens 3900 of FIG. 39. In some implementations, the reflective component 2700 can be used with the projection lens 4000 of FIG. 40.

[0256] The reflective component 2700 includes a filter 2702. The filter 2702 can be a dichroic filter. The filter 2702 can facilitate the guiding of one or more types of light, either alone or in conjunction with at least one other component. In some implementations, the filter 2702 can reflect the emitted light and transmit the autofocus light. For example, the filter 2702 can have an antireflection coating that prevents the reflection of (i.e., facilitates the transmission of) the autofocus light and reflects the emitted light. In other implementations, the filter 2702 can be configured to prevent the reflection of (i.e., facilitate the transmission of) the emitted light and reflect the autofocus light.

[0257] The reflective component 2700 includes a tent prism 2704. The tent prism 2704 can include one or more reflective surfaces and can be positioned behind the filter 2702 in the direction of travel of the incident light. The tent prism can have a triangular shape. In some implementations, the tent prism 2704 reflects the light that has passed through the filter 2702, and the reflection directs the light towards the sensor. For example, the tent prism 2704 can reflect some (but not all) of the autofocus light reflected from the substrate. The tent prism 2704 can have optical properties based on the type of autofocus light used. In some implementations, the tent prism 2704 is reflective at least in part in the near-infrared wavelength range (e.g., reflection of any of approximately 750 nm to approximately 1400 nm). In some implementations, the light 2706 passing through the filter 2702 is reflected by the tent prism 2704. For example, the light 2706 includes autofocus light reflected from the S1 surface and / or the S2 surface of the sample substrate. In some implementations, the light 2708 passing through the filter 2702 is not (e.g., is absorbed) reflected by the reflective component 2700. The reflective component 2700 can include an absorbing material 2710 where the light 2708 is incident. For example, the light 2708 includes autofocus light reflected from the S4 surface and / or the S5 surface of the sample substrate.

[0258] FIG. 28 shows one embodiment 2800 of a reflective component. The reflective component 2800 can be used with or incorporated into one or more other embodiments described herein. In some implementations, the reflective component 2800 can be used with or incorporated into the system 100 of FIG. 1. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 200 of FIG. 2. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 500 of FIG. 5. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 800 of FIG. 8A. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 820 of FIG. 8B. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 1100 of FIG. 11. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 1200 of FIG. 12. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 1300 of FIG. 13. In some implementations, the reflective component 2800 can be used with or incorporated into the optical system 1400 of FIG. 14. In some implementations, the reflective component 2800 can be used with or incorporated into the imaging module 1800 of FIGS. 18 and 19A-19B. In some implementations, the reflective component 2800 can be used with or incorporated into the imaging module 2100 of FIG. 21. In some implementations, the reflective component 2800 can be used with or incorporated into the imaging module 2200 of FIG. 22.In some implementations, the reflective component 2800 can be used with or included in the imaging module 2400 of FIG. 24. In some implementations, the reflective component 2800 can be used with or included in the optical system 2500 of FIG. 25. In some implementations, the reflective component 2800 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, the reflective component 2800 can include or be used with the reflective component 2700 of FIG. 27. In some implementations, the reflective component 2800 can generate the autofocus light 2900 of FIG. 29. In some implementations, the reflective component 2800 can generate the autofocus light 3000 of FIG. 30. In some implementations, the reflective component 2800 can generate the autofocus light 3100 of FIGS. 31A - 31C. In some implementations, the reflective component 2800 can be used with the laser engine heat sink 3200 of FIGS. 32A - 32C. In some implementations, the reflective component 2800 can be used with the laser engine heat sink 3300 of FIGS. 33A - 33C. In some implementations, the reflective component 2800 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the reflective component 2800 can be used with the RIGS 3500 of FIG. 35. In some implementations, the reflective component 2800 can be used with the RIGS 3600 of FIG. 36. In some implementations, the reflective component 2800 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the reflective component 2800 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the reflective component 2800 can be used with the projection lens 3900 of FIG. 39. In some implementations, the reflective component 2800 can be used with the projection lens 4000 of FIG. 40.

[0259] The reflective component 2800 includes a filter 2802. The filter 2802 can be a dichroic filter. The filter 2802, alone or together with at least one other component, can facilitate the guidance of one or more types of light. In some implementations, the filter 2802 can reflect the emitted light and transmit the autofocus light. For example, the filter 2802 can have an antireflection coating that prevents reflection of the autofocus light (i.e., facilitates transmission of the autofocus light) and reflects the emitted light. In other implementations, the filter 2802 can be configured to prevent reflection of the emitted light (i.e., facilitate transmission) and reflect the autofocus light.

[0260] The reflective component 2800 includes a reflective surface 2804. The reflective surface 2804 can include one or more reflective surfaces and can be positioned behind the filter 2802 in the direction of travel of the incident light. In some implementations, the reflective surface 2804 reflects the light that has passed through the filter 2802, and the reflection directs the light towards the sensor. For example, the reflective surface 2804 can reflect some (but not all) of the autofocus light reflected from the substrate. The reflective surface 2804 can have optical properties based on the type of autofocus light used. In some implementations, the reflective surface 2804 is reflective at least in part in the near-infrared wavelength range (e.g., any reflection from about 750 nm to about 1400 nm). In some implementations, the light 2806 that passes through the filter 2802 is reflected by the reflective surface 2804. For example, the light 2806 includes autofocus light reflected from the S1 surface and / or the S2 surface of the sample substrate. In some implementations, the light 2808 that passes through the filter 2802 is not reflected (e.g., is absorbed) by the reflective component 2800. The reflective component 2800 can include an absorbing material 2810 onto which the light 2808 is incident. For example, the light 2808 includes autofocus light reflected from the S4 surface and / or the S5 surface of the sample substrate.

[0261] The reflective component 2800 can include one or more instances of a reflective surface 2804 positioned behind the filter 2802 in the direction of travel of the arriving light. In some implementations, two instances of the reflective surface 2804 are used to reflect each of at least one respective beam of light 2806 (e.g., as shown in FIG. 28). In other implementations, a single instance of the reflective surface 2804 is positioned behind the filter 2802 in the direction of travel of the arriving light. The reflective surface 2804 can then reflect one or more beams of light 2806. For example, referring briefly again to FIGS. 10B - 10C, the angles of surfaces 1008A - 1008B (e.g., with respect to surface 1006) can be adjusted such that two or more spots of autofocus light approach each other on the flow cell, thereby enabling the use of a single instance of the reflective surface 2804 for reflection.

[0262] Figure 29 shows an example of autofocus light 2900 detected by a sensor. The autofocus light 2900 can be detected using one or more embodiments described herein. In some implementations, the autofocus light 2900 can be detected using the system 100 of FIG. 1. In some implementations, the autofocus light 2900 can be detected using the optical system 200 of FIG. 2. In some implementations, the autofocus light 2900 can be detected using the optical system 500 of FIG. 5. In some implementations, the autofocus light 2900 can be detected using the optical system 800 of FIG. 8A. In some implementations, the autofocus light 2900 can be detected using the optical system 820 of FIG. 8B. In some implementations, the autofocus light 2900 can be detected using the optical system 1100 of FIG. 11. In some implementations, the autofocus light 2900 can be detected using the optical system 1200 of FIG. 12. In some implementations, the autofocus light 2900 can be detected using the optical system 1300 of FIG. 13. In some implementations, the autofocus light 2900 can be detected using the optical system 1400 of FIG. 14. In some implementations, the autofocus light 2900 can be detected using the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the autofocus light 2900 can be created using the SIM assembly 2000 of FIG. 20. In some implementations, the autofocus light 2900 can be detected using the imaging module 2100 of FIG. 21. In some implementations, the autofocus light 2900 can be detected using the imaging module 2200 of FIG. 22. In some implementations, the autofocus light 2900 can be detected using the imaging module 2400 of FIG. 24. In some implementations, the autofocus light 2900 can be detected using the optical system 2500 of FIG. 25.In some implementations, the autofocus light 2900 can be detected using the optical system 2600 of FIG. 26. In some implementations, the autofocus light 2900 can be detected using the reflective component 2700 of FIG. 27. In some implementations, the autofocus light 2900 can be detected using the reflective component 2800 of FIG. 28. In some implementations, the autofocus light 2900 can be created using the SIM assembly 3400 of FIG. 34. In some implementations, the autofocus light 2900 can be created using the RIGS 3500 of FIG. 35. In some implementations, the autofocus light 2900 can be created using the RIGS 3600 of FIG. 36. In some implementations, the autofocus light 2900 can be created using the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the autofocus light 2900 can be created using the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the autofocus light 2900 can be detected using the projection lens 3900 of FIG. 39. In some implementations, the autofocus light 2900 can be detected using the projection lens 4000 of FIG. 40. In some implementations, the autofocus light 2900 can be detected using the field of view 4100 of FIG. 41.

[0263] Here, the autofocus light 2900 is shown in a simulation detected within the tile 2902 defined with respect to the substrate 2904. For example, the autofocus light 2900 can be captured using an implementation that includes the imaging module 2400 of FIG. 24 and the optical system 2500 of FIG. 25. The autofocus light 2900 can include two or more spots of autofocus light corresponding to reflections from a layer of the substrate or other surface. The distance between the spots can indicate the distance between the substrate and the objective lens that captures the autofocus light 2900. For example, the distance between the spots of the autofocus light 2900 is here about 0.390 mm.

[0264] Figure 30 shows an example of autofocus light 3000 detected by a sensor. The autofocus light 3000 can be detected using one or more embodiments described herein. In some implementations, the autofocus light 3000 can be detected using the system 100 of FIG. 1. In some implementations, the autofocus light 3000 can be detected using the optical system 200 of FIG. 2. In some implementations, the autofocus light 3000 can be detected using the optical system 500 of FIG. 5. In some implementations, the autofocus light 3000 can be detected using the optical system 800 of FIG. 8A. In some implementations, the autofocus light 3000 can be detected using the optical system 820 of FIG. 8B. In some implementations, the autofocus light 3000 can be detected using the optical system 1100 of FIG. 11. In some implementations, the autofocus light 3000 can be detected using the optical system 1200 of FIG. 12. In some implementations, the autofocus light 3000 can be detected using the optical system 1300 of FIG. 13. In some implementations, the autofocus light 3000 can be detected using the optical system 1400 of FIG. 14. In some implementations, the autofocus light 3000 can be detected using the imaging module 1800 of FIGS. 18 and 19A-19B. In some implementations, the autofocus light 3000 can be created using the SIM assembly 2000 of FIG. 20. In some implementations, the autofocus light 3000 can be detected using the imaging module 2100 of FIG. 21. In some implementations, the autofocus light 3000 can be detected using the imaging module 2200 of FIG. 22. In some implementations, the autofocus light 3000 can be detected using the imaging module 2400 of FIG. 24. In some implementations, the autofocus light 3000 can be detected using the optical system 2500 of FIG. 25.In some implementations, the autofocus light 3000 can be detected using the optical system 2600 of FIG. 26. In some implementations, the autofocus light 3000 can be detected using the reflective component 2700 of FIG. 27. In some implementations, the autofocus light 3000 can be detected using the reflective component 2800 of FIG. 28. In some implementations, the autofocus light 3000 can be created using the SIM assembly 3400 of FIG. 34. In some implementations, the autofocus light 3000 can be created using the RIGS 3500 of FIG. 35. In some implementations, the autofocus light 3000 can be created using the RIGS 3600 of FIG. 36. In some implementations, the autofocus light 3000 can be created using the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the autofocus light 3000 can be created using the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the autofocus light 3000 can be detected using the projection lens 3900 of FIG. 39. In some implementations, the autofocus light 3000 can be detected using the projection lens 4000 of FIG. 40. In some implementations, the autofocus light 3000 can be detected using the field of view 4100 of FIG. 41.

[0265] Here, the autofocus light 3000 is shown in a simulation detected within the tile 3002 defined with respect to the substrate 3004. For example, the autofocus light 3000 can be captured using implementations that include the imaging module 1800 of FIGS. 18 and 19A-19B, the SIM assembly 2000 of FIG. 20, and the optical system 2600 of FIG. 26. As another example, the autofocus light 3000 can be captured using an implementation that includes the imaging module 2200 of FIG. 22. The autofocus light 3000 can include two or more spots of autofocus light corresponding to reflections from a layer of the substrate or other surface. The distance between the spots can indicate the distance between the substrate and the objective lens that captures the autofocus light 3000. For example, the distance between the spots of the autofocus light 3000 is here about 1.067 mm. In some implementations, the autofocus procedure can be adjusted to exclude or reduce an incidence where one or more spots of the autofocus light 3000 are outside the tile 3002.

[0266] Figures 31A - 31C show examples of autofocus light detected by a sensor. The autofocus light can be detected using one or more embodiments described herein. In some implementations, the autofocus light can be detected using the system 100 of FIG. 1. In some implementations, the autofocus light can be detected using the optical system 200 of FIG. 2. In some implementations, the autofocus light can be detected using the optical system 500 of FIG. 5. In some implementations, the autofocus light can be detected using the optical system 800 of FIG. 8A. In some implementations, the autofocus light can be detected using the optical system 820 of FIG. 8B. In some implementations, the autofocus light can be detected using the optical system 1100 of FIG. 11. In some implementations, the autofocus light can be detected using the optical system 1200 of FIG. 12. In some implementations, the autofocus light can be detected using the optical system 1300 of FIG. 13. In some implementations, the autofocus light can be detected using the optical system 1400 of FIG. 14. In some implementations, the autofocus light can be detected using the imaging module 1800 of FIGS. 18 and 19A - 19B. In some implementations, the autofocus light can be created using the SIM assembly 2000 of FIG. 20. In some implementations, the autofocus light can be detected using the imaging module 2100 of FIG. 21. In some implementations, the autofocus light can be detected using the imaging module 2200 of FIG. 22. In some implementations, the autofocus light can be detected using the imaging module 2400 of FIG. 24. In some implementations, the autofocus light can be detected using the optical system 2500 of FIG. 25. In some implementations, the autofocus light can be detected using the optical system 2600 of FIG. 26. In some implementations, the autofocus light can be detected using the reflective component 2700 of FIG. 27.In some implementations, the autofocus light can be detected using the reflective component 2800 of FIG. 28. In some implementations, the autofocus light can be created using the SIM assembly 3400 of FIG. 34. In some implementations, the autofocus light can be created using the RIGS 3500 of FIG. 35. In some implementations, the autofocus light can be created using the RIGS 3600 of FIG. 36. In some implementations, the autofocus light can be created using the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the autofocus light can be created using the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the autofocus light can be detected using the projection lens 3900 of FIG. 39. In some implementations, the autofocus light can be detected using the projection lens 4000 of FIG. 40. In some implementations, the autofocus light can be detected using the field of view 4100 of FIG. 41.

[0267] FIG. 31A shows the autofocus light 3100. Here, the autofocus light 3100 is shown in a simulation detected within the tile 3102 defined with respect to the substrate 3104. For example, the autofocus light can be captured using an implementation that includes the imaging module 2400 of FIG. 24 and the optical system 2500 of FIG. 25. The autofocus light 3100 can include two or more spots of autofocus light corresponding to reflections from layers or other surfaces of the substrate. The distance between the spots can indicate the distance between the substrate and the objective lens that captures the autofocus light 3100. For example, the distance between the spots of the autofocus light 3100 is here about 0.390 mm.

[0268] FIG. 31B shows autofocus light 3106. Here, the autofocus light 3106 is shown in a simulation detected within tile 3108 defined with respect to substrate 3110. For example, the autofocus light 3106 can be captured using an implementation including the imaging module 1800 of FIGS. 18 and 19A - 19B, the SIM assembly 2000 of FIG. 20, and the optical system 2600 of FIG. 26. As another example, the autofocus light 3106 can be captured using an implementation including the imaging module 2200 of FIG. 22. The autofocus light 3106 can include two or more spots of autofocus light corresponding to reflections from layers or other surfaces of the substrate. The distance between the spots can indicate the distance between the substrate and the objective lens that captures the autofocus light 3106. For example, the distance between the spots of the autofocus light 3106 is here about 1.067 mm. In some implementations, the autofocus procedure can be adjusted to exclude or reduce an incidence where one or more spots of the autofocus light 3106 are outside of tile 3108.

[0269] Figure 31C shows the autofocus light 3112. Here, the autofocus light 3112 is shown in a simulation detected within the tile 3114 defined with respect to the substrate 3116. For example, the autofocus light 3106 can be captured using an implementation including the imaging module 1800 of FIGS. 18 and 19A - 19B, the SIM assembly 2000 of FIG. 20, and the optical system 2600 of FIG. 26. As another example, the autofocus light 3106 can be captured using an implementation including the imaging module 2200 of FIG. 22. The autofocus light 3106 can include two or more spots of autofocus light corresponding to reflections from a layer of the substrate or other surface. The distance between the spots can indicate the distance between the substrate and the objective lens that captures the autofocus light 3106. For example, the distance between the spots of the autofocus light 3106 is here about 1.067 mm. In some implementations, the autofocus procedure can be adjusted to exclude or reduce the incidence of one or more spots of the autofocus light 3112 being outside the tile 3114.

[0270] Power management can be performed in one or more embodiments described herein. In some implementations, power management includes applying one or more power algorithms. The power algorithms can be associated with one or more color channels. For example, the combined green power algorithm for a laser engine can be defined as follows.

Number

[0271] Figures 32A - 32C illustrate an embodiment of a laser engine heat sink 3200. Figures 33A - 33C illustrate an embodiment of a laser engine heat sink 3300. The laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, one or more other embodiments described herein. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the system 100 of FIG. 1. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the optical system 200 of FIG. 2. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the optical system 500 of FIG. 5. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the optical system 820 of FIG. 8B. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the optical system 1100 of FIG. 11. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the optical system 1200 of FIG. 12. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the optical system 1300 of FIG. 13. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the optical system 1400 of FIG. 14. In some implementations, the laser engine heat sink 3200 and / or 3300 can be used with, or incorporated within, the imaging module 1800 of FIGS. 18 and 19A - 19B.In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with or included in the imaging module 2100 of FIG. 21. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with or included in the imaging module 2200 of FIG. 22. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with or included in the imaging module 2400 of FIG. 24. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with or included in the optical system 2500 of FIG. 25. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with or included in the optical system 2600 of FIG. 26. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the reflective component 2700 of FIG. 27. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the SIM assembly 3400 of FIG. 34. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the RIGS 3500 of FIG. 35. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the RIGS 3600 of FIG. 36. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the piezoelectric phase shifter 3700 of FIG. 37. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the piezoelectric phase shifter 3800 of FIG. 38. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the projection lens 3900 of FIG. 39. In some implementations, the laser engine heat sinks 3200 and / or 3300 can be used with the projection lens 4000 of FIG. 40.

[0272] The laser engine heat sink 3200 can include a heat sink 3202. The laser engine heat sink 3300 can include a heat sink 3302. The heat sink 3200 and / or 3300 can include one or more heat sink materials. In some implementations, the heat sink material can be aluminum or copper. For example, the heat sink 3202 can include copper, and the heat sink 3302 can include aluminum. The heat sink 3202 and / or 3302 can have heat sink fins of a predetermined size. In some implementations, the size of the heat sink fins of the heat sink 3302 can be larger than the size of the heat sink fins of the heat sink 3202. For example, the size of the heat sink fins of the heat sink 3302 can be about 20 mm larger than the size of the heat sink fins of the heat sink 3202. In some implementations, the thermal resistance of the heat sink 3302 can be lower than the thermal resistance of the heat sink 3302. For example, the thermal resistance of the heat sink 3302 can be about 30 - 40% lower, for example about 36% lower, than the thermal resistance of the heat sink 3302. In some implementations, the air flow of the laser engine heat sink 3300 can be higher than the air flow of the laser engine heat sink 3200. For example, the air flow of the laser engine heat sink 3300 can be about 40 - 50% higher, for example about 45% higher, than the air flow of the laser engine heat sink 3200. In some implementations, the heat sink 3202 can have a size of about 80×80×30 mm. In some implementations, the heat sink 3302 can have a size of about 80×90×50 mm. In some implementations, the duct size of the heat sink 3302 can be larger than the duct size of the heat sink 3202. In some implementations, the heat sink 3302 can have a duct made of a material different from the duct of the heat sink 3202. For example, the heat sink 3302 can have a molded plastic duct. For example, the heat sink 3202 can have a sheet metal duct. The laser engine heat sink 3200 can include a housing 3204.The laser engine heat sink 3300 can include a housing 3304. In some implementations, the laser engine heat sink 3300 can include a gasket 3306. For example, the gasket 3306 can provide duct sealing between the heat sink 3302 and the housing 3304.

[0273] FIG. 34 shows one embodiment of a SIM assembly 3400. The SIM assembly 3400 can be used with or included in one or more other embodiments described herein. In some implementations, the SIM assembly 3400 can be used with or included in the system 100 of FIG. 1. In some implementations, the SIM assembly 3400 can be used with or included in the optical system 200 of FIG. 2. In some implementations, the SIM assembly 3400 can be used with or included in the optical system 500 of FIG. 5. In some implementations, the SIM assembly 3400 can be used with or included in the optical system 820 of FIG. 8B. In some implementations, the SIM assembly 3400 can be used with or included in the optical system 1100 of FIG. 11. In some implementations, the SIM assembly 3400 can be used with or included in the optical system 1200 of FIG. 12. In some implementations, the SIM assembly 3400 can be used with or included in the optical system 1300 of FIG. 13. In some implementations, the SIM assembly 3400 can be used with or included in the optical system 1400 of FIG. 14. In some implementations, the SIM assembly 3400 can be used with the lateral displacement prism 1600 of FIGS. 16A-16B. In some implementations, the SIM assembly 3400 can include or be used with the beam splitter 1700 of FIG. 17. In some implementations, the SIM assembly 3400 can be used with or included in the im...

Claims

Claim 1 A method comprising: generating autofocus light using a first light source of an optical system; directing the autofocus light through an objective lens of the optical system and then towards a substrate having first and second surfaces, wherein the autofocus light is reflected as first autofocus light at the first surface and the autofocus light is reflected as second autofocus light at the second surface; generating excitation light using a second light source of the optical system; directing the excitation light through the objective lens and then towards the substrate; directing the first autofocus light towards a sensor using the objective lens and a first reflective surface; preventing the second autofocus light from reaching the sensor; and directing emitted light towards the sensor using the objective lens and a second reflective surface, wherein the emitted light is generated from a sample of the substrate that receives the excitation light; comprising further comprising directing the first autofocus light towards the second reflective surface, the second reflective surface being transparent to the first autofocus light, and the first reflective surface being positioned behind the second reflective surface with respect to the direction of travel of the first autofocus light. Claim 2 The method of claim 1, further comprising directing the second autofocus light towards the second reflective surface, the second reflective surface being transparent to the second autofocus light, and the first reflective surface being transparent to the second autofocus light so as to prevent the second autofocus light from reaching the sensor. Claim 3 The first reflective surface is positioned on a first reflective component, the second reflective surface is positioned on a second reflective component, the first reflective component is separated from the second reflective component, and the method further comprises orienting the first reflective component independently of the orientation of the second reflective component. The method according to claim 1. Claim 4 Orienting the first reflective component includes directing the first autofocus light onto the sensor, independent of the position of the emitted light on the sensor, according to the method of claim 3.

5. Further comprising using a lateral displacement prism to form left and right autofocus lights that diverge from each other at a predetermined angle, wherein the first autofocus light includes a first left autofocus light from the reflection of the left autofocus light from the first surface of the substrate, the first autofocus light further includes a first right autofocus light from the reflection of the right autofocus light from the first surface of the substrate, the second autofocus light includes a second left autofocus light from the reflection of the left autofocus light from the second surface of the substrate, and the second autofocus light further includes a second right autofocus light from the reflection of the right autofocus light from the second surface of the substrate. Directing the first autofocus light toward the sensor includes using the objective lens and the first reflective surface to direct the first left autofocus light and the first right autofocus light toward the sensor. Preventing the second autofocus light from reaching the sensor includes preventing the second left autofocus light and the second right autofocus light from reaching the sensor, according to the method of claim 1.

6. The substrate further includes a third surface, the left autofocus light forms a third left autofocus light upon reflection from the third surface, the right autofocus light forms a third right autofocus light upon reflection from the third surface, and the method further includes using the objective lens and the first reflective surface to direct the third left autofocus light and the third right autofocus light toward the sensor, according to the method of claim 5.

7. Further comprising adjusting the distance between the objective lens and the substrate based on the first autofocus light, according to the method of claim 1.

8. A method comprising: Forming left and right autofocus lights that diverge from each other at a predetermined angle using a first light source of an optical system; Directing the left autofocus light and the right autofocus light through the objective lens toward the first surface of the substrate; After reflection from the first surface, directing at least a first portion of the left autofocus light and at least a first portion of the right autofocus light toward the sensor, wherein the fact that the distance between the first portion of the left autofocus light and the first portion of the right autofocus light at the sensor is a predefined distance indicates that the substrate is at the focus of the objective lens; Using a second light source of the optical system to generate excitation light; Directing the excitation light through the objective lens and then toward the substrate; and Using the objective lens and the reflective surface to direct the emitted light toward the sensor, where the emitted light is generated from a sample of the substrate that receives the excitation light; comprising further comprising directing the first portion of the left autofocus light and the first portion of the right autofocus light toward a second reflective surface, the second reflective surface being transparent to the first portion of the left autofocus light and the first portion of the right autofocus light, and the first reflective surface being positioned behind the second reflective surface with respect to the traveling direction of the first portion of the left autofocus light and the first portion of the right autofocus light, a method.

9. The method according to claim 8, wherein the substrate further comprises a second surface, the reflection of the left autofocus light from the first surface forms a first left autofocus light, the reflection of the left autofocus light from the second surface forms a second left autofocus light, at the sensor, the first portion of the left autofocus light includes the first left autofocus light and the second left autofocus light, the reflection of the right autofocus light from the first surface forms a first right autofocus light, the reflection of the right autofocus light from the second surface forms a second right autofocus light, and at the sensor, the first portion of the right autofocus light includes the first right autofocus light and the second right autofocus light.

10. The fact that the distance between the first left autofocus light and the first right autofocus light in the sensor is a predefined first distance indicates that the first surface of the substrate is at the focus of the objective lens. The method according to claim 9.

11. The fact that the distance between the second left autofocus light and the second right autofocus light in the sensor is a predefined second distance indicates that the second surface of the substrate is at the focus of the objective lens. The method according to claim 10.

12. Directing the first portion of the left autofocus light and the first portion of the right autofocus light towards the sensor using a first reflective surface includes directing the first portion of the left autofocus light and the first portion of the right autofocus light towards the sensor. The method according to claim 8.

13. The substrate further includes a second surface, the second portion of the left autofocus light is formed upon reflection of the left autofocus light from the second surface, the second portion of the right autofocus light is formed upon reflection of the right autofocus light from the second surface, the method further includes directing the second portion of the left autofocus light and the second portion of the right autofocus light towards the second reflective surface, the second reflective surface is also transparent to the second portion of the left autofocus light and the second portion of the right autofocus light, and the first reflective surface is transparent to the second portion of the left autofocus light and the second portion of the right autofocus light to prevent the second portion of the left autofocus light and the second portion of the right autofocus light from reaching the sensor. The method according to claim 8.

14. The first reflective surface is positioned on a first reflective component, the second reflective surface is positioned on a second reflective component, the first reflective component is separated from the second reflective component, and the method further includes orienting the first reflective component independently of the orientation of the second reflective component. The method according to claim 8.

15. Orienting the first reflective component causes the guiding of the first portions of the left autofocus light and the right autofocus light on the sensor, independent of the position of the emitted light on the sensor, according to the method of claim 14.

16. The method of claim 8, further comprising adjusting a distance between the objective lens and the substrate based on the first portion of the left autofocus light and the first portion of the right autofocus light.

17. A structured illumination microscope assembly, A light source that provides a first light, An anamorphic prism for providing a second light by converting the first light, A first grating, A second grating separated from the first grating, A rotatable mirror configured to take a first position (i) for redirecting the second light towards the first grating and a second position (ii) for receiving the second light from the second grating, the rotatable mirror not redirecting the second light towards the second grating at the second position, a structured illumination microscope assembly comprising.

Images