Improved autofocus functionality in optical sample analysis

Abstract

The invention relates to an improved autofocus function in optical sample analysis. A method includes directing a first auto-focused light toward a sensor using an objective lens and a first reflective surface, the first auto-focused light being reflected from a first surface of a substrate; preventing the second auto-focused light from reaching the sensor, the second auto-focused light being reflected from the second surface of the substrate; and directing emitted light from the sample at the substrate to the sensor using the objective lens and the second reflective surface.

Description

[0001] This application is a divisional application of the application with application date of December 30, 2020, application number 202011613363.4, and invention name “Improved autofocus function in optical sample analysis”.

[0002] CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] This application claims priority to U.S. Provisional Application No. 62 / 959,681, filed on January 10, 2020, entitled “IMPROVED AUTOFOCUS FUNCTIONALITY IN OPTICAL SAMPLE ANALYSIS.” This application also claims priority to U.S. Provisional Application No. 62 / 956,083, filed on December 31, 2019, entitled “IMPROVED AUTOFOCUS FUNCTIONALITY IN OPTICAL SAMPLE ANALYSIS.” The contents of both provisional applications are incorporated herein by reference.

[0004] background

[0005] One or more types of optical systems can be used to analyze samples of different materials. Optical systems sometimes include a focus tracking function to help adjust the optical components to improve the quality of the measurement and, in turn, the quality of the final sample analysis. The focus tracking system is typically integrated with the optical system, but operates in some sense independently of the functionality of the optical system. For example, the focus tracking component may use a dedicated light source, one or more optical components (e.g., a lens), and / or a light detector. That is, these components may be used solely for the purpose of focus tracking. Having dedicated components for the focus tracking system may increase the manufacturing cost of the optical system. As another example, having a larger number of components on a board may increase the likelihood that the system will require repair.

[0006] Overview

[0007] In a first aspect, a method includes directing first autofocus light to a sensor using an objective lens and a first reflective surface, the first autofocus light reflected from a first surface of a substrate; preventing second autofocus light from reaching the sensor, the second autofocus light reflected from a second surface of the substrate; and directing emission light to the sensor using the objective lens and the second reflective surface, the emission light originating from a sample at the substrate.

[0008] Implementations may include any or all of the following features. The method also includes directing the first autofocus light to the second reflective surface, the second reflective surface being transparent to the first autofocus light, wherein the first reflective surface is positioned behind the second reflective surface relative to the direction of travel of the first autofocus light. The method also includes also directing the second autofocus light to the second reflective surface, the second reflective surface being transparent to the second autofocus light, wherein the first reflective surface is transparent to the second autofocus light to prevent the second autofocus light from reaching the sensor. The first reflective surface is positioned on a first reflective component, wherein the second reflective surface is positioned on a second reflective component, and wherein the first reflective component is separated from the second reflective component, the method also including orienting the first reflective component independently of the orientation of the second reflective component. Orienting the first reflective component includes manipulating the first autofocus light on the sensor independently of the positioning of the emitted light on the sensor. The method also includes: using a lateral displacement prism to form a left auto-focus light and a right auto-focus light that are offset from each other by a predetermined angle, wherein the first auto-focus light includes a first left auto-focus light resulting from a reflection of the left auto-focus light from the first surface of the substrate, wherein the first auto-focus light also includes a first right auto-focus light resulting from a reflection of the right auto-focus light from the first surface of the substrate, wherein the second auto-focus light includes a second left auto-focus light resulting from a reflection of the left auto-focus light from the second surface of the substrate, and wherein the second auto-focus light also includes a second right auto-focus light resulting from a reflection of the right auto-focus light from the second surface of the substrate; wherein directing the first auto-focus light to the sensor includes directing the first left auto-focus light and the first right auto-focus light to the sensor using the objective lens and the first reflective surface; and wherein preventing the second auto-focus light from reaching the sensor includes preventing the second left auto-focus light and the second right auto-focus light from reaching the sensor. The substrate further includes a third surface, wherein the left auto-focus light forms a third left auto-focus light when reflected from the third surface, and wherein the right auto-focus light forms a third right auto-focus light when reflected from the third surface, the method further including directing the third left auto-focus light and the third right auto-focus light toward the sensor using the objective lens and the first reflective surface. The method further includes adjusting a distance between the objective lens and the substrate based on the first auto-focus light.

[0009] In a second aspect, a system includes: a substrate that holds a sample for analysis; a sensor; an objective lens; a first reflective surface that is used to direct first autofocus light to the sensor, the first autofocus light being reflected from the first surface of the substrate and transmitted through the objective lens; a second reflective surface that is used to direct emitted light to the sensor, the emitted light being emitted from the sample and transmitted through the objective lens; and a structure that prevents second autofocus light from reaching the sensor, the second autofocus light being reflected from the second surface of the substrate and transmitted through the objective lens.

[0010] Implementations may include any or all of the following features. The first reflective surface is positioned behind the second reflective surface relative to the direction of travel of the first autofocus light, and wherein the second reflective surface is transparent to the first autofocus light. The first reflective surface is positioned on a first reflective component, wherein the second reflective surface is positioned on a second reflective component, and wherein the first reflective component is separated from the second reflective component. The second reflective surface is positioned on a front surface of a reflective component relative to the direction of travel of the first autofocus light, wherein the first reflective surface covers a first portion of a rear surface of the reflective component relative to the direction of travel of the first autofocus light, and wherein the structure covers a second portion of the rear surface of the reflective component. The system further includes a lateral displacement prism that forms left and right autofocus lights that are offset from each other by a predetermined angle, wherein the first autofocus light includes a first left autofocus light resulting from a reflection of the left autofocus light from a first surface of the substrate, wherein the first autofocus light also includes a first right autofocus light resulting from a reflection of the right autofocus light from the first surface of the substrate, wherein the second autofocus light includes a second left autofocus light resulting from a reflection of the left autofocus light from a second surface of the substrate, and wherein the second autofocus light also includes a second right autofocus light resulting from a reflection of the right autofocus light from the second surface of the substrate. The lateral displacement prism includes a plurality of exit surfaces having non-zero angles relative to each other. The lateral displacement prism includes: a first surface; a second surface, the second surface of the lateral displacement prism being parallel to the first surface of the lateral displacement prism; a third surface; a fourth surface; a fifth surface, the 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 boundaries of the fourth surface and the fifth surface. The first surface of the lateral displacement prism has boundaries with the third surface, the fourth surface, and the fifth surface; and the second surface of the lateral displacement prism has boundaries with the third surface, the fourth surface, and the fifth surface. The third surface is an incident surface, wherein the fourth surface is an exit surface for the left autofocus light, and wherein the fifth surface is an exit surface for the right autofocus light.The lateral displacement prism includes: a first prism having a first wedge-shaped profile including a first side forming a non-zero angle relative to a first exit side; a second prism having a second wedge-shaped profile including a second side forming a non-zero angle relative to the second exit side; and a third prism having a parallelogram-shaped profile including a third side parallel to a fourth side and a fifth side parallel to a sixth side, the third side of the parallelogram-shaped profile being a portion of an incident surface of the lateral displacement prism; wherein each of the first side of the first prism and the second side of the second prism faces the fourth side of the third prism. The system is configured to analyze nucleic acid material at the substrate.

[0011] In a third aspect, a method includes: forming left auto-focus light and right auto-focus light that are offset from each other by a predetermined angle; directing the left auto-focus light and the right auto-focus light to a first surface of a substrate through an objective lens; and directing at least a first portion of the left auto-focus light and at least a first portion of the right auto-focus light to a sensor after reflection from the first surface, wherein a predetermined interval between the first portion of the left auto-focus light and the first portion of the right auto-focus light at the sensor indicates that the substrate is in focus of the objective lens.

[0012] Implementations may include any or all of the following features. The substrate further comprises a second surface, wherein the left auto-focus light is reflected from the first surface to form a first left auto-focus light, wherein the left auto-focus light is reflected from the second surface to form a second left auto-focus light, wherein a first portion of the left auto-focus light at the sensor comprises the first left auto-focus light and the second left auto-focus light, wherein the right auto-focus light is reflected from the first surface to form a first right auto-focus light, wherein the right auto-focus light is reflected from the second surface to form a second right auto-focus light, wherein a first portion of the right auto-focus light at the sensor comprises the first right auto-focus light and the second right auto-focus light. A first predetermined interval between the first left auto-focus light and the first right auto-focus light at the sensor indicates that the first surface of the substrate is in focus of the objective lens. A second predetermined interval between the second left auto-focus light and the second right auto-focus light at the sensor indicates that the second surface of the substrate is in focus of the objective lens. Directing the first portion of the left auto-focus light and the first portion of the right auto-focus light toward the sensor includes directing the first portion of the left auto-focus light and the first portion of the right auto-focus light toward the sensor using a first reflective surface. The method also includes directing emitted light from the sample at the substrate toward the sensor using the objective lens and the second reflective surface. The method also includes directing the first portion of the left auto-focus light and the first portion of the right auto-focus light toward the second reflective surface, the second reflective surface being transparent to the first portion of the left auto-focus light and the first portion of the right auto-focus light, wherein the first reflective surface is positioned behind the second reflective surface relative to a direction of travel of the first portion of the left auto-focus light and the first portion of the right auto-focus light. The substrate also includes a second surface, wherein the second portion of the left auto-focus light is formed when the left auto-focus light is reflected from the second surface, and wherein the second portion of the right auto-focus light is formed when the right auto-focus light is reflected from the second surface, and the method also includes directing the second portion of the left auto-focus light and the second portion of the right auto-focus light to the second reflective surface, the second reflective surface also being transparent to the second portion of the left auto-focus light and the second portion of the right auto-focus light, wherein the first reflective surface is transparent to the second portion of the left auto-focus light and the second portion of the right auto-focus light to prevent the second portion of the left auto-focus light and the second portion of the right auto-focus light from reaching the sensor.The first reflective surface is positioned on a first reflective component, wherein the second reflective surface is positioned on a second reflective component, and wherein the first reflective component is separated from the second reflective component, the method further comprising orienting the first reflective component independently of the orientation of the second reflective component. The first reflective component is oriented such that the first portion of the left autofocus light and the first portion of the right autofocus light on the sensor are manipulated independently of the positioning of the emitted light on the sensor. The method further comprises 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.

[0013] In a fourth aspect, a system comprises: a beam splitter for forming a left auto-focus light and a right auto-focus light that are offset from each other by a predetermined angle; an objective lens for transmitting the left auto-focus light and the right auto-focus light to a first surface of a substrate; and a sensor for receiving at least the first portion of the left auto-focus light and at least the first portion of the right auto-focus light after the at least first portion of the left auto-focus light and the at least first portion of the right auto-focus light are reflected from the first surface, wherein a predetermined interval between the first portion of the left auto-focus light and the first portion of the right auto-focus light at the sensor indicates that the substrate is in focus of the objective lens.

[0014] Implementations may include any or all of the following features. The beam splitter is part of a lateral displacement prism. The lateral displacement prism includes a plurality of exit surfaces having a non-zero angle relative to one another. The lateral displacement prism includes: a first surface; a second surface, the second surface of the lateral displacement prism being parallel to the first surface of the lateral displacement prism; a third surface; a fourth surface; a fifth surface, the 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 a boundary between the fourth surface and the fifth surface. The first surface of the lateral displacement prism has a boundary with the third surface, the fourth surface, and the fifth surface; and the second surface of the lateral displacement prism has a boundary with the third surface, the fourth surface, and the fifth surface. The third surface is an incident surface, wherein the fourth surface is an exit surface for the left autofocus light, and wherein the fifth surface is an exit surface for the right autofocus light. The lateral displacement prism includes: a first prism, the first prism having a first wedge-shaped cross-section, the first wedge-shaped cross-section including a first side forming a non-zero angle relative to the first exit side; a second prism, the second prism having a second wedge-shaped cross-section, the second wedge-shaped cross-section including a second side forming a non-zero angle relative to the second exit side; and a third prism, the third prism having a parallelogram cross-section, the parallelogram cross-section including a third side parallel to the fourth side and a fifth side parallel to the sixth side, the third side of the parallelogram cross-section being part of the incident surface of the lateral displacement prism; wherein each of the first side of the first prism and the second side of the second prism faces 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 at 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 and the right autofocus light is incident after being formed at the partially reflective layer. The system also 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 also includes a second reflective surface for directing emitted light, which originates from a sample at the substrate and is transmitted through the objective lens, toward the sensor.The substrate further includes a second surface, wherein the second portion of the left auto-focus light is formed when the left auto-focus light is reflected from the second surface of the substrate, and wherein the second portion of the right auto-focus light is formed when the right auto-focus light is reflected from the second surface of the substrate, and the system further includes a structure that prevents the second portion of the left auto-focus light and the second portion of the right auto-focus light from reaching the sensor. The first reflective surface is positioned behind the second reflective surface relative to a direction of travel of the first portion of the left auto-focus light, the second portion of the left auto-focus light, the first portion of the right auto-focus light, and the second portion of the right auto-focus light, wherein the second reflective surface is transparent to the first portion of the left auto-focus light, the second portion of the left auto-focus light, the first portion of the right auto-focus light, and the second portion of the right auto-focus light. The first reflective surface is positioned on a first reflective component, wherein the second reflective surface is positioned on a second reflective component, and wherein the first reflective component is separate from the second reflective component. The second reflective surface is positioned on a front surface of a second reflective component relative to a direction of travel of the first portion of the left auto-focus light, the second portion of the left auto-focus light, the first portion of the right auto-focus light, and the second portion of the right auto-focus light, wherein the first reflective surface covers a first portion of a rear surface of the second reflective component relative to the direction of travel of the first portion of the left auto-focus light, the second portion of the left auto-focus light, the first portion of the right auto-focus light, and the second portion of the right auto-focus light, and wherein the structure covers a second portion of the rear surface of the second reflective component. The system is configured to analyze nucleic acid material at the substrate.

[0015] In a fifth aspect, an autofocus component comprises: a prism, the prism comprising: a first surface; a second surface, the second surface being parallel to the first surface; a third surface; a fourth surface; a fifth surface, the 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, the partially reflective layer extending between the third surface and the boundary between the fourth surface and the fifth surface; and a light source, the light source being used to direct light to the prism, the prism forming a first autofocus light and a second autofocus light from the light, the first autofocus light and the second autofocus light being offset from each other by a predetermined angle.

[0016] Implementations may include any or all of the following features. The fourth surface and the fifth surface form an exit surface having a non-zero angle relative 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 incident surface. The prism includes: a first prism having a first wedge-shaped cross-section, the first prism forming the fourth surface, the first wedge-shaped cross-section including a first side forming a non-zero angle relative to the fourth surface; a second prism having a second wedge-shaped cross-section, the second prism forming the fifth surface, the second wedge-shaped cross-section including a second side forming a non-zero angle relative to the fifth surface; and a third prism having a parallelogram cross-section, the parallelogram cross-section including a third side parallel to the fourth side and a fifth side parallel to the sixth side, the third side defining the third surface; wherein each of the first side of the first prism and the second side of the second prism faces the fourth side of the third prism.

[0017] It should be appreciated that all combinations of the foregoing concepts and the additional concepts discussed in more detail below (provided that these concepts are not mutually inconsistent) are contemplated as part of the overall subject matter disclosed herein. In particular, all combinations of the claimed subject matter appearing at the end of this disclosure are contemplated as part of the disclosed subject matter disclosed herein. BRIEF DESCRIPTION OF THE DRAWINGS

[0019] Figure 1 An embodiment of a system that can be used to analyze a sample is shown.

[0020] Figure 2 An embodiment of an optical system is shown.

[0021] Figure 3 is a diagram illustrating an example of desired and undesired reflections generated from multiple surfaces of a multi-layer sample substrate in some embodiments.

[0022] Figures 4A-4C The autofocus light recorded at the sensor is shown.

[0023] Figure 5 An embodiment of an optical system is shown.

[0024] Figures 6A-6C The autofocus light recorded at the sensor is shown.

[0025] Figures 7A-7C The autofocus light recorded at the sensor is shown.

[0026] Figure 8AAn embodiment of an optical system is shown.

[0027] Figure 8B An embodiment of an optical system is shown.

[0028] Figure 9A-9B is a diagram illustrating an example of desired and undesired reflections generated from multiple surfaces of a multi-layer sample substrate in some embodiments.

[0029] Figures 10A-10C An embodiment of a laterally displacing prism is shown.

[0030] Figure 11 An optical system with a laterally displaced prism is schematically shown.

[0031] Figure 12 An optical system with a laterally displaced prism is schematically shown.

[0032] Figure 13 An optical system with a laterally displaced prism is schematically shown.

[0033] Figure 14 An optical system with a laterally displaced prism is schematically shown.

[0034] Figure 15 An embodiment of automatically focusing light at a sensor is illustrated.

[0035] Figures 16A-16B An embodiment of a laterally displacing prism is shown.

[0036] Figure 17 An embodiment of a beam splitter is shown.

[0037] Figure 18 An embodiment of an imaging system is shown.

[0038] Figures 19A-19B Shown Figure 18 Embodiment of the imaging module.

[0039] Figure 20 An embodiment of a structured illumination microscopy (SIM) assembly is shown.

[0040] Figure 21 An embodiment of an imaging module is shown.

[0041] Figure 22 An embodiment of an imaging module is shown.

[0042] Figure 23 A graph showing error rates is shown.

[0043] Figure 24 An embodiment of an imaging module is shown.

[0044] Figure 25 An embodiment of an optical system is shown.

[0045] Figure 26 An embodiment of an optical system is shown.

[0046] Figure 27 An embodiment of a reflective component is shown.

[0047] Figure 28 An embodiment of a reflective component is shown.

[0048] Figure 29 An example of autofocus light detected by a sensor is shown.

[0049] Figure 30 An example of autofocus light detected by a sensor is shown.

[0050] Figures 31A-31C An example of autofocus light detected by a sensor is shown.

[0051] Figures 32A-32C An embodiment of a laser engine heat sink is shown.

[0052] Figures 33A-33C An embodiment of a laser engine heat sink is shown.

[0053] Figure 34 An embodiment of a SIM assembly is shown.

[0054] Figure 35 An example of a rotating in-plane grating switcher (RIGS) is shown.

[0055] Figure 36 An example of RIGS is shown.

[0056] Figure 37 An embodiment of a piezoelectric phase shifter is shown.

[0057] Figure 38 An embodiment of a piezoelectric phase shifter is shown.

[0058] Figure 39 An embodiment of a projection lens is shown.

[0059] Figure 40 An embodiment of a projection lens is shown.

[0060] Figure 41 An example of the field of view is shown.

[0061] Figure 42 is a schematic diagram of an example system that can be used for biological and / or chemical analysis.

[0062] Figure 43 An example architecture of a computing device that can be used to implement aspects of the present disclosure is illustrated.

[0063] Detailed description

[0064] The present disclosure describes systems, techniques, and / or articles of manufacture related to corresponding improvements regarding autofocus functionality. When using a focus tracking system or other autofocus system, stray reflections may appear on the detector, the stray reflections originating from multiple optical interfaces (e.g., layers or other surfaces) which can interfere with the focus tracking algorithm. In some implementations, additional optical devices for steering the light beam can be used to direct reflections related to autofocus to the image sensor while preventing irrelevant reflections from reaching the sensor. Such an approach can provide that focus tracking reflections of interest can be selectively steered to a predetermined area of ​​the detector that is not interfered with by stray reflections. This can increase the focus tracking capability of the system. One or more implementations described herein can facilitate integration of 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 at the sample.

[0065] In some implementations, the optical system can include a filter having a coating that reflects emitted light toward the sensor, the filter transmitting both relevant and irrelevant reflections. The optical device for manipulating the light beam can be positioned after the filter and can include a reflective material (e.g., a mirror) positioned in the relevant reflection path and out of the irrelevant reflection path. An absorbing material can be placed in the irrelevant reflection path. The reflective material can be movable to direct the relevant reflection relative to the sensor (e.g., direct the relevant reflection away from the emitted light). In another implementation, the reflective material can include a coating at the back of the filter, and a high-transmittance coating can be used to allow irrelevant reflections to leave the filter.

[0066] In some implementations, the beams of autofocus light can be formed so that they deviate from each other after being split. For example, an angled exit surface at a beam splitting component (e.g., using a custom prism, or using an off-the-shelf prism with an attached wedge prism) can be used to provide a diverging autofocus beam. As another example, an arrangement of a mirror, a 50% reflective filter, and a glass plate forming an angled exit surface can be used to provide a diverging autofocus beam. Each diverging AFM beam forms a corresponding spot on the sensor that is offset to opposite sides of the center of the field of view. The angled exit surface of the beam splitting component is configured to introduce a predetermined distance between the spots reflected from the same surface, so that a measure of the difference between the measured distance between the 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 a best focus that is more easily measured without affecting the alignment of the emission optics.

[0067] The examples described herein relate to the analysis of one or more samples. As used herein, the term sample includes various substances of interest that undergo an imaging process in which optical signals from the sample are observed. In certain embodiments, the sample may include biological substances of interest and / or chemical substances of interest. Optionally, the sample may include an optical substrate or support structure that supports the biological substance or chemical substance. Thus, the sample may or may not include an optical substrate or support structure. As used herein, the term biological substance or chemical substance may include various biological or chemical substances suitable for imaging or inspection using the optical system described herein. For example, biological or chemical substances include biomolecules such as nucleosides, nucleic acids, polynucleotides, oligonucleotides, proteins, enzymes, polypeptides, antibodies, antigens, ligands, receptors, polysaccharides, carbohydrates, polyphosphates, nanopores, organelles, lipid layers, cells, tissues, organisms, and biologically active compounds, such as analogs or mimetics of the above species. Other chemical substances include labels that can be used for identification, examples of which include fluorescent labels. Analysis of samples can include, but is not limited to, gene sequencing (e.g., determining the structure of genetic material), genotyping (e.g., determining differences in the genetic makeup of individuals), gene expression (e.g., using genetic information to synthesize gene products), proteomics (e.g., the large-scale study of proteins), or a combination thereof.

[0068] The examples herein refer to substrates. A substrate can refer to any material that provides at least a substantially rigid structure, or a structure that maintains its shape rather than taking on the shape of a container placed in contact with it. The material can have a surface to which another material can be attached, including, for example, smooth supports (e.g., metal, glass, plastic, silicon, and ceramic surfaces) and textured and / or porous materials. Possible substrates include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylic resins, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethane, polytetrafluoroethylene, TM The substrate can be a polymer (e.g., polysaccharides, nylon or nitrocellulose), resins, silica or silicon-based materials (including silicon and modified silicon), carbon, metals, inorganic glass, plastics, fiber optic bundles, and various other polymers. Generally, the substrate allows optical detection and does not emit significant fluorescence itself.

[0069] The examples described herein relate to flow cells. A flow cell can be considered as a substrate for preparing and accommodating or carrying one or more samples in at least one stage of an analytical process. The flow cell is made of a material compatible with the sample material (e.g., genetic material), irradiation, and the chemical reaction to which it will be exposed. The substrate can have one or more channels in which the sample material can be deposited. A substance (e.g., liquid) can flow through the channel where the sample genetic material is located to trigger one or more chemical reactions and / or remove unwanted materials. The flow cell can be imaged in the following manner: the sample in the flow cell channel can be subjected to irradiation light and any fluorescence response from the sample can be detected. Some implementations of the system can be designed to be used with at least one flow cell, but during one or more stages, such as during transportation or when delivered to a customer, a flow cell may not be included. The flow cell can have one or more surfaces configured to accommodate a sample (e.g., a sample of, but not limited to, nucleic acid material). In some implementations, the surface is coated with one or more polymers. For example, the polymer can comprise poly(N-(5-azidoacetamidylpentyl)acrylamide-co-acrylamide), sometimes referred to as PAZAM.

[0070] Examples described herein relate to autofocus light. An autofocus module in a sample analysis system can use the autofocus light 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 use the autofocus light to optically measure the distance between two or more objects (e.g., an optical component and a substrate). In some implementations, the autofocus module uses the autofocus light to perform triangulation with respect to the two or more objects. For example, an autofocus light source (e.g., a laser diode) can generate a light beam that impinges on and is reflected by at least one surface of the substrate. A light detector (e.g., a photosensor) can record the reflection of the light beam from the at least one surface. The location of the reflection (e.g., a light spot) on the light detector is an indication of the distance to the substrate. The autofocus light can have any suitable wavelength, taking into account the type of material in the sample (i.e., so that the autofocus light does not significantly degrade the sample or otherwise alter its chemical properties) and / or the light detector (i.e., so that the light detector can detect the autofocus light). In some implementations, the autofocus light can have one or more wavelengths within a range of approximately 770 nanometers to approximately 880 nanometers.

[0071] The examples described herein relate to emitted light. One or more types of emitted light can be caused to be emitted from a sample as part of performing or preparing the sample for analysis with respect to one or more features. In some implementations, the emitted light includes fluorescent light (sometimes referred to as fluorescence) emitted by one or more fluorescent markers or labels on the sample material. For example, the emission of fluorescence can be triggered or excited by subjecting the sample to excitation light (including but not limited to directing a laser at the sample).

[0072] The examples described herein relate to surfaces that are reflective or that are reflective surfaces. A surface can reflect at least substantially all wavelengths of light, or can reflect only one or more predetermined wavelengths (e.g., wavelengths of one or more bands). The surface can exhibit specular reflection, meaning that an image contained in the incident light is at least substantially preserved in the reflected light. Reflectivity does not necessarily include reflection of all incident light, or reflection of all incident light of a predetermined wavelength. Rather, a surface can be considered reflective if it reflects a certain amount (e.g., greater than zero) of incident light or light of a predetermined wavelength. A reflective surface can be formed on any type of substrate, and the surface can include any of a variety of reflective materials. A reflective surface can be formed by applying one or more layers to a substrate. In some implementations, the reflective surface operates based on thin film interference involving the top surface of the layer and the top surface of the substrate.

[0073] A reflective surface may be referred to as a filter in an optical system. For example, a reflective surface may include a dichroic filter. As used herein, the term filter in an optical system is intended to refer to a device used to selectively pass or reject radiation in a wavelength-, polarization-, or frequency-dependent manner. The term may include interference filters, in which multiple layers of dielectric material pass or reflect radiation based on constructive or destructive interference between reflections from different layers. Interference filters are also known in the art as dichroic filters or dielectric filters. The term may also include absorptive filters, which prevent the passage of radiation having a selective wavelength or wavelength range by absorption. Absorptive filters include, for example, colored glass or liquids.

[0074] The examples described herein relate to transparent surfaces, or surfaces that act as transparent surfaces. The surface can be transparent to at least substantially all wavelengths of light, or can be transparent only to one or more predetermined wavelengths (e.g., one or more wavelength bands). Transparency does not necessarily involve the transmission of all incident light or the transmission of all incident light of a predetermined wavelength. Instead, if the surface transmits a certain amount (e.g., greater than zero) of incident light or light with a predetermined wavelength, the surface can be considered transparent. The transparent surface can be formed on any type of substrate, and the surface can include any of a variety of transparent materials. The transparent surface can be formed by applying one or more anti-reflective materials to the substrate. Examples of suitable anti-reflective materials that can be used include, but are not limited to, any transparent material having a refractive index equal to the square root of the product of the refractive index of the substrate and the surrounding medium. Some examples of anti-reflective materials include magnesium fluoride (MgF2), fluoropolymers, mesoporous silica nanoparticles, alternating layers of silica and a higher refractive index material, or other anti-reflective materials that exhibit desired anti-reflective properties within the desired emission band / wavelength used.

[0075] Examples described herein relate to one or more structures that prevent light (e.g., autofocus light) from being transmitted to a predetermined component or in a predetermined direction. In some implementations, the structure can prevent transmission to the predetermined component or in a predetermined direction by absorbing the light. For example, the structure can include an absorbing material to absorb at least substantially all of the energy in the light impinging on the structure. In some implementations, the structure can prevent transmission to the predetermined component or in a predetermined direction by not reflecting the light toward the predetermined component or in a predefined direction. For example, the structure can include a material that is transparent to the wavelength being sought to prevent reaching the predetermined component or preventing transmission in a predetermined direction.

[0076] Examples described herein involve using modifiers such as "left" or "right" to refer to portions of light. The terms left and right are used herein for illustrative purposes only and do not necessarily reflect the spatial arrangement of any components or the relative position of any portion of light. In some implementations, an alternative to the modifiers left and right may be the terms first and second, respectively. For example, in some cases, the left autofocus light and the right autofocus light may be referred to as the first autofocus light and the second autofocus light, respectively.

[0077] The examples described herein involve parts of a light using modifiers such as "top" or "bottom." The terms top and bottom are used herein for illustrative purposes only and do not necessarily reflect the spatial arrangement of any components. In some implementations, alternatives to the modifiers top and bottom can be the terms first and second, respectively. For example, the top surface and bottom surface can, in some cases, be referred to as the first surface and the second surface, respectively.

[0078] The examples described herein relate to components that are "after" or "in front of" another component or "in front of" or "behind" another component. The terms after, in front of, and behind are used herein for illustrative purposes only and do not necessarily reflect only one of multiple spatial arrangements or the only possible spatial arrangement of any component. In some implementations, the terms after, 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 after a second item relative to the direction of travel of light, meaning that the light reaches the second item before reaching the first item. As another example, the first item can be characterized as in front of the second item relative to the direction of travel of light, meaning that the light reaches the first item before reaching the second item. As another example, a surface of a component can be referred to as a front surface relative to the direction of propagation of light, meaning that light reaches the front surface before reaching other aspects of the component. As another example, a surface of a component can be referred to as a back surface relative to the direction of propagation of light, meaning that light reaches other aspects of the component before reaching the back surface.

[0079] The examples described herein relate to light detectors. In some implementations, the light detectors can be sensitive to one or more forms of electromagnetic radiation. The detectors can include devices or apparatuses having several elements that convert the energy of contacting photons into an electrical response. Such elements can be referred to as sensors, or arrays of these elements can be collectively referred to as sensors. The sensors can include charge-coupled devices (CCDs), in which the elements are photosensitive charge collection points that accumulate charge in response to impinging photons. The sensors can include complementary metal oxide semiconductor (CMOS) detector arrays, photodiode arrays, avalanche photodiode (APD) detector arrays, and / or Geiger-mode photon counter detector arrays. The elements of the sensor can have any of a variety of arrangements. For example, a rectangular sensor array has elements arranged orthogonally in two dimensions, where the first dimension, referred to as the "horizontal" dimension, can be longer than the second dimension, referred to as the "vertical" dimension. A square sensor array has elements arranged orthogonally in two dimensions, where the first and second dimensions in the arrangement are the same length. The sensor can detect light and generate a corresponding output from one or more pixels. In some implementations, the separation between two or more portions of light at the sensor can be determined (e.g., as part of an autofocus operation). For example, the separation can be measured using pixel distance or using a suitable linear distance unit.

[0080] The examples described herein involve an objective lens. An objective lens is part of an optical system, which 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 optical signals. For example, an optical component can perform at least one of the following: redirect, filter, shape, amplify, or focus an optical signal. Optical signals that may be affected include those upstream of the sample and those downstream of the sample. In a fluorescence detection system, upstream components include those that direct excitation radiation toward the sample, while downstream components include those that direct emission radiation away from the sample. Optical components can include, for example, reflectors, dichroic filters, dichroic mirrors, beam splitters, collimators, lenses, filters, optical wedges, prisms, mirrors, detectors, and the like. 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 transmit an image of an object to a detector. For example, a lens can be positioned to transmit an image emitted from the objective lens to a detector array. The objective lens can support depth of field control (DFC). In some implementations, a DFC can facilitate selection between different depths of field. For example, a DFC controls the distance between the closest object and the farthest object in focus.

[0081] The example described herein relates to the parts on the focus of the object lens. Due to the inherent limitations of the physical optical system (contrary to the ideal system), there may not be a precise focus relative to the parts and the object lens. Instead, there may be a best focus range that is applicable to the parts and the object lens, and this is sometimes referred to as the parts being in the best focus of the object lens. As used herein, focusing or defocusing (for example, best focus or deviation from best focus) comprise the process of adjusting the detection system to obtain the desired feature of 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 another example, the optical detection system can be adjusted to obtain the image with the uniformity of expectation, and in a particular embodiment, the image can have the uniformity of expectation and the MTF higher than the minimum value of definition. The MTF of the image can be different at different positions of the detected sample. For example, at two independent positions of the sample, the MTF can be different to allow the image to have one or more other features that are similar or within the desired range at each position.

[0082] Examples described herein relate to beam splitters. A beam splitter is 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 wavelength range. For example, a beam splitter can split autofocus light into two separate (e.g., at least substantially equal) beams. The beam splitter can include a partially reflective layer. The partially reflective layer can include any material with optical properties (e.g., refractive index and / or thickness) that reflect a portion of the light and transmit another portion due to frustrated total internal reflection. In some implementations, the partially reflective layer can have a reflectivity of approximately 45-55%. The reflectivity can be applicable to a predetermined wavelength or wavelength range. For example, the reflectivity can be measured at one or more wavelengths between approximately 77 nanometers and approximately 880 nanometers. The reflectivity can be applicable to one or more angles of incidence. For example, the reflectivity can be applied at one or more angles of incidence between approximately 45 degrees and approximately 55 degrees.

[0083] Examples herein involve prisms. A prism is an optical element with flat, smooth surfaces that form an angle with respect to one another, wherein the prism is transparent to at least one wavelength of light. Two adjacent surfaces of a prism form an angle with respect to one another and are separated by a boundary. For example, the boundary can be an edge defined by the intersection of a plane of one surface with a plane of another surface at the boundary. The prism can include one or more optically active components. In some implementations, the prism includes a partially reflective layer.

[0084] A prism may involve having a predefined cross-section, meaning that the geometry of at least a portion of the prism is represented by at least some of the boundaries of the prism. In some implementations, the cross-section of the prism corresponds to the shape of the prism (i.e., the shape of at least some of the visible boundaries) when viewed from at least one direction. In some implementations, the prism may have a wedge-shaped cross-section. A prism with a wedge-shaped cross-section may have a first side of the wedge-shaped cross-section that forms a non-zero angle with respect to a second side of the wedge-shaped cross-section, wherein the first side and the second side either share a common boundary or do not share a common boundary. In some implementations, the prism may have a parallelogram cross-section. A prism with a parallelogram cross-section may have a first side of the parallelogram cross-section and a second side of the parallelogram cross-section that are parallel to each other, and may have a third side of the parallelogram cross-section and a fourth side of the parallelogram cross-section that are parallel to each other.

[0085] Due to the lateral displacement of one or more light beams relative to at least one other light beam, a prism used to form the corresponding light beam can be referred to as a laterally displaced prism. A laterally displaced prism can include a beam splitter, including but not limited to a partially reflective layer. In some implementations, the prism can be made of any material that is transparent to one or more wavelengths of light. For example, the prism can be made of one or more glasses (e.g., optical borosilicate crown glass), plastic, or fluorite. The surface of the prism can be polished to a predetermined flatness and smoothness.

[0086] Examples herein relate to structured illumination microscopy (SIM). SIM imaging is based on spatially structured light. For example, the structure may consist of or include a pattern in the illuminating light that contributes to improving the resolution of the image obtained. In some implementations, the structure may include a stripe pattern. The stripes of light may be generated by shining a light beam on a diffraction grating (referred to as a grating for simplicity) so that reflective or transmissive diffraction occurs. The structured light may be directed onto a sample, illuminating the sample according to corresponding stripes that may appear in a certain periodicity. For example, an image of the sample may be obtained at different phases of the stripes in the structured light (sometimes referred to as the corresponding pattern phase of the image). This may allow different locations on the sample to be exposed to a variety of illumination intensities. The pattern of the structured light may be rotated relative to the sample, and the images just mentioned may be captured for each rotation angle.

[0087] Examples herein relate to a blue channel of emitted light (e.g., detected by a blue sensor assembly) and / or a green channel of emitted light (e.g., detected by a green sensor assembly). The emitted illumination can be identified by wavelength bands, each of which can be categorized into a corresponding color channel. For example, the wavelength bands of the emitted illumination can correspond to blue (e.g., 450 nm-525 nm) and / or green (e.g., 525 nm-570 nm). In some implementations, the wavelength bands can be defined based on two or more wavelengths of light present during simultaneous illumination. For example, when only 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 to emitted light from approximately 450 nm to 510 nm (e.g., 486 nm-506 nm). In some cases, the blue wavelength band can simply have an upper limit, such as approximately 500 nm-510 nm or approximately 506 nm. Similarly, the green wavelength band can be set to emitted light from approximately 525 nm to 650 nm (e.g., 584 nm-637 nm). While the aforementioned green band may extend into yellow and red, when analyzing emitted light expected only in the blue and green ranges, the upper and / or lower boundaries of the band may be expanded to capture additional emitted light above or below the wavelengths of those colors. In some cases, the green band may simply have a lower limit, such as approximately 550-600 nanometers or approximately 584 nanometers.

[0088] Figure 1 An embodiment of a system 100 that can be used to analyze a sample is shown. The system 100 can include, or be used with, one or more of the other embodiments described herein. In some implementations, the system 100 can include Figure 42 System 4200 in, or can Figure 42 In some implementations, the system 100 may include Figure 43 At least some components of the computing device 4300 in, or can be used with Figure 43 In some implementations, system 100 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the system 100 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the system 100 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the system 100 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the system 100 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the system 100 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the system 100 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the system 100 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the system 100 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the system 100 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the system 100 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the system 100 may include Figure 18 and Figures 19A-19B The imaging module 1800 in the embodiment of the present invention may be used in conjunction with Figure 18 and Figures 19A-19B In some implementations, the system 100 may include Figure 20 SIM component 2000 in the Figure 20 In some implementations, the system 100 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the system 100 may include Figure 22 The imaging module 2200 in the embodiment of the present invention may be used in conjunction with Figure 22 In some implementations, the system 100 may include Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the system 100 may include Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the system 100 may include Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the system 100 may include an optical system 2600 configured to be used with Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the system 100 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the system 100 can generate Figure 29 In some implementations, the system 100 may generate an autofocus light 2900. Figure 30 In some implementations, the system 100 may generate an autofocus light 3000. Figures 31A-31C In some implementations, the system 100 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the system 100 may include Figures 33A-33C Laser engine radiator 3300, or can be used with Figures 33A-33C In some implementations, the system 100 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the system 100 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the system 100 may include Figure 36 RIGS3600 in the Figure 36 In some implementations, the system 100 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the system 100 may include Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the system 100 may include Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the system 100 may include, or may be used with, the projection lens 3900 in FIG. Figure 40 In some implementations, the system 100 can generate Figure 41 The field of view is 4100.

[0089] The 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, the system 100 can be configured to analyze nucleic acid materials at a substrate. The 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 the fluorescence (sometimes referred to as emitted light) generated at the sample for the purpose of performing analysis on the sample. For example, the autofocus module 102 can automatically determine the best focus to be applied by the fluorescence collection optical system 104 to the sample to be analyzed, and the fluorescence collection optical system 104 can apply the best focus accordingly.

[0090] The autofocus module 102 includes one or more autofocus components 106. In some implementations, the autofocus component 106 includes an autofocus light source (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 aspheric lens (e.g., for collimating light from the light source). For example, as described below, one or more other components used by the autofocus module 102 can be shared with the fluorescence collection optical system 104.

[0091] The fluorescence collection optical system 104 includes one or more fluorescent components 108. The fluorescent component 108 participates in the collection of fluorescence in one or more ways. In some implementations, the fluorescent component 108 can trigger the emission of fluorescence. For example, the fluorescent component 108 can include one or more excitation lasers that generate excitation light with a certain wavelength and energy, and the excitation light with a certain wavelength and energy will activate one or more fluorescent tags on the sample material, and the activation causes the fluorescent tags to emit fluorescence. In some implementations, the fluorescent component 108 can control the sample in preparation for imaging and / or during imaging. For example, the fluorescent component 108 can condition the sample for analysis (e.g., by heat treatment and / or the use of chemicals) and / or position a substrate that holds the sample for imaging. In some implementations, the fluorescent 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 and thereby determine one or more characteristics of the sample.

[0092] System 100 may include one or more shared components 110. Shared components 110 may be used by autofocus module 102, by fluorescence collection optical system 104, or by both autofocus module 102 and fluorescence collection optical system 104. The use may occur simultaneously or at different times. For example, autofocus module 102 may use shared components 110 during an autofocus process that is performed prior to an analysis process (e.g., involving sample imaging) performed by fluorescence collection optical system 104.

[0093] Shared components 110 may include one or more objective lenses 112. For example, objective lenses 112 may be used to direct autofocus light toward a substrate and to transmit reflected autofocus light away from the substrate to perform an autofocus procedure. For example, objective lenses 112 may be used to direct excitation light toward a sample and to transmit emitted fluorescence light away from the sample for collection.

[0094] The shared component 110 may include one or more reflective / transparent components 114. The reflective / transparent components 114 may include one or more reflective components (e.g., mirrors), and / or one or more transparent components (e.g., filters), and / or one or more components that are both reflective and transparent (e.g., partially reflective layers), and / or refractive components (e.g., lenses). In some implementations, the reflective / transparent components 114 are used to manipulate one or more types of light away from one or more other types of light. For example, the reflective / transparent components 114 may include at least one filter 116. This manipulation by the reflective / transparent components 114 may be used to distinguish currently relevant light from currently irrelevant light, thereby improving the detection of autofocus light by the autofocus module 102.

[0095] Shared component 110 may include one or more detectors 118. Detector 118 may be used to record autofocus light reflected from the sample for the purpose of the autofocus process. Detector 118 may be used to record emitted light (e.g., fluorescence) during the analysis process. Detector 118 may include one or more sensors 120. For example, sensor 120 may include light-sensitive elements arranged in a rectangular array.

[0096] Figure 2 An embodiment of a battery system 200 is illustrated. The system 200 may include, or be used with, one or more of the other embodiments described herein. In some implementations, the optical system 200 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 200 may be included in Figure 1 In some implementations, the optical system 200 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the optical system 200 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 200 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 200 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 200 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 200 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 200 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the optical system 200 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 200 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 200 may include Figure 18 and Figures 19A-19B The imaging module 1800 in the embodiment of the present invention may be used in conjunction with Figure 18 and Figures 19A-19B In some implementations, the optical system 200 may include Figure 20 SIM component 2000 in the Figure 20 In some implementations, the optical system 200 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the optical system 200 may include Figure 22The imaging module 2200 in the embodiment of the present invention may be used in conjunction with Figure 22 In some implementations, the optical system 200 may include Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the optical system 200 may include Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the optical system 200 may include Figure 26 The optical system 2600 in, or with Figure 26 In some implementations, the optical system 200 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 200 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 200 can generate Figure 29 In some implementations, the optical system 200 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 200 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 200 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the optical system 200 may include Figures 33A-33C Laser engine radiator 3300, or can be used with Figures 33A-33C In some implementations, the optical system 200 may include Figure 34 SIM component 3400 in, or can be used with Figure 34 In some implementations, the optical system 200 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 200 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 200 may include Figure 37The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 200 may include Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the optical system 200 may include Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 200 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 200 can generate Figure 41 The field of view is 4100.

[0097] The optical system 200 includes a substrate 202. The substrate 202 can be used to hold one or more samples to be analyzed. In some implementations, the sample at the substrate 202 can include nucleic acid material. For example, the substrate 202 can include a flow cell for imaging nucleic acid material.

[0098] Optical system 200 may include objective lens 204. Objective lens 204 may be a component directly upstream of substrate 202. For example, objective lens 204 may be used to direct autofocus light toward substrate 202 and to transmit reflected autofocus light away from substrate 202 to perform an autofocus procedure. For example, objective lens 204 may be used to direct excitation light toward a sample on substrate 202 and to transmit emitted fluorescence light away from the sample for collection.

[0099] The optical system 200 includes an optical filter 206. The optical filter 206 can be a component directly upstream of the objective lens 204. The optical filter 206 can be a dichroic filter. The optical filter 206 can allow one or more types of light to enter the flow cell. For example, excitation light from an excitation light source (not shown) can be added through the optical filter 206 and thus transmitted toward the substrate 202.

[0100] Optical system 200 includes an optical filter 208. Optical filter 208 can be a component directly upstream of optical filter 206. Optical filter 206 can be a dichroic filter. In some implementations, optical filter 208 can reflect autofocus light reflected from substrate 202 and emission light generated at the sample, thereby facilitating the transmission of the autofocus light and emission light to other aspects of optical system 200. Optical filter 208 can allow one or more types of light to enter the flow cell. For example, autofocus light can be added by optical filter 208, thereby transmitting it toward substrate 202.

[0101] Optical system 200 includes structure 210. Structure 210 can be a component directly upstream of optical filter 208. Structure 210 can be used to block one or more light beams arriving from optical filter 208 from being transmitted to other aspects of system 200. In some implementations, structure 210 can block one or more aspects of autofocus light that has been reflected at substrate 202. For example, structure 210 can block autofocus light from being reflected from the top surface of a flow cell.

[0102] The optical system 200 includes an optical filter 212. The optical filter 212 can be a component directly upstream of the structure 210. The amplifier 212 can be a dichroic light filter. In some implementations, the optical filter 212 can transmit the autofocus light reflected at the substrate 202 and the emission light generated at the sample, thereby helping the autofocus light and the emission light to be transmitted to other aspects of the optical system 200. The optical filter 212 can separate the emission light from the substrate 202 into two or more paths. In some implementations, each path can be associated with a corresponding color channel. For example, the components upstream of the optical 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.

[0103] Optical system 200 includes at least one tube lens 214. Tube lens 214 can be a component directly upstream of filter 212. In some implementations, tube lens 214 can be used to focus incident light in preparation for detection. For example, tube lens 214 can focus autofocus light for detection as part of an autofocus process. As another example, tube lens 214 can focus emitted light for detection as part of an analysis process.

[0104] Optical system 200 includes an optical filter 216. Optical filter 216 can be a component directly upstream of tube lens 214. Optical filter 216 can be a dichroic filter. Optical filter 216 can facilitate manipulation of one or more types of light, either alone or in conjunction with at least one other component. In some implementations, optical filter 216 can reflect emitted light and transmit autofocus light. For example, optical filter 216 can have an antireflective coating that prevents reflection of the autofocus light (i.e., promotes transmission) while actually reflecting emitted light. In other embodiments, optical filter 216 can be configured to prevent reflection of emitted light (i.e., promotes transmission) while reflecting the autofocus light.

[0105] Optical system 200 includes filter 218. Filter 218 can be a component directly upstream of filter 216. Amplifier 218 can be a dichroic filter. In some implementations, filter 218 can condition the light in one or more aspects to prepare for detection. For example, filter 218 can provide bandpass filtering based on the wavelength of the reflected autofocus light and the wavelength of the emitted light to eliminate noise.

[0106] Optical system 200 includes sensor 220. Sensor 220 can be a component directly upstream of filter 218. Sensor 220 can detect reflected autofocus light during an autofocus process and / or detect emitted light during an analysis process. For example, sensor 220 can include a rectangular array of light-sensitive elements that can detect the corresponding positions of one or more portions of light incident on sensor 220.

[0107] Optical system 200 includes one or more autofocus light sources (not shown). Connector 222 can represent the point of entry of laser light used as the autofocus light into optical system 200. In some implementations, the laser light can be provided by a superluminescent diode via a fiber optic cable. The superluminescent diode provides the autofocus light based on superluminescence (e.g., spontaneous emission amplified by stimulated emission). For example, the autofocus light can be collimated by passing it through an aspheric lens.

[0108] The initial autofocus light can be split (or laterally shifted) into two or more portions of autofocus light. The optical system 200 includes a lateral displacement prism 224. The lateral displacement prism 224 can be positioned proximate to the optical filter 208. For example, the lateral displacement prism 224 is positioned at a side of the optical filter 208 opposite to the side that reflects the autofocus light and the emission light generated at the sample. The side of the optical filter 208 that faces the lateral displacement prism 224 can be transparent to the autofocus light from the lateral displacement prism 224 to allow the autofocus light to be transmitted toward the substrate 202. For example, as described below, the lateral displacement prism 224 can form corresponding portions of the autofocus light that are offset from each other.

[0109] The optical system 200 includes one or more reflective components 226. The reflective components 226 can include one or more reflective surfaces and can be positioned after the filter 216 in the direction of travel of light arriving from the tube lens 214. In some implementations, the reflective components 226 reflect light transmitted through the filter 216, which causes the light to be directed toward the sensor 220. For example, the reflective components 226 can reflect some (but not all) autofocus light that has been reflected at the substrate 202. The reflective components 226 can have optical properties based on the type of autofocus light used. In some implementations, the reflective components 226 are reflective in at least a portion of the near-infrared wavelength range (e.g., reflection somewhere between approximately 750 nanometers and approximately 1400 nanometers).

[0110] The optical system 200 can include one or more structures 228. The structures 228 can be positioned after the filter 216 in the direction of travel of light arriving from the tube lens 214. In some implementations, the structures 228 absorb light transmitted through the filter 216, which prevents the light from reaching the sensor 220 or another area of ​​the optical system 200. For example, the structures 228 can absorb some (but not all) autofocus light that has been reflected at the substrate 202.

[0111] During operation of optical system 200, autofocus light 230A and autofocus light 230B can be formed by lateral displacement prism 224. Autofocus light 230A and autofocus light 230B are offset from each other by a predetermined angle. Each of autofocus light 230A and autofocus light 230B can be transmitted through filter 208 and objective lens 204 and illuminated on substrate 202. In some implementations, reflections of autofocus light 230A and autofocus light 230B at substrate 202 can form autofocus light 232A, autofocus light 232B, autofocus light 234A, and autofocus light 234B. For example, autofocus lights 232A-232B can be generated by reflections of autofocus light 230A-230B, respectively, from a first layer or other surface at substrate 202. In this manner, optical system 200 can direct autofocus light 232A-232B toward filter 216. As another example, autofocus lights 234A-234B may be generated by reflections of autofocus lights 230A-230B, respectively, off a second layer or other surface of substrate 202. Thus, optical system 200 may direct autofocus lights 234A-234B toward filter 216.

[0112] The autofocus lights 232A-232B and the autofocus lights 234A-234B may be transmitted through the optical filter 216. For example, the autofocus lights 232A-232B and the autofocus lights 234A-234B may have wavelengths outside the wavelength range reflected by the optical filter 216. The reflective component 226 may be positioned in space so that one or more, but not all, of the autofocus lights 232A-232B and the autofocus lights 234A-234B are incident on the reflective component 226. For example, the autofocus lights 232A and 232B may be incident on the reflective component 226. In this way, the reflective component 226 may 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. Instead, autofocus light 234A and autofocus light 234B can be incident on structure 228. In some implementations, structure 228 absorbs autofocus light 234A and autofocus light 234B. This can prevent autofocus light 234A and autofocus light 234B from reaching sensor 220, for example.

[0113] 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 predetermined distance on the sensor 220 corresponding to the substrate 202 being focused on the objective lens can be specified. Thus, the optical system 200 can automatically adjust the distance between the objective lens 204 and the substrate 202 based on the distance between the autofocus light 232A and the autofocus light 232B detected at the sensor 220.

[0114] Optical system 200 illustrates an example of a method that includes directing a first autofocus light toward a sensor using an objective lens and a first reflective surface. For example, optical system 200 uses objective lens 204 and the reflective surface of reflective component 226 to direct autofocus light 232A and autofocus light 232B toward sensor 220. The first autofocus light is reflected from a first surface of a substrate. The method includes preventing a second autofocus light from reaching the sensor, the second autofocus light being reflected from a second surface of the substrate. For example, optical system 200 includes structure 210 that is capable of blocking some of the autofocus light reflected from substrate 202. As another example, optical system 200 includes structure 228 that is capable of preventing autofocus light 234A and autofocus light 234B from reaching sensor 220.

[0115] Optical system 200 illustrates an example of a system including 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 that directs a first autofocus light toward the sensor. The first autofocus light is reflected from the first surface of the substrate and transmitted through the objective lens. For example, optical system 200 includes a reflective surface at reflective component 226. The system includes a second reflective surface that directs emitted light from the sample toward the sensor. The emitted light is transmitted through the objective lens. For example, optical system 200 includes a filter 216 that can direct emitted light (not shown) toward sensor 220. The system includes structure that prevents a second autofocus light from reaching the sensor. The second autofocus light is reflected from the second surface of the substrate and transmitted through the objective lens. For example, optical system 200 includes structure 210 that blocks some of the autofocus light reflected from substrate 202. As another example, optical system 200 includes structure 228 that prevents autofocus light 234A and autofocus light 234B from reaching sensor 220.

[0116] Optical system 200 illustrates an example of a system including a beam splitter for forming left and right autofocus lights offset from each other by a predetermined angle. For example, optical system 200 includes a beam splitter within lateral displacement prism 224 for forming autofocus lights 230A and 230B offset from each other by a predetermined angle. The system includes an objective lens for transmitting the left and right autofocus lights toward a first surface facing a substrate. For example, optical system 200 includes objective lens 204 for transmitting autofocus lights 230A-230B toward substrate 202. The system includes a sensor for receiving at least a first portion of the left and right autofocus lights after they are reflected from the first surface. For example, optical system 200 includes sensor 220. At the sensor, a predetermined separation between the first portion of the left and right autofocus lights indicates that the substrate is in focus of the objective lens. For example, optical system 200 may determine the distance between autofocus lights 230A- 230B at sensor 220 .

[0117] Figure 3 is a diagram illustrating an example of desired and undesired reflections generated from multiple surfaces of a multi-layer sample substrate in some embodiments. Reflections 300 may be generated by one or more embodiments described herein. In some implementations, the Figure 1 to generate reflection 300. In some implementations, the system 100 may be used Figure 2 The optical system 200 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the optical system 200 in the embodiment of the present invention can be used to generate the reflection 300. Figure 5 to produce the reflection 300. In some implementations, the Figure 8A to produce the reflection 300. In some implementations, the Figure 8B The optical system 820 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the optical system 820 in the embodiment of the present invention can be used to generate the reflection 300. Figure 11 The optical system 1100 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the optical system 1100 in the embodiment of the present invention can be used to generate the reflection 300. Figure 12 The optical system 1200 in FIG. 3 is used to generate the reflection 300. In some implementations, the Figure 13 In some implementations, the optical system 1300 may be used to generate the reflection 300. Figure 14 The optical system 1400 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the optical system 1400 in the embodiment of the present invention can be used to generate the reflection 300. Figure 18 and Figures 19A-19B The imaging module 1800 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the imaging module 1800 in the embodiment of the present invention can be used to generate the reflection 300. Figure 20 SIM assembly 2000 in the embodiment of the present invention is used to generate reflection 300. In some implementations, the SIM assembly 2000 in the embodiment of the present invention can be used to generate reflection 300. Figure 21 The imaging module 2100 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the imaging module 2100 in the embodiment of the present invention can be used to generate the reflection 300. Figure 22 The imaging module 2200 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the imaging module 2200 in the embodiment of the present invention can be used to generate the reflection 300. Figure 24 The imaging module 2400 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the imaging module 2400 in the embodiment of the present invention can be used to generate the reflection 300. Figure 25 to produce the reflection 300. In some implementations, the Figure 26 The optical system 2600 in the embodiment of the present invention is used to generate the reflection 300. In some implementations, the optical system 2600 in the embodiment of the present invention can be used to generate the reflection 300. Figure 27 In some implementations, the reflective component 2700 may be used to generate the reflection 300. Figure 28 In some implementations, the reflective component 2800 may be used to generate the reflection 300. Figure 34 SIM assembly 3400 in the embodiment to generate reflection 300. In some implementations, the Figure 35 RIGS 3500 in to generate reflection 300. In some implementations, the Figure 36 RIGS 3600 in to generate reflection 300. In some implementations, the Figure 37 In some implementations, the piezoelectric phase shifter 3700 in the embodiment of the present invention can be used to generate the reflection 300. Figure 38 In some implementations, the piezoelectric phase shifter 3800 in the embodiment of the present invention can be used to generate the reflection 300. Figure 39The projection lens 3900 in the image is used to generate the reflection 300. In some implementations, the image may be used Figure 40 The projection lens 4000 in the image is used to generate the reflection 300. In some implementations, the image may be used Figure 41 The field of view 4100 in the image is used to generate the reflection 300.

[0118] Reflection 300 is caused by light 302 being transmitted from objective lens 304 to flow cell 306. For simplicity, objective lens 304 and flow cell 306 are shown schematically. In some implementations, light 302 is autofocus light. For example, light 302 can be one beam (e.g., a left beam) of a pair of autofocus light beams formed such that light 302 is offset by a predetermined angle relative to another beam (not shown) (e.g., a right beam).

[0119] In some implementations, the flow cell 306 includes a substrate 308 (e.g., a cladding of a transparent material), a substrate 310 (e.g., a cladding of a transparent material), and a channel 312 (e.g., a fluid channel) formed between the substrates 308 and 310. For example, a sample (e.g., a sample of nucleic acid material) and / or one or more chemical substances (e.g., sequencing reagents) can be located in and / or flow through the channel 312. One or more additional layers or other surfaces can be associated with the flow cell 306. Here, layer 314 is positioned on a side of the substrate 310 opposite the channel 312. In some implementations, the layer 314 bonds the flow cell 306 to another structure. For example, the layer 314 can include a pressure-sensitive adhesive that bonds the flow cell 306 to a carrier.

[0120] Flow cell 306 includes multiple layers or other surfaces. Here, surface S1 can be characterized as the top surface of substrate 308. Surface S2 can be referred to as the bottom surface of substrate 308, or the top surface of channel 312, or both. Surface S3 can be referred to as the bottom surface of channel 312, or the top surface of substrate 310, or both. Surface S4 can be characterized as the bottom surface of substrate 310. Surface S5 can be characterized as the bottom surface of layer 314.

[0121] When light 302 is incident on flow cell 306, light 302 may be reflected by one or more surfaces S1-S5, which may produce a corresponding reflection 300. In some implementations, reflection 300A is formed by light 302 reflecting from surface S1. In some implementations, reflection 300B is formed by light 302 reflecting from surface S2. In some implementations, reflection 300C is formed by light 302 reflecting from surface S3. In some implementations, reflection 300D is formed by light 302 reflecting from surface S4. In some implementations, reflection 300E is formed by light 302 reflecting from surface S5.

[0122] One or more reflected portions of the autofocus light can be considered more relevant than other portions. In some implementations, autofocus light reflected from surfaces where sample material is located or intended to be located can be relatively more relevant than from surfaces where sample material should not be located. For example, reflections 300B-300C (i.e., reflections from surfaces S2 and S3) can be considered relatively more relevant here than reflection 300A (i.e., from S1), reflection 300D (i.e., from S4), or reflection 300E (i.e., from S5).

[0123] If relevant autofocus light is present on the sensor together with less relevant autofocus light, the autofocus process may be more difficult to perform and / or may produce less satisfactory results. Figures 4A-4C The autofocus light recorded at the sensor is shown. Detection of the light is shown using graphs 400, 402, and 404. Here, graph 400 corresponds to adjustment of the optical system out of focus, where the z distance between the objective lens and the substrate is 25 micrometers (μm) greater than the optimal value. Graph 402 corresponds to adjustment of the optical system in optimal focus, where the z distance between the objective lens and the substrate is optimal. Graph 404 corresponds to adjustment of the optical system out of focus, where the z distance between the objective lens and the substrate is 25 μm less than the optimal value.

[0124] However, during the autofocus process, the above focus situation (i.e., whether the objective lens is at -25 meters from the best focus position, at the best focus position, or at +25 meters from the best focus position) may not be known. Instead, the autofocus process attempts to identify when the optical system is or is not in best focus. The optical system based on which the graphs 400, 402, and 404 are generated does not have the benefits of certain aspects of the present subject matter. For example, the optical system is capable of steering relevant autofocus light away from less relevant autofocus light. In each of the graphs 400, 402, and 404, the optical system is not in the best focus position. Figure 3 ) will reflect the light spot from surface S2-S3 ( Figure 3) overlap. For example, although each light point in light point cluster 400A originates from the same beam of autofocus light (e.g., the right beam), these points are spatially distributed and difficult to distinguish from each other. As another example, although each light point in light point cluster 400B originates from the same beam of autofocus light (e.g., the left beam), these points are spatially distributed and difficult to distinguish from each other. Due to the overlap, it is challenging for the autofocus module to determine when relevant aspects of light point clusters 400A-400B (e.g., light points reflected from surfaces S2-S3) are separated by a predetermined distance. This may affect autofocus or other focus tracking processes.

[0125] In some implementations, relevant autofocus light can be steered away from less relevant autofocus light. Figure 5 An embodiment of an optical system 500 is shown. The optical system 500 can include, or be used with, one or more of the other examples described herein. In some implementations, the optical system 500 can be included in Figure 1 In some implementations, the optical system 500 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 500 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the optical system 500 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 500 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 500 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 500 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 500 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 500 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14In some implementations, the optical system 500 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 500 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 500 may include Figure 18 and Figures 19A-19B The imaging module 1800 in the embodiment of the present invention may be used in conjunction with Figure 18 and Figures 19A-19B In some implementations, the optical system 500 may include Figure 20 SIM component 2000 in the Figure 20 In some implementations, the optical system 500 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the optical system 500 may include: Figure 22 The imaging module 2200 in the embodiment of the present invention may be used in conjunction with Figure 22 In some implementations, the optical system 500 may include: Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the optical system 500 may include: Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the optical system 500 may include Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the optical system 500 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 500 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 500 can generate Figure 29 In some implementations, the optical system 500 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 500 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 500 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the optical system 500 may include Figures 33A-33C Laser engine radiator 3300, or can be used with Figures 33A-33C In some implementations, the optical system 500 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the optical system 500 may include Figure 35 RIGS3500 in the Figure 35 In some implementations, the optical system 500 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 500 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 500 may include: Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the optical system 500 may include: Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 500 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 500 can generate Figure 41 The field of view is 4100.

[0126] Optical system 500 includes optical components 502. Optical components 502 may include a substrate (not shown). The substrate may be used to hold one or more samples to be analyzed. In some implementations, the sample at the substrate may include nucleic acid material. For example, the substrate may include a flow cell for imaging nucleic acid material.

[0127] Optical components 502 include an objective lens (not shown). For example, the objective lens can be used to direct autofocus light toward the substrate and transmit reflected autofocus light away from the substrate for performing an autofocus process. For example, the objective lens can be used to direct excitation light toward a sample on the substrate and transmit emitted fluorescence away from the sample for collection.

[0128] The optical component 502 may include one or more filters (not shown). The filter may be a dichroic filter. In some implementations, the filter may be used to remove one or more irrelevant portions of light transmitted toward and / or away from the substrate. For example, the filter may be used to remove excitation light reflected on the substrate. As another example, the filter may reflect autofocus light reflected on the substrate and emission light generated on the sample, thereby facilitating the autofocus light and emission light being transmitted to other aspects of the optical system 500. The filter may allow one or more types of light to enter the flow cell. For example, the autofocus light may be added by the filter to transmit it toward the substrate.

[0129] 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 be used to block one or more light beams arriving from the optical component 502 from being transmitted to other aspects of the optical system 500. In some implementations, the structure 504 can block one or more aspects of the autofocus light that has been reflected on the substrate. For example, the structure 504 can block the autofocus light from the top surface of the flow cell (e.g., Figure 3 Autofocus light reflected by surface S1 in the image.

[0130] The optical system 500 includes an optical filter 506. The optical filter 506 can be a component directly upstream of the structure 504. The amplifier 506 can be a dichroic filter. In some implementations, the optical filter 506 can transmit the autofocus light reflected at the substrate and the emission light generated at the sample, thereby facilitating the autofocus light and the emission light to be transmitted to other aspects of the optical system 500. The optical filter 506 can separate the emission light from the substrate into two or more paths. In some implementations, each path can be associated with a corresponding color channel. For example, the components upstream of the optical filter 506 can be associated with one color channel (e.g., a blue or green channel), while other components (not shown) can be associated with another color channel.

[0131] 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 be used to focus incident light in preparation for 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 emitted light for detection as part of an analysis process.

[0132] Optical system 200 includes an optical filter 510. Optical filter 510 can be a component directly upstream of tube lens 508. Optical filter 510 can be a dichroic filter. Optical filter 510 can facilitate manipulation of one or more types of light, either alone or in conjunction with at least one other component. In some implementations, optical filter 510 can reflect emitted light and transmit autofocus light. For example, optical filter 510 can have an antireflective coating that prevents reflection of autofocus light (i.e., promotes transmission) while actually reflecting emitted light. In other embodiments, optical filter 510 can be configured to prevent reflection of emitted light (i.e., promotes transmission) while reflecting autofocus light.

[0133] Optical system 500 includes an optical filter 512. Optical filter 512 can be a component directly upstream of optical filter 510. Optical filter 512 can be a dichroic filter. In some implementations, optical filter 512 can condition light in one or more aspects in preparation for detection. For example, filter 512 can provide bandpass filtering based on the wavelength of reflected autofocus light and based on the wavelength of emitted light to eliminate noise.

[0134] Optical system 500 includes sensor 514. Sensor 514 can be a component immediately upstream of filter 512. Sensor 514 can detect reflected autofocus light during an autofocus process and / or detect emitted light during an analysis process. For example, sensor 514 can include a rectangular array of light-sensitive elements that can detect the corresponding positions of one or more portions of light incident on sensor 514.

[0135] The optical system 500 includes one or more autofocus light sources (not shown). In some implementations, the laser light can be provided by a superluminescent diode via a fiber optic cable, which provides the autofocus light based on superluminescence (e.g., spontaneous emission amplified by stimulated emission). For example, the autofocus light can be collimated by passing it through an aspheric lens.

[0136] The initial autofocus light can be split (or laterally shifted) into two or more portions of autofocus light. Optical system 500 includes a beam splitter (not shown). The beam splitter can be included in the lateral displacement prism. The beam splitter can be positioned near optical component 502 to inject the autofocus light to be transmitted to the substrate. For example, as described below, the beam splitter can form corresponding portions of the autofocus light that are offset from each other.

[0137] The optical system 200 includes one or more reflective components 516. The reflective components 516 can include one or more reflective surfaces and can be positioned after the optical filter 510 in the direction of travel of light arriving from the tube lens 508. In some implementations, the reflective components 516 reflect light transmitted through the optical filter 510, and this reflection causes the light to be directed toward the sensor 514. For example, the reflective components 516 can reflect some (but not all) autofocus light that has been reflected on the substrate. The reflective components 516 can have optical properties based on the type of autofocus light used. In some implementations, the reflective components 516 are reflective in at least a portion of the near-infrared wavelength range (e.g., somewhere between approximately 750 nanometers and approximately 1400 nanometers).

[0138] As shown, system 500 can include one or more structures 518. Structures 518 can be positioned after filter 510 in the direction of travel of light arriving from tube lens 508. In some implementations, structures 518 absorb light that passes through filter 510, which prevents the light from reaching sensor 514 or another area of ​​optical system 500. For example, structures 518 can absorb some (but not all) autofocus light that has been reflected on the substrate.

[0139] In operation of the optical system 500, the left auto-focus light and the right auto-focus light can be formed by a beam splitter. The left auto-focus light and the right auto-focus light are offset from each other by a predetermined angle. Each of the left auto-focus light and the right auto-focus light can be transmitted through the optical component 502 and irradiated on the substrate. In some implementations, the reflection of the left auto-focus light and the right auto-focus light at the substrate can form auto-focus light 520A, auto-focus light 520B, auto-focus light 522A, and auto-focus light 522B. For example, the auto-focus lights 520A-520B can be formed by the left auto-focus light and the right auto-focus light, respectively, on a first layer or other surface (e.g., Figure 3 In this way, the optical system 500 can guide the autofocus lights 520A-520B to the filter 510. As another example, the autofocus lights 522A-522B can be generated by the left autofocus light and the right autofocus light on the second layer or other surface of the substrate (e.g., Figure 3In this way, the optical system 500 can guide the autofocus light 522A-522B to the filter 510.

[0140] Autofocus lights 520A-520B and 522A-522B may be transmitted through optical filter 510. For example, autofocus lights 520A-520B and 522A-522B may have wavelengths outside the wavelength range reflected by optical filter 510. Reflective component 516 may be positioned in space such that one or more, but not all, of autofocus lights 520A-520B and 522A-522B are incident on reflective component 516. For example, autofocus lights 520A and 520B may be incident on reflective component 516. In this way, reflective component 516 can direct autofocus lights 520A and 520B to sensor 514. On the other hand, autofocus lights 522A and 522B may not be incident on reflective component 516. Instead, autofocus lights 522A and 522B may be incident on structure 518. In some implementations, structure 518 absorbs autofocus light 522A and autofocus light 522B. This can prevent autofocus light 522A and autofocus light 522B from reaching sensor 514, for example.

[0141] 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 and the substrate of the optical component 502. For example, a predetermined distance on the sensor 514 corresponding to the substrate being in 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 distance between the autofocus light 520A and the autofocus light 520B detected at the sensor 514.

[0142] Figures 6A-6C The autofocus light recorded at the sensor is shown. The recording of the autofocus light is illustrated using graphs 600, 602, and 604. Graphs 600, 602, and 604 can be generated using one or more embodiments described herein. In some implementations, graphs 600, 602, and 604 can be generated using Figure 1 In some implementations, graphs 600, 602, and 604 may be generated using the system 100 in FIG. Figure 2 In some implementations, graphs 600, 602, and 604 may be generated using the optical system 200 in FIG. Figure 5In some implementations, graphs 600, 602, and 604 may be generated using the optical system 500 in FIG. Figure 8A In some implementations, graphs 600, 602, and 604 may be generated using the optical system 800 in FIG. Figure 8B In some implementations, the graphs 600, 602, and 604 may be generated using the optical system 820 in FIG. Figure 11 In some implementations, graphs 600, 602, and 604 may be generated using the optical system 1100 in FIG. Figure 12 In some implementations, the graphs 600, 602, and 604 may be generated using the optical system 1200 in FIG. Figure 13 In some implementations, graphs 600, 602, and 604 may be generated using the optical system 1300 in FIG. Figure 14 In some implementations, graphs 600, 602, and 604 may be generated using the optical system 1400 in FIG. Figure 18 and Figures 19A-19B In some implementations, graphs 600, 602, and 604 may be generated using imaging module 1800 in FIG. Figure 20 In some implementations, the graphs 600, 602, and 604 may be generated using the SIM component 2000 in FIG. Figure 21 In some implementations, graphs 600, 602, and 604 may be generated using the imaging module 2100 in FIG. Figure 22 In some implementations, graphs 600, 602, and 604 may be generated using the imaging module 2200 in FIG. Figure 24 In some implementations, graphs 600, 602, and 604 may be generated using the imaging module 2400 in FIG. Figure 25 In some implementations, graphs 600, 602, and 604 may be generated using the optical system 2500 in FIG. Figure 26 In some implementations, graphs 600, 602, and 604 may be generated using the optical system 2600 in FIG. Figure 27 In some implementations, the graphs 600, 602, and 604 may be generated using the reflective component 2700 in FIG. Figure 28 In some implementations, the graphs 600, 602, and 604 may be generated using the reflective component 2800 in FIG. Figure 34 In some implementations, charts 600, 602, and 604 may be generated using the SIM component 3400 in FIG. Figure 35 In some implementations, charts 600, 602, and 604 may be generated using RIGS 3500 in FIG. Figure 36In some implementations, charts 600, 602, and 604 may be generated using RIGS 3600. Figure 37 In some implementations, graphs 600, 602, and 604 may be generated using the piezoelectric phase shifter 3700 in FIG. Figure 38 In some implementations, graphs 600, 602, and 604 may be generated using the piezoelectric phase shifter 3800 in FIG. Figure 39 In some implementations, graphs 600, 602, and 604 may be generated using the projection lens 3900 in FIG. Figure 40 In some implementations, graphs 600, 602, and 604 may be generated using projection lens 4000 in FIG. Figure 41 The field of view 4100 is generated.

[0143] In graphs 600, 602, and 604, light spot 606A corresponds to an autofocus beam (eg, left autofocus light) being emitted from a substrate surface (eg, Figure 3 , and the light spot 606B corresponds to another autofocus light beam (eg, right autofocus light) reflected from the substrate surface (eg, Figure 3 In graphs 600, 602, and 604, light spot 608A corresponds to an autofocus beam (e.g., left autofocus light) reflected from another substrate surface (e.g., Figure 3 , and the light spot 608B corresponds to another autofocus light beam (eg, right autofocus light) reflected from another substrate surface (eg, Figure 3 The reflection of the S3 surface in the image.

[0144] Here, graphs 600, 602, and 604 are plotted according to the S2 surface ( Figure 3 ) is currently focused; that is, according to whether the distance between the light spots 606A-606B in graphs 600, 602, and 604 is equal to a predetermined interval 610 associated with the optical system. In graph 600, the distance between the light spots 606A-606B is greater than the predetermined interval 610; that is, graph 600 corresponds to an adjustment of the optical system that is out of focus, wherein the z distance between the objective lens and the substrate is 25 micrometers (μm) less than the optimal value. In graph 602, the distance between the light spots 606A-606B is equal to the predetermined interval 610; that is, graph 602 corresponds to an adjustment of the optical system that is in optimal focus, wherein the z distance between the objective lens and the substrate is optimal. In graph 604, the distance between the light spots 606A-606B is shorter than the predetermined interval 610; that is, graph 604 corresponds to an adjustment of the optical system that is out of focus, wherein the z distance between the objective lens and the substrate is 25 μm greater than the optimal value.

[0145] However, during the autofocus process, the above focus situation (i.e., whether the objective lens is at -25 meters from the best focus position, at the best focus position, or at +25 meters from the best focus position) may not be known. Instead, the autofocus process attempts to identify when the optical system is in the best focus state or when it is not in the best focus state. The optical system based on which the graphs 600, 602, and 604 are generated has the benefits of at least some aspects of the present subject matter. For example, the optical system is capable of steering relevant autofocus light away from less relevant autofocus light. In each of the graphs 600, 602, and 604, from the surface S4-S5 ( Figure 3 ) is not visible and therefore does not correspond to the light reflected from surface S2-S3 ( Figure 3 ) reflected light spots overlap. The autofocus module can therefore more accurately determine when the distance between the light spots 606A-606B is equal to the predetermined interval 610. This can improve the autofocus or other focus tracking process.

[0146] Figures 7A-7C The autofocus light recorded at the sensor is shown. The registration of the autofocus light is shown using graphs 700, 702, and 704. Graphs 700, 702, and 704 can be generated using one or more embodiments described herein. In some implementations, graphs 700, 702, and 704 can be generated using Figure 1 In some implementations, graphs 700, 702, and 704 may be generated using the system 100 in FIG. Figure 2 In some implementations, graphs 700, 702, and 704 may be generated using the optical system 200 in FIG. Figure 5 In some implementations, graphs 700, 702, and 704 may be generated using the optical system 500 in FIG. Figure 8A In some implementations, graphs 700, 702, and 704 may be generated using the optical system 800 in FIG. Figure 8B In some implementations, graphs 700, 702, and 704 may be generated using the optical system 820 in FIG. Figure 11 In some implementations, graphs 700, 702, and 704 may be generated using the optical system 1100 in FIG. Figure 12 In some implementations, graphs 700, 702, and 704 may be generated using the optical system 1200 in FIG. Figure 13 In some implementations, graphs 700, 702, and 704 may be generated using the optical system 1300 in FIG. Figure 14 In some implementations, the images 700, 702, and 704 may be generated using the optical system 1400 in FIG. Figure 18 and Figures 19A-19BIn some implementations, graphs 700, 702, and 704 may be generated using imaging module 1800 in FIG. Figure 20 In some implementations, charts 700, 702, and 704 may be generated using the SIM component 2000 in FIG. Figure 21 In some implementations, graphs 700, 702, and 704 may be generated using the imaging module 2100 in FIG. Figure 22 In some implementations, graphs 700, 702, and 704 may be generated using the imaging module 2200 in FIG. Figure 24 In some implementations, graphs 700, 702, and 704 may be generated using the imaging module 2400 in FIG. Figure 25 In some implementations, graphs 700, 702, and 704 may be generated using the optical system 2500 in FIG. Figure 26 In some implementations, graphs 700, 702, and 704 may be generated using the optical system 2600 in FIG. Figure 27 In some implementations, charts 700, 702, and 704 may be generated using the reflective component 2700 in FIG. Figure 28 In some implementations, charts 700, 702, and 704 may be generated using the reflective component 2800 in FIG. Figure 34 In some implementations, charts 700, 702, and 704 may be generated using the SIM component 3400 in FIG. Figure 35 In some implementations, charts 700, 702, and 704 may be generated using RIGS 3500 in FIG. Figure 36 In some implementations, charts 700, 702, and 704 may be generated using RIGS 3600. Figure 37 In some implementations, graphs 700, 702, and 704 may be generated using the piezoelectric phase shifter 3700 in FIG. Figure 38 In some implementations, graphs 700, 702, and 704 may be generated using the piezoelectric phase shifter 3800 in FIG. Figure 39 In some implementations, graphs 700, 702, and 704 may be generated using projection lens 3900 in FIG. Figure 40 In some implementations, graphs 700, 702, and 704 may be generated using projection lens 4000 in FIG. Figure 41 The field of view 4100 is generated.

[0147] In graphs 700, 702, and 704, light spot 706A corresponds to an autofocus beam (eg, left autofocus light) being emitted from a substrate surface (eg, Figure 3The light spot 706B corresponds to the reflection of another autofocus light beam (eg, right autofocus light) from the substrate surface (eg, Figure 3 In the graphs 700, 702 and 704, the light spot 708A corresponds to an autofocus beam (e.g., the left autofocus light) reflected from another substrate surface (e.g., Figure 3 , and the light spot 708B corresponds to another autofocus light beam (eg, right autofocus light) reflected from another substrate surface (eg, Figure 3 The reflection of the S3 surface in the image.

[0148] Here, graphs 700, 702, and 704 are plotted according to the S3 surface ( Figure 3 ) is currently focused; that is, according to whether the distance between points 708A-708B in graphs 700, 702, and 704 is equal to a predetermined interval 710 associated with the optical system. In graph 700, the distance between points 708A-708B is greater than the predetermined interval 710; that is, graph 700 corresponds to an adjustment of the optical system that is out of focus, wherein the z distance between the objective lens and the substrate is 25 micrometers (μm) less than the optimal value. In graph 702, the distance between points 708A-708B is equal to the predetermined interval 710; that is, graph 702 corresponds to an adjustment of the optical system that is in optimal focus, wherein the z distance between the objective lens and the substrate is optimal. In graph 704, the distance between points 708A-708B is shorter than the predetermined interval 710; that is, graph 704 corresponds to an adjustment of the optical system that is out of focus, wherein the z distance between the objective lens and the substrate is 25 μm greater than the optimal value.

[0149] However, during the autofocus process, the above focus situation (i.e., whether the objective lens is at -25 meters from the best focus position, at the best focus position, or at +25 meters from the best focus position) may not be known. Instead, the autofocus process attempts to identify when the optical system is in the best focus state or when it is not in the best focus state. The optical system based on which the graphs 700, 702, and 704 are generated has the benefits of at least some aspects of the present subject matter. For example, the optical system is capable of steering relevant autofocus light away from less relevant autofocus light. In each of the graphs 700, 702, and 704, from the surface S4-S5 ( Figure 3 ) is not visible and therefore does not correspond to the light reflected from surface S2-S3 ( Figure 3 ) reflected light spots overlap. The autofocus module can therefore more accurately determine when the distance between the light spots 708A-708B is equal to the predetermined interval 710. This can improve the autofocus or other focus tracking process.

[0150] Figure 8AAn embodiment of an optical system 800 is illustrated. The optical system 800 can include or be used with one or more other embodiments described herein. In some implementations, the optical system 800 can be included in Figure 1 In some implementations, the optical system 800 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 800 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 800 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 800 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 800 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 800 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 800 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 800 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the optical system 800 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 800 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 800 may include Figure 18 and Figures 19A-19B The imaging module 1800 in the embodiment of the present invention may be used in conjunction with Figure 18 and Figures 19A-19B In some implementations, the optical system 800 may include Figure 20 SIM component 2000 in the Figure 20 In some implementations, the optical system 800 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the optical system 800 may include: Figure 22 The imaging module 2200 in the embodiment of the present invention may be used in conjunction with Figure 22 In some implementations, the optical system 800 may include: Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the optical system 800 may include: Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the optical system 800 may include Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the optical system 800 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 800 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 800 can generate Figure 29 In some implementations, the optical system 800 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 800 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 800 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the optical system 800 may include Figures 33A-33C Laser engine radiator 3300 in, or can be used with Figures 33A-33C In some implementations, the optical system 800 may include Figure 34 SIM component 3400 in, or can be used with Figure 34 In some implementations, the optical system 800 may include Figure 35RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 800 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 800 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 800 may include: Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the optical system 800 may include: Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 800 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 800 can generate Figure 41 The field of view is 4100.

[0151] For clarity, only a portion of optical system 800 is shown. Optical system 800 includes at least one tube lens 802. In some implementations, tube lens 802 can be used to focus incident light in preparation for detection. For example, tube lens 802 can focus autofocus light for detection as part of an autofocus process. As another example, tube lens 802 can focus emitted light for detection as part of an analysis process.

[0152] Optical system 800 includes an optical filter 804. Optical filter 804 can be a component directly upstream of tube lens 802. Optical filter 804 can be a dichroic filter. Optical filter 804 can facilitate manipulation of one or more types of light, either alone or in conjunction with at least one other component. In some implementations, optical filter 804 can reflect emitted light and transmit autofocus light. For example, optical filter 804 can have an antireflective coating that prevents reflection of the autofocus light (i.e., promotes transmission) while actually reflecting the emitted light. In other implementations, optical filter 804 can be configured to prevent reflection of the emitted light (i.e., promotes transmission) and reflect the autofocus light.

[0153] Optical system 800 includes an optical filter 806. Optical filter 806 can be a component directly upstream of optical filter 804. Optical filter 806 can be a dichroic filter. In some implementations, optical filter 806 can condition light in one or more aspects to prepare it for detection. For example, filter 806 can provide bandpass filtering based on the wavelength of reflected autofocus light and the wavelength of emitted light to eliminate noise.

[0154] Optical system 800 includes sensor 808. Sensor 808 can be a component directly upstream of filter 806. Sensor 808 can detect reflected autofocus light during an autofocus process and / or detect emitted light during an analysis process. For example, sensor 808 can include a rectangular array of light-sensitive elements that can detect the corresponding positions of one or more portions of light incident on sensor 808.

[0155] The optical system 800 may include a substrate (not shown). The substrate may be used to hold one or more samples to be analyzed. In some implementations, the sample at the substrate may include a nucleic acid material. For example, the substrate may include a flow cell for imaging nucleic acid material. The optical system 800 may include one or more other optical components (not shown). Other optical components may include, but are not limited to, one or more objective lenses, optical filters, structures that block one or more light beams, autofocus light sources, or beam splitters.

[0156] 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 after the optical filter 804 in the direction of travel of light arriving from the tube lens 802. In some implementations, any one or both of the reflective components 810A-810B reflects light transmitted through the optical filter 804, and this reflection causes the light to be directed to the sensor 808. For example, one or both of the reflective components 810A-810B can reflect some (but not all) of the autofocus light that has been 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 in at least a portion of the near-infrared wavelength range (e.g., reflecting somewhere between approximately 750 nanometers and approximately 1400 nanometers).

[0157] One or more reflective components 810A-810B may be movable. The movability may include one or more of translation or rotation of at least one of the reflective components 810A-810B. The reflective component 810A may be separate from the filter 804. In some implementations, the reflective component 810A may be oriented independently of the orientation of the filter 804. For example, the reflective component 810A may 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 separate from the filter 804. The reflective component 810B may be separate from the reflective component 810A. In some implementations, the reflective component 810B may be oriented independently of the orientation of the filter 804. For example, the reflective component 810B may be coupled to a motor or actuator that controls the orientation of the reflective component 810B without affecting the orientation of the filter 804.

[0158] As shown, the optical system 800 may include one or more structures 812. The structures 812 can be positioned after the filter 804 in the direction of travel of light arriving from the tube lens 802. In some implementations, the structures 812 absorb light transmitted through the filter 804, which prevents the light from reaching the sensor 808 or another area of ​​the optical system 800. For example, the structures 812 can absorb some (but not all) autofocus light that has been reflected on the substrate.

[0159] In operation of the optical system 800, the left auto-focus light and the right auto-focus light can be formed by a beam splitter. The left auto-focus light and the right auto-focus light are offset from each other by a predetermined angle. Each of the left auto-focus light and the right auto-focus light can be transmitted through one or more optical components and irradiated on the substrate. In some implementations, the reflection of the left auto-focus light and the right auto-focus light on the substrate can form auto-focus light 814A, auto-focus light 814B, auto-focus light 816A, and auto-focus light 816B. For example, the auto-focus lights 814A-814B can be formed by the left auto-focus light and the right auto-focus light on the first layer or other surface of the substrate (e.g., Figure 3 Thus, the optical system 800 can direct the autofocus lights 814A-814B to the filter 804. As another example, the autofocus lights 816A-816B can be generated by the left autofocus light and the right autofocus light, respectively, reflecting off the second layer or other surface of the substrate (e.g., Figure 3 In this way, the optical system 800 can guide the autofocus light 816A-816B to the filter 804.

[0160] Autofocus lights 814A-814B and autofocus lights 816A-816B can be transmitted through filter 804. For example, autofocus lights 814A-814B and autofocus lights 816A-816B can have wavelengths outside the wavelength range reflected by filter 804. Reflective component 810A can be positioned in space so that autofocus light 814A, but not autofocus light 814B or autofocus lights 816A-816B, will be incident on reflective component 810A. In this way, reflective component 810A can direct autofocus light 814A toward sensor 808. For example, movement (e.g., rotation) of reflective component 810A can manipulate autofocus light 814A at sensor 808. Reflective component 810B can be positioned in space so that autofocus light 814B, but not autofocus light 814A or autofocus lights 816A-816B, will be incident on reflective component 810B. In this manner, reflective member 810B can direct autofocus light 814B toward sensor 808. For example, movement (e.g., rotation) of reflective member 810B can manipulate autofocus light 814B at sensor 808. Autofocus light 816A and autofocus light 816B can be incident on structure 812. In some implementations, structure 812 absorbs autofocus light 816A and autofocus light 816B. This can, for example, prevent autofocus light 816A and autofocus light 816B from reaching sensor 808.

[0161] The autofocus process can be performed based on one or more portions of the autofocus light detected by the sensor 808. In some implementations, the distance between the autofocus light 814A and the autofocus light 814B at the sensor 808 can indicate the distance between the objective lens of the optical system 800 and the substrate. For example, a predetermined distance on the sensor 808 corresponding to the substrate being in 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 distance between the autofocus light 814A and the autofocus light 814B detected at the sensor 808.

[0162] Figure 8B An embodiment of an optical system 820 is shown. System 820 can be used with or included in one or more other embodiments described herein. In some implementations, optical system 820 can be included in system 100. In some implementations, optical system 820 can be used with Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the optical system 820 can be configured to Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the optical system 820 can be configured to Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the optical system 820 can be configured to Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the optical system 820 can be configured to Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the optical system 820 can be configured to Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the optical system 820 can be configured to Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the optical system 820 can be configured to Figure 18 and Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 and Figures 19A-19B In some implementations, the optical system 820 can be used with the imaging module 1800. Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the optical system 820 can be used with the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the optical system 820 can be used with the imaging module 2200. Figure 24 The imaging module 2400 may be used in conjunction with, or may be included in Figure 24 In some implementations, the optical system 820 can be used with the imaging module 2400. Figure 25 The optical system 2500 may be used in conjunction with, or may be included in Figure 25 In some implementations, the optical system 820 can be configured to Figure 26 The optical system 2600 may be used in conjunction with, or may be included in Figure 26 In some implementations, the optical system 820 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27In some implementations, the optical system 820 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 820 can generate Figure 29 In some implementations, the optical system 820 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 820 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 820 can be used with the autofocus light 3100. Figures 32A-32C In some implementations, the optical system 820 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the optical system 820 can be used with the laser engine heat sink 3300 in FIG. Figure 34 In some implementations, the optical system 820 can be used with the SIM assembly 3400 in FIG. Figure 35 In some implementations, the optical system 820 can be used with the RIGS3500 in FIG. Figure 36 In some implementations, the optical system 820 can be used with the RIGS 3600 in FIG. Figure 37 In some implementations, the optical system 820 can be used with the piezoelectric phase shifter 3700 in FIG. Figure 38 In some implementations, the optical system 820 can be used with the piezoelectric phase shifter 3800 in FIG. Figure 39 In some implementations, the optical system 820 can be used with the projection lens 3900 in FIG. Figure 40 In some implementations, the optical system 820 can generate Figure 41 The field of view is 4100.

[0163] For clarity, only a portion of the optical system 820 is shown. The filter monitoring system 820 includes an optical filter 822. The optical filter 822 can be a dichroic filter. The optical filter 822 can facilitate manipulation of one or more types of light, either alone or in conjunction with at least one other component. In some implementations, the optical filter 822 can have an anti-reflective coating 824 that prevents reflection of the autofocus light (i.e., promotes transmission) and does reflect the emitted light. For example, the anti-reflective coating 824 can be positioned at the front surface of the optical filter 822 in the direction of travel of the light reaching the optical filter 822. In other implementations, the anti-reflective coating 824 can be configured to prevent reflection of the emitted light (i.e., promote transmission) and reflect the autofocus light.

[0164] 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 may include one or more reflective surfaces and may be positioned at the surface of the optical filter 822. For example, the reflective components 826A-826B may be positioned at the rear surface of the optical filter 822 in the direction of travel of the light reaching the optical filter 822. In some implementations, any one or both of the reflective components 826A-826B reflect light transmitted through the optical filter 822, and the reflection causes the light to be directed to another part of the optical system 820 (e.g., a guide sensor). For example, the reflective component 826A may reflect autofocus light 828A. Each of the reflective components 826A-826B may have optical properties based on the type of autofocus light used. In some implementations, each of the reflective components 826A-826B is reflective in at least a portion of the near-infrared wavelength range (eg, reflective somewhere between approximately 750 nanometers and approximately 1400 nanometers).

[0165] Optical system 820 may include one or more structures 830. Structures 830 may be positioned at the rear surface of filter 822 in the direction of travel of autofocus light 828A. In some implementations, structures 830 absorb light transmitted through filter 822, which prevents the light from reaching a sensor or another area of ​​optical system 820. For example, structure 830 may absorb some (but not all) autofocus light 828B. As another example, structure 830 may transmit autofocus light 828B, as schematically shown by autofocus light 828B′. In some implementations, structure 830 may be omitted from optical system 820.

[0166] That is, during operation of the optical system 820, the reflective component 826A can reflect the autofocus light 828A, thereby allowing manipulation of the autofocus light 828A at the sensor of the optical system 820. As another example, the reflective component 826B can reflect other autofocus light (not shown), thereby allowing manipulation of the other autofocus light at the sensor of the optical system 820. Simultaneously with the just-mentioned reflection, and / or at another time, the anti-reflective coating 824 can reflect the emitted light 832 toward another portion of the optical system 820 (e.g., toward the sensor). For example, the emitted light 832 can include fluorescent light generated at the sample for imaging the sample for analysis.

[0167] Figure 9A-9Bis a diagram illustrating an example of generating desired reflections 900 and unwanted reflections 900' from multiple surfaces of a sample substrate in some embodiments. Reflections 900 and 900' can be generated by one or more embodiments described herein. In some implementations, the Figure 1 In some implementations, the system 100 may be used to generate reflections 900 and 900'. Figure 2 The optical system 200 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the optical system 200 in the embodiment of the present invention can be used to generate reflections 900 and 900'. Figure 5 The optical system 500 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the optical system 500 in the embodiment of the present invention can be used to generate reflections 900 and 900'. Figure 8A In some implementations, the optical system 800 can be used to generate reflections 900 and 900'. Figure 8B The optical system 820 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the optical system 820 in the embodiment of the present invention can be used to generate reflections 900 and 900'. Figure 11 The optical system 1100 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the optical system 1100 in the embodiment of the present invention can be used to generate reflections 900 and 900'. Figure 12 In some implementations, the optical system 1200 may be used to generate reflections 900 and 900'. Figure 13 In some implementations, the optical system 1300 can be used to generate reflections 900 and 900'. Figure 14 In some implementations, the optical system 1400 may be used to generate reflections 900 and 900'. Figure 18 and Figures 19A-19B The imaging module 1800 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the imaging module 1800 in the embodiment of the present invention can be used to generate reflections 900 and 900'. Figure 20 SIM assembly 2000 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the Figure 21 In some implementations, the imaging module 2100 may be used to generate reflections 900 and 900'. Figure 22 In some implementations, the imaging module 2200 may be used to generate reflections 900 and 900'. Figure 24 The imaging module 2400 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the imaging module 2400 in the embodiment of the present invention can be used to generate reflections 900 and 900'. Figure 25 In some implementations, the optical system 2500 may be used to generate reflections 900 and 900'. Figure 26 In some implementations, the optical system 2600 can be used to generate reflections 900 and 900'. Figure 27 In some implementations, the reflective component 2700 in the embodiment can be used to generate reflections 900 and 900'. Figure 28The reflective component 2800 in the embodiment of the present invention is used to generate reflections 900 and 900'. In some implementations, the reflections 900 and 900' can be Figure 34 In some implementations, reflections 900 and 900' may be generated using the SIM component 3400 in FIG. Figure 35 In some implementations, reflections 900 and 900' may be generated using RIGS 3500. Figure 36 In some implementations, the RIGS 3600 can be used to generate Figure 37 In some implementations, the piezoelectric phase shifter 3700 can be used to generate reflections 900 and 900'. Figure 38 In some implementations, the piezoelectric phase shifter 3800 can be used to generate reflections 900 and 900'. Figure 39 The projection lens 3900 in the image is used to generate reflections 900 and 900'. In some implementations, the image may be used Figure 40 In some implementations, the projection lens 4000 may be used to generate reflections 900 and 900'. Figure 41 The field of view 4100 in the image is used to generate reflections 900 and 900'.

[0168] In some implementations, reflections 900 and 900' can be generated by corresponding portions of the autofocus light incident on the substrate. For example, reflection 900 is generated by light 902 being transmitted from objective lens 904 to flow cell 906, where light 902 is the left autofocus light (e.g., a portion of the output from the beam splitter). For example, reflection 900' is generated by light 902' being transmitted from objective lens 904 to flow cell 906, where light 902' is the right autofocus light (e.g., another portion of the output from the beam splitter). Light 902 and light 902' can be offset from each other by a predetermined angle. For simplicity, objective lens 904 and flow cell 906 are schematically illustrated.

[0169] In some implementations, the flow cell 906 includes a substrate 908 (e.g., a cladding of transparent material), a substrate 910 (e.g., a cladding of transparent material), and a channel 912 (e.g., a fluid channel) formed between the substrates 908 and 910. For example, a sample (e.g., nucleic acid material) and / or one or more chemical substances (e.g., sequencing reagents) can be located in and / or flow through the channel 912. One or more additional layers or other surfaces can be associated with the flow cell 906. Here, layer 914 is positioned on a side of the substrate 910 opposite the channel 912. In some implementations, the layer 914 bonds the flow cell 906 to another structure. For example, the layer 914 can include a pressure-sensitive adhesive that bonds the flow cell 906 to a carrier.

[0170] Flow cell 906 includes multiple layers or other surfaces. Here, surface S1 can be characterized as the top surface of substrate 908. Surface S2 can be referred to as the bottom surface of substrate 908, or the top surface of channel 912, or both. Surface S3 can be referred to as the bottom surface of channel 912, or the top surface of substrate 910, or both. Surface S4 can be characterized as the bottom surface of substrate 910. Surface S5 can be characterized as the bottom surface of layer 914.

[0171] When light 902 is incident on flow cell 906, light 902 may be reflected by one or more surfaces S1-S5, which may produce a corresponding reflection 900. In some implementations, reflection 900A is formed by reflection of light 902 from surface S1. In some implementations, reflection 900B is formed by reflection of light 902 from surface S2. In some implementations, reflection 900C is formed by reflection of light 902 from surface S3. In some implementations, reflection 900D is formed by reflection of light 902 from surface S4. In some implementations, reflection 900E is formed by reflection of light 902 from surface S5.

[0172] One or more reflected portions of the autofocus light can be considered more relevant than another portion. In some implementations, autofocus light reflected from surfaces where sample material is located or intended to be located can be relatively more relevant than surfaces where sample material should not be located. For example, reflections 900B-900C (i.e., reflections from surfaces S2 and S3) can be considered relatively more relevant here than reflection 900A (i.e., reflection from S1), reflection 900D (i.e., reflection from S4), or reflection 900E (i.e., reflection from S5).

[0173] When light 902' is incident on flow cell 906, light 902' may be reflected by one or more surfaces S1-S5, which may produce a corresponding reflection 900'. In some implementations, reflection 900A' is formed by reflection of light 902' from surface S1. In some implementations, reflection 900B' is formed by reflection of light 902' from surface S2. In some implementations, reflection 900C' is formed by reflection of light 902' from surface S3. In some implementations, reflection 900D' is formed by reflection of light 902' from surface S4. In some implementations, reflection 900E' is formed by reflection of light 902' from surface S5.

[0174] One or more reflected portions of the autofocus light can be considered more relevant than another portion. In some implementations, autofocus light reflected from a surface where the sample material is located or intended to be located can be relatively more relevant than a surface where the sample material should not be located. For example, reflections 900B'-900C' (i.e., reflections from surfaces S2 and S3) can be considered relatively more relevant here than reflection 900A' (i.e., reflection from S1), reflection 900D' (i.e., reflection from S4), or reflection 900E' (i.e., reflection from S5).

[0175] Figures 10A-10C An embodiment of a lateral displacement prism 1000 is shown. Lateral displacement prism 1000 can be used with or included in one or more other embodiments described herein. In some implementations, lateral displacement prism 1000 can be used with Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the lateral displacement prism 1000 can be used with Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the lateral displacement prism 1000 can be used with the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the lateral displacement prism 1000 can be used with the optical system 500. Figure 8A The optical system 800 may be used in conjunction with, or may be included in Figure 8A In some implementations, the lateral displacement prism 1000 can be used with the optical system 800. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the lateral displacement prism 1000 can be used with the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the lateral displacement prism 1000 can be used with the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the lateral displacement prism 1000 can be used with the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the lateral displacement prism 1000 can be used with the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the lateral displacement prism 1000 can be used with the optical system 1400. Figure 18 and Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 and Figures 19A-19B In some implementations, the lateral displacement prism 1000 can be used with the imaging module 1800. Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the lateral displacement prism 1000 can be used with the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the lateral displacement prism 1000 can be used with the imaging module 2200. Figure 24 The imaging module 2400 may be used in conjunction with, or may be included in Figure 24 In some implementations, the lateral displacement prism 1000 can be used with the imaging module 2400. Figure 25 The optical system 2500 may be used in conjunction with, or may be included in Figure 25 In some implementations, the lateral displacement prism 1000 can be used with the optical system 2500. Figure 26 The optical system 2600 may be used in conjunction with, or may be included in Figure 26 In some implementations, the lateral displacement prism 1000 can be used with the optical system 2600. Figure 27 In some implementations, the lateral displacement prism 1000 can be used with the reflective component 2700 in FIG. Figure 28 In some implementations, the lateral displacement prism 1000 can generate Figure 29 In some implementations, the lateral displacement prism 1000 can generate the autofocus light 2900. Figure 30 In some implementations, the lateral displacement prism 1000 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the lateral displacement prism 1000 can be used with the Figures 32A-32C In some implementations, the lateral displacement prism 1000 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the lateral displacement prism 1000 can be used with the laser engine heat sink 3300 in FIG. Figure 34 In some implementations, the lateral displacement prism 1000 can be used with the SIM assembly 3400 in FIG. Figure 35In some implementations, the lateral displacement prism 1000 can be used with the RIGS 3500 in FIG. Figure 36 In some implementations, the lateral displacement prism 1000 can be used with the RIGS 3600 in FIG. Figure 37 In some implementations, the lateral displacement prism 1000 can be used with the piezoelectric phase shifter 3700 in FIG. Figure 38 In some implementations, the lateral displacement prism 1000 can be used with the piezoelectric phase shifter 3800 in FIG. Figure 39 In some implementations, the lateral displacement prism 1000 can be used with the projection lens 3900 in FIG. Figure 40 Used together with the projection lens 4000 in.

[0176] Lateral displacement prism 1000 includes surface 1002. In some implementations, surface 1002 can be considered the top surface of lateral displacement prism 1000. Lateral displacement prism 1000 includes surface 1004 that is parallel to surface 1002. In some implementations, surface 1004 can be considered the bottom surface of lateral displacement prism 1000. Lateral displacement prism 1000 includes surface 1006. In some implementations, surface 1006 can be considered a side surface of lateral displacement prism 1000. For example, surface 1006 can be considered the entrance surface of lateral displacement prism 1000. Lateral displacement prism 1000 includes surface 1008A. In some implementations, surface 1008A can be considered the exit surface of lateral displacement prism 1000. Lateral displacement prism 1000 includes surface 1008B. In some implementations, surface 1008B can be considered the exit surface of lateral displacement prism 1000. Each surface 1008A-1008B forms a common angle with surface 1006. In some implementations, surfaces 1008A-1008B can have a non-zero angle relative to each other. Lateral displacement prism 1000 includes a partially reflective layer 1010. In some implementations, lateral displacement prism 1000 can be manufactured by assembling two prism sheets that are at least substantially identical to each other, with partially reflective layer 1010 positioned at the junction between the two prism sheets. Surface 1002 can have a boundary with at least surfaces 1006, 1008A, and 1008B. Surface 1004 can have a boundary with at least surfaces 1006, 1008A, and 1008B.

[0177] Light 1012 can enter lateral displacement prism 1000 through surface 1006. For example, light 1012 is autofocus light generated by a light source (e.g., a laser diode). After at least one reflection within lateral displacement prism 1000, or after no reflection within lateral displacement prism 1000, light 1012 can be incident on partially reflective layer 1010. As a result, light 1012A reflected by partially reflective layer 1010 can exit lateral displacement prism 1000 through surface 1008A. In addition, light 1012B transmitted through partially reflective layer 1010 can exit lateral displacement prism 1000 through surface 1008B after at least one reflection within lateral displacement prism 1000, or after no reflection within lateral displacement prism 1000. Light 1012A and light 1012B are offset from each other by a predetermined angle. In some implementations, each of the lights 1012A-1012B is offset from the normal to the surface 1006 by an angle between about 1 degree and about 3 degrees. For example, each of the lights 1012A-1012B can be offset from the normal to the surface 1006 by an angle between about 1.4 degrees (e.g., about 1.464 degrees). Thus, the lights 1012A-1012B can be offset from each other by an angle between about 2 degrees and about 6 degrees. For example, the lights 1012A-1012B can be offset from each other by an angle between about 2.9 degrees (e.g., 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 portions of at least substantially equal size. As another example, surfaces 1008A-1008B may have dimensions that are at least substantially equal to one another.

[0178] Lateral displacement prism 1000 can be included in an autofocus assembly. In some implementations, the autofocus assembly includes at least lateral displacement prism 1000 and a light source that directs light (e.g., light 1012) toward lateral displacement prism 1000. For example, the light source can be autofocus component 106 ( Figure 1 In such an autofocus assembly, lateral displacement prism 1000 may form a first autofocus light (e.g., light 1012A) and a second autofocus light (e.g., light 1012B) from light, such that the first autofocus light and the second autofocus light are offset from each other by a predetermined angle.

[0179] Figure 11 Schematically illustrates an optical system 1100 having a lateral displacement prism 1102. The optical system 1100 can include, or be used with, one or more of the other examples described herein. In some implementations, the optical system 1100 can include Figure 1 In some implementations, the optical system 1100 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 1100 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 1100 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the optical system 1100 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 1100 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 1100 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 1100 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 1100 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the optical system 1100 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 1100 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 1100 may be included in Figure 18 and Figures 19A-19B In some implementations, the optical system 1100 can be integrated with the imaging module 1800. Figure 20 In some implementations, the optical system 1100 may be included in Figure 21 In some implementations, the optical system 1100 may be included in the imaging module 2100. Figure 22In some implementations, the optical system 1100 may be included in the imaging module 2200. Figure 24 In some implementations, process 1100 may be included in the imaging module 2400. Figure 25 In some implementations, process 1100 can be included in the optical system 2500. Figure 26 In some implementations, the optical system 1100 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 1100 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 1100 can generate Figure 29 In some implementations, the optical system 1100 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 1100 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 1100 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the optical system 1100 may include Figures 33A-33C Laser engine radiator 3300, or can be used with Figures 33A-33C In some implementations, the optical system 1100 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the optical system 1100 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 1100 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 1100 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 1100 may include: Figure 38 The piezoelectric phase shifter 3800 in the Figure 38In some implementations, the optical system 1100 may include: Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 1100 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 1100 can generate Figure 41 The field of view is 4100.

[0180] Light 1104 may enter lateral displacement prism 1102 through an incident surface. For example, light 1104 may be autofocus light generated by a light source (e.g., a laser diode). Light 1104A may exit lateral displacement prism 1102 through an exit surface. Light 1104B may exit lateral displacement prism 1102 through another exit surface. Light 1104A and light 1104B may be offset from each other by a predetermined angle.

[0181] Optical system 1100 includes substrate 1106. Substrate 1106 can be used to hold one or more samples to be analyzed. In some implementations, the sample on substrate 1106 can include nucleic acid material. For example, substrate 1106 can include a flow cell for imaging nucleic acid material. Reflection of light 1104A from the surface of substrate 1106 can form light 1108A. Reflection of light 1104B from the surface of substrate 1106 can form light 1108B.

[0182] Light 1108A-1108B may be transmitted and / or reflected and / or refracted by at least one other component (not shown) in optical system 1100. Here, line 1110 schematically illustrates additional components of optical system 1100 and the processing of light 1108A-1108B performed at the additional components.

[0183] Optical system 1100 includes sensor 1112. Sensor 1112 can detect reflected autofocus light during an autofocus process and / or detect emitted light during an analysis process. In some implementations, sensor 1112 includes a rectangular array of light-sensitive elements that can detect the respective positions of one or more portions of light incident on sensor 1112. For example, light 1108A-1108B can be incident on sensor 1112.

[0184] The sensor 1112 can be used to determine one or more characteristics of the light 1108A-1108B. In some implementations, the distance 1114 between the light 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 predetermined distance on the sensor 1112 corresponding to the substrate 1106 being at the focal point of the objective lens can be specified.

[0185] Optical system 1100 illustrates an example of performing a method that includes forming a left autofocus light (e.g., light 1104A) and a right autofocus light (e.g., light 1104B) that are offset from each other by a predetermined angle (e.g., via laterally displacing prism 1102). The method includes directing the left autofocus light and the right autofocus light toward a first surface of a substrate (e.g., substrate 1106) through an objective lens. The method includes, 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 to a sensor (e.g., sensor 1112). A predetermined distance 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 in focus of the objective lens. For example, distance 1114 may or may not be equal to the predetermined distance.

[0186] Figure 12 Schematically illustrates an optical system 1200 having a laterally displaced prism 1202. The system 1200 can include or be used with one or more of the other embodiments described herein. In some implementations, the optical system 1200 can be included in Figure 1 In some implementations, the optical system 1200 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 1200 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 1200 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the optical system 1200 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 1200 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 1200 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 1200 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 1200 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the optical system 1200 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 1200 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 1200 may be included in Figure 18 and Figures 19A-19B In some implementations, the optical system 1200 can be integrated with the imaging module 1800. Figure 20 In some implementations, the optical system 1200 may be included in Figure 21 In some implementations, the optical system 1200 may be included in the imaging module 2100. Figure 22 In some implementations, the optical system 1200 may be included in the imaging module 2200. Figure 24 In some implementations, process 1200 may be included in the imaging module 2400. Figure 25 In some implementations, process 1200 can be included in the optical system 2500. Figure 26 In some implementations, the optical system 1200 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 1200 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 1200 can generate Figure 29 In some implementations, the optical system 1200 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 1200 can generate the autofocus light 3000. Figures 31A-31CIn some implementations, the optical system 1200 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the optical system 1200 may include Figures 33A-33C Laser engine radiator 3300, or can be used with Figures 33A-33C In some implementations, the optical system 1200 may include Figure 34 SIM component 3400 in, or can be used with Figure 34 In some implementations, the optical system 1200 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 1200 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 1200 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 1200 may include: Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the optical system 1200 may include: Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 1200 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 1200 can generate Figure 41 The field of view is 4100.

[0187] Light 1204 may enter lateral displacement prism 1202 through an incident surface. For example, light 1204 may be autofocus light generated by a light source (e.g., a laser diode). Light 1204A may exit lateral displacement prism 1202 through an exit surface. Light 1204B may exit lateral displacement prism 1202 through another exit surface. Light 1204A and light 1204B may be offset from each other by a predetermined angle.

[0188] Optical system 1200 includes substrate 1206. Substrate 1206 can be used to hold one or more samples to be analyzed. In some implementations, the sample on substrate 1206 can include nucleic acid material. For example, substrate 1206 can include a flow cell for imaging nucleic acid material. Substrate 1206 can include at least surface 1206A and surface 1206B. Reflection of light 1204A from surface 1206A can form light 1208A. Reflection of light 1204A from surface 1206B can form light 1210A. Reflection of light 1204B from surface 1206A can form light 1208B. Reflection of light 1204B from surface 1206B can form light 1210B.

[0189] Light 1208A-1208B and 1210A-1210B may be transmitted and / or reflected and / or refracted by at least one other component (not shown) in optical system 1200. Here, line 1212 schematically illustrates additional components of optical system 1200 and the processing of light 1208A-1208B and 1210A-1210B performed at the additional components.

[0190] Optical system 1200 includes sensor 1214. Sensor 1214 can detect reflected autofocus light during an autofocus procedure and / or detect emitted light during an analysis procedure. In some implementations, sensor 1214 includes a rectangular array of light-sensitive elements that can detect corresponding positions of one or more portions of light incident on sensor 1214. For example, light 1208A-1208B and 1210A-1210B can be incident on sensor 1214.

[0191] Sensor 1214 can be used to determine one or more characteristics of lights 1208A-1208B and 1210A-1210B. In some implementations, a predetermined interval 1216 can be specified corresponding to when substrate 1206 is in focus of an objective lens of optical system 1200. For example, optical system 1200 can determine whether the distance between lights 1208A-1208B at sensor 1214 is at least substantially equal to predetermined interval 1216, indicating that surface 1206A is currently in focus. As another example, optical system 1200 can determine whether the distance between lights 1210A-1210B at sensor 1214 is at least substantially equal to predetermined interval 1216, indicating that surface 1206B is currently in focus.

[0192] Figure 13Schematically illustrates an optical system 1300 having a laterally displaced prism 1302. The optical system 1300 can include, or be used with, one or more of the other examples described herein. In some implementations, the optical system 1300 can be included in Figure 1 In some implementations, the optical system 1300 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 1300 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 1300 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the optical system 1300 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 1300 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 1300 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 1300 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 1300 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the optical system 1300 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 1300 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 1300 may be included in Figure 18 and Figures 19A-19B In some implementations, the optical system 1300 can be integrated with the imaging module 1800. Figure 20In some implementations, the optical system 1300 may be included in Figure 21 In some implementations, the optical system 1300 may be included in the imaging module 2100. Figure 22 In some implementations, the optical system 1300 may be included in the imaging module 2200. Figure 24 In some implementations, the optical system 1300 may be included in the imaging module 2400. Figure 25 In some implementations, the optical system 1300 may be included in the optical system 2500. Figure 26 In some implementations, the optical system 1300 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 1300 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 1300 can generate Figure 29 In some implementations, the optical system 1300 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 1300 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 1300 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the optical system 1300 may include Figures 33A-33C Laser engine radiator 3300, or can be used with Figures 33A-33C In some implementations, the optical system 1300 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the optical system 1300 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 1300 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 1300 may include Figure 37The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 1300 may include: Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the optical system 1300 may include: Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 1300 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 1300 can generate Figure 41 The field of view is 4100.

[0193] Light 1304 may enter lateral displacement prism 1302 through an incident surface. For example, light 1304 may be autofocus light generated by a light source (e.g., a laser diode). Light 1304A may exit lateral displacement prism 1302 through an exit surface. Light 1304B may exit lateral displacement prism 1302 through another exit surface. Light 1304A and light 1304B may be offset from each other by a predetermined angle.

[0194] Optical system 1300 includes sensor 1306. Substrate 1306 can be used to hold one or more samples to be analyzed. In some implementations, the sample on substrate 1306 can include nucleic acid material. For example, substrate 1306 can include a flow cell for imaging nucleic acid material. Substrate 1306 can include at least surface 1306A and surface 1306B. Reflection of light 1304A from surface 1306A can form light 1308A. Reflection of light 1304A from surface 1306B can form light 1310A. Reflection of light 1304B from surface 1306A can form light 1308B. Reflection of light 1304B from surface 1306B can form light 1310B.

[0195] Light 1308A-1308B and 1310A-1310B may be transmitted and / or reflected and / or refracted by at least one other component (not shown) in optical system 1300. Here, line 1312 schematically illustrates additional components of optical system 1300 and the processing of light 1308A-1308B and 1310A-1310B performed at the additional components.

[0196] Optical system 1300 includes sensor 1314. Sensor 1314 can detect reflected autofocus light during an autofocus procedure and / or detect emitted light during an analysis procedure. In some implementations, sensor 1314 includes a rectangular array of light-sensitive elements that can detect the respective positions of one or more portions of light incident on sensor 1314. For example, light 1310A-1310B can be incident on sensor 1314.

[0197] Optical system 1300 can include one or more structures. Here, optical system 1300 includes structure 1316A and structure 1316B. Structure 1316A can be used to block one or more light beams from being transmitted to sensor 1314. In some implementations, structure 1316A can block one or more aspects of autofocus light that has been reflected from substrate 1306. For example, structure 1316A can block light 1308A. Structure 1316B can be used to block one or more light beams from being transmitted to sensor 1314. In some implementations, structure 1316B can block one or more aspects of autofocus light that has been reflected from substrate 1306. For example, structure 1316B can block light 1308B.

[0198] Sensor 1314 can be used to determine one or more characteristics of lights 1310A-1310B. In some implementations, a predetermined interval 1318 can be specified corresponding to substrate 1306 being in focus of an objective lens of optical system 1300. For example, optical system 1300 can determine whether the distance between lights 1310A-1310B at sensor 1314 is at least substantially equal to predetermined interval 1216, indicating that surface 1306B is currently in focus.

[0199] Figure 14 Schematically illustrates an optical system 1400 having a laterally displaced prism 1402. The optical system 1400 can include, or be used with, one or more of the other examples described herein. In some implementations, the optical system 1400 can include Figure 1 In some implementations, the optical system 1400 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 1400 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 1400 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8AIn some implementations, the optical system 1400 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 1400 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 1400 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 1400 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 1400 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 1400 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 1400 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 1400 may be included in Figure 18 and Figures 19A-19B In some implementations, the optical system 1400 can be integrated with the imaging module 1800. Figure 20 In some implementations, the optical system 1400 may be included in Figure 21 In some implementations, the optical system 1400 may be included in the imaging module 2100. Figure 22 In some implementations, the optical system 1400 may be included in the imaging module 2200. Figure 24 In some implementations, the optical system 1400 may be included in the imaging module 2400. Figure 25 In some implementations, the optical system 1400 may be included in the optical system 2500. Figure 26 In some implementations, the optical system 1400 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27In some implementations, the optical system 1400 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 1400 can generate Figure 29 In some implementations, the optical system 1400 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 1400 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 1400 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the optical system 1400 may include Figures 33A-33C Laser engine radiator 3300 in, or can be used with Figures 33A-33C In some implementations, the optical system 1400 may include Figure 34 SIM component 3400 in, or can be used with Figure 34 In some implementations, the optical system 1400 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 1400 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 1400 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 1400 may include: Figure 38 Piezoelectric phase shifter 3800 in, or with Figure 38 In some implementations, the optical system 1400 may include: Figure 39 The projection lens 3900 in the Figure 39 In some implementations, the optical system 1400 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 1400 can generate Figure 41 The field of view is 4100.

[0200] Light 1404 can enter lateral displacement prism 1402 through an incident surface. For example, light 1404 is autofocus light generated by a light source (e.g., a laser diode). Light 1404A can exit lateral displacement prism 1402 through an exit surface. Light 1404B can exit lateral displacement prism 1402 through another exit surface. Light 1404A and light 1404B are offset from each other by a predetermined angle.

[0201] Optical system 1400 includes substrate 1406. Substrate 1406 can be used to hold one or more samples to be analyzed. In some implementations, the sample on substrate 1406 can include nucleic acid material. For example, substrate 1406 can include a flow cell for imaging nucleic acid material. Substrate 1406 can include at least surface 1406A, surface 1406B, and surface 1406C. Reflection of light 1404A from surface 1406A can form light 1408A. Reflection of light 1404A from surface 1406B can form light 1410A. Reflection of light 1404A from surface 1406C can form light 1412A. Reflection of light 1404B from surface 1406A can form light 1408B. Reflection of light 1404B from surface 1406B can form light 1410B. Reflection of light 1404B from surface 1406C can form light 1412B.

[0202] Light 1408A-1408B, 1410A-1410B, and 1412A-1412B may be transmitted and / or reflected and / or refracted by at least one other component (not shown) in optical system 1400. Here, line 1414 schematically illustrates additional components of optical system 1400 and the processing of light 1408A-1408B, 1410A-1410B, and 1412A-1412B performed at the additional components.

[0203] Optical system 1400 includes sensor 1416. Sensor 1416 can detect reflected autofocus light during an autofocus procedure and / or detect emitted light during an analysis procedure. In some implementations, sensor 1416 includes a rectangular array of light-sensitive elements that can detect corresponding positions of one or more portions of light incident on sensor 1416. For example, light 1408A-1408B and 1410A-1410B can be incident on sensor 1416.

[0204] Optical system 1400 can include one or more structures. Here, optical system 1400 includes structure 1418A and structure 1418B. Structure 1418A can be used to block one or more light beams from being transmitted to sensor 1416. In some implementations, structure 1418A can block one or more aspects of autofocus light that has been reflected from substrate 1406. For example, structure 1418A can block light 1412A. Structure 1418B can be used to block one or more light beams from being transmitted to sensor 1416. In some implementations, structure 1418B can block one or more aspects of autofocus light that has been reflected from substrate 1406. For example, structure 1418B can block light 1412B.

[0205] Sensor 1416 can be used to determine one or more characteristics of lights 1408A-1408B and 1410A-1410B. In some implementations, a predetermined interval 1420 can be specified corresponding to when substrate 1406 is in focus of an objective lens of optical system 1400. For example, optical system 1400 can determine whether the distance between lights 1408A-1408B at sensor 1416 is at least substantially equal to predetermined interval 1420, indicating that surface 1406A is currently in focus. As another example, optical system 1400 can determine whether the distance between lights 1410A-1410B at sensor 1416 is at least substantially equal to predetermined interval 1420, indicating that surface 1406B is currently in focus.

[0206] Figure 15 An embodiment of autofocusing light at sensor 1500 is illustrated. Sensor 1500 can be used with or included in one or more other embodiments described herein. In some implementations, sensor 1500 can be included in Figure 1 In some implementations, the sensor 1500 can be connected to the system 100. Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the sensor 1500 can be connected to the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the sensor 1500 can be connected to the optical system 500. Figure 8A The optical system 800 may be used in conjunction with, or may be included in Figure 8A In some implementations, the sensor 1500 can be connected to the optical system 800. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8BIn some implementations, the sensor 1500 can be connected to the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the sensor 1500 can be connected to the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the sensor 1500 can be connected to the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the sensor 1500 can be connected to the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the sensor 1500 can be connected to the optical system 1400. Figure 18 and Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 and Figures 19A-19B In some implementations, the sensor 1500 can be used with the imaging module 1800. Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the sensor 1500 can be used with the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the sensor 1500 can be used with the imaging module 2200. Figure 24 The imaging module 2400 may be used in conjunction with, or may be included in Figure 24 In some implementations, the sensor 1500 can be used with the imaging module 2400. Figure 25 The optical system 2500 may be used in conjunction with, or may be included in Figure 25 In some implementations, the sensor 1500 can be connected to the optical system 2500. Figure 26 The optical system 2600 may be used in conjunction with, or may be included in Figure 26 In some implementations, process 1500 can be performed with Figure 27 In some implementations, process 1500 can be used with the reflective component 2700 in FIG. Figure 28 In some implementations, the sensor 1500 can receive Figure 29 In some implementations, the sensor 1500 may receive the autofocus light 2900. Figure 30In some implementations, the sensor 1500 may receive the autofocus light 3000. Figures 31A-31C In some implementations, the sensor 1500 can be used with the Figures 32A-32C In some implementations, the sensor 1500 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the sensor 1500 can be used with the laser engine heat sink 3300 in FIG. Figure 34 In some implementations, the sensor 1500 can be used with the SIM assembly 3400 in FIG. Figure 35 In some implementations, the sensor 1500 can be used with the RIGS 3500 in Figure 36 In some implementations, the sensor 1500 can be used with the RIGS 3600 in FIG. Figure 37 In some implementations, the sensor 1500 can be used with the piezoelectric phase shifter 3700 in FIG. Figure 38 In some implementations, the sensor 1500 can be used with the piezoelectric phase shifter 3800 in FIG. Figure 39 In some implementations, the sensor 1500 can be used with the projection lens 3900 in FIG. Figure 40 In some implementations, the sensor 1500 can capture Figure 41 The field of view is 4100.

[0207] Sensor 1500 illustrates light spots corresponding to sensor 1500's registration of incident light. In some implementations, the light spots correspond to portions of the autofocus light that have reflected from corresponding surfaces of the substrate. For example, a light spot labeled "S2" may have reflected from the top surface of a fluid channel in a flow cell. As another example, a light spot labeled "S3" may have reflected from the bottom surface of a fluid channel in a flow cell. The spacing between two S2 light spots tracks the distance between the S2 surface and the objective lens of the optical system. The spacing between two S3 light spots tracks the distance between the S3 surface and the objective lens of the optical system. Sensor 1500 illustrates that forming a controlled deviation between beams of autofocus light (e.g., using a lateral displacement prism), and / or manipulating at least one of a desired autofocus reflection or an unwanted autofocus reflection, can provide a clear image that helps to efficiently and accurately track focus in an optical system.

[0208] Figures 16A-16BAn embodiment of a lateral displacement prism 1600 is shown. Lateral displacement prism 1600 can be used with or included in one or more other embodiments described herein. In some implementations, lateral displacement prism 1600 can be used with Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the lateral displacement prism 1600 can be used with the system 100. Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the lateral displacement prism 1600 can be used with the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the lateral displacement prism 1600 can be used with the optical system 500. Figure 8A The optical system 800 may be used in conjunction with, or may be included in Figure 8A In some implementations, the lateral displacement prism 1600 can be used with the optical system 800. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the lateral displacement prism 1600 can be used with the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the lateral displacement prism 1600 can be used with the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the lateral displacement prism 1600 can be used with the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the lateral displacement prism 1600 can be used with the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the lateral displacement prism 1600 can be used with the optical system 1400. Figure 18 and Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 and Figures 19A-19B In some implementations, the lateral displacement prism 1600 can be used with the imaging module 1800. Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21In some implementations, the lateral displacement prism 1600 can be used with the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the lateral displacement prism 1600 can be used with the imaging module 2200. Figure 24 The imaging module 2400 may be used in conjunction with, or may be included in Figure 24 In some implementations, the lateral displacement prism 1600 can be used with the imaging module 2400. Figure 25 The optical system 2500 may be used in conjunction with, or may be included in Figure 25 In some implementations, the lateral displacement prism 1600 can be used with the optical system 2500. Figure 26 The optical system 2600 may be used in conjunction with, or may be included in Figure 26 In some implementations, the lateral displacement prism 1600 can be used with the optical system 2600. Figure 27 In some implementations, the lateral displacement prism 1600 can be used with the reflective component 2700 in FIG. Figure 28 In some implementations, the lateral displacement prism 1600 can generate Figure 29 In some implementations, the lateral displacement prism 1600 can generate the autofocus light 2900. Figure 30 In some implementations, the lateral displacement prism 1600 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the lateral displacement prism 1600 can be used with the Figures 32A-32C In some implementations, the lateral displacement prism 1600 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the lateral displacement prism 1600 can be used with the laser engine heat sink 3300 in FIG. Figure 34 In some implementations, the lateral displacement prism 1600 can be used with the SIM assembly 3400 in FIG. Figure 35 In some implementations, the lateral displacement prism 1600 can be used with the RIGS 3500 in FIG. Figure 36 In some implementations, the lateral displacement prism 1600 can be used with the RIGS 3600 in FIG. Figure 37 In some implementations, the lateral displacement prism 1600 can be used with the piezoelectric phase shifter 3700 in FIG. Figure 38 In some implementations, the lateral displacement prism 1600 can be used with the piezoelectric phase shifter 3800 in FIG. Figure 39In some implementations, the lateral displacement prism 1600 can be used with the projection lens 3900 in FIG. Figure 40 Used together with the projection lens 4000 in.

[0209] Lateral displacement prism 1600 includes a partially reflective layer 1602. In some implementations, lateral displacement prism 1600 can be manufactured by assembling prism sheet 1604A and prism sheet 1604B together, wherein partially reflective layer 1602 is positioned at the junction between the two prism sheets, wherein prism sheets 1604A-1604B are at least substantially identical to each other. As shown in the present figure, each prism sheet 1604A-1604B has a parallelogram cross-section. In some implementations, prism sheet 1604A is a quadrilateral having sides 1606A and 1606B that are parallel to each other and having sides 1606C and 1606D that are parallel to each other. In some implementations, prism sheet 1604B is a quadrilateral having sides 1608A and 1608B that are parallel to each other and having sides 1608C and 1608D that are parallel to each other. The assembly of the prismatic sheets 1604A-1604B and the partially reflective layer 1602 also has a parallelogram-shaped cross-section, as shown in the present figure.

[0210] Lateral displacement prism 1600 includes prism 1610 and prism 1612. Each prism 1610-1612 can have a wedge-shaped cross-section. For example, the wedge-shaped cross-section can include a triangular shape. In some implementations, prism 1610 has side 1610A that can be considered the exit side of prism 1610. For example, side 1610B can be opposite side 1610A in prism 1610, and sides 1610A-1610B can form a non-zero angle relative to each other. In some implementations, prism 1612 has side 1612A that can be considered the exit side of prism 1612. For example, side 1612B can be opposite side 1612A in prism 1612, and sides 1612A-1612B can form a non-zero angle relative to each other. Lateral displacement prism 1600 can be assembled by placing side 1610B of prism 1610 against side 1606B of prism sheet 1604A, and placing side 1612B of prism 1612 against side 1608B of prism sheet 1604B. In some implementations, this facilitates the use of sides 1610A and 1612A as exit surfaces for laterally displacement prism 1600. For example, such an arrangement can provide exit surfaces for laterally displacement prism 1600 that have a non-zero angle relative to each other.

[0211] Lateral displacement prism 1600 may also or alternatively include prism 1610' and prism 1612', such as Figure 16BAs shown. Each of prism 1610' and prism 1612' can have a wedge-shaped cross-section. For example, the wedge-shaped cross-section can include a truncated triangular shape. In some implementations, prism 1610' has a side 1610A' that can be considered an exit side of prism 1610'. For example, side 1610B' can be opposite to side 1610A' in prism 1610', and sides 1610A' and 1610B' can form a non-zero angle with each other. In some implementations, prism 1612' has a side 1612A' that can be considered an exit side of prism 1612'. For example, side 1612B' can be opposite to side 1612A' in prism 1612', and sides 1612A' and 1612B' can form a non-zero angle with respect to each other. Lateral displacement prism 1600 can be assembled by placing side 1610B' of prism 1610' against side 1606B of prism sheet 1604A, and placing side 1612B' of prism 1612' against side 1608B of prism sheet 1604B. In some implementations, this facilitates sides 1610A' and 1612A' serving as exit surfaces for laterally displacement prism 1600. For example, such an arrangement can provide exit surfaces for laterally displacement prism 1600 that have a non-zero angle relative to each other.

[0212] Figure 17 An embodiment of a beam splitter 1700 is shown. The beam splitter 1700 can be used with or included in one or more other embodiments described herein. In some implementations, the beam splitter 1700 can be used with Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the beam splitter 1700 can be used with the system 100. Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the beam splitter 1700 can be used with the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the beam splitter 1700 can be used with the optical system 500. Figure 8A The optical system 800 may be used in conjunction with, or may be included in Figure 8A In some implementations, the beam splitter 1700 can be used with the optical system 800. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the beam splitter 1700 can be used with the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11In some implementations, the beam splitter 1700 can be used with the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the beam splitter 1700 can be used with the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the beam splitter 1700 can be used with the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the beam splitter 1700 can be used with the optical system 1400. Figure 18 and Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 and Figures 19A-19B In some implementations, the beam splitter 1700 can be used with the imaging module 1800. Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the beam splitter 1700 can be used with the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the beam splitter 1700 can be used with the imaging module 2200. Figure 24 The imaging module 2400 may be used in conjunction with, or may be included in Figure 24 In some implementations, the beam splitter 1700 can be used with the imaging module 2400. Figure 25 The optical system 2500 may be used in conjunction with, or may be included in Figure 25 In some implementations, the beam splitter 1700 can be used with the optical system 2500. Figure 26 The optical system 2600 may be used in conjunction with, or may be included in Figure 26 In some implementations, the beam splitter 1700 can be used with the optical system 2600. Figure 27 In some implementations, the beam splitter 1700 can be used with the reflective component 2700 in FIG. Figure 28 In some implementations, the beam splitter 1700 can generate Figure 29 In some implementations, the beam splitter 1700 can generate Figure 30 In some implementations, the beam splitter 1700 can generate Figures 31A-31C In some implementations, the beam splitter 1700 can be used with Figures 32A-32C In some implementations, the beam splitter 1700 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the beam splitter 1700 can be used with the laser engine heat sink 3300 in FIG. Figure 34 In some implementations, the beam splitter 1700 can be used with the SIM assembly 3400 in FIG. Figure 35 In some implementations, the beam splitter 1700 can be used with the RIGS 3500 in FIG. Figure 36 In some implementations, the beam splitter 1700 can be used with the RIGS 3600 in FIG. Figure 37 In some implementations, the beam splitter 1700 can be used with the piezoelectric phase shifter 3700 in FIG. Figure 38 In some implementations, the beam splitter 1700 can be used with the piezoelectric phase shifter 3800 in FIG. Figure 39 In some implementations, the beam splitter 1700 can be used with the projection lens 3900 in FIG. Figure 40 Used together with the projection lens 4000 in.

[0213] Beam splitter 1700 includes a partially reflective layer 1702. Beam splitter 1700 includes a reflective surface 1704 and a reflective surface 1706. Light 1708 may enter beam splitter 1700. For example, light 1708 is autofocus light generated by a light source (e.g., a laser diode). After being reflected at reflective surface 1704, light 1708 may be incident on partially reflective layer 1702. Thus, light 1708A reflected at partially reflective layer 1702 may be formed by beam splitter 1700. In addition, light 1708B may be transmitted through partially reflective layer 1702 and reflected at reflective surface 1706. Light 1708A and light 1708B are offset from each other by a predetermined angle.

[0214] Figure 18 An embodiment of an imaging module 1800 is shown. The imaging module 1800 may include, or be used with, one or more of the other examples described herein. In some implementations, the imaging module 1800 may include Figure 42 System 4200 in, or can be used with Figure 42 In some implementations, imaging module 1800 may include Figure 43 At least some components of the computing device 4300 in, or can be used with Figure 43 In some implementations, imaging module 1800 may be included in Figure 1In some implementations, the imaging module 1800 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the imaging module 1800 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the imaging module 1800 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the imaging module 1800 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the imaging module 1800 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the imaging module 1800 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the imaging module 1800 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the imaging module 1800 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the imaging module 1800 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the imaging module 1800 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the imaging module 1800 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the imaging module 1800 may include Figure 18 and Figures 19A-19B The imaging module 1800 in the embodiment of the present invention may be used in conjunction with Figure 18 and Figures 19A-19B In some implementations, the imaging module 1800 may include Figure 20SIM component 2000 in the Figure 20 In some implementations, the imaging module 1800 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the imaging module 1800 may include Figure 22 The imaging module 2200 in the embodiment of the present invention may be used in conjunction with Figure 22 In some implementations, the imaging module 1800 may include Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the imaging module 1800 may include Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the imaging module 1800 may include Figure 26 The optical system 2600 in, or with Figure 26 In some implementations, the imaging module 1800 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the imaging module 1800 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the imaging module 1800 can generate Figure 29 In some implementations, the imaging module 1800 may generate the autofocus light 2900. Figure 30 In some implementations, the imaging module 1800 may generate the autofocus light 3000. Figures 31A-31C In some implementations, the imaging module 1800 may include Figures 32A-32C Laser engine radiator 3200, or can be used with Figures 32A-32C In some implementations, the imaging module 1800 may include Figures 33A-33C Laser engine radiator 3300, or can be used with Figures 33A-33C In some implementations, the imaging module 1800 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the imaging module 1800 may include Figure 35RIGS 3500 in, or can be used with Figure 35 In some implementations, the imaging module 1800 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the imaging module 1800 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the imaging module 1800 may include Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the imaging module 1800 may include Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the imaging module 1800 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the imaging module 1800 can generate Figure 41 The field of view is 4100.

[0215] The imaging module 1800 includes a plurality of components and / or devices that can be integrated to operate in unison 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, which is only partially visible in the current view. 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 the SIM light from the SIM assembly 1802 and apply the SIM light to a substrate (not shown) holding 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 (here referred to as the z distance) between the objective lens 1804 and the substrate holding the sample.

[0216] Imaging module 1800 can include one or more portions of a housing. In some implementations, the housing can substantially enclose components of imaging module 1800. For example, housing 1808 can at least partially enclose SIM assembly 1802. As another example, housing 1810 can at least partially enclose emission optics (e.g., one or more tube lenses and / or sensors) of imaging module 1800. As another example, housing 1812 can at least partially enclose SIM assembly 1802 and / or at least partially enclose detection optics.

[0217] Imaging module 1800 may be missing one or more housings, which may make some components visible. This may occur during assembly and / or during maintenance or repair, to name a few examples. Figures 19A-19B Shown Figure 18 1800. The imaging module 1800 is shown in a partially unassembled or disassembled state. For example, the housing 1808 and 1810 ( Figure 18 ) is not currently located at imaging module 1800. At least partially visible in the current view are SIM assembly 1802, autofocus module 1814, compensator 1816, and launch optics 1818. Shown for illustrative purposes, SIM assembly 1802, autofocus module 1814, compensator 1816, and launch optics 1818, along with objective lens 1804, can be used when imaging module 1800 (in an operational state) performs imaging of substrate 1820. For example, optical system 1814 can include one or more autofocus functions described elsewhere herein.

[0218] In some implementations, the emission optics 1818 includes a filter assembly 1822. The filter assembly 1822 may include at least one filter. For example, the filter assembly 1822 may include Figure 2 Filter 212 or Figure 5 In some implementations, the emission optics 1818 may include a tube lens 1824. For example, the tube lens 1824 may be Figure 2 The tube lens 214 in Figure 5 The tube lens 508 or Figure 8A 1824 can be assigned to the blue detector channel. In some implementations, the emission optics 1818 can include a tube lens 1826. The tube lens 1826 can be assigned to the green detector channel. For example, the tube lens 1826 can be Figure 2 The tube lens 214 in Figure 5 The tube lens 508 or Figure 8AIn some implementations, the emission optics 1818 include a filter assembly 1828. For example, the filter assembly 1828 may include Figure 2 As another example, the filter assembly 1828 may include one or more of the filter 216, the reflective component 226, or the structure 228. Figure 5 As another example, the filter assembly 1828 may include one or more of the filter 510, the reflective component 516, or the structure 518. Figure 8A One or more of the filter 804, reflective components 810A-810B, or structure 812.

[0219] In some implementations, the emission optics 1818 includes a sensor assembly 1830. The sensor assembly 1830 can be assigned to the blue detector channel. The sensor assembly 1830 can include one or more sensors for emission light and / or autofocus light. For example, the sensor assembly 1830 can include one or more of the following: Figure 1 Sensor 120 in; Figure 2 Sensor 220 in; Figure 5 Sensor 514 in FIG. 8 ; sensor 808 in FIG. 8 ; Figure 11 Sensor 1112 in; Figure 12 Sensor 1214 in; Figure 13 Sensor 1314 in; or Figure 14 1416 in the emission optics. In some implementations, the emission optics 1818 includes a sensor assembly 1832. The sensor assembly 1832 can be assigned to the green detector channel. The sensor assembly 1832 can include one or more sensors for emission light and / or autofocus light. For example, the sensor assembly 1832 can include one or more of the following: Figure 1 Middle sensor 120; Figure 2 Sensor 220 in; Figure 5 Sensor 514 in FIG. 8 ; sensor 808 in FIG. 8 ; Figure 11 Sensor 1112 in; Figure 12 Sensor 1214 in; Figure 13 Sensor 1314 in; or Figure 14 Sensor 1416 in.

[0220] Figure 20 An embodiment of a SIM assembly 2000 is shown. The SIM assembly 2000 can be used with or included in one or more of the other examples described herein. In some implementations, the SIM assembly 2000 can be used with Figure 1system 100 for use with, or may be included in Figure 1 In some implementations, the SIM component 2000 can be used with the system 100. Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the SIM assembly 2000 can be used with the optical system 200 in FIG. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the SIM assembly 2000 can be used with the optical system 500. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the SIM assembly 2000 can be used with the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the SIM assembly 2000 can be used with the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the SIM assembly 2000 can be used with the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the SIM assembly 2000 can be used with the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the SIM assembly 2000 can be used with the optical system 1400. Figure 18 or Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 or Figures 19A-19B In some implementations, the SIM assembly 2000 can be used with the imaging module 1800. Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the SIM assembly 2000 can be used with the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the SIM assembly 2000 may include Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the SIM assembly 2000 may include Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the SIM assembly 2000 may include Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the SIM assembly 2000 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the SIM assembly 2000 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the SIM assembly 2000 can generate Figure 29 In some implementations, the SIM assembly 2000 can generate an autofocus light 2900. Figure 30 In some implementations, the SIM assembly 2000 may generate an autofocus light 3000. Figures 31A-31C In some implementations, the SIM assembly 2000 can be used with the Figures 32A-32C In some implementations, the SIM assembly 2000 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the SIM assembly 2000 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the SIM assembly 2000 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the SIM assembly 2000 may include Figure 36 RIGS3600 in the Figure 36 In some implementations, the SIM assembly 2000 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the SIM assembly 2000 may include Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the SIM assembly 2000 may include: Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39In some implementations, the SIM assembly 2000 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the SIM assembly 2000 can generate Figure 41 The field of view is 4100.

[0221] SIM assembly 2000 includes a rotatable mirror 2002. SIM assembly 2000 includes a light source 2004. In some implementations, light source 2004 provides light, which in turn receives light via at least one fiber optic cable 2006. For example, light source 2004 and fiber optic cable 2006 may be collectively referred to as a fiber optic transmission module. SIM assembly 2000 includes a grating 2008 and a grating 2010. In some implementations, gratings 2008 and / or 2010 may function as diffraction elements for light from light source 2004. For example, gratings 2008 and / or 2010 may include a substrate having a periodic structure combined with a prism. Gratings 2008 and 2010 may be positioned relative to each other according to one or more arrangements. Here, gratings 2008 and 2010 face each other in system 2000. Gratings 2008 and 2010 may be substantially identical to each other, or may have one or more differences. The size, periodicity, or other spatial aspect of one of the gratings 2008 and 2010 can differ from the size, periodicity, or other spatial aspect of the other grating. The grating orientation (i.e., the spatial orientation of the periodic structure) of one of the gratings 2008 and 2010 can differ from the grating orientation of the other grating. In some implementations, the grating orientations (i.e., the orientations of the gratings themselves facing each other) of the gratings 2008 and 2010 can be substantially perpendicular to each other or at any other angle relative to each other. In some implementations, the gratings 2008 and 2010 can be in an offset position relative to the rotatable mirror 2002. In some implementations, the gratings 2008 and / or 2010 can be in a fixed position relative to the light source 2004.

[0222] System 2000 may include one or more components (e.g., such as a phase selector) that facilitate phase selection of light to be applied to the sample. Here, SIM assembly 2000 includes phase shifter 2012. In some implementations, phase shifter 2012 comprises a piezoelectric fringe shifter. In some implementations, phase shifter 2012 may receive light from gratings 2008 and / or 2010 and may perform phase selection on some or all of the light. For example, phase shifter 2012 may be used to control the phase of a structured light pattern that is used to capture a particular image. Phase shifter 2012 may include a piezoelectric actuator. For example, a piezoelectric piston system may be used to achieve phase selection. Other methods may also be used. For example, a tilted optical plate may be used for phase selection. For example, here, SIM assembly 2000 is implemented on plate 2014, and one or more regions of plate 2014 may 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, for example, by a piezoelectric actuator. The light emitted from the phase shifter 2012 is sometimes referred to as phase-selective 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.

[0223] The SIM assembly includes a projection lens 2016, which may include one or more optical components (e.g., lenses) that condition the light received from the phase shifter 2012. For example, the projection lens 2016 may be positioned after the light enters the objective lens (e.g., Figure 2 The characteristics of the light are controlled before the objective lens 204 in the image.

[0224] Rotatable mirror 2002 can be used to redirect at least one beam of light toward one or more of gratings 2008 or 2010, and / or to redirect at least one beam of light arriving from one or more of gratings 1308 or 1310. Rotatable mirror 2002 can include one or more materials to sufficiently reflect the electromagnetic waves with which the sample is to be illuminated. In some implementations, the light from light source 2004 includes a laser beam of one or more wavelengths. For example, metal-coated mirrors and / or dielectric mirrors can be used. Rotatable mirror 2002 can be double-sided. For example, if rotatable mirror 2002 is capable of performing reflection on at least a portion of its two sides (e.g., reflecting at a first end for a first beam path and reflecting at a second end opposite the first end for a second beam path), then rotatable mirror 1302 can be considered double-sided.

[0225] The rotatable reflector 2002 can include an elongated member. The rotatable reflector 2002 can have any of a variety of form factors or other shape characteristics. The rotatable reflector 2002 can have a generally flat configuration. The rotatable reflector 2002 can have a substantially square or other rectangular shape. The rotatable reflector 2002 can have rounded corners. The rotatable reflector 2002 can have a substantially constant thickness. The reflective surface of the rotatable reflector 2002 can be substantially planar.

[0226] The rotatable mirror 2002 can be supported by a shaft 2018 of the SIM assembly 2000. The shaft 2018 can allow the rotatable mirror 2002 to rotate about the shaft 2018 in either or both directions. The shaft 2018 can be made of a material sufficiently rigid to hold and manipulate the rotatable mirror 2002, including, but not limited to, metal. The shaft 2018 can be coupled substantially at the center of the rotatable mirror 2002. For example, the rotatable mirror 2002 can have an opening in the center or a cutout extending from one side to the center to facilitate coupling with the shaft 2018. The shaft 2018 can extend at least substantially to one side of the rotatable mirror 2002. As another example, the shaft 2018 can include separate shaft portions that couple to respective faces of the rotatable mirror 2002 without requiring any openings in the rotatable mirror 2002. The shaft 2018 can have at least one suspension 2014 relative to the plate 2014. Here, the suspension is positioned at the ends of shaft 2018 on either side of the rotatable mirror 2002. The suspension may include bearings or other features that facilitate low friction operation.

[0227] 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 shaft 2018 and used to rotate the shaft 2018 and assume the desired position, thereby rotating the rotatable mirror 2002 and assuming the desired position. In some implementations, the rotatable mirror 2002 rotates in the same direction (e.g., always clockwise or always counterclockwise around the axis of rotation of the shaft 2018) toward the new position. In some implementations, the rotatable mirror 2002 reciprocates between two or more positions (e.g., alternately clockwise or counterclockwise around the axis of rotation of the shaft 2018).

[0228] In some implementations, light source 2004 can generate light that initially propagates toward mirror 2024. After reflecting at mirror 2024, the light propagates toward grating 2010. Rotatable mirror 2002 is currently positioned (e.g., oriented about the axis of rotation of axis 2018) such that first end 2022 of rotatable mirror 2002 does not block the light. Currently, first end 2022 can be positioned closer to the observer than light propagating in the plane of the figure would. That is, the reflective surface of rotatable mirror 2002 facing light source 2004 does not currently block the light because first end 2022 does not block the path of the light. Therefore, the light propagates (through air, vacuum, or another fluid) until it reaches grating 2010.

[0229] Light interacts with the grating 2010 in one or more ways. In some implementations, the light undergoes diffraction based on the grating 2010. Here, based on the light's interaction with the grating 2010, the light emitted from the grating 2010 can be structured light (e.g., light having one or more patterned fringes). The light emitted from the grating 2010 initially propagates substantially in a direction generally toward the projection lens 2016. However, the rotatable mirror 2002 is positioned such that the second end 2026 of the rotatable mirror 2002 blocks the light. The second end 2026 can be opposite 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 (e.g., any angle between 0 and 180 degrees). Currently, the second end 2026 can be positioned approximately as close to the observer as the light. That is, the reflective surface 202B of the rotatable mirror 2002 facing the grating 2010 blocks the light emitted from the grating 2010 because the second end 2026 blocks the light's path. Thus, depending on the light, the rotatable mirror 2002 directs the light toward the phase shifter 2012 .

[0230] Phase shifter 2012 performs phase selection on the light. For example, phase shifter 2012 selects the phase of the pattern that the sample will experience under the current illumination (e.g., for the purpose of capturing one or more specific images). Light is emitted from phase shifter 2012 and propagates toward and enters projection lens 2016. The light corresponds to the specific phase selection made using phase shifter 2012. Therefore, the light can be characterized as phase-selected light. The light can then continue to propagate through the system, for example, to illuminate the sample.

[0231] Here, the phase-selective electromagnetic wave characteristics of the light entering the projection lens 2016 correspond to the fact that the light is diffracted by the grating 2010 and the phase selection is performed by the phase shifter 2012. Moreover, the intervention of the grating 2010 is here a result of the positioning of the rotatable mirror 2002 so that its second end 2026 blocks the light while the first end 2022 does not.

[0232] What is now presented is that rotatable reflector 2002 is alternatively placed in a different location. Here, light source 2004 generates light that is initially reflected by reflector 2024 and therefore propagates toward grating 2010. Rotatable reflector 2002 is positioned (e.g., oriented around the axis of rotation of shaft 2018) so that a first end 2022 of rotatable reflector 2002 blocks the light. Currently, first end 2022 can be positioned approximately as close to the observer as the light. That is, the reflective surface of rotatable reflector 2002 facing light source 2004 blocks the light because first end 2022 blocks the path of the light. Therefore, light propagates (through air, vacuum, or another fluid) until it reaches grating 2008.

[0233] Light interacts with grating 2008 in one or more ways. In some implementations, the light undergoes diffraction based on grating 2008. Here, the light is structured light (e.g., having one or more patterned fringes) emitted from the grating based on the interaction of the light with grating 2008. The light propagates substantially in a direction toward phase shifter 2012. The rotatable mirror 2002 is positioned so that the second end 2026 of the rotatable mirror 2002 does not block the light. Currently, the second end 2026 can be positioned closer to the observer than the light. In other words, the reflective surface of the rotatable mirror 2002 currently does not block the light because the second end 2026 does not block the light's path. Therefore, the light propagates until it reaches the phase shifter 2012.

[0234] Phase shifter 2012 performs phase selection on the light. For example, phase shifter 2012 selects the phase of the pattern that the sample will experience under the current illumination (e.g., for the purpose of capturing one or more specific images). Light is emitted from phase shifter 2012 and propagates toward and enters projection lens 2016. The light corresponds to the specific phase selection made using phase shifter 2012. Therefore, the light can be characterized as phase-selected light. The light can then continue to propagate through the system, for example, to illuminate the sample.

[0235] Here, the characteristic of the phase-selective electromagnetic wave of light corresponds to the fact that the light is diffracted by the grating 2008 and the phase selection is performed by the phase shifter 2012. In addition, the intervention of the grating 2008 is the result of the positioning of the rotatable mirror 2002 so that its first end 2022 blocks the light while the second end 2026 does not block the light. The rotatable mirror 2002 can repeatedly assume different positions through various rotations. For example, the rotatable mirror 2002 can reciprocate between multiple positions. As another example, the rotatable mirror 2002 can rotate in the same direction (e.g., clockwise or counterclockwise from the perspective of the stepper motor 2020) to repeatedly assume different positions.

[0236] SIM assembly 2000 may include one or more anamorphic prisms 2028. When a single anamorphic prism is used, light may exit the prism at an angle. A pair of anamorphic prisms may be arranged so that the exiting light is parallel to the incident light. In some implementations, anamorphic prism 2028 may transform the light from light source 2004 in one or more aspects. The light from light source 2004 (e.g., the exit face of fiber optic cable 2006) may have a specific geometric shape (e.g., a square shape) and be imaged onto the flow cell and then onto the system's sensor. Furthermore, the sensor may have a different geometry than the light from light source 2004 (e.g., a rectangular shape), and the anamorphic prism may alter the shape of the light based on the sensor geometry. For example, anamorphic prism 2028 may stretch a square fiber face into a rectangular shape. As another example, anamorphic prism 2028 may transform an elliptical beam into a circular beam, and / or may transform a circular beam into an elliptical beam. Insufficient irradiance at the sample plane may be due to the challenges of generating a rectangular illumination footprint using a square multimode laser fiber as an excitation source. This technical challenge may result in decreased sequencing performance due to less DNA cluster signal reaching the sensor. This is addressed by demagnifying the square fiber in one axis using at least one deformable prism (including but not limited to one or more deformable prism pairs). While custom rectangular laser fibers can be implemented in some cases, square fibers may be preferred due to manufacturability and / or applicability. That is, issues with custom fibers may be due to tolerances. Matching the required numerical aperture may be difficult and / or less reliable during the fiber preforming stage. Additionally, custom rectangular fibers may also be difficult to form into the core dimensions required to produce the desired illumination coverage area. Finally, the fiber bend radii of the two axes of a custom rectangular fiber may be less known than those of a square fiber.

[0237] A rectangular illumination footprint ensures that all laser power reaches the sample, accounting for all transmission losses through the excitation path. For this projection, the laser illumination footprint of the APP was converted from a square to a rectangular shape. The square footprint does not match the sample planar tile size. Allowing full square illumination to reach the sensor would cause unnecessary illumination of adjacent tiles, which could prematurely reduce intensity in the process. In early prototype stages, a baffle was included in the excitation path to clip the top and bottom of the square illumination footprint, but this resulted in reduced irradiance from the square fiber. Instead, an anamorphic prism pair was included in the SIM beam path. The 0.9 mm x 1.2 mm sample tile size was designed to match the aspect ratio of the integrated imaging module sensor. The introduction of the anamorphic prism pair shrinks the output of the square fiber and reshapes it into a rectangular shape. This allows the instrument to optimize the amount of laser power that excites the sample. This is demonstrated by comparing the imaging tile area of ​​a rectangular FOV to a square FOV. This was done to determine how much laser power a rectangular footprint can deliver compared to a square footprint:

[0238] Overlap between cylinder and rectangle [%] = (area_cylinder) / (area_rectangle) = 0.968 / 1.08 = 0.896 = 89.6%

[0239] Overlap between the cylinder and the square [%] = (area_cylinder) / (area_square) = 0.968 / 1.44 = 0.672 = 67.2%.

[0240] That is, by using an anamorphic prism pair to reshape the square fiber output, the power increase is (rectangular overlap with the barrel %) / (square overlap with the barrel %) = 89.6 / 67.2 = 1.3333%. The implementation of the anamorphic prism pair eliminates the need for cropping the top and bottom portions of the laser, while also increasing the irradiance at the sample plane by 33%.

[0241] Stepper motor 2020 may be referred to as an in-plane rotary grating switcher (RIGS). In some implementations, stepper motor 2020 actuates shaft 2018, which causes rotatable mirror 2002 to rotate (i.e., "rotate" in RIGS). Rotatable mirror 2002 rotates within a plane (i.e., "in-plane" in RIGS). Rotation of rotatable mirror 2002 causes grating 2008 or grating 2010 to be applied (i.e., a "grating switcher" in RIGS).

[0242] Figure 21 An embodiment of an imaging module 2100 is shown. The imaging module 2100 can be used with or included in one or more other embodiments described herein. In some implementations, the imaging module 2100 can include Figure 42 System 4200 in, or can be used with Figure 42 In some implementations, the imaging module 2100 may include Figure 43 At least some components of the computing device 4300 in, or can be used with Figure 43 In some implementations, the imaging module 2100 can be used with at least some components of the computing device 4300 in FIG. Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the imaging module 2100 can be used with the system 100. Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the imaging module 2100 can be used with the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the imaging module 2100 can be used with the optical system 500. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the imaging module 2100 can be used with the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the imaging module 2100 can be used with the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the imaging module 2100 can be used with the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the imaging module 2100 can be used with the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the imaging module 2100 can be used with the optical system 1400. Figure 18 or Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 or Figures 19A-19B In some implementations, the imaging module 2100 can be used with Figure 20 In some implementations, the imaging module 2100 can be used with the SIM assembly 2000 in FIG. Figure 22 In some implementations, the imaging module 2100 may include Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the imaging module 2100 may include Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the imaging module 2100 may include Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the imaging module 2100 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the imaging module 2100 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the imaging module 2100 can generate Figure 29 In some implementations, the imaging module 2100 may generate an autofocus light 2900. Figure 30 In some implementations, the imaging module 2100 may generate the autofocus light 3000. Figures 31A-31C In some implementations, the imaging module 2100 can be used with the autofocus light 3100 in the image sensor. Figures 32A-32C In some implementations, the imaging module 2100 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the imaging module 2100 may include Figure 34 SIM component 3400 in, or can be used with Figure 34 In some implementations, the imaging module 2100 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the imaging module 2100 may include Figure 36 RIGS3600 in the Figure 36 In some implementations, the imaging module 2100 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the imaging module 2100 may include Figure 38 Piezoelectric phase shifter 3800 in, or with Figure 38In some implementations, the imaging module 2100 may include Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the imaging module 2100 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the imaging module 2100 can generate Figure 41 The field of view is 4100.

[0243] The imaging module 2100 includes multiple components and / or devices that can be integrated to operate in unison 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 component 2102, which is only partially visible in the current view. For example, the SIM component 2102 can generate spatially structured light for illuminating the 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 component 2102 and apply the SIM light to a substrate 2114 holding 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 (here referred to as the z distance) between the objective lens 2104 and the substrate holding the sample.

[0244] Imaging module 2100 can include one or more portions of a housing. In some implementations, the housing can substantially enclose components of imaging module 2100. For example, housing 2108 can at least partially enclose SIM assembly 2102. As another example, housing 2110 can at least partially enclose emission optics (e.g., one or more tube lenses and / or sensors) of imaging module 2100. As another example, housing 2112 can at least partially enclose SIM assembly 2102 and / or at least partially enclose detection optics.

[0245] Imaging module 2100 may be missing one or more housings, which may make some components visible. This may occur during assembly and / or during maintenance or repair, to name a few examples.

[0246] In some implementations, one or more of the housings 2108, 2110, or 2112 of imaging module 2100 can comprise aluminum. For example, housing 2108, 2110, or 2112 can comprise two pieces of welded aluminum that can be assembled using side fasteners. Tolerances can be defined regarding mounting holes, and assembly can include matching drill holes where applicable. Implementations can be designed to reduce or eliminate absolute camera tilt, which can otherwise result in unit-to-unit variations in the force applied to the main substrate in imaging module 2100.

[0247] Figure 22 An embodiment of an imaging module 2200 is shown. The imaging module 2200 can be used with or included in one or more other embodiments described herein. In some implementations, the imaging module 2200 can include Figure 42 System 4200 or with Figure 42 In some implementations, the imaging module 2200 may include Figure 43 At least some components of the computing device 4300 in, or can be used with Figure 43 In some implementations, the imaging module 2200 can be used with at least some components of the computing device 4300 in FIG. Figure 1 system 100 for use with, or included in Figure 1 In some implementations, the imaging module 2200 can be used with the system 100. Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the imaging module 2200 can be used with the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the imaging module 2200 can be used with the optical system 500. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the imaging module 2200 can be used with the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the imaging module 2200 can be used with the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the imaging module 2200 can be used with the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the imaging module 2200 can be used with the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the imaging module 2200 can be used with the optical system 1400. Figure 18 or Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 or Figures 19A-19B In some implementations, the imaging module 2200 can be used with Figure 20 used in conjunction with the SIM assembly 2000, or may be included in the Figure 20 In some implementations, the imaging module 2200 can be connected to the SIM component 2000. Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the imaging module 2200 may include Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the imaging module 2200 may include Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the imaging module 2200 may include Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the imaging module 2200 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the imaging module 2200 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the imaging module 2200 can generate Figure 29 In some implementations, the imaging module 2200 may generate an autofocus light 2900. Figure 30 In some implementations, the imaging module 2200 may generate the autofocus light 3000. Figures 31A-31C In some implementations, the imaging module 2200 can be used with the autofocus light 3100 in the image sensor. Figures 32A-32C In some implementations, the imaging module 2200 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33CIn some implementations, the imaging module 2200 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the imaging module 2200 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the imaging module 2200 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the imaging module 2200 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the imaging module 2200 may include Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the imaging module 2200 may include Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the imaging module 2200 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the imaging module 2200 can generate Figure 41 The field of view is 4100.

[0248] The imaging module 2200 includes a plurality of components and / or devices that can be integrated to operate in unison 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, which is only partially visible in the current view. For example, the SIM assembly 2202 can generate spatially structured light for illuminating the sample material. The imaging module 2200 includes an objective lens 2204. In some implementations, the objective lens 2204 can transmit the SIM light from the SIM assembly 2202 and apply the SIM light to a substrate (not shown) holding 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 (here referred to as the z distance) between the objective lens 2204 and the substrate holding the sample.

[0249] Imaging module 2200 can include one or more portions of a housing. In some implementations, the housing can substantially enclose components of imaging module 2200. For example, housing 2208 can at least partially enclose SIM assembly 2202. As another example, housing 2210 can at least partially enclose emission optics (e.g., one or more tube lenses and / or sensors) of imaging module 2200. As another example, housing 2212 can at least partially enclose SIM assembly 2202 and / or at least partially enclose detection optics.

[0250] Imaging module 2200 may be missing one or more housings, which may make some components visible. This may occur during assembly and / or during maintenance or repair, to name a few examples.

[0251] In some implementations, one or more of the housings 2208, 2210, or 2212 of the imaging module 2200 can comprise aluminum. The housings 2208, 2210, or 2212 can comprise aluminum components that are assembled (e.g., bolted together) without welding. For example, this approach can allow for greater tolerance for component variability. In some implementations, a seal can be provided to prevent light intrusion and / or escape, and / or a seal to prevent particle intrusion and / or escape. For example, adhesive tape can be used for the seal.

[0252] Figure 23 A graph 2300 of error rates is shown. The error rate (e.g., measured as a positive number) is shown on the vertical axis, where the vertical axis has a scale ranging between 0 and 10. The number of cycles is shown on the horizontal axis, where the horizontal axis has a scale ranging between 0 and 110. In some implementations, the amount of data generated by RIGS (e.g., Figure 20The invention provides a method for reducing the effects of vibrations of optical components caused by the movement of the stepper motor 2020 in the grating. For example, otherwise, such vibrations may affect the fringe stability and thereby the imaging quality. The RIGS may operate according to an S-curve movement profile. For example, this may prevent the SIGS from suddenly accelerating or decelerating. In some implementations, the S-curve movement profile may be optimized to minimize the generation of vibrations. In some implementations, the order in which the RIGS assumes its states may be specified to reduce the effects of vibrations. For example, in one state of the RIGS, the vibrated reflective component may be downstream (e.g., behind) the grating in the optical flow, while in another state of the RIGS, the vibrated reflective component (or another reflective component) may be upstream (e.g., in front) of the grating. The upstream positioning may be more sensitive to vibrations of the reflective component than the downstream positioning. In some implementations, the effects of vibrations may be eliminated or reduced by designing the time and / or order in which the RIGS assumes the corresponding states. For example, in the operation of the RIGS, the upstream positioning may be processed before the downstream positioning, and vice versa. As another example, a delay may be implemented after the RIGS movement or RIGS reset sequence. In some implementations, one or more methods for RIGS can reduce or eliminate the effects of vibration on the imaging process, for example, reducing error rates.

[0253] Figure 24 An embodiment of an imaging module 2400 is shown. The imaging module 2400 can be used with or included in one or more other embodiments described herein. In some implementations, the imaging module 2400 can include Figure 42 System 4200 in, or can be used with Figure 42 In some implementations, the imaging module 2400 may include Figure 43 At least some components of the computing device 4300 in, or can be used with Figure 43 In some implementations, the imaging module 2400 can be used with at least some components of the computing device 4300 in FIG. Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the imaging module 2400 can be used with the system 100. Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the imaging module 2400 can be used with the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the imaging module 2400 can be used with the optical system 500. Figure 8BThe optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the imaging module 2400 can be used with the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the imaging module 2400 can be used with the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the imaging module 2400 can be used with the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the imaging module 2400 can be used with the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the imaging module 2400 can be used with the optical system 1400. Figure 18 or Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 or Figures 19A-19B In some implementations, the imaging module 2400 can be used with Figure 20 In some implementations, the imaging module 2400 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the imaging module 2400 can be used with the imaging module 2100 in FIG. Figure 22 In some implementations, the imaging module 2400 may include Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the imaging module 2400 may include Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the imaging module 2400 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the imaging module 2400 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the imaging module 2400 can generate Figure 29In some implementations, the imaging module 2400 may generate an autofocus light 2900. Figure 30 In some implementations, the imaging module 2400 may generate the autofocus light 3000. Figures 31A-31C In some implementations, the imaging module 2400 can be used with the autofocus light 3100 in the image sensor. Figures 32A-32C In some implementations, the imaging module 2400 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the imaging module 2400 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the imaging module 2400 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the imaging module 2400 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the imaging module 2400 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the imaging module 2400 may include Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the imaging module 2400 may include Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the imaging module 2400 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the imaging module 2400 can generate Figure 41 The field of view is 4100.

[0254] Imaging module 2400 includes multiple components and / or devices that can be integrated to operate in unison as a system to perform one or more tasks. In some implementations, imaging module 2400 performs imaging as part of analyzing a sample. For example, imaging module 2400 can detect fluorescence emitted from a sample of genetic material. Imaging module 2400 includes SIM assembly 2402, which is only partially visible in the current view. In some implementations, SIM assembly 2402 can generate spatially structured light for illuminating the sample material. For example, SIM assembly 2402 can include RIGS. Imaging module 2400 includes objective lens 2404. In some implementations, objective lens 2404 can transmit SIM light from SIM assembly 2402 and apply the SIM light to substrate 2406 holding the sample. 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 objective lens 2404 and substrate 2406.

[0255] Imaging module 2400 may include one or more portions of a housing. In some implementations, the housing may substantially enclose components of imaging module 2400. For example, housing 2408 may at least partially enclose SIM assembly 2402. Imaging module 2400 may lack one or more portions of the housing, which may allow some components to be visible. This may occur during assembly and / or during maintenance or repair, to name a few examples.

[0256] The imaging module 2400 may include an emission optics 2410. In some implementations, the emission optics 2410 includes a filter assembly 2412. The filter assembly 2412 may include at least one filter. For example, the filter assembly 2412 may include Figure 2 Filter 212 or Figure 5 In some implementations, the emission optics 2410 can include a tube lens 2414. For example, the tube lens 2414 can be one or more of the following: Figure 2 The tube lens 214 in Figure 5 The tube lens 508 or Figure 8A 802 in FIG. 804 . Tube lens 2414 can be assigned to the blue detector channel. In some implementations, emission optics 2410 can include tube lens 2416. Tube lens 2416 can be assigned to the green detector channel. For example, tube lens 2416 can be one or more of the following: Figure 2 The tube lens 214 in Figure 5 The tube lens 508 or Figure 8A802 in the tube lens. In some implementations, the emission optics 2410 includes a filter assembly 2418. For example, the filter assembly 2418 can include one or more of the following: Figure 2 216, reflective component 226, or structure 228. As another example, filter assembly 2418 can include one or more of the following: Figure 5 510, reflective component 516, or structure 518. As another example, filter assembly 2418 can include one or more of the following: Figure 8A The filter 804, reflective components 810A-810B or structure 812 in.

[0257] In some implementations, the emission optics 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 emission light and / or autofocus light. For example, the sensor assembly 2420 can include one or more of the following: Figure 1 Sensor 120 in; Figure 2 Sensor 220 in; Figure 5 Sensor 514 in FIG. 8 ; sensor 808 in FIG. 8 ; Figure 11 Sensor 1112 in; Figure 12 Sensor 1214 in; Figure 13 Sensor 1314 in; or Figure 14 1416 in the emission optics 2410. In some implementations, the emission optics 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 emission light and / or autofocus light. For example, the sensor assembly 2422 can include one or more of the following: Figure 1 Sensor 120 in; Figure 2 Sensor 220 in; Figure 5 Sensor 514 in FIG. 8 ; sensor 808 in FIG. 8 ; Figure 11 Sensor 1112 in; Figure 12 Sensor 1214 in; Figure 13 Sensor 1314 in; or Figure 14 Sensor 1416 in.

[0258] Figure 25 An embodiment of an optical system 2500 is illustrated. The optical system 2500 can include, or can be used with, one or more of the other examples described herein. In some implementations, the optical system 2500 can include Figure 42System 4200 in, or can be used with Figure 42 In some implementations, the optical system 2500 may include Figure 43 At least some components of the computing device 4300 in, or can be used with Figure 43 In some implementations, the optical system 2500 can be used with at least some components of the computing device 4300 in FIG. Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the optical system 2500 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 2500 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 2500 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the optical system 2500 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 2500 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 2500 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 2500 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 2500 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 2500 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the optical system 2500 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 2500 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 2500 can be used with the beam splitter 1700 in FIG. Figure 18 or Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 or Figures 19A-19B In some implementations, the optical system 2500 can be used with the imaging module 1800. Figure 20 In some implementations, the optical system 2500 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the optical system 2500 can be used with the imaging module 2100 in FIG. Figure 22 In some implementations, the optical system 2500 may include: Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the optical system 2500 may include: Figure 26 The optical system 2600 in the embodiment of the present invention may be Figure 26 In some implementations, the optical system 2500 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 2500 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 2500 can generate Figure 29 In some implementations, the optical system 2500 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 2500 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 2500 can be used with the autofocus light 3100 in FIG. Figures 32A-32C In some implementations, the optical system 2500 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the optical system 2500 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the optical system 2500 may include Figure 35RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 2500 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 2500 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 2500 may include: Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the optical system 2500 may include: Figure 39 The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 2500 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 2500 can generate Figure 41 The field of view is 4100.

[0259] The optical path 2500 may include an objective lens. In some implementations, the objective lens 2502 may be used to direct excitation light to a sample at a substrate and to receive emission light from the sample at the substrate. The optical system 2500 includes an optical filter 2504. In some implementations, the optical filter 2504 may be used to add one or more types of light to the transmitted light and / or to remove one or more types of light from the transmitted light. For example, the optical filter 2504 may allow (e.g., from Figure 24Excitation light (from SIM assembly 2402 in the optical system) is introduced and transmitted toward objective lens 2502. Optical system 2500 includes filter 2506. Filter 2506 can redirect light to another layer of optical system 2500. For example, filter 2506 can redirect emitted light in a horizontal direction. Optical system 2500 includes filter 2508. Filter 2508 can redirect light to another layer of optical system 2500. In some implementations, filter 2508 can redirect emitted light in a vertical direction. For example, filter 2508 can separate blue channel light from green channel light, or vice versa. Optical system 2500 includes filter 2510. Filter 2510 can redirect light in a horizontal direction. Optical system 2500 includes tube lens 2512. For example, tube lens 2512 can condition light for detection. Optical system 2500 includes sensor 2514. In some implementations, sensor 2514 can be used to receive emission light and / or autofocus light. Optical system 2500 includes filter 2516. Filter 2516 can redirect light in a horizontal direction. Optical system 2500 includes tube lens 2518. For example, tube lens 2518 can condition light for detection. Optical system 2500 includes sensor 2520. In some implementations, sensor 2520 can be used to receive emission light and / or autofocus light. In some implementations, optical system 2500 corresponds to Figure 24 System layout of the imaging module 2400.

[0260] Figure 26 An embodiment of an optical system 2600 is shown. The optical system 2600 can include, or can be used with, one or more of the other examples described herein. In some implementations, the optical system 2600 can include Figure 42 System 4200 in, or can be used with Figure 42 In some implementations, the optical system 2600 may include Figure 43 At least some components of the computing device 4300 in, or can be used with Figure 43 In some implementations, the optical system 2600 can be used with at least some components of the computing device 4300 in FIG. Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the optical system 2600 may include Figure 2 The optical system 200 in the embodiment of the present invention may be Figure 2 In some implementations, the optical system 2600 may include Figure 5 The optical system 500 in the embodiment of the present invention may be Figure 5 In some implementations, the optical system 2600 may include Figure 8A The optical system 800 in the embodiment of the present invention may be Figure 8A In some implementations, the optical system 2600 may include Figure 8B The optical system 820 in the embodiment of the present invention may be Figure 8B In some implementations, the optical system 2600 may include Figures 10A-10C The lateral displacement prism 1000 in the Figures 10A-10C In some implementations, the optical system 2600 may include Figure 11 The optical system 1100 in the embodiment of the present invention may be Figure 11 In some implementations, the optical system 2600 may include Figure 12 The optical system 1200 in the embodiment of the present invention may be Figure 12 In some implementations, the optical system 2600 may include Figure 13 The optical system 1300 in the embodiment of the present invention may be Figure 13 In some implementations, the optical system 2600 may include Figure 14 The optical system 1400 in the embodiment of the present invention may be Figure 14 In some implementations, the optical system 2600 may include Figures 16A-16B The lateral displacement prism 1600 in the Figures 16A-16B In some implementations, the optical system 2600 may include Figure 17 The beam splitter 1700 in the Figure 17 In some implementations, the optical system 2600 can be used with the beam splitter 1700 in FIG. Figure 18 or Figures 19A-19B The imaging module 1800 may be used in conjunction with, or may be included in Figure 18 or Figures 19A-19B In some implementations, the optical system 2600 can be used with the imaging module 1800. Figure 20 In some implementations, the optical system 2600 may include Figure 21 The imaging module 2100 in the embodiment of the present invention may be used in conjunction with Figure 21 In some implementations, the optical system 2600 can be used with the imaging module 2100 in FIG. Figure 22In some implementations, the optical system 2600 may include: Figure 24 The imaging module 2400 in the embodiment of the present invention may be used in conjunction with Figure 24 In some implementations, the optical system 2600 may include: Figure 25 The optical system 2500 in the embodiment of the present invention may be Figure 25 In some implementations, the optical system 2600 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the optical system 2600 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the optical system 2600 can generate Figure 29 In some implementations, the optical system 2600 can generate the autofocus light 2900. Figure 30 In some implementations, the optical system 2600 can generate the autofocus light 3000. Figures 31A-31C In some implementations, the optical system 2600 can be used with the autofocus light 3100. Figures 32A-32C In some implementations, the optical system 2600 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the optical system 2600 may include Figure 34 SIM assembly 3400 in, or can be used with Figure 34 In some implementations, the optical system 2600 may include Figure 35 RIGS 3500 in, or can be used with Figure 35 In some implementations, the optical system 2600 may include Figure 36 RIGS 3600 in, or can be used with Figure 36 In some implementations, the optical system 2600 may include Figure 37 The piezoelectric phase shifter 3700 in the Figure 37 In some implementations, the optical system 2600 may include: Figure 38 The piezoelectric phase shifter 3800 in the Figure 38 In some implementations, the optical system 2600 may include: Figure 39The projection lens 3900 in the embodiment of the present invention may be used in conjunction with Figure 39 In some implementations, the optical system 2600 may include Figure 40 The projection lens 4000 in the Figure 40 In some implementations, the optical system 2600 can generate Figure 41 The field of view is 4100.

[0261] The optical system 2600 may include an objective lens. In some implementations, the objective lens 2602 may be used to direct excitation light to a sample at the substrate and receive emission light from the sample at the substrate. The optical system 2600 includes an optical filter 2604. In some implementations, the optical filter 2604 may be used to add one or more types of light to the transmitted light and / or to remove one or more types of light from the transmitted light. For example, the optical filter 2604 may allow (e.g., from Figure 24 Excitation light (from SIM assembly 2402 in the optical system) is introduced and transmitted toward objective lens 2602. Optical system 2600 includes filter 2606. Filter 2606 can redirect light to another layer of optical system 2600. For example, filter 2606 can redirect emission light in a horizontal direction. Optical system 2600 includes filter 2608. Filter 2608 can redirect light to another layer of optical system 2600. In some implementations, filter 2608 can redirect emission light in a horizontal direction. For example, filter 2608 can separate blue channel light from green channel light, or vice versa. Optical system 2500 includes tube lens 2610. For example, tube lens 2610 can condition light for detection. Optical system 2600 includes sensor 2612. In some implementations, sensor 2612 can be used to receive emission light and / or autofocus light. Optical system 2600 includes tube lens 2614. For example, the tube lens 2614 can condition the light for detection. The optical system 2600 includes a filter 2616. The filter 2616 can redirect the light in a 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 the autofocus light. In some implementations, the optical system 2600 corresponds to Figure 18 and Figures 19A-19B System layout of the imaging module 1800.

[0262] The optical performance between two or more systems can be compared. The comparison can include one or more simulated measurements. The following table shows values ​​for three systems labeled A, B, and C. In some implementations, system A can correspond to the system Figure 18 and 19A- Imaging module 1800 in 19B, Figure 20 SIM component 2000 and Figure 26 In some implementations, system B may correspond to a reference system. For example, the reference system may include an objective lens that supports DFC. In some implementations, system C may correspond to a reference system that is involved in Figure 24 The imaging module 2400 and Figure 25 Implementation of the optical system 2500 in FIG.

[0263]

[0264]

[0265] Figure 27 An embodiment of a reflective component 2700 is shown. 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 Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the reflective component 2700 can be configured to Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the reflective component 2700 can be connected to the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the reflective component 2700 can be connected to the optical system 500. Figure 8A The optical system 800 may be used in conjunction with, or may be included in Figure 8A In some implementations, the reflective component 2700 can be connected to the optical system 800. Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the reflective component 2700 can be connected to the optical system 820. Figure 11 The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the reflective component 2700 can be connected to the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the reflective component 2700 can be connected to the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13In some implementations, the reflective component 2700 can be connected to the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the reflective component 2700 can be connected to the optical system 1400. Figure 18 and 19A -19B may be used with, or may be included in, the imaging module 1800 Figure 18 and 19A -19B in the imaging module 1800. In some implementations, the reflective component 2700 can be Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the reflective component 2700 may be connected to the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the reflective component 2700 may be connected to the imaging module 2200. Figure 24 The imaging module 2400 may be used in conjunction with, or may be included in Figure 24 In some implementations, the reflective component 2700 may be connected to the imaging module 2400. Figure 25 The optical system 2500 may be used in conjunction with, or may be included in Figure 25 In some implementations, the reflective component 2700 can be connected to the optical system 2500. Figure 26 The optical system 2600 may be used in conjunction with, or may be included in Figure 26 In some implementations, the reflective component 2700 may include Figure 28 The reflective component 2800 in the embodiment of the present invention may be Figure 28 In some implementations, the reflective component 2700 can generate Figure 29 In some implementations, the reflective component 2700 can generate an autofocus light 2900. Figure 30 In some implementations, the reflective component 2700 may generate an autofocus light 3000. Figures 31A-31C In some implementations, the reflective component 2700 can be configured to automatically focus light 3100 in the image. Figures 32A-32C In some implementations, the reflective member 2700 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the reflective member 2700 can be used with the laser engine heat sink 3300 in FIG. Figure 34 In some implementations, the reflective member 2700 may be used with the SIM assembly 3400 in FIG. Figure 35 In some implementations, the reflective component 2700 can be used with the RIGS 3500 in FIG. Figure 36 In some implementations, the reflective component 2700 can be used with the RIGS 3600 in FIG. Figure 37 In some implementations, the reflective component 2700 can be used with the piezoelectric phase shifter 3700 in FIG. Figure 38 As another example, the reflective component 2700 can be used with the piezoelectric phase shifter 3800 in FIG. Figure 39 As another example, the reflective member 2700 may be used with the projection lens 3900 in FIG. Figure 40 Used together with the projection lens 4000 in.

[0266] Reflective component 2700 includes filter 2702. Filter 2702 can be a dichroic filter. Filter 2702 can facilitate manipulation of one or more types of light, alone or in conjunction with at least one other component. In some implementations, filter 2702 can reflect emitted light and transmit autofocus light. For example, filter 2702 can have an anti-reflective coating that prevents reflection of autofocus light (i.e., promotes transmission) and does reflect emitted light. In other implementations, filter 2702 can be configured to prevent reflection of emitted light (i.e., promotes transmission) and reflect autofocus light.

[0267] Reflective component 2700 includes a tent prism 2704. Tent prism 2704 may include one or more reflective surfaces and may be positioned after filter 2702 in the direction of travel of the incoming light. The tent prism may be triangular in shape. In some implementations, tent prism 2704 reflects light transmitted through filter 2702, causing this reflection to be directed toward the sensor. For example, tent prism 2704 may reflect some (but not all) autofocus light that has reflected on the substrate. Tent prism 2704 may have optical characteristics based on the type of autofocus light used. In some implementations, tent prism 2704 is reflective in at least a portion of the near-infrared wavelength range (e.g., reflecting somewhere between approximately 750 nanometers and approximately 1400 nanometers). In some implementations, light 2706 that passes through filter 2702 is reflected by tent prism 2704. For example, light 2706 includes autofocus light reflected from the S1 surface and / or the S2 surface of the sample substrate. In some implementations, light 2708 passing through the filter 2702 is not reflected by the reflective component 2700 (e.g., absorbed by the reflective component 2700). The reflective component 2700 can include an absorbing material 2710 on which 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.

[0268] Figure 28 An embodiment of a reflective component 2800 is shown. The reflective component 2800 can be used with or included in one or more other embodiments described herein. In some implementations, the reflective component 2800 can be used with Figure 1 system 100 for use with, or may be included in Figure 1 In some implementations, the reflective component 2800 can be configured to Figure 2 The optical system 200 may be used in conjunction with, or may be included in Figure 2 In some implementations, the reflective component 2800 can be connected to the optical system 200. Figure 5 The optical system 500 may be used in conjunction with, or may be included in Figure 5 In some implementations, the reflective component 2800 can be connected to the optical system 500. Figure 8A The optical system 800 may be used in conjunction with, or may be included in Figure 8A In some implementations, the reflective component 2800 can be Figure 8B The optical system 820 may be used in conjunction with, or may be included in Figure 8B In some implementations, the reflective component 2800 can be connected to the optical system 820. Figure 11The optical system 1100 may be used in conjunction with, or may be included in Figure 11 In some implementations, the reflective component 2800 can be connected to the optical system 1100. Figure 12 The optical system 1200 may be used in conjunction with, or may be included in Figure 12 In some implementations, the reflective component 2800 can be connected to the optical system 1200. Figure 13 The optical system 1300 may be used in conjunction with, or may be included in Figure 13 In some implementations, the reflective component 2800 can be connected to the optical system 1300. Figure 14 The optical system 1400 may be used in conjunction with, or may be included in Figure 14 In some implementations, the reflective component 2800 can be connected to the optical system 1400. Figure 18 and 19A -19B may be used with, or may be included in, the imaging module 1800 Figure 18 and 19A -19B in the imaging module 1800. In some implementations, the reflective component 2800 can be Figure 21 The imaging module 2100 may be used in conjunction with, or may be included in Figure 21 In some implementations, the reflective component 2800 may be connected to the imaging module 2100. Figure 22 The imaging module 2200 may be used in conjunction with, or may be included in Figure 22 In some implementations, the reflective component 2800 may be connected to the imaging module 2200. Figure 24 The imaging module 2400 may be used in conjunction with, or may be included in Figure 24 In some implementations, the reflective component 2800 may be connected to the imaging module 2400. Figure 25 The optical system 2500 may be used in conjunction with, or may be included in Figure 25 In some implementations, the reflective component 2800 can be connected to the optical system 2200. Figure 26 The optical system 2600 may be used in conjunction with, or may be included in Figure 26 In some implementations, the reflective component 2800 may include Figure 27 The reflective component 2700 in the embodiment of the present invention may be Figure 27 In some implementations, the reflective component 2800 can generate Figure 29 In some implementations, the reflective component 2800 may generate an autofocus light 2900. Figure 30 In some implementations, the reflective component 2800 may generate an autofocus light 3000. Figures 31A-31C In some implementations, the reflective member 2800 may be configured to automatically focus light 3100 in the image. Figures 32A-32C In some implementations, the reflective member 2800 can be used with the laser engine heat sink 3200 in FIG. Figures 33A-33C In some implementations, the reflective member 2800 can be used with the laser engine heat sink 3300 in FIG. Figure 34 In some implementations, the reflective member 2800 may be used with the SIM assembly 3400 in FIG. Figure 35 In some implementations, the reflective component 2800 can be used with the RIGS 3500 in FIG. Figure 36 In some implementations, the reflective component 2800 can be used with the RIGS 3600 in FIG. Figure 37 In some implementations, the reflective component 2800 can be used with the piezoelectric phase shifter 3700 in FIG. Figure 38 As another example, the reflective component 2800 can be used with the piezoelectric phase shifter 3800 in FIG. Figure 39 As another example, the reflective component 2800 can be used with the projection lens 3900 in FIG. Figure 40 Used together with the projection lens 4000 in.

[0269] Reflective component 2800 includes a filter 2802. Filter 2802 can be a dichroic filter. Filter 2802 can facilitate manipulation of one or more types of light, alone or in conjunction with at least one other component. In some implementations, filter 2802 can reflect emitted light and transmit autofocus light. For example, filter 2802 can have an anti-reflective coating that prevents reflection of autofocus light (i.e., promotes transmission) while actually reflecting emitted light. In other implementations, filter 2802 can be configured to prevent reflection of emitted light (i.e., promotes transmission) and reflect autofocus light.

[0270] Reflective component 2800 includes a reflective surface 2804. Reflective surface 2804 may include one or more reflective surfaces and may be positioned after filter 2802 in the direction of travel of the incoming light. In some implementations, reflective surface 2804 reflects light transmitted through filter 2802, causing the light to be directed toward the sensor. For example, reflective surface 2804 may reflect some (but not all) autofocus light that has reflected on the substrate. Reflective surface 2804 may have optical characteristics based on the type of autofocus light used. In some implementations, reflective surface 2804 is reflective in at least a portion of the near-infrared wavelength range (e.g., reflecting somewhere between approximately 750 nanometers and approximately 1400 nanometers). In some implementations, light 2806 that passes through filter 2802 is reflected by reflective surface 2804. For example, light 2806 includes autofocus light reflected from the S1 surface and / or the S2 surface of the sample substrate. In some implementations, light 2808 passing through the filter 2802 is not reflected by the reflective component 2800 (e.g., absorbed by the reflective component 2800). The reflective component 2800 can include an absorbing material 2810 on 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.

[0271] The reflective component 2800 may include one or more instances of a reflective surface 2804 positioned after the filter 2802 in the direction of travel of the arriving light. In some implementations, two instances of the reflective surface 2804 are used (e.g., Figure 28 2806 . In other embodiments, a single instance of reflective surface 2804 is positioned after filter 2802 in the direction of travel of the arriving light. Reflective surface 2804 can then reflect one or more beams of light 2806 . For example, again briefly referring to Figures 10B-10C , the angles of surfaces 1008A-1008B (e.g., relative to surface 1006) can be adjusted so that the spots of two or more autofocus light are relatively closer to each other on the flow cell, thereby allowing reflection using a single instance of reflective surface 2804.

[0272] Figure 29 An example of autofocus light 2900 detected by a sensor is shown. 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 Figure 1 to detect the autofocus light 2900. In some implementations, the optical system 100 may be used Figure 2 The optical system 200 in the embodiment of the present invention detects the autofocus light 2900. In some implementations, the optical system 200 in the embodiment of the present invention can be used to detect the autofocus light 2900. Figure 5The optical system 500 in the embodiment of the present invention detects the autofocus light 2900. In some implementations, the optical system 500 in the embodiment of the present invention can be used to detect the autofocus light 2900. Figure 8A The optical system 800 in the embodiment of the present invention detects the autofocus light 2900. In some implementations, the optical system 800 in the embodiment of the present invention can be used to detect the autofocus light 2900. Figure 8B The optical system 820 in the embodiment of the present invention detects the autofocus light 2900. In some implementations, the optical system 820 in the embodiment of the present invention can be used to detect the autofocus light 2900. Figure 11 The optical system 1100 in the embodiment of the present invention detects the autofocus light 2900. In some implementations, the optical system 1100 in the embodiment of the present invention can be used to detect the autofocus light 2900. Figure 12 The optical system 1200 in the embodiment of the present invention detects the autofocus light 2900. In some implementations, the optical system 1200 in the embodiment of the present invention can be used to detect the autofocus light 2900. Figure 13 The optical system 1300 in the embodiment of the present invention detects the autofocus light 2900. In some implementations, the optical system 1300 in the embodiment of the present invention can be used to detect the autofocus light 2900. Figure 14 The optical system 1400 in the embodiment of the present invention is used to detect the autofocus light 2900. In some implementations, the optical system 1400 in the embodiment of the present invention can be used to detect the autofocus li...

Claims

1. An automatic focusing method, comprising: forming a left auto-focusing light and a right auto-focusing light that are offset from each other by a predetermined angle; directing the left auto-focusing light and the right auto-focusing light to the first surface of the substrate through an objective lens; as well as After reflecting from the first surface, at least a first portion of the left autofocus light and at least a first portion of the right autofocus light are directed to a sensor, wherein, at the sensor, a predetermined spacing between the first portion of the left autofocus light and the first portion of the right autofocus light indicates that the substrate is in focus of the objective lens.

2. The method according to claim 1, wherein: The substrate also includes a second surface, wherein the left auto-focusing light is reflected from the first surface to form a first left auto-focusing light, wherein the left auto-focusing light is reflected from the second surface to form a second left auto-focusing light, wherein, at the sensor, a first part of the left auto-focusing light includes the first left auto-focusing light and the second left auto-focusing light, wherein the right auto-focusing light is reflected from the first surface to form a first right auto-focusing light, wherein the right auto-focusing light is reflected from the second surface to form a second right auto-focusing light, wherein, at the sensor, a first part of the right auto-focusing light includes the first right auto-focusing light and the second right auto-focusing light.

3. The method according to claim 2, wherein: At the sensor, a first predetermined interval between the first left auto focus light and the first right auto focus light indicates that the first surface of the substrate is in focus of the objective lens.

4. The method according to claim 3, wherein: At the sensor, a second predetermined interval between the second left auto focus light and the second right auto focus light indicates that the second surface of the substrate is in focus of the objective lens.

5. The method according to claim 1, wherein: Directing the first portion of the left auto-focus light and the first portion of the right auto-focus light to the sensor includes directing the first portion of the left auto-focus light and the first portion of the right auto-focus light to the sensor using a first reflective surface.

6. The method of claim 5, further comprising directing emission light toward the sensor using the objective lens and a second reflective surface, the emission light originating from the sample at the substrate.

7. The method of claim 6, further comprising directing the first portion of the left auto-focus light and the first portion of the right auto-focus light to the second reflective surface, the second reflective surface being transparent to the first portion of the left auto-focus light and the first portion of the right auto-focus light, wherein The first reflective surface is positioned behind the second reflective surface relative to a direction of travel of the first portion of the left auto focus light and the first portion of the right auto focus light.

8. The method according to claim 7, wherein: The substrate also includes a second surface, wherein the second portion of the left auto-focus light is formed when the left auto-focus light is reflected from the second surface, and wherein the second portion of the right auto-focus light is formed when the right auto-focus light is reflected from the second surface, and the method also includes directing the second portion of the left auto-focus light and the second portion of the right auto-focus light to the second reflecting surface, and the second reflecting surface is also transparent to the second portion of the left auto-focus light and the second portion of the right auto-focus light, wherein the first reflecting surface is transparent to the second portion of the left auto-focus light and the second portion of the right auto-focus light to prevent the second portion of the left auto-focus light and the second portion of the right auto-focus light from reaching the sensor.

9. The method according to claim 6, wherein: The first reflective surface is positioned on a first reflective component, wherein the second reflective surface is positioned on a second reflective component, and wherein the first reflective component is separate from the second reflective component, the method further comprising orienting the first reflective component independently of an orientation of the second reflective component.

10. The method according to claim 9, wherein: The first reflective component is oriented so as to steer the first portion of the left autofocus light and the first portion of the right autofocus light onto the sensor independently of positioning of the emitted light onto the sensor.

11. The method of any one of claims 1 to 10, 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.

12. An automatic focusing system, comprising: A beam splitter, the beam splitter being used to form a left auto-focusing light and a right auto-focusing light that are offset from each other by a predetermined angle; an objective lens, the objective lens being used to transmit the left auto-focusing light and the right auto-focusing light to the first surface of the substrate; and A sensor for receiving at least the first portion of the left auto-focus light and at least the first portion of the right auto-focus light after they are reflected from the first surface, wherein at the sensor, a predetermined interval between the first portion of the left auto-focus light and the first portion of the right auto-focus light indicates that the substrate is in focus of the objective lens.

13. The system according to claim 12, wherein: The beam splitter is part of a lateral displacement prism.

14. The system according to claim 13, wherein: The lateral displacement prism includes a plurality of exit surfaces having a non-zero angle relative to each other.

15. The system of claim 13, wherein: The lateral displacement prism comprises: a first surface; a second surface, wherein the second surface of the lateral displacement prism is parallel to the first surface of the lateral displacement prism; third surface; fourth surface; 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 extends between the third surface and the boundaries of the fourth surface and the fifth surface.

16. The system of claim 15, wherein: The first surface of the lateral displacement prism has a boundary with the third surface, the fourth surface and the fifth surface; and The second surface of the lateral displacement prism has a boundary with the third surface, the fourth surface and the fifth surface.

17. A system according to any one of claims 15 to 16, wherein: The third surface is an incident surface, wherein the fourth surface is an exit surface of the left auto focus light, and wherein the fifth surface is an exit surface of the right auto focus light.

18. The system of claim 13, wherein: The lateral displacement prism comprises: a first prism having a first wedge-shaped cross-section including a first side forming a non-zero angle with respect to a first exit side; a second prism having a second wedge-shaped cross-section including a second side forming a non-zero angle with respect to a second exit side; and a third prism having a parallelogram cross-section including a third side parallel to the fourth side and a fifth side parallel to the sixth side, the third side of the parallelogram cross-section being a portion of an incident surface of the laterally displaced prism; Wherein, each of the first side of the first prism and the second side of the second prism faces the fourth side of the third prism.

19. The system of claim 12, wherein: The beam splitter comprises: a first reflecting surface on which the initial autofocus light is incident; a partial reflective layer on which the initial auto-focusing light is incident after being reflected at the first reflective surface, the partial reflective layer forming the left auto-focusing light and the right auto-focusing light; and A second reflective surface on which one of the left auto focus light or the right auto focus light is incident after being formed at the partially reflective layer.

20. The system of claim 12, further comprising 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.

21. The system of claim 20, further comprising a second reflective surface for directing emission light toward the sensor, the emission light originating from the sample at the substrate and transmitted through the objective lens.

22. The system of claim 21, wherein: The substrate also includes a second surface, wherein the second portion of the left auto-focus light is formed when the left auto-focus light is reflected from the second surface of the substrate, and wherein the second portion of the right auto-focus light is formed when the right auto-focus light is reflected from the second surface of the substrate, and the system also includes a structure that prevents the second portion of the left auto-focus light and the second portion of the right auto-focus light from reaching the sensor.

23. The system of claim 22, wherein: The first reflecting surface is positioned behind the second reflecting surface relative to the traveling directions of the first part of the left auto-focusing light, the second part of the left auto-focusing light, the first part of the right auto-focusing light, and the second part of the right auto-focusing light, wherein the second reflecting surface is transparent to the first part of the left auto-focusing light, the second part of the left auto-focusing light, the first part of the right auto-focusing light, and the second part of the right auto-focusing light.

24. The system of claim 23, wherein: The first reflective surface is positioned on a first reflective component, wherein the second reflective surface is positioned on a second reflective component, and wherein the first reflective component is separated from the second reflective component.

25. The system of claim 23, wherein: The second reflecting surface is positioned on the front surface of the second reflecting component relative to the traveling directions of the first part of the left auto-focusing light, the second part of the left auto-focusing light, the first part of the right auto-focusing light and the second part of the right auto-focusing light, wherein the first reflecting surface covers the first part of the rear surface of the second reflecting component relative to the traveling directions of the first part of the left auto-focusing light, the second part of the left auto-focusing light, the first part of the right auto-focusing light and the second part of the right auto-focusing light, and wherein the structure covers the second part of the rear surface of the second reflecting component.

26. The system of any one of claims 12 to 25, configured for analyzing nucleic acid material at the substrate.

27. An automatic focusing component, comprising: A prism, the prism comprising: a first surface; a second surface, the second surface being parallel to the first surface; third surface; fourth surface; 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 boundaries of the fourth and fifth surfaces; and A light source is used to direct light to the prism, and the prism forms a first auto-focusing light and a second auto-focusing light from the light, and the first auto-focusing light and the second auto-focusing light are offset from each other by a predetermined angle.

28. The autofocus assembly of claim 27, wherein: The fourth surface and the fifth surface form an exit surface having a non-zero angle with respect to each other.

29. The autofocus assembly of claim 27, wherein: 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.

30. An autofocus assembly according to any one of claims 27 to 29, wherein: The third surface is an incident surface.

31. The autofocus assembly of claim 27, wherein: The prism comprises: a first prism, the first prism having a first wedge-shaped cross-section, the first prism forming the fourth surface, the first wedge-shaped cross-section including a first side forming a non-zero angle with respect to the fourth surface; a second prism, the second prism having a second wedge-shaped cross-section, the second prism forming the fifth surface, the second wedge-shaped cross-section including a second side forming a non-zero angle with respect to the fifth surface; and a third prism having a parallelogram cross-section including a third side parallel to the fourth side and a fifth side parallel to the sixth side, the third side defining the third surface; Wherein, each of the first side of the first prism and the second side of the second prism faces the fourth side of the third prism.

32. A structured illumination microscope assembly comprising: a light source, the light source providing a first light; a deformable prism configured to provide a second light by transforming the first light; First grating; The second grating; as well as A rotatable mirror is configured to assume a first position for redirecting the second light toward the first grating and a second position for receiving the second light from the second grating.

Images