Method, carrier assembly and system for imaging sample for biological or chemical analysis

Abstract

The invention relates to a method, carrier assembly and system for imaging a sample for biological or chemical analysis. The method includes positioning a first carrier assembly on a system table. The first carrier assembly includes a support frame having an inner frame edge defining a window of the support frame. The first carrier assembly includes a first substrate located within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting an optical signal from a sample of a first substrate. The method further includes replacing the first carrier assembly on the system table with a second carrier assembly on the system table. The second carrier assembly includes a support frame and a tipping plate held by the support frame. The second carrier assembly has a second substrate held by the tipping plate, the second substrate having a sample thereon. The method further includes detecting an optical signal from the sample of the second substrate.

Description

[0001] This application is a divisional application of an application with application date of March 22, 2016, application number 202011181966.1, and invention name “Methods, carrier components and systems for imaging samples for biological or chemical analysis”.

[0002] The application with the application date of March 22, 2016, the application number of 202011181966.1, and the invention name of “Methods, carrier components and systems for imaging samples for biological or chemical analysis” is a divisional application of the application with the application date of March 22, 2016, the application number of 201680024922.3, and the invention name of “Methods, carrier components and systems for imaging samples for biological or chemical analysis”. CROSS-REFERENCE TO RELATED APPLICATIONS

[0003] This application claims the benefit of U.S. Provisional Patent Application No. 62 / 137,600, filed on March 24, 2015, which is incorporated herein by reference in its entirety. Background of the Invention

[0004] Embodiments of the present invention relate generally to biological or chemical analysis, and more particularly to methods, carrier assemblies, and systems for detecting optical signals from a sample for use in biological or chemical analysis.

[0005] Various assay protocols for biological or chemical research involve performing a large number of controlled reactions. In some cases, the controlled reactions are performed on a support surface. The specified reactions can then be observed and analyzed to help identify the properties or characteristics of the chemical substances involved in the specified reactions. For example, in some protocols, a chemical component including an identifiable label (e.g., a fluorescent label) can be selectively bound to another chemical component under controlled conditions. These chemical reactions can be observed by exciting the label with radiation and detecting the light emission from the label.

[0006] Examples of these schemes include DNA sequencing and multiplex array-based assays. In a sequencing by synthesis (SBS) scheme, clusters of clonal amplicons are formed on the surface of a channel of a flow cell by bridge PCR. After generating clusters of clonal amplicons, the amplicons can be "linearized" to make single-stranded DNA (sstDNA). A predetermined sequence of reagents can flow into the flow cell to complete a sequencing cycle. Each sequencing cycle extends the sstDNA by a single nucleotide (e.g., A, T, G, C) with a unique fluorescent label. Each nucleotide has a reversible terminator that allows only a single base to be incorporated in a cycle. After the nucleotides are added to the sstDNA cluster, images in four channels are acquired (i.e., there is one channel for each fluorescent label). After imaging, the fluorescent label and terminator are chemically separated from the sstDNA, and the growing DNA chain is prepared for another cycle. Several cycles of reagent delivery and optical detection can be repeated to determine the sequence of the nucleic acid of the clonal amplicons.

[0007] In some assays based on multiple arrays, groups of different probe molecules are fixed to the substrate surface. Probes can be distinguished based on the address of each probe on the substrate surface. For example, each group of probe molecules can have a known position (e.g., coordinates on a grid) on the substrate surface. The probe molecules are exposed to the target analyte under controlled conditions so that due to the specific interaction between the target analyte and the probe, detectable changes occur at one or more addresses. For example, the fluorescently labeled target analyte bound to a specific probe can be identified based on the aggregation of the fluorescent marker to the address of the probe. The address on the array can be determined by the assay system to identify which groups react with the analyte. By knowing the chemical structure of the probe molecules that react with the analyte, the nature of the analyte can be determined. In other multiple assays, the specified reaction is carried out on the surface of individually identifiable particles that can be scanned and analyzed.

[0008] Different assay protocols (such as those described above) may include specific features or involve specific steps that do not occur in other assay protocols. For example, different assay protocols may use different types of reagents or reagents with unique modifications, labels with different emission spectra, different types of optical substrates for supporting samples (e.g., flow cells, open-face substrates, microarrays, wells, microparticles), different light sources with different excitation spectra, different optical components (e.g., objective lenses), thermal conditions, and software. In addition, because detection occurs at a resolution of a few microns or less, the equipment typically operates at a high level of precision. As a result, the platforms that exist today are typically directed to performing only one type of assay protocol.

[0009] Therefore, a need exists for an assay system and corresponding components that are capable of performing more than one type of assay protocol. Brief description of the invention

[0010] This disclosure provides the following: 1. A method comprising: positioning a first carrier assembly on a system stage, the first carrier assembly comprising a support frame having an inner frame edge defining a window of the support frame, the first carrier assembly comprising a removable first substrate positioned within the window and surrounded by the inner frame edge, the first substrate having a sample thereon positioned within an imaging region of the optical system; detecting an optical signal from the sample on the first substrate using the optical system according to a first imaging scheme; replacing the first carrier assembly with a second carrier assembly on the system stage, the second carrier assembly having a removable second substrate having a sample thereon located within the imaging region of the optical system, wherein the first substrate and the second substrate are different types of substrates; and The optical system is used to detect an optical signal from the sample of the second substrate according to a second imaging scheme different from the first imaging scheme.

[0011] 2. The method of 1, wherein each of the first carrier assembly and the second carrier assembly includes a hole extending into the corresponding carrier assembly, the hole receiving a corresponding datum of the system stage when the corresponding carrier assembly is located on the system stage, wherein the second carrier assembly includes an adapter plate that holds the second substrate, the datum engaging the first substrate when the first carrier assembly is located on the system stage and engaging the adapter plate when the second carrier assembly is located on the system stage.

[0012] 3. The method of 1, wherein the optical system comprises an objective lens, wherein detecting the light signal from the first substrate comprises moving the objective lens and the first substrate relative to each other, wherein detecting the light signal from the second substrate comprises moving the objective lens and the second substrate relative to each other, wherein the optical system detects the light signal from the first substrate along a first imaging area, and the optical system detects the light signal from the second substrate along a second imaging area, the first imaging area and the second imaging area are different in size, and wherein the first imaging scheme and the second imaging scheme comprise automatically moving the objective lens along different paths relative to the first substrate and the second substrate, respectively.

[0013] 4. The method of 1, wherein the second carrier assembly includes a holding mechanism, the holding mechanism includes a movable reference block, the method further comprising pressing the reference block to position the second substrate on the second carrier assembly, and releasing the reference block, the reference block engaging the second substrate to hold the second substrate on the second carrier assembly, wherein the reference block does not hold the first substrate relative to the first carrier assembly.

[0014] 5. The method of 1, wherein the first substrate and the second substrate have different thicknesses and respectively have a first substrate surface and a second substrate surface, wherein detecting the optical signal from the first substrate and the second substrate comprises detecting the optical signal from the first substrate surface and the second substrate surface, respectively, and the first substrate surface and the second substrate surface are in a common plane or offset by 100 microns or less.

[0015] 6. The method of 1, wherein the second substrate comprises a microarray of features, and detecting the optical signal from the second substrate comprises capturing a series of images of overlapping portions of the microarray of features, each of the features having a designated probe molecule immobilized thereon, the microarray having a target analyte attached thereto; The method further comprises: analyzing light intensities associated with corresponding features in the image and determining a data representation of the image, the data representation having a corresponding subarray of data features based on corresponding features of the microarray, each of the data features having a corresponding position relative to the other data features and a signal value based on one or more of the light intensities; and combining data representations of adjacent images based on a comparison of signal values ​​of data features of the data representations of adjacent images to generate a data representation of the microarray; The data representation of the microarray is analyzed to determine a property or characteristic of the sample.

[0016] 7. The method of claim 1, wherein the first substrate is a flow cell.

[0017] 8. The method of claim 7, wherein the flow cell comprises a flow channel extending between an inlet and an outlet of the flow cell, the inlet and outlet being fluidly coupled to a manifold for flowing liquid through the flow channel.

[0018] 9. The method of claim 7, wherein the flow cell comprises a plurality of flow channels extending between respective inlets and outlets of the flow cell, the inlets and outlets being fluidly coupled to a manifold for flowing liquid through the flow channels.

[0019] 10. The method of claim 7, further comprising repeatedly flowing reagents through the flow cell to perform a sequencing by synthesis (SBS) protocol.

[0020] 11. The method of claim 1, wherein the first imaging scheme and the second imaging scheme include moving the objective lens and / or the system stage relative to each other along different paths.

[0021] 12. The method of claim 1, wherein the second substrate is an open-face substrate having a biological or chemical substance immobilized to an outer surface of the open-face substrate.

[0022] 13. The method of 12, wherein the open-face substrate comprises a microarray along the outer surface.

[0023] 14. The method of 13, wherein the microarray comprises a plurality of feature strips extending parallel to each other, each of the feature strips having an array of reaction sites.

[0024] 15. The method of 1, wherein each of the first carrier assembly and the second carrier assembly includes an aperture extending into the corresponding carrier assembly, the aperture receiving a corresponding fiducial when the corresponding carrier assembly is positioned on the system stage.

[0025] 16. The method of 15, wherein the first substrate engages the datum and the second substrate does not engage the datum.

[0026] 17. The method of 1, wherein the first substrate is larger than the second substrate.

[0027] 18. The method of 1, wherein the optical system comprises an objective lens, wherein detecting the optical signal from the first substrate comprises moving the objective lens and the first substrate relative to each other, and wherein detecting the optical signal from the second substrate comprises moving the objective lens and the second substrate relative to each other.

[0028] 19. The method of 13, wherein the optical system detects the light signal from the first substrate along a first imaging area, and the optical system detects the light signal from the second substrate along a second imaging area, and the first imaging area and the second imaging area are different in size.

[0029] 20. The method of 18, wherein the first imaging scheme and the second imaging scheme include automatically moving the objective lens along different paths relative to the first substrate and the second substrate, respectively.

[0030] 21. The method of claim 1, wherein the first carrier assembly and the second carrier assembly engage the system stage in substantially the same manner.

[0031] 22. A method comprising: positioning a first carrier assembly on a system stage, the first carrier assembly comprising a support frame having an inner frame edge defining a window of the support frame, the first carrier assembly comprising a first substrate positioned within the window and surrounded by the inner frame edge, the first substrate having a sample thereon positioned within an imaging region of the optical system; detecting an optical signal from the sample on the first substrate using the optical system; replacing the first carrier assembly with a second carrier assembly on the system stage, the second carrier assembly comprising a support frame and an adapter plate coupled to the support frame, the second carrier assembly having a second substrate held by the adapter plate, the second substrate having a sample thereon, the sample of the second substrate being located within the imaging region of the optical system; and An optical signal from the sample of the second substrate is detected using the optical system.

[0032] 23. The method of 22, wherein each of the first carrier assembly and the second carrier assembly includes a hole extending into the corresponding carrier assembly, the hole receiving a corresponding datum of the system stage when the corresponding carrier assembly is positioned on the system stage, the datum engaging the first substrate when the first carrier assembly is positioned on the system stage and engaging the adapter plate when the second carrier assembly is positioned on the system stage.

[0033] 24. The method of 22, wherein the optical system comprises an objective lens, wherein detecting the light signal from the first substrate comprises moving the objective lens and the first substrate relative to each other, wherein detecting the light signal from the second substrate comprises moving the objective lens and the second substrate relative to each other, wherein the optical system detects the light signal from the first substrate along a first imaging area, and the optical system detects the light signal from the second substrate along a second imaging area, the first imaging area and the second imaging area are different in size, and wherein the first imaging scheme and the second imaging scheme comprise automatically moving the objective lens relative to the first substrate and the second substrate, respectively, along different paths.

[0034] 25. The method of 22, wherein the second carrier assembly includes a retaining mechanism, the retaining mechanism includes a movable reference block, the method further comprising depressing the reference block to position the second substrate on the second carrier assembly, and releasing the reference block, the reference block engaging the second substrate to retain the second substrate on the second carrier assembly, wherein the reference block does not retain the first substrate relative to the first carrier assembly.

[0035] 26. The method of 22, wherein the first substrate and the second substrate have different thicknesses and have a first substrate surface and a second substrate surface, respectively, wherein detecting the optical signal from the first substrate and the second substrate comprises detecting the optical signal from the first substrate surface and the second substrate surface, respectively, and the first substrate surface and the second substrate surface are in a common plane or offset by 100 microns or less.

[0036] 27. The method of 26, wherein the second substrate comprises a microarray of features, and detecting the optical signal from the second substrate comprises capturing a series of images of overlapping portions of the microarray of features, each of the features having a designated probe molecule immobilized thereon, the microarray having a target analyte attached thereto; The method further comprises: analyzing light intensities associated with corresponding features in the image and determining a data representation of the image, the data representation having a corresponding subarray of data features based on corresponding features of the microarray, each of the data features having a corresponding position relative to the other data features and a signal value based on one or more of the light intensities; and combining the data representations of adjacent images based on a comparison of the signal values ​​of the data features of the data representations of adjacent images to generate a data representation of the microarray; The data representation of the microarray is analyzed to determine a property or characteristic of the sample.

[0037] 28. The method of 22, wherein the first substrate is a flow cell.

[0038] 29. The method of 28, wherein the flow cell comprises a flow channel extending between an inlet and an outlet of the flow cell, the inlet and outlet being fluidly coupled to a manifold for flowing liquid through the flow channel.

[0039] 30. The method of 28, wherein the flow cell comprises a plurality of flow channels extending between respective inlets and outlets of the flow cell, the inlets and outlets being fluidly coupled to a manifold for flowing liquid through the flow channels.

[0040] 31. The method of claim 30, wherein the flow channels extend parallel to each other through the imaging region.

[0041] 32. The method of claim 28, further comprising repeatedly flowing reagents through the flow cell to perform a sequencing by synthesis (SBS) protocol.

[0042] 33. The method of 22, wherein the second substrate is an open-face substrate having a biological or chemical substance fixed to an outer surface of the open-face substrate.

[0043] 34. The method of 33, wherein the open-face substrate comprises a microarray along the outer surface.

[0044] 35. The method of 22, wherein the first substrate is larger than the second substrate.

[0045] 36. The method of 22, wherein the support frame of the first carrier assembly and the support frame of the second carrier assembly are the same support frame.

[0046] 37. The method of 22, wherein the support frame of the first carrier assembly and the support frame of the second carrier assembly are different support frames having respective edges defining a same perimeter.

[0047] 38. The method of 22, wherein the first base is slidable within the window along an XY plane extending parallel to an edge of the inner frame, and wherein the adapter plate is slidable within the window along the XY plane.

[0048] 39. The method of claim 22, wherein said system stage includes a plurality of fiducials, said fiducials engaging said first substrate and engaging said adapter plate during said positioning and replacing operations.

[0049] 40. The method of 22, wherein the adapter plate includes an inner panel edge defining a receiving portion, the second substrate being disposed within the receiving portion and engaged with the inner panel edge.

[0050] 41. The method of 22, wherein the optical system comprises an objective lens, wherein detecting the optical signal from the first substrate comprises moving the objective lens and the first substrate relative to each other, and wherein detecting the optical signal from the second substrate comprises moving the objective lens and the second substrate relative to each other.

[0051] 42. The method of 41, wherein the optical system detects the light signal from the first substrate along a first imaging area, and the optical system detects the light signal from the second substrate along a second imaging area, and the first imaging area and the second imaging area are different in size.

[0052] 43. The method of 41, wherein the sample of the first substrate and the sample of the second substrate are located in different sections of the window.

[0053] 44. The method of 22, wherein replacing the first carrier assembly with the second carrier assembly comprises removing the first substrate from the support frame of the first carrier assembly and positioning the second substrate within the adapter plate.

[0054] 45. The method of claim 40, further comprising a retaining mechanism, the retaining mechanism comprising a movable reference block disposed within a portion of the receiving portion, the method further comprising pressing the reference block to position the second substrate within the receiving portion, and releasing the reference block, the reference block engaging the second substrate to retain the second substrate in the receiving portion.

[0055] 46. ​​The method of 45, wherein the retaining mechanism comprises a biasing spring, the biasing spring providing a spring force for retaining the second substrate in the receiving portion.

[0056] 47. A carrier assembly comprising: a support frame having an inner frame edge defining a window of the support frame; an adapter plate coupled to the support frame and positioned within the window, the adapter plate comprising a plate body having an inner plate edge defining a receiving portion for receiving a substrate having a size smaller than the window, the inner plate edge further defining a retaining recess open to the receiving portion; and A movable reference block is located in the retaining recess, the reference block is movable between a retracted position and an engaged position, and the reference block is configured to engage the substrate and press the substrate against the opposing surface of the adapter plate to retain the substrate in the receiving portion when the reference block is in the engaged position.

[0057] 48. The carrier assembly of 47, wherein the adapter plate extends parallel to the XY plane and faces in a direction along the Z axis, and the datum block provides a retention force oriented along the XY plane.

[0058] 49. The carrier assembly of 47, wherein the receiving portion is at least one of: coincident with a receiving plane intersecting the edge of the inner frame or located below the receiving plane.

[0059] 50. The carrier assembly of 47, wherein the inner frame edge defines an aperture opening into the window, the aperture being configured to receive a datum when the carrier assembly is positioned on a system stage.

[0060] 51. The carrier assembly of 50, wherein the support frame comprises a first body side and a second body side, the first body side being configured to face the objective lens during an imaging operation, and the second body side being configured to be located on a base surface during the imaging operation, the hole of the support frame opening toward the second body side and extending from the second body side toward the first body side.

[0061] 52. The carrier assembly of claim 47, wherein the adapter plate is slidable within the window along an XY plane.

[0062] 53. The carrier assembly of claim 47, wherein the adapter plate includes an opening that opens into the receiving portion.

[0063] 54. The carrier assembly of 47, wherein the receiving portion is sized and shaped to receive a planar chip or a slider.

[0064] 55. A carrier assembly comprising: a support frame having an inner frame edge defining a window of the support frame; and an adapter plate coupled to the support frame and positioned within the window, the inner frame edge defining a substrate receiving recess positioned above the adapter plate, the substrate receiving recess being configured to receive a first planar substrate, the adapter plate comprising a plate body having an inner plate edge defining a receiving portion for receiving a second planar substrate having a smaller size than the first planar substrate, the receiving portion at least partially existing below the substrate receiving recess.

[0065] 56. The carrier assembly of 55, further comprising a datum block movable between a retracted position and an engaged position, the datum block being configured to engage the substrate and press the substrate against an opposing surface of the adapter plate to retain the substrate within the receiving portion when the datum block is in the engaged position.

[0066] 57. The carrier assembly of 56, wherein the adapter plate extends parallel to the XY plane and faces in a direction along the Z axis, and the datum block provides a retention force oriented along the XY plane.

[0067] 58. The carrier assembly of 55, wherein the inner frame edge defines an aperture opening into the window, the aperture being configured to receive a datum when the carrier assembly is positioned on a system stage.

[0068] 59. The carrier assembly of 58, wherein the support frame comprises a first body side and a second body side, the first body side being configured to face the objective lens during an imaging operation, and the second body side being configured to lie on a base surface during the imaging operation, the hole of the support frame opening toward the second body side and extending from the second body side toward the first body side.

[0069] 60. The carrier assembly of 55, wherein the adapter plate is slidable within the window along an XY plane.

[0070] 61. The carrier assembly of 55, wherein the receiving portion is sized and shaped to receive a planar chip or a slider.

[0071] 62. The carrier assembly of 55, wherein the adapter plate includes a fluid opening providing access to the substrate receiving recess.

[0072] 63. The carrier assembly of 62, wherein at least one of the fluid openings is located at a first end of the adapter plate and at least one of the fluid openings is located at an opposing second end of the adapter plate.

[0073] 64. A measurement system comprising: a system stage having a base surface extending parallel to an XY plane and a plurality of fiducials coupled to the base surface, the fiducials including protrusions extending away from the base surface along a Z axis perpendicular to the XY plane; an optical system comprising an objective lens configured to move relative to the system stage along the XY plane; a fluid control system configured to control the flow of one or more fluids through the flow cell when the flow cell is mounted on the system stage; and a system controller configured to control the fluid control system and the optical system to perform different first and second assay protocols with a first sample and a second sample, respectively, wherein during the first assay protocol, the system controller commands the fluid control system to direct one or more fluids through the flow cell on the system stage and commands the optical system to detect an optical signal from the first sample on the flow cell, and wherein during the second assay protocol, the system controller commands the optical system to detect an optical signal from the second sample on an open-face substrate on the system stage without flowing fluid through the second sample.

[0074] 65. The assay system of 64, wherein the first assay protocol is a sequencing by synthesis (SBS) protocol and the second assay protocol comprises imaging a microarray.

[0075] 66. The assay system of 64, further comprising a carrier sensor configured to detect a type of carrier assembly mounted to the system stage, wherein the assay system is configured to provide a notification when the carrier assembly does not match the selected assay protocol.

[0076] 67. The assay system of 64, further comprising a carrier assembly having a support frame defining a window, the support frame configured to couple to an adapter plate extending across and covering the window.

[0077] 68. A method comprising: capturing a series of images of overlapping portions of a microarray of features, each of the features having a designated probe molecule immobilized thereto, the microarray having a target analyte attached thereto; analyzing light intensities associated with corresponding features in the image and determining a data representation of the image having a corresponding subarray of data features based on the corresponding features of the microarray, each of the data features having a corresponding position relative to the other data features and a signal value based on one or more of the light intensities; and combining data representations of adjacent images based on a comparison of signal values ​​of data features of the data representations of adjacent images to generate a data representation of the microarray; The data representation of the microarray is analyzed to determine a property or characteristic of the sample.

[0078] 69. The method of 68, wherein each of the data representations of the image includes a plurality of columns of the data features, and wherein the comparing includes comparing a signal value of a column of one data representation with a signal value of a column of an adjacent data representation, wherein the method includes calculating a correlation value based on the comparing, and if the correlation value satisfies a specified threshold, then the column of the one data representation and the column of the adjacent data representation are designated as overlapping columns having the same features.

[0079] 70. The method of 68, wherein each of the data representations of the image includes a plurality of columns of the data features, and wherein the comparing includes comparing signal values ​​of the plurality of columns of one data representation with signal values ​​of the plurality of columns of an adjacent data representation, wherein the method includes calculating a correlation value based on the comparing, and if the correlation value satisfies a specified threshold, then the plurality of columns of the one data representation and the plurality of columns of the adjacent data representation are designated as overlapping columns having the same features.

[0080] 71. The method of claim 68, wherein the combining operation is repeated for each pair of adjacent images to generate a data representation of the microarray.

[0081] 72. The method of 68, wherein analyzing the data representation of the microarray is performed after comparing the number of features within the data representation of the microarray to an expected number of features.

[0082] 73. The method of claim 68, wherein the features of the microarray have known sizes and shapes and a known order or arrangement relative to each other within the microarray.

[0083] 74. The method of claim 68, wherein each of the features corresponds to a plurality of pixels in the corresponding image.

[0084] In an embodiment, a method is provided, which includes positioning a first carrier assembly on a system stage. The first carrier assembly includes a support frame having an inner frame edge defining a window of the support frame. The first carrier assembly includes a removable first substrate located within the window and surrounded by the inner frame edge. The first substrate has a sample located within an imaging zone of an optical system thereon. The method also includes detecting an optical signal from the sample of the first substrate using the optical system according to a first imaging scheme. The method also includes replacing the first carrier assembly with a second carrier assembly on the system stage. The second carrier assembly has a removable second substrate. The second substrate has a sample located within an imaging zone of the optical system thereon, wherein the first and second substrates are different types of substrates. The method also includes detecting an optical signal from the sample of the second substrate using the optical system according to a second imaging scheme different from the first imaging scheme. Optionally, the first imaging scheme and / or the second imaging scheme are automated.

[0085] According to an embodiment, a method is provided, which includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge defining a window of the support frame. The first carrier assembly includes a first substrate located within the window and surrounded by the inner frame edge. The first substrate has a sample thereon that is located within an imaging area of ​​an optical system. The method includes detecting an optical signal from the sample of the first substrate using an optical system. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes a support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate, the second substrate having a sample thereon. The sample of the second substrate is located within the imaging area of ​​the optical system. The method also includes detecting an optical signal from the sample of the second substrate using an optical system.

[0086] According to an embodiment, a carrier assembly is provided, which includes a support frame having an inner frame edge defining a window of the support frame and an adapter plate coupled to the support frame and located within the window. The adapter plate includes a plate body having an inner plate edge that defines a receiving portion (pocket) for receiving a substrate having a size smaller than the window. The inner plate edge also defines a retaining recess open to the receiving portion. The carrier assembly also includes a movable reference block located in the retaining recess. The reference block is movable between a retracted position and an engagement position. The reference block is configured to engage the substrate when the reference block is in the engagement position, and to press the substrate against the opposing surface of the adapter plate to retain the substrate in the receiving portion.

[0087] According to an embodiment, a carrier assembly is provided, which includes a support frame having an inner frame edge defining a window of the support frame. The carrier assembly also includes an adapter plate coupled to the support frame and located within the window. The inner frame edge defines a substrate receiving recess located above the adapter plate. The substrate receiving recess is configured to receive a first planar substrate. The adapter plate includes a plate body having an inner plate edge, the inner plate edge defining a receiving portion for receiving a second planar substrate having a smaller size than the first planar substrate. The receiving portion is at least partially present below the substrate receiving recess.

[0088] According to an embodiment, a measurement system is provided, which includes a system stage having a base extending parallel to an XY plane and a plurality of references coupled to the base. The reference includes a protrusion extending away from the base along a Z axis perpendicular to the XY plane. The measurement system also includes an optical system having an objective lens. The objective lens is configured to move relative to the system stage along the XY plane. The measurement system also includes a fluid control system, which is configured to control the flow of one or more fluids through the flow cell when the flow cell is mounted on the system stage. The measurement system also includes a system controller, which is configured to control the fluid control system and the optical system to perform different first and second measurement schemes with the first and second samples, respectively. During the first measurement scheme, the system controller commands the fluid control system to guide one or more fluids through the flow cell on the system stage, and commands the optical system to detect the light signal from the first sample on the flow cell. During the second measurement scheme, the system controller commands the optical system to detect the light signal from the second sample on the open surface substrate on the system stage without passing the flowing fluid through the second sample.

[0089] In an embodiment, a method is provided for capturing a series of images of overlapping portions of a microarray of features. Each of the features has a designated probe molecule fixed thereto. The microarray has a target analyte attached thereto. The method also includes analyzing the light intensities associated with the corresponding features in the image to determine a data representation of the image. The data representation has a corresponding subarray of data features based on the corresponding features of the microarray. Each of the data features has a corresponding position relative to other data features and a signal value based on one or more light intensities. The method also includes combining the data representations of adjacent images based on a comparison of the signal values ​​of the data features of the data representations of adjacent images, thereby generating a data representation of the microarray. The method also includes analyzing the data representation of the microarray to determine a property or characteristic of the sample. BRIEF DESCRIPTION OF THE DRAWINGS

[0090] Figure 1 is a block diagram of an assay system for performing a biological or chemical assay formed in accordance with one embodiment.

[0091] Figure 2 is a perspective view showing imaging of a sample according to one embodiment.

[0092] Figure 3 is Figure 2 A side cross-sectional view of the illustration in FIG.

[0093] Figure 4 Various optical configurations that can be used for different imaging sessions are shown.

[0094] Figure 5 The optical layout for a microfluorometer is shown.

[0095] Figure 6 Shown is the arrangement of four microfluorometers relative to a flow cell with two channels.

[0096] Figure 7 is a perspective view of a portion of a system table according to an embodiment.

[0097] Figure 8 is a perspective view of a carrier assembly formed in accordance with an embodiment.

[0098] Fig. 9 yes Figure 8 A plan view of a carrier assembly having a substrate located thereon.

[0099] Fig.10 yes Figure 8 A plan view of a carrier assembly having another substrate located thereon.

[0100] Fig.11is an enlarged view of a portion of the carrier assembly showing the retention mechanism in greater detail.

[0101] Fig.12 is a perspective view of a carrier assembly formed in accordance with an embodiment.

[0102] Fig.13 yes Fig.12 A plan view of a carrier assembly located on a system table.

[0103] Fig.14A yes Fig.12 Cross section of a carrier assembly.

[0104] Fig. 14B Shown are the flow cell and open-face substrate side by side.

[0105] Fig.15 Shown relative to Fig.10 The imaging area of ​​the optical system of the substrate.

[0106] Fig.16 Shown relative to Fig. 9 The imaging area of ​​the optical system of the substrate.

[0107] Fig.17 is a flow chart illustrating a method according to an embodiment.

[0108] Fig.18 is an image of a microarray according to one embodiment.

[0109] Fig.19 yes Fig.18 A magnified view of an image showing the feature locator positioned relative to the microarray.

[0110] Fig. 20 Shown is a series of overlapping data representations in accordance with an embodiment.

[0111] Fig.21 According to an embodiment, after the data representation has undergone a splicing operation, Fig. 20 A series of overlapping data representations.

[0112] Fig. 22 is a flow chart illustrating a method according to an embodiment. Detailed description of the invention

[0113] Embodiments described herein include various methods and systems for detecting an optical signal provided by a sample. The optical signal can be a light emission generated in response to an excitation light or a light emission generated by a label without excitation (e.g., a radioactive or chemiluminescent component in a sample). Specific embodiments include systems or system components that can be used when performing more than one type of assay protocol. For example, embodiments can be used to perform or facilitate the execution of a sequencing protocol in which sstDNA is sequenced and imaged in a flow cell and a microarray protocol in which a microarray is imaged for various applications.

[0114] The components of the system may include a carrier assembly located on the system stage. The carrier assembly may be capable of holding different substrates with samples thereon. In a particular embodiment, the carrier assembly is reconfigurable so that one or more components may be added or removed. In a first configuration, the carrier assembly may be configured to hold a first substrate, such as a flow cell, during a sequencing scheme in which a fluid is directed through the flow cell. When the flow cell is located on the system stage, the fluid flows through the inner surface of the flow channel. The fluid delivers the reagent to the sample on the inner surface. Then, the optical system may detect the light signal from the inner surface. In a second configuration, the carrier assembly may be configured to hold a second substrate, such as an open face substrate, with a sample located on the outer surface of the second substrate. The second substrate may include, for example, probes arranged in an array on the outer surface of the second substrate. Unlike the flow cell, the second substrate may not have a fluid flow across the outer surface while the second substrate is located on the system stage. Therefore, the carrier assembly may be configured to hold different substrates on the same system stage for different assay schemes. Although two specific configurations are described above, the carrier assembly may be capable of having a configuration different from the configuration described above and / or more than two configurations.

[0115] One or more aspects of the subject matter described herein may be similar to the subject matter described in U.S. Patent Nos. 8,951,781, 8,748,789, 7,769,548, and 8,481,903 and in U.S. Patent Publication No. 2013 / 0260372, each of which is incorporated herein by reference in its entirety.

[0116] As used herein, the term "optical signal" includes electromagnetic energy that is capable of being detected. The term includes light emission from labeled biological or chemical substances, and also includes transmitted light refracted or reflected by an optical substrate. For example, a sample may include coded microparticles that convert incident light into an optical signal that identifies the microparticles (or a substance fixed to the microparticles). The converted optical signal can form a detectable pattern representing the code of the irradiated microparticles. The optical signal can also include incident light that is directed onto the sample to excite a label or reflected / refracted by the sample.

[0117] The optical signal (including the excitation radiation incident on the sample and the light emission provided by the sample) can have one or more spectral patterns. For example, more than one type of label can be excited in an imaging session. In this case, different types of labels can be excited by a common excitation light source, or can be excited by different excitation light sources that provide incident light at the same time. Each type of label can emit a light signal having a spectral pattern different from the spectral pattern of other labels. For example, the spectral pattern can have a different emission spectrum. The light emission can be filtered to detect light signals from other emission spectra separately. As used herein, when the term "different" is used with respect to emission spectra, the emission spectrum can have a wavelength range that at least partially overlaps as long as at least a portion of one emission spectrum does not completely overlap with another emission spectrum. Different emission spectra may have other non-overlapping characteristics, such as emission anisotropy or fluorescence lifetime. When the light emission is filtered, the wavelength range of the emission spectrum may be narrowed.

[0118] In some embodiments, an optical signal is directed through an optical column having a plurality of optical components. The optical signal is directed to a detector (e.g., an image sensor). In particular embodiments, the optical components of the optical column may be selectively movable. As used herein, when the term "selectively" is used in conjunction with "move" and similar terms, the phrase means that the position of the optical component can be changed in a desired manner. For example, at least one of the position and orientation of the optical component can be changed. The phrase "selectively move" includes removing the optical component from the optical path, adjusting the orientation of the optical component in the optical path (e.g., rotating the optical component), or moving the optical component so that the orientation does not change, but the position of the optical component does change. In particular embodiments, the optical component is selectively moved between imaging sessions. However, in other embodiments, the optical component may be selectively moved during an imaging session.

[0119] Different elements and components can be removably coupled. As used herein, when two or more elements or components are "removably coupled" (or "removably engaged"), the elements are easy to separate without destroying the coupled components. When the elements can be separated from each other without a lot of time or too much effort spent on separating the components, the elements are easy to separate. For example, in some embodiments, the adapter plate of the carrier assembly can be removably coupled to the support frame many times during the life of the carrier assembly. When removably coupled, the adapter plate and the support frame can be operated together in a suitable manner to maintain the substrate. In a specific embodiment, the elements are automatically removably coupled by a machine or system. In addition, in some embodiments, the removably coupled elements are directly connected to each other so that some contacts are formed between the coupled elements. In other embodiments, the removably coupled elements have an intermediate element that is convenient for removably coupling. For example, the adapter plate can be directly attached to a gasket or an intermediate layer, which is directly attached to the support frame. Therefore, the adapter plate and the support frame do not necessarily contact each other. Exemplary modes for removably coupling components include, but are not limited to, indirect interaction by frictional engagement (eg, interference fit, snap fit), magnetism, vacuum, electrical charge, mild adhesion, mechanical clamping, and the like.

[0120] In other embodiments, different elements and components may not be easily separated. For example, the support frame and the adapter plate may be different parts of the same single body. The support frame and the adapter plate may be injection molded and formed by a common mold. In some embodiments, the support frame and the adapter plate may be discrete components that are fixed to each other so that the components are not easily separated. For example, one or more portions of the support frame and the adapter plate may be fused together. As used herein, the phrase "[element A] is coupled to [element B]" may include elements A and B being discrete elements that are removably coupled to each other, fixed to each other, or parts of the same single structure.

[0121] An imaging session includes a time period during which at least a portion of a sample is imaged. A sample may undergo or be subjected to multiple imaging sessions. For example, a sample may be subjected to two different imaging sessions, each of which attempts to detect light signals from one or more different markers. As a specific example, a first scan along at least a portion of a nucleic acid sample may detect markers associated with nucleotides A and C, and a second scan along at least a portion of the sample may detect markers associated with nucleotides G and T.

[0122] During an imaging session, an optical signal provided by a sample is observed by an optical system. Various types of imaging can be used with the embodiments described herein. For example, an embodiment can be configured to perform at least one of epi-fluorescent imaging and total internal reflection fluorescence (TIRF) imaging. In a specific embodiment, the sample imager is a scanning time delay integration (TDI) system. In addition, an imaging session can include "line scanning" one or more samples so that a linear focal region of light is scanned across the sample. For example, some methods of line scanning are described in U.S. Patent No. 7,329,860 and International Publication No. WO 2009 / 137435, the complete subject matter of which is incorporated herein by reference in its entirety. An imaging session can also include moving a point focal region of light in a raster pattern over a sample. Optionally, one or more regions of a sample can be irradiated at once in a "step and shoot" manner. In other embodiments, an imaging session can include detecting light emissions generated without illumination and based entirely on the emission characteristics of a marker within the sample (e.g., a radioactive or chemiluminescent component in the sample).

[0123] Systems that may be capable of performing one or more of the assay protocols described herein include systems developed by Illumina, Inc., such as the MiSeq, HiSeq 2500, HiSeq X Ten, NeoPrep, HiScan, NextSeq, and iScan systems. Systems capable of performing one or more of the assay protocols described herein are described in U.S. Pat. Nos. 8,951,781, 8,748,789, 7,769,548, and 8,481,903, and in U.S. Patent Publication No. 2013 / 0260372, each of which is incorporated herein by reference in its entirety.

[0124] As used herein, the term "sample" includes various substances of interest that undergo an imaging session, wherein light signals from the sample are observed. In a particular embodiment, the sample may include an organism or chemical substance of interest. As used herein, the term "organism or chemical substance" may include various organisms or chemicals that are suitable for imaging or inspection with an optical system as described herein. For example, the organism or chemical substance includes 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 bioactive chemical components, such as analogs or mimetics of the above-mentioned types. Other chemicals include labels that can be used for identification, examples of which include fluorescent labels and other labels described in more detail below.

[0125] Different types of samples can be coupled to different types of optical substrates or support structures that affect incident light in different ways. In a specific embodiment, the sample to be detected can be attached to one or more surfaces of the substrate or support structure. For example, an open-face substrate (such as some microarrays and chips) has biological or chemical substances fixed to the outer surface of the open-face substrate. Therefore, when collecting light signals from above, the light signals to be detected are projected from the outer surface through the air and possibly through liquids with different refractive indices. However, a flow cell or a capillary flow optical substrate can include one or more flow channels. In a flow cell, the flow channel can be separated from the surrounding environment by the top and bottom layers of the flow cell. Therefore, the light signal to be detected is projected from the support structure and can be transmitted through multiple layers of materials with different refractive indices. For example, when detecting light signals from the inner bottom surface of the flow channel and when detecting light signals from above the flow channel, it is expected that the light signal to be detected can be propagated through a fluid with a refractive index, through one or more layers of a flow cell with different refractive indices, and through a surrounding environment with different refractive indices. In some embodiments, the light signal propagated from the open-face substrate may be affected differently from the light signal propagated from the surface of the flow channel. In this case, embodiments described herein can facilitate adjusting or modifying the optical train that directs the light signal from the sample to the detector assembly. However, in other embodiments, the optical train is not adjusted for different samples. For example, the same optical train can detect light signals from the flow cell and light signals from the open-face substrate. Embodiments can adjust or modify the optical train as described in U.S. Patent No. 8,481,903, which is incorporated herein by reference in its entirety.

[0126] The optical substrate or support structure includes a flow cell having a flow channel in which, for example, nucleic acids are sequenced. In other embodiments, the optical substrate may include one or more glass slides, open-face substrates, planar chips (such as those used in microarrays), or microparticles. In the case where the optical substrate includes a plurality of microparticles supporting biological or chemical substances, the microparticles may be held by another optical substrate (such as a glass slide, a pit array, or a groove plate). In a specific embodiment, the optical substrate includes a coding optical identification element based on a diffraction grating similar or identical to those described in pending U.S. patent application serial number 10 / 661,234, entitled "Diffraction Grating Based Optical Identification Element" filed on September 12, 2003, which is incorporated herein by reference in its entirety and discussed more below. The bead unit or plate for holding optical recognition elements can be similar or identical to the elements described in pending U.S. patent application serial number 10 / 661,836, entitled “Method and Apparatus for Aligning Microbeads in Order to Interrogate the Same,” filed on September 12, 2003, and U.S. Patent No. 7,164,533, entitled “Hybrid Random Bead / Chip Based Microarray,” issued on January 16, 2007, and U.S. patent application serial number 60 / 609,583, entitled “Improved Method and Apparatus for Aligning Microbeads in Order to Interrogate the Same,” filed on September 13, 2004, and serial number 60 / 610,910, entitled “Method and Apparatus for Aligning Microbeads in Order to Interrogate the Same,” filed on September 17, 2004, each of which is incorporated herein by reference in its entirety.

[0127] The optical system described herein can also be used to scan samples including microarrays. Microarrays can include a population of different probe molecules attached to one or more substrates so that different probe molecules can be distinguished from each other according to relative positions. The array can include different probe molecules or populations of probe molecules, each of which is located at different addressable positions on the substrate. Alternatively, the microarray can include a separate optical substrate, such as a bead, and each optical substrate supports a population of different probe molecules or probe molecules, which can be identified according to the position of the optical substrate on the surface to which the substrate is attached or according to the position of the substrate in the liquid. The exemplary arrays in which the separate substrate is located on the surface include, without limitation, BeadChip arrays available from Inc. (San Diego, California) or other arrays including beads in the well, such as those described in U.S. Patent Nos. 6,266,459, 6,355,431, 6,770,441, 6,859,570 and 7,622,294 and PCT Publication No. WO 00 / 63437, each of which is hereby incorporated by reference. Other arrays having particles on the surface include those described in US 2005 / 0227252, WO 05 / 033681, and WO 04 / 024328, each of which is hereby incorporated by reference.

[0128] Any of various microarrays known in the art can be used, including those described herein, for example. Typical microarrays include reaction sites sometimes referred to as features, each reaction site having a colony of probes. The probe colony at each reaction site is usually homogeneous, with a single type of probe, but in some embodiments, the colony can be heterogeneous. The reaction sites or features of the array are usually discrete, separated by intervals between each other. The size of the probe site and / or the spacing between the reaction sites can be changed so that the array can be high-density, medium-density or low-density. The high-density array is characterized in having reaction sites separated less than about 15 μm. The medium-density array has reaction sites separated by about 15 to 30 μm, and the low-density array has reaction sites separated by more than 30 μm. Arrays useful in the present invention can have sites separated by less than 100 μm, 50 μm, 10 μm, 5 μm, 1 μm or 0.5 μm. The device or method of an embodiment of the present invention can be used for imaging the array with a resolution sufficient to distinguish the sites under the above-mentioned density or density range.

[0129] Additional examples of commercially available microarrays that can be used include, for example, Affymetrix® GeneChip® microarrays or other microarrays synthesized according to a technique sometimes referred to as VLSIPS. (Very Large Scale Immobilized Polymer Synthesis) technology, as described, for example, in U.S. Pat. Nos. 5,324,633; 5,744,305; 5,451,683; 5,482,867; 5,491,074; 5,624,711; 5,795,716; 5,831,070; 5,856,101; 5,858,659; 5,874,219; 5,968,740; 5,989,911; 74,164, 5,981,185, 5,981,956, 6,025,601, 6,033,860, 6,090,555, 6,136,269, 6,022,963, 6,083,697, 6,291,183, 6,309,831, 6,416,949, 6,428,752 and 6,482,591, each of which is hereby incorporated by reference. Spotted microarrays can also be used in methods according to embodiments of the present invention. An exemplary spotted microarray is a CodeLink™ array available from Amersham Biosciences. Another useful microarray is a microarray using an inkjet printing method such as SurePrint available from Agilent Technologies. TM Microarrays fabricated using PCR technology.

[0130] The system and method set forth herein can be used for detecting the presence of a specific target molecule in a sample contacted with a microarray. This can be determined, for example, based on the combination of a marked target analyte with a specific probe of a microarray or due to the target-related modification of a specific probe to merge, remove or change the mark at the probe position. Any of several assays can be used to identify or characterize a target using a microarray, as described, for example, in U.S. Patent Application Publication Nos. 2003 / 0108867, 2003 / 0108900, 2003 / 0170684, 2003 / 0207295 or 2005 / 0181394, wherein each patent is hereby incorporated by reference.

[0131] In addition, the optical system described herein can be constructed to include various components and assemblies as described in PCT application PCT / US07 / 07991, entitled "System and Devices for Sequence by Synthesis Analysis", filed on March 30, 2007, and / or include various components and assemblies as described in International Publication No. WO 2009 / 042862, entitled "Fluorescence Excitation and Detection System and Method", filed on September 26, 2008, the entire subject matter of both patents is incorporated herein by reference in its entirety. In a specific embodiment, the optical system can include various components and assemblies as described in U.S. Patent Nos. 7,329,860 and WO 2009 / 137435, the entire subject matter of which is incorporated herein by reference in its entirety. The optical system can also include various components and assemblies as described in U.S. Patent Application Serial No. 12 / 638,770, filed on December 15, 2009, the entire subject matter of which is incorporated herein by reference in its entirety.

[0132] In a specific embodiment, the methods and optical systems described herein can be used to sequence nucleic acids. For example, sequencing by synthesis (SBS) schemes are particularly applicable. In SBS, multiple fluorescently labeled modified nucleotides are used to sequence dense clusters of amplified DNA (possibly millions of clusters) present on the surface of an optical substrate (e.g., the surface of a channel in a flow cell that is at least partially defined). The flow cell can contain a nucleic acid sample for sequencing, wherein the flow cell is placed in a suitable flow cell support frame. The sample for sequencing can take the form of single nucleic acid molecules separated from each other so as to become a separate decomposable amplification population of nucleic acid molecules in the form of beads of one or more molecules of a cluster or other features or attached to the nucleic acid. Nucleic acids can be prepared so that they include oligonucleotide primers adjacent to an unknown target sequence. In order to initiate the first SBS sequencing cycle, one or more differently labeled nucleotides and DNA polymerases, etc., can flow into / flow through the flow cell through a fluid flow subsystem (not shown). A single type of nucleotide can be added at a time, or the nucleotides used in the sequencing process can be specially designed to have a reversible termination property, thereby allowing each cycle of the sequencing reaction to occur simultaneously when several types of labeled nucleotides (e.g., A, C, T, G) are present. The nucleotides can include a detectable labeling portion, such as a fluorophore. When four nucleotides are mixed together, the polymerase can select the correct base to be incorporated, and each sequence is extended by a single base. Unincorporated nucleotides can be washed away by passing a wash solution through the flow cell. One or more lasers can excite the nucleic acid and induce fluorescence. The fluorescence emitted from the nucleic acid is based on the fluorophore of the incorporated base, and different fluorophores can emit light of different wavelengths. Unsealing agents can be added to the flow cell to remove the reversible terminator group from the extended and detected DNA chain. Unsealing agents can then be washed away by passing a wash solution through the flow cell. The flow cell then begins to prepare for another cycle of sequencing with the introduction of labeled nucleotides as described above. The fluid and detection steps can be repeated several times to complete the sequencing run. Exemplary sequencing methods are described in, e.g., Bentley et al. (Nature 456:53-59 (2008)), WO 04 / 018497, U.S. Pat. No. 7,057,026, WO 91 / 06678, WO 07 / 123,744, U.S. Pat. No. 7,329,492, U.S. Pat. No. 7,211,414, U.S. Pat. No. 7,315,019, U.S. Pat. No. 7,405,281, and US2008 / 0108082, each of which is incorporated herein by reference.

[0133] In some embodiments, nucleic acid can be attached to the surface and amplified before or during sequencing. For example, bridge amplification can be used to amplify. Useful bridge amplification methods are described in, for example, U.S. Patent No. 5,641,658, U.S. Patent Publication No. 2002 / 0055100, U.S. Patent No. 7,115,400, U.S. Patent Publication No. 2004 / 0096853, U.S. Patent Publication No. 2004 / 0002090, U.S. Patent Publication No. 2007 / 0128624 and U.S. Patent Publication No. 2008 / 0009420. Another useful method for amplifying nucleic acid from the surface is rolling circle amplification (RCA), for example, as described in Nat. Genet. 19:225-232 (1998) and US 2007 / 0099208 A1 of people such as Lizardi, wherein each is incorporated herein by reference. Emulsion PCR on beads can also be used, for example, as described in Dressman et al., Proc. Natl. Acad. Sci. USA 100:8817-8822 (2003), which is incorporated herein by reference.

[0134] Other sequencing techniques suitable for the methods and systems described herein are pyrophosphate sequencing, nanopore sequencing, and sequencing by ligation. Particularly useful exemplary pyrophosphate sequencing techniques and examples are described in U.S. Patent No. 6,210,891, U.S. Patent No. 6,258,568, U.S. Patent No. 6,274,320, and Ronaghi's Genome Research 11:3-11 (2001), each of which is incorporated herein by reference. Exemplary nanopore techniques and examples that are also useful are described in Acc. Chem. Res. 35:817-825 (2002) by Deamer et al., Nat. Mater. 2:611-615 (2003) by Li et al., Clin Chem. 53:1996-2001 (2007) by Soni et al., Nanomed. 2:459-481 (2007) by Healy et al., and J. am. Chem. Soc. 130:818-820 by Cockroft et al., and U.S. Pat. No. 7,001,792, which are incorporated herein by reference. In particular, these methods utilize repeated steps of reagent delivery. The apparatus or method described herein can be configured with reservoirs, valves, fluid lines, and other fluid components together with control systems for those components to introduce reagents and detect signals according to a desired protocol, such as those described in the references cited above. Any of a variety of samples may be used in these systems, such as substrates with beads generated by emulsion PCR, substrates with zero mode waveguides, substrates with integrated CMOS detectors, substrates with biological nanopores in lipid bilayers, solid-state substrates with synthetic nanopores, and other substrates known in the art. Such examples are described in the context of various sequencing technologies in the references cited above and further in US 2005 / 0042648, US 2005 / 0079510, US 2005 / 0130173, and WO 05 / 010145, each of which is incorporated herein by reference.

[0135] Exemplary labels that can be detected according to various embodiments include, for example, when present on or in a support structure, chromophores, luminophores, fluorophores, optically encoded nanoparticles, particles encoded with diffraction gratings, electrochemiluminescent labels (such as Ru(bpy).sup.32+), or moieties that can be detected based on optical properties. Potentially useful fluorophores include, for example, fluorescent lanthanide complexes, including europium and terbium, fluorescein, rhodamine, tetramethylrhodamine, eosin, erythrosine, coumarin, methylcoumarin, pyrene, Malacite green, Cy3, Cy5, stilbene, fluorescent yellow, Cascade Blue, and fluorescein. TM, Texas Red, Alexa dyes, phycoerythrin, bodipy, and other substances known in the art, such as those described in Haugland's Molecular Probes Handbook (Eugene, Oreg.) 6th edition, The Synthegen catalog (Houston, Texas), Lakowicz's Principles of Fluorescence Spectroscopy (2nd edition), Plenum Press New York (1999), or WO 98 / 59066, each of which is incorporated herein by reference. In some embodiments, a pair of labels can be excited by a first excitation wavelength, while another pair of labels can be excited by a second excitation wavelength.

[0136] Although embodiments are illustrated with respect to detection of samples including biological or chemical substances supported by an optical substrate, it will be understood that other samples may be imaged by the embodiments described herein. Other exemplary samples include, but are not limited to, biological specimens (such as cells or tissues), electronic chips (such as those used in computer processors), etc. Some examples of applications include microscopy, satellite scanners, high-resolution copying technology, fluorescence image acquisition, analysis and sequencing of nucleic acids, DNA sequencing, sequencing by synthesis, imaging of microarrays, imaging of holographic encoded microparticles, etc.

[0137] Figure 1 1 is a block diagram of an assay system 100 for biological or chemical analysis formed according to one embodiment. The assay system 100 may be a workbench that may be similar to a desktop device or a desktop computer. For example, most of the systems and components for performing a desired reaction may be within a common housing 115 of the assay system 100. In some embodiments, the assay system 100 includes one or more components, assemblies, or systems remotely located from the assay system 100. In addition, the assay system 100 may include various components, assemblies, and systems (or subsystems) that interact with each other to perform one or more predetermined methods or assay protocols for biological or chemical analysis. In some embodiments, the protocol may be executed in an automated manner after the protocol is started without user interaction.

[0138] For example, the assay system 100 includes a system controller 102 that can communicate with various components, assemblies, and subsystems of the assay system 100. As shown, the assay system 100 has an optical system 104, an excitation source assembly 106, a detector assembly 108, and a docking station or system 110 that supports one or more carrier assemblies 112 having a substrate with a sample thereon. In some embodiments, the optical system 104 includes the excitation source assembly 106 and / or the detector assembly 108. In some embodiments, the optical system 104 is configured to direct incident light from the excitation source assembly 106 onto the sample. The excitation source assembly 106 can include one or more excitation light sources configured to excite a marker associated with the sample. The excitation source assembly 106 can also be configured to provide incident light that is reflected and / or refracted by the sample. As shown, the sample can provide an optical signal including light emission 116 and / or transmitted light 118. The docking system 110 and the optical system 104 can be moved relative to each other. In certain embodiments, docking system 110 includes a system stage 130 and a motor assembly 132 that moves system stage 130 relative to optical system 104. In other embodiments, motor assembly 132 can be operably coupled to optical system 104 and can move optical system 104 in addition to or as an alternative to docking system 110. Optical system 104 can be or include an optical train having a plurality of optical components.

[0139] The optical system 104 may also be configured to direct the light emission 116 and / or the transmitted light 118 to a detector assembly 108. The detector assembly 108 may include one or more image sensors. The image sensor may be, by way of example only, a CMOS imager, a CCD camera, or a photodiode. The optical system 104 may include an optical adjustment system (or subsystem) 120. The optical adjustment system 120 is configured to selectively move one or more optical components of the optical system 104. For example, the optical adjustment system 120 may selectively move a path compensator 122 and / or an optical device 124 located upstream or downstream of the sample. Components may also be shared between two or more optical trains. For example, one or more components may be optionally positioned to contact different light paths (e.g., emissions from different samples).

[0140] Also shown, the assay system 100 may include a fluid control system 134 to control the flow of fluids throughout a fluid network 135 (indicated by solid lines) of the assay system 100. The fluid control system 134 may deliver reagents to a sample during, for example, a sequencing protocol. The assay system 100 may also include a fluid storage system 136 configured to hold fluids that may be used by the assay system 100 and a temperature control system 138 that regulates the temperature of the fluids. The temperature control system 138 may also regulate the temperature of the assay system 100, typically using, for example, a radiator and a blower. An exemplary temperature control system is described in U.S. Serial No. 12 / 565,606, which is incorporated herein by reference.

[0141] In some embodiments, the fluid network 135 includes one or more umbilicals (not shown) that operatively couple the fluid control system 134 and the fluid storage system 136 to the system station 130 and other components of the assay system 100. The carrier assembly 112 may include a flow cell configured to flow a solution therethrough during an assay protocol. The solution may be delivered via the umbilical. For example, the umbilical may be fluidically coupled to the flow cell and a multi-port pump, which in turn is fluidically coupled to various fluids (e.g., reagents, buffers, etc.) in the fluid storage system 136. The pump may receive instructions for delivering different solutions to the flow cell. The umbilical may include one or more fluid lines and also one or more communication lines (e.g., electrical or optical) that transmit instructions.

[0142] Also shown, the assay system 100 may include a user interface 140 for interacting with a user. For example, the user interface 140 may include a display 142 that displays or requests information from a user and a user input device 144 that receives user input. In some embodiments, the display 142 and the user input device 144 are the same device (e.g., a touch screen). As will be discussed in more detail below, the assay system 100 may communicate with various components to perform a desired reaction. The assay system 100 may also be configured to analyze the detection data to provide the desired information to the user.

[0143] The fluid control system 134 is configured to direct and regulate the flow of one or more fluids through the fluid network 135. The fluid network 135 can be in fluid communication with at least one of a substrate and a fluid storage system 136. For example, a selected fluid can be drawn from the fluid storage system 136 and directed in a controlled manner to the carrier assembly 112 having the substrate, or a fluid can be drawn from the substrate and directed toward a waste reservoir, such as in the fluid storage system 136. Although not shown, the fluid control system 134 can include a flow sensor that detects the flow rate or pressure of the fluid within the fluid network. The sensor can communicate with the system controller 102.

[0144] The temperature control system 138 is configured to regulate the temperature of the fluid at different zones of the fluid network 135, the fluid storage system 136, and / or the substrate. For example, the temperature control system 138 may include a thermal cycler (not shown) connected to the substrate (or carrier assembly 112) and controlling the temperature of the fluid flowing along the sample. The temperature control system 138 may also regulate the temperature of the sample or solid elements or components of the assay system 100 or the sample. Although not shown, the temperature control system 138 may include a sensor to detect the temperature of the fluid or other components. The sensor may communicate with the system controller 102.

[0145] Fluid storage system 136 is communicated with sample fluid, and can store various reaction components or reactants for carrying out desired reaction therein. Fluid storage system 136 can store fluid for washing or cleaning fluid network 135 or sample and also for diluting reactants. For example, fluid storage system 136 can include various reservoirs for storing reagents, enzymes, other biomolecules, buffer solutions, aqueous and non-polar solutions, etc. In addition, fluid storage system 136 can also include a waste reservoir for receiving waste.

[0146] The docking system 110 is configured to engage one or more carrier assemblies 112, for example, in at least one of a mechanical, electrical, and fluidic manner. The docking system 110 can maintain the carrier assembly 112 in a desired orientation to facilitate the flow of fluid through the carrier assembly 112 and / or imaging of the sample. The docking system can be configured to deliver fluid to one sample, rather than another sample. The system can be configured to deliver different fluids to different samples. Alternatively or in addition, the fluid can be delivered to different samples in different time sequences, amounts, flow rates, or durations. In some embodiments, the docking system 110 includes a carrier sensor 113. The carrier sensor 113 can determine the type of sample by, for example, scanning a bar code on the substrate of the carrier assembly 112 or by detecting an RF signal from an RFID tag that identifies the type of sample.

[0147] The system controller 102 may include any processor-based or microprocessor-based system, including systems using microcontrollers, reduced instruction set computers (RISC), application-specific integrated circuits (ASICs), field programmable gate arrays (FPGAs), logic circuits, and any other circuits or processors capable of performing the functions described herein. These functions may be performed within a commercially reasonable time period. The above examples are exemplary only, and therefore are not necessarily intended to limit the definition and / or meaning of the term system controller in any way. In an exemplary embodiment, the system controller 102 executes an instruction set stored in one or more storage elements, memories, or modules to perform at least one of the following: obtaining detection data and analyzing detection data. The storage element may be in the form of an information source or physical storage element within the determination system 100. The embodiment includes a non-temporary computer-readable medium, which includes an instruction set for executing or implementing one or more processes described herein. The non-temporary computer-readable medium may include all computer-readable media, except for the temporary propagation signal itself. The non-temporary computer-readable medium may generally include any tangible computer-readable medium, including, for example, permanent memory (such as a magnetic disk and / or optical disk, ROM and PROM) and volatile memory (such as RAM). Computer-readable media may store instructions for execution by one or more processors.

[0148] The instruction set may include various commands that instruct the measurement system 100 to perform specific operations, such as the methods and processes of the various embodiments described herein. The instruction set may be in the form of a software program. As used herein, the terms "software" and "firmware" are interchangeable and include any computer program stored in a memory (including RAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatile RAM (NVRAM) memory) for execution by a computer. The above memory types are exemplary only, and therefore are not limiting as to the types of memory that may be used for storage of computer programs.

[0149] Components of the assay system may include or represent hardware circuits or circuit systems that include and / or are connected to one or more processors (such as one or more computer microprocessors). The operation of the methods and assay systems described herein may be sufficiently complex that the operations cannot be mentally performed by an average person or person of ordinary skill in the art within a commercially reasonable period of time.

[0150] The software may be in various forms, such as system software or application software. In addition, the software may be in the form of a collection of separate programs or in the form of a program module or a portion of a program module within a larger program. The software may also include modular programming in the form of object-oriented programming. After the detection data is obtained, the detection data may be automatically processed by the measurement system 100, processed in response to user input, or processed in response to a request made by another processing machine (e.g., a remote request via a communication link).

[0151] The system controller 102 can be connected to other components or subsystems of the assay system 100 via a communication link (indicated by a dotted line). The system controller 102 can also be communicatively connected to an off-site system or server. The communication link can be hardwired or wireless. The system controller 102 can receive user input or commands from a user interface 140. The user input device 144 can include a keyboard, a mouse, a touch screen panel, and / or a voice recognition system, etc. Alternatively or in addition, the user input device 144 can also be a display 142.

[0152] In some embodiments, the assay system 100 can have interchangeable or exchangeable devices (e.g., plug and play). For example, the docking system 110 or the system station 130 can be easily replaced or substituted with a different docking system 110 or system station 130. This may occur when different types of samples need to be used. In some embodiments, the sample is easily exchanged from the system station 130. In addition, the fluid storage system 136 can be a container that is easily separated from the fluid network and replaced by another container. This can occur when the fluid in the container is exhausted, expired, or a different container is needed because the user of the assay system 100 wishes to run different assay protocols. In addition, the system controller 102 can have exchangeable devices (e.g., if the user wishes to use the assay system 100 to perform different assay protocols).

[0153] Figure 1 A block diagram of the system controller 102 is also shown. In one embodiment, the system controller 102 includes one or more processors or modules that can communicate with each other. The system controller 102 is conceptually shown as a collection of modules, but can be implemented using any combination of dedicated hardware boards, DSPs, processors, etc. Alternatively, the system controller 102 can be implemented using an off-the-shelf PC with a single processor or multiple processors, where the functional operations are distributed between the processors. As another option, the modules described below can be implemented using a hybrid configuration, where certain modular functions are performed using dedicated hardware, while the remaining modular functions are performed using an off-the-shelf PC, etc. Modules can also be implemented as software modules within a processing unit.

[0154] The system controller 102 may include a plurality of modules 151-158 that communicate with a system control module 150. The system control module 150 may communicate with a user interface 140. Although the modules 151-158 are shown as communicating directly with the system control module 150, the modules 151-158 may also communicate directly with each other, the user interface 140, or other systems. In addition, the modules 151-158 may communicate with the system control module 150 through other modules.

[0155] The plurality of modules 151-158 include system modules 151-153 that communicate with the subsystems. The fluid control module 151 can communicate with the fluid control system 134 to control valves and flow sensors of the fluid network 135 for controlling the flow of one or more fluids through the fluid network 135. The fluid storage module 152 can notify the user when the fluid is low or when the waste reservoir must be replaced. The fluid storage module 152 can also communicate with the temperature control module 153 so that the fluid can be stored at a desired temperature.

[0156] The plurality of modules 151-158 may also include an optical adjustment (or correction) module 154 that communicates with the optical adjustment system 120 and an identification module 155 that determines identification information associated with the sample. For example, the carrier assembly 112 may be scanned to identify the type of sample before an imaging session or before being placed on the system stage 130. The optical adjustment module 154 may communicate with various devices that are capable of selectively moving optical components such as a transfer device or a rotatable optical device. The plurality of modules 151-158 may also include a detection data analysis module 158 that receives and analyzes detection data (e.g., image data) from the detector assembly 108. The processed detection data may be stored for subsequent analysis, or may be sent to the user interface 140 to display desired information to the user. In addition, there may be a sample module that communicates with the sample (e.g., receives a signal about the sample temperature or the flow rate of a fluid in the sample).

[0157] The protocol modules 156 and 157 communicate with the system control module 150 to control the operation of the subsystems when performing a predetermined test protocol. The protocol modules 156 and 157 may include a set of instructions for instructing the assay system 100 to perform specific operations according to a predetermined protocol. The protocol modules 156 and 157 include a sequencing by synthesis (SBS) module 156, which may be configured to issue various commands for performing a sequencing by synthesis process. In some embodiments, the SBS module 156 may also process the detection data. The protocol module 157 may be configured to scan a microarray or perform other assay protocols.

[0158] As an example, the SBS module 156 can be configured to issue a command for a sequencing by synthesis process. For example, the SBS module 156 can issue a command to perform bridge PCR, in which a cluster of cloned amplicons is formed on a local area within a channel (or passage) of a flow cell. After the amplicon is generated by bridge PCR, the SBS module 156 can provide instructions to linearize or denature the amplicon to make sstDNA and add sequencing primers so that the sequencing primers can hybridize to a universal sequence located on the side of the region of interest. Each sequencing cycle extends the sstDNA by a single base and is achieved by a modified DNA polymerase and a mixture of four types of nucleotides, the delivery of which can be indicated by the SBS module 156. Different types of nucleotides have unique fluorescent labels, and each nucleotide has a reversible terminator that allows only single base incorporation to occur in each cycle. After a single base is added to the sstDNA, the SBS module 156 can indicate a washing step to remove non-incorporated nucleotides by flowing a wash solution through the flow cell. The SBS module 156 can also instruct the excitation source assembly and the detector assembly to perform an image session to detect fluorescence in each of the four channels (i.e., one for each fluorescent marker). After imaging, the SBS module 156 can instruct the delivery of the deblocking reagent to chemically cleave the fluorescent marker and terminator from the sstDNA. The SBS module 156 can instruct the washing step to remove the deblocking reagent and the product of the deblocking reaction. The result can produce another similar sequencing cycle. In such a sequencing scheme, the SBS module 156 can instruct the fluid control system 134 to direct the flow of reagents and enzyme solutions through the sample.

[0159] In some embodiments, the SBS module 156 may also be configured to issue various commands for executing the steps of the pyrophosphate sequencing protocol. In this case, the sample may include millions of wells, each of which has a single capture bead with clonally amplified sstDNA thereon. Each well may also include other smaller beads that may carry immobilized enzymes (e.g., ATP sulfurylase and luciferase), for example, or facilitate the retention of capture beads in the well. The SBS module 156 may be configured to issue commands to the fluid control module 151 to run consecutive cycles of fluids carrying a single type of nucleotide (e.g., first cycle: A; second cycle: G; third cycle: C; fourth cycle: T; fifth cycle: A; sixth cycle: G; seventh cycle: C; eighth cycle: T; etc.). When the nucleotide is incorporated into the DNA, the pyrophosphate is released, causing a chain reaction in which a beam of light is generated. This beam of light may be detected by a sample detector of the detector assembly. The detection data may be passed to the system control module 150, the detection data analysis module 158, and / or the SBS module 156 for processing. The detection data may be stored for later analysis, or may be analyzed by the system controller 102 , and the images may be sent to the user interface 140 .

[0160] The scheme module 157 can be configured to send instructions for scanning unknown analytes in the microarray. Before or after performing an imaging session, the scheme module 157 can instruct the optical adjustment system 120 to move optical components in the light path, move optical components into the light path, or remove optical components from the light path. For example, the scheme module 157 can request that the path compensator 122 be inserted into the light path or removed from the light path. The scheme module 157 can also request to reposition another optical component. Any of the various removable or adjustable optical components set forth herein can be moved, adjusted, or otherwise manipulated in response to instructions sent from the scheme module 157 or any other appropriate module of the system controller. Once the common arrangement of optical components is established as required, the scheme module 157 can instruct the excitation source assembly to provide incident light to the sample and instruct the detector assembly to detect the light signal provided by the sample.

[0161] In some embodiments, the user can provide user input through the user interface 140 to select the assay scheme run by the assay system 100. In other embodiments, the assay system 100 can automatically detect the type of sample that has been inserted into the docking system 110, and confirm the assay scheme to be run with the user. For example, the carrier sensor 113 can identify the type of sample in the carrier assembly by scanning or detecting a signal from a substrate or a carrier assembly. Alternatively, the assay system 100 can provide a limited number of assay schemes that can be run with a sample of a determined type. The user can select a desired assay scheme, and then the assay system 100 can perform the selected assay scheme based on preprogrammed instructions.

[0162] Figure 2 and Figure 3 2 is a diagram showing a perspective view and a side cross-sectional view of imaging a sample 202 according to one embodiment, respectively. In the illustrated embodiment, the sample 202 includes an optical substrate 204 represented as a flow cell. However, in an optional embodiment, the sample 202 may include a microarray as described above. As shown, the optical substrate 204 may include a first plate or layer 206 and a second plate or layer 208, with an internal volume or channel 210 extending between the first layer 206 and the second layer 208. The internal channel 210 may be configured to allow the flow of reagents through it. The first layer 206 and the second layer 208 may be formed by various substrate materials. The substrate material may be substantially transparent to the wavelength of the incident light and the optical signal provided from the sample. For example, the substrate material may be substantially transparent to the optical signal emitted by one or more markers in the sample, or may be substantially transparent to the optical signal reflected or refracted by the sample. The first layer 206 and the second layer 208 may have biological components 212 and 214 on their respective inner surfaces 216 and 218, respectively.

[0163] In various embodiments, the sample 202 can be illuminated by the excitation light or radiation 220 along a linear focal zone 222 (also referred to as a radiation line). However, in other embodiments, the focal zone can have other configurations (e.g., point, elliptical). The focal zone 222 can be formed by the excitation radiation 220 from one or more excitation light sources through the objective lens 224. The excitation light source can generate a light beam that is processed and shaped to provide the focal zone 222 on the sample 202. The focused light beam can include light signals with different emission spectra that excite the associated fluorophores of the biological components 212 and 214. When excited, the fluorophores emit light signals that may have different emission spectra. In some embodiments, the optical system can first direct the excitation radiation 220 to the inner surface 216 of the optical substrate 204 to illuminate the biological component 212. In addition, the optical substrate 204 and the objective lens 224 can be moved in a relative manner relative to each other so that the sample 202 is translated in the direction indicated by the arrow 226. Therefore, the focal zone 222 can gradually illuminate the biological component along the inner surface 216. As focal region 222 translates along interior surface 216, the focused light beam may continuously scan region 228, thereby scanning the entire interior surface 216 of optical substrate 204. After scanning interior surface 216, objective lens 224 and sample 202 may be moved relative to each other, and the same process may be repeated to scan interior surface 218 of optical substrate 204.

[0164] In certain embodiments, the device or method can be used to generate a 3D image of the image at least about 0.01 mm in diameter. 2 / second to detect features on the surface. Depending on the particular application, faster rates may also be used, including, for example, at least about 0.02 mm over the area being scanned or otherwise detected. 2 / sec, 0.05 mm 2 / sec, 0.1mm 2 / sec, 1mm 2 / sec, 1.5mm 2 / sec, 5mm 2 / sec, 10mm 2 / sec, 50mm 2 / sec, 100mm 2 / second or faster. For example, if necessary, in order to reduce noise, the detection rate can have a rate of about 0.05mm 2 / sec, 0.1mm 2 / sec, 1mm 2 / sec, 1.5mm 2 / sec, 5mm 2 / sec, 10mm 2 / sec, 50mm 2 / sec or 100mm 2 / second upper limit.

[0165] In some embodiments, biological materials can be immobilized on multiple surfaces of optical substrate 204. For example, Figure 3 An optical substrate 204 is shown having biological components 212 and 214 attached to inner surfaces 216 and 218, respectively. In the illustrated embodiment, an attachment layer 230 may be formed on both inner surfaces 216 and 218. The attachment layer 230 may facilitate the immobilization of the biological components 212 and 214 thereon. As shown, a first excitation radiation 232 may be used to illuminate the biological component 212 on the inner surface 216 of the optical substrate 204. Light emissions 234 from the illuminated biological component 212 may be returned through the layer 206. Simultaneously or sequentially, a second excitation radiation 236 may be used to illuminate the biological component 214 on the inner surface 218 of the optical substrate 204. Light emissions 238 may be returned from the illuminated biological component 214 through the channel 210 and the layer 206.

[0166] In certain embodiments, a path compensator may be used when imaging a sample through an objective lens having a high numerical aperture (NA) value. An exemplary high NA range includes NA values ​​of at least about 0.6. For example, the NA value may be at least about 0.65, 0.7, 0.75, 0.8, 0.85, 0.9, 0.95, or higher. Those skilled in the art will recognize that, depending on the refractive index of the medium in which the lens operates, the NA may be higher, including, for example, up to 1.0 for air, 1.33 for pure water, or higher for other media such as oil. The compensator may also be used in an objective lens having a lower NA value than the examples listed above. Typically, the NA value of an objective lens is a measure of the width of an angle for which the objective lens can receive light. For a given fixed magnification, the higher the NA value, the more light that can be collected by the objective lens. As a result, when using an objective lens having a higher NA value, multiple objects may be more easily distinguished because a higher feature density may be possible.

[0167] Figure 4Different optical configurations 281-283 of the optical system 250 that can be used during different imaging sessions are shown. The optical system 250 includes an objective lens 256 having a focusing end 294. It is also shown that the carrier assembly 260 is positioned near the focusing end 294 of the objective lens 256. The carrier assembly 260 can include a first substrate 252A or a second substrate 252B. In an exemplary embodiment, the first substrate 252A is a flow cell and the second substrate 252B is an open-face substrate. As will be described in more detail below, the embodiments described herein include adjustable or modifiable optical systems and assemblies. For example, the common arrangement of optical components that affect the optical signal provided by the sample can be changed for different imaging sessions. Changing the common arrangement of the optical components causes a change in the propagation of the optical signal from the sample or a change in the spectrum of the detected optical signal. The common arrangement can be modified by removing or repositioning one or more optical components. In addition, the common arrangement can be modified by exchanging filters along the optical path so that different optical signals are detected by the detector assembly.

[0168] As shown, a work distance WD can exist between the sample 252A and the focusing end 294 of the objective lens 256. In some embodiments, the working distance WD is less than about 5000 microns. In a specific embodiment, the working distance WD is less than about 2000 microns, and more particularly less than about 1000 microns.

[0169] exist Figure 4 In the embodiment, the carrier assembly 260 includes the same support frame 262 for supporting the first and second substrates 252A and 252B. When supporting the second substrate 252B, the carrier assembly 260 may also include an adapter plate (not shown). In an exemplary embodiment, the first substrate 252A includes a flow cell having a flow channel at least partially defined by the first and second material layers. The optical signal propagates from the marker in the flow channel through one or more layers and possible fluids to the outer surface of the flow cell. The optical signal then propagates from the outer surface to the objective lens. However, the second substrate 252B may be an open-face substrate so that the marker is located near the corresponding outer surface of the open-face substrate and provides an optical signal therefrom. In some cases, due to the structure of the first and second substrates 252A, 252B, the optical signal emitted from the markers of the first and second substrates 252A, 252B will be affected differently before reaching the objective lens 256. Therefore, the embodiments described herein may change the common arrangement of the optical system so that the optical signal can be appropriately detected.

[0170] Figure 4The different optical configurations 281-283 shown in the figure represent specific examples of how the path compensators 293 and 295 can be selectively moved to provide different common arrangements. The path compensators 293 and 295 adjust the optical path of the optical signal provided by the sample. In various embodiments, the optical components can be selectively moved so that the path compensator 295 can be located between the second substrate 252B and the objective lens 256, and / or the path compensator 293 can be located in an out-of-focus position relative to the objective lens 256.

[0171] As shown, optical configuration 281 includes objective lens 256 without any optical components (e.g., path compensators) located out of focus or between objective lens 256 and first substrate 252A. As an example, optical configuration 281 can be used during an imaging session where it is desired to image the bottom surface of a flow channel in a flow cell, such as Figure 4 As shown. When imaging the bottom surface of the flow channel, the input light signal is transmitted through the top layer of the flow cell and then through the cavity defined between the top layer and the bottom layer. After imaging the bottom surface of the flow channel, the measurement system can be moved to image other surfaces of the sample (e.g., the top surface of the flow channel or the outer surface of the flow cell or another sample). In this case, the light signal is no longer transmitted through the top layer and the cavity. More specifically, if the measurement system subsequently images the top surface of the flow channel or the outer surface of a different sample, it may be desirable to adjust the light path or the focal area to compensate for the reduced layer.

[0172] Thus, the optical configuration 282 includes a path compensator 293 located at an out-of-focus position relative to the objective lens 256. The path compensator 293 can be selectively moved to the out-of-focus position by a transfer device, such as a transfer device similar to that described in US 2009 / 0272914 or U.S. Pat. No. 8,481,903, each of which is incorporated herein by reference. The optical configuration 282 can be used during an imaging session in which it is desired to image the top surface of a flow channel in a flow cell.

[0173] The optical configuration 283 includes a path compensator 295 located between the light-collecting end 294 of the objective lens 256 and the second substrate 252B at the imaging position. In the imaging position, the path compensator 295 and the light-collecting end 294 can be spaced apart from each other by a fixed distance. However, the path compensator 295 and the second substrate 252B can be spaced apart by an adjustable distance. More specifically, the second substrate 252B and the objective lens 256 can move toward or away from each other during an imaging session.

[0174] The path compensator 295 can be selectively moved to an imaging position by a transport device. During an imaging session, the path compensator 295 can have a fixed position relative to the objective lens 256. In some embodiments, the path compensator 295 is operably coupled to the objective lens 256 through one or more intermediate components. In an optional embodiment, the path compensator 295 is directly attached to the focusing end 294 of the objective lens 256. The optical configuration 283 can be used to scan the outer surface of, for example, a microarray.

[0175] Figure 5 An exploded view of an exemplary microfluorometer is shown for the purpose of demonstrating the functional arrangement for at least some of the optical components. Two excitation sources are shown, including a green LED (LEDG) and a red LED (LEDR). Excitation light from each excitation source passes through a green LED condenser lens L6 and a red LED condenser lens L7, respectively. LED fold mirror M1 reflects the green excitation radiation to a combiner dichroic mirror F5, which passes through an excitation filter F2, then through a laser diode beam splitter F3, then through an excitation field stop FS, then through an excitation projection lens group L2 to an excitation / emission dichroic mirror F4, which reflects the green excitation radiation to the surface of a flow cell FC through a stationary objective lens group L3 and a translation objective lens group L4. Red excitation radiation passes from the red LED condenser lens L7 to the combiner dichroic mirror F5, after which the red excitation radiation follows the same path as the green excitation radiation to the surface of the flow cell FC. Focusing is initiated by moving the translation objective lens group L4 up and down (i.e., along the Z dimension), as shown. The emission from the surface of the flow cell FC is passed through the translation objective lens group L4 and then through the stationary objective lens group L3 back to the excitation / emission dichroic mirror F4, which passes the emission radiation to the emission projection lens group L1 to the emission filter and then to the CMOS image sensor S1. The laser diode LD is also guided to the laser diode beam splitter F3 via the laser diode coupling lens group L5, which reflects the laser diode radiation to the flow cell FC through the excitation field stopper FS, the excitation projection lens group L2, the excitation / emission dichroic mirror F4, the stationary objective lens group L3 and the translation objective lens group L4.

[0176] like Figure 5As demonstrated by the exemplary embodiments of , each of the microfluorometers may include a beam splitter and a detector, wherein the beam splitter is positioned to direct the excitation radiation from the excitation radiation source to the objective lens and to direct the emission radiation from the objective lens to the detector. Each microfluorometer may optionally include an excitation radiation source such as an LED. In this case, each microfluorometer may include a dedicated radiation source so that the read head includes several radiation sources, each of which is separated into a separate microfluorometer. In some embodiments, two or more microfluorometers may receive excitation radiation from a common radiation source. Thus, two or more microfluorometers may share a radiation source. In an exemplary configuration, a single radiation source may direct radiation to a beam splitter, which is positioned to separate the excitation radiation into two or more beams and direct the beams to two or more corresponding microfluorometers. Additionally or alternatively, the excitation radiation may be directed from the radiation source to one, two or more microfluorometers via one or more optical fibers.

[0177] It will be understood that the specific components shown in the drawings are exemplary and can be replaced with components having similar functions. For example, any of a variety of radiation sources can be used instead of LEDs. Particularly useful radiation sources are arc lamps, lasers, semiconductor light sources (SLS), or laser diodes. LEDs can be purchased from, for example, Luminus (Billerica, Massachusetts). Similarly, various detectors are useful, including but not limited to charge coupled device (CCD) sensors, photomultiplier tubes (PMTs), or complementary metal oxide semiconductor (CMOS) sensors. A particularly useful detector is a 5 megapixel CMOS sensor (MT9P031) available from Aptina Imaging (San Jose, California).

[0178] Figure 5 An exemplary embodiment of a microfluorometer including two excitation sources is provided. This configuration is useful for detecting at least two fluorophores that are excited at different wavelengths, respectively. If desired, the microfluorometer can be configured to include more than two excitation sources. For example, the microfluorometer can include at least 2, 3, 4 or more different excitation sources (i.e., sources that produce different wavelengths from each other). Alternatively or in addition, beam splitters and optical filters can be used to expand the range of excitation wavelengths available from a single radiation source. For embodiments in which several microfluorometers share excitation from one or more radiation sources, similar use of multiple radiation sources and / or optical filtering to separate the excitation beams can be used. As further described in detail elsewhere herein, the availability of multiple excitation wavelengths is particularly useful for sequencing applications that utilize several different fluorophore labels.

[0179] Figure 6An exemplary arrangement of four microfluorometers in a single readhead or carrier 300 is shown. The four microfluorometers are arranged in a staggered layout relative to the first and second channels 302 and 304 of the flow cell 306. In the arrangement shown, two of the microfluorometers (corresponding to detectors 310A and 310C) are configured to image the separation region of the first channel 302, while the other two microfluorometers (corresponding to detectors 310B and 310D) are configured to image the separation region of the second channel 304. As shown, the microfluorometers (corresponding to detectors 310A and 310C) are staggered in the x-dimension relative to the microfluorometers (corresponding to detectors 310B and 310D) so that two pairs of microfluorometers can detect adjacent first and second channels 302 and 304, respectively. The microfluorometers each have orthogonal emission and excitation paths, and the radiation source 312 is located on the same side of the readhead opposite the flow cell 306. Two of the detectors 310A and 310C are located on a first side of the readhead, while the other two detectors 310B and 310D are located on an opposite side, both of which are orthogonal to the side where the excitation source is located. Figure 6 In the exemplary embodiment shown, four radiation sources are in thermal contact with a single large heat sink 314. A single large heat sink provides a greater degree of heat dissipation than many configurations that use a separate heat sink for each radiation source. However, if desired, separate radiation sources can be thermally coupled to separate heat sinks. Figure 6 An advantage of the arrangement of the microfluorometers shown is the provision of a compact readhead. Similar advantages may be derived for embodiments in which the relative positions of the excitation source and detector in each microfluorometer are interchanged, Figure 6 The read head 300 is shown positioned to scan in the y dimension. The y dimension is parallel to the length of the flow cell 306, so that movement of the read head 300 in a scanning operation will result in imaging of an area along the length of the flow cell 306. The detectors 310A-310D are located on opposite sides of the read head 300 and on opposite sides of the flow cell 306, the sides of the flow cell extending along the scanning direction. The orientation of the read head 300 relative to the flow cell 306 and the scanning direction is merely exemplary, and other orientations may be used.

[0180] A microfluorometer or a read head with several microfluorometers can be located above the flow cell (arrow relative to gravity), as illustrated for several embodiments described herein. However, it is also possible to position the microfluorometer or read head below the flow cell. Thus, the flow cell can be transparent on the top side, bottom side, or both sides relative to the wavelength of the excitation and emission radiation used. In fact, in some embodiments, it may be desirable to position the microfluorometer on both sides of the flow cell or to position the read head on both sides of the flow cell. Other orientations relative to gravity are also possible, including, for example, a side-by-side orientation between the flow cell and the microfluorometer (or read head).

[0181] The microfluorometer or readhead can be configured to detect two opposing inner surfaces of the flow cell from a single side of the flow cell. For example, the microfluorometer or readhead can use an optical compensator that is inserted and removed to detect an alternative surface of the flow cell. Exemplary methods and devices for detecting opposing inner surfaces of a flow cell, such as the use of an optical compensator, are described in U.S. Pat. No. 8,039,817, which is incorporated herein by reference in its entirety. The compensator is optional, for example depending on the NA and / or optical resolution of the device.

[0182] Figure 7 is configured to receive a carrier assembly (such as carrier assemblies 400 and 500 (respectively Figure 8 and Fig.12 )) is a perspective view of a portion of a system stage 320. The system stage 320 includes a stage body or platform 321 having a base surface 322 and a plurality of references 324-326 positioned along the base surface 322. The references 324-326 have fixed positions relative to the base surface 322. Figure 7 In the embodiment, the stage body 321 is block-shaped, but it should be understood that various shapes can be used. The base surface 322 is shaped to be connected to the substrate and / or the carrier assembly. For example, at least a portion of the base surface 322 can be planar for connection to the flow cell. In some embodiments, the base surface 322 is configured to transfer thermal energy toward or away from the substrate of the carrier assembly. More specifically, the base surface 322 can be thermally coupled to a thermal cycler. As an example, when the flow cell is held by the carrier assembly and is located on the base surface 322, the base surface 322 can conduct heat toward the flow cell or absorb heat from the flow cell. In the illustrated embodiment, the base surface 322 connected to the carrier assembly is planar. However, in other embodiments, the base surface 322 can be non-planar. For example, the base surface 322 can be shaped to supplement the shape of the carrier assembly.

[0183] The datums 324-326 are configured to provide a fixed reference point or surface for engaging the substrate for holding the substrate in a fixed position relative to the optical system or more particularly the objective lens. In the illustrated embodiment, the datums 324-326 are cylindrical protrusions (e.g., posts) extending from the base surface 322, but in alternative embodiments the datums 324-326 may have other shapes. The position of the datums 324-326 relative to each other and the base surface 322 may be based on the design of the carrier assembly, the shape of the substrate (e.g., a flow cell), and / or the shape of the adapter plate.

[0184] Also shown, the system stage 320 (or docking system) can include an alignment mechanism 330 configured to engage a carrier assembly and / or a substrate. In the illustrated embodiment, the alignment mechanism 330 includes a movable arm 332 configured to rotate about an axis 333. The movable arm 332 is operably connected to a motor 334 configured to drive the movable arm 332. The datums 324-326 and the movable arm 332 generally define a carrier receiving area 336 of the base surface 322 therebetween. The carrier receiving area 336 is configured to allow a carrier assembly to be positioned thereon. When the carrier assembly is positioned on the carrier receiving area 336, the motor 334 can drive the movable arm 332 toward the carrier assembly. The movable arm 332 can engage the carrier assembly and push the carrier assembly toward the datums 324-326.

[0185] In the illustrated embodiment, the movable arm 332 is rotated. However, in other embodiments, the movable arm 332 can be moved in other ways. For example, the movable arm 332 can move in a linear manner. In some embodiments, a single stroke that moves the movable arm 332 to engage the carrier assembly can include movement in multiple directions. For example, the movable arm 332 can initially move in a first linear direction and then move in a second linear direction or rotate in another direction. In other embodiments, more than one alignment mechanism can be used. In addition, optional methods can also be used to keep the carrier assembly in a specified position. For example, a pneumatic pump can use a gas (e.g., ambient air) to push or pull the carrier assembly in a specified manner.

[0186] Figure 7 As also shown in FIG. 1 , the system stage 320 may include a plurality of manifold ports 340 . The manifold ports 340 are configured to align with ports of a substrate, such as ports of a flow cell. Fluids may be provided or withdrawn through the manifold ports 340 .

[0187] Figure 8 is a perspective view of a carrier assembly 400 according to one embodiment. The carrier assembly 400 is configured to hold a sample during an imaging operation in which an optical signal from a substrate is detected. The carrier assembly 400 may be used with a Figure 1The assay system 100 is used in conjunction with an assay system and is located at a system station such as a system station 320 ( Figure 7 ) system stage. The carrier assembly 400 includes a support frame 402. The support frame 402 includes a frame body 404 having first and second body sides 408, 410. The first body side 408 is configured to face an objective lens of an optical system such as objective lens 256. The second body side 410 is configured to face an objective lens of an optical system such as system stage 320 ( Figure 7 )’s system station.

[0188] The support frame 402 can define a sample area 406. In some embodiments, the sample area 406 includes an adapter plate 420. In other embodiments, the sample area 406 includes an open window or one or more through holes extending completely between the first and second body sides 408, 410. In some embodiments, the sample area 406 is a window extending completely through the frame body 404, so that the window is accessible through either of the body sides 408, 410. The adapter plate 420 can be located within the window and coupled to the support frame 402. The adapter plate 420 can block all or most of the window. In some embodiments, the adapter plate 420 and the support frame 402 form a continuous structure. In other embodiments, the adapter plate 420 is removably coupled to the support frame 402. In optional embodiments, the adapter plate 420 is not part of the carrier assembly 400. For example, during an SBS protocol, the carrier assembly 400 can include only the support frame 402 with a flow cell located within the sample area 406. During a microarray imaging protocol, the carrier assembly 400 may include an adapter plate 420 and an open-faced substrate such as a bead chip.

[0189] The frame body 404 also includes an inner frame edge 412 and an outer frame edge 414. In some embodiments, the inner frame edge 412 can define the sample area 406. The outer frame edge 414 defines the perimeter of the frame body 404 and is configured to engage an alignment feature of a docking system (not shown). The alignment feature can include, for example, an alignment mechanism, such as alignment mechanism 330 ( Figure 7 ). The frame body 404 has a thickness 416 measured between the first and second body sides 408, 410. The support frame 402 is configured to be located on a system stage and allow the objective lens to move along a designated path alongside the support frame 402 during an imaging operation. As used herein, the objective lens can "move" when the objective lens and / or the system stage are moved, so that an object desired to be imaged moves relative to the objective lens. In the illustrated embodiment, the thickness 416 is substantially uniform, so that the frame body 404 is substantially planar. In other embodiments, the frame body 404 can include non-planar features. The non-planar features can be located outside the designated path of the objective lens.

[0190] Also there Figure 8 As shown, the adapter plate 420 has a plate body 421. The adapter plate 420 is located within the sample area 406. In the illustrated embodiment, the adapter plate 420 covers all of the sample area 406, except for the passage or through hole 422 and the holes 464, 465, 466 of the adapter plate 420. In some embodiments, at least a portion of the adapter plate 420 can extend next to or engage the second body side 410. The plate body 421 includes an inner plate edge 424. The inner plate edge 424 defines a receiving portion 426 of the adapter plate 420. The plate body 421 can also include a substrate or chip platform 428 within the receiving portion 426. The chip platform 428 has a platform surface 430, which is configured to have a substrate located thereon. The plate body 421 also includes a recess 432. In the illustrated embodiment, the recess 432 surrounds a majority of the platform 428.

[0191] Figure 8 4, the carrier assembly 400 may include a retaining mechanism 418. The retaining mechanism 418 may be coupled to the adapter plate 420 and / or the frame body 404. The retaining mechanism 418 is configured to engage a substrate within the receiving portion 426 to retain the substrate in a fixed position within the receiving portion 426. The retaining mechanism 418 includes a movable reference block 440. In an exemplary embodiment, the reference block 440 is spring-loaded so that the reference block 440 can be deflected or moved to a compressed state and then released to engage a substrate (not shown) within the receiving portion 426 and retain the substrate within the receiving portion 426.

[0192] Fig. 9 4 is a plan view of a carrier assembly 400 having a substrate 434 positioned within a receiving portion 426 of an adapter plate 420. The substrate 434 is retained by a retaining mechanism 418. More specifically, a datum block 440 of the retaining mechanism 418 applies a retaining force 436 that presses a substrate edge 438 against an inner plate edge 424. The retaining force 436 is applied in a direction parallel to the XY plane. Thus, the substrate 434 is held in a fixed position relative to the adapter plate 420. In other embodiments, the retaining force 436 may be applied at least partially in a direction perpendicular to the XY plane so that the substrate 434 is pressed against the adapter plate 420. For example, the substrate 434 may be pressed against the platform surface 430 ( Figure 8 ).

[0193] In some embodiments, the adapter plate 420 can be movable along the XY plane relative to the frame body 404. For example, the adapter plate 420 can include an outer plate edge 442 configured to face the inner frame edge 412. In some cases, the outer plate edge 442 can represent the outermost edge of the adapter plate 420. However, in other cases, the outer plate edge 442 is not the outermost edge of the adapter plate 420. For example, a portion of the plate body 421 can be below the frame body 404 (e.g., Fig. 9 shown) and beside the main body side 410 ( Figure 8 ) extension. Fig. 9 As shown, the outer panel edge 442 and the inner frame edge 412 may be separated by a tolerance gap 444 and a tolerance gap 446. The tolerance gap 444 has a distance measured along the X-axis, while the tolerance gap 446 is a distance measured along the Y-axis.

[0194] In other embodiments, however, the adapter plate 420 may have a fixed position relative to the frame body 404. In certain embodiments, the adapter plate 420 and the frame body 404 may be molded within a common mold such that the frame body 404 and the adapter plate 420 are part of a single piece of material. Alternatively, the frame body 404 and the adapter plate 420 may be separate components that are secured to each in a fixed position relative to each other.

[0195] exist Fig. 9 438. The passage 422 is at least partially defined between an edge of the adapter plate 420 and a portion of the substrate edge 438. The passage 422 is sized and shaped to allow a portion of an individual's digit (e.g., finger) to be inserted therein and engage the substrate edge 438 for loading or removing the substrate 434. The passage 422 of the adapter plate 420 is positioned so that the individual can position the substrate 434 within the receiving portion 426 when grasping the substrate 434. For example, the passage 422A can receive the tip of an index finger or thumb, and the passage 422B can receive the tip of the thumb or index finger when the substrate 434 is located within the receiving portion 426. During the positioning operation, the retaining mechanism 418 can be activated, compressed to move the reference block 440 away from the receiving portion 426. When the substrate 434 is positioned within the receiving portion 426 or after the substrate 434 is positioned in the receiving portion 426, the reference block 440 can be released so that the reference block 440 can move back toward the substrate 434 and engage the substrate edge 438. As shown, the substrate 434 is an open-faced substrate having a microarray 448 thereon. Other types of substrates 434 can also be used in other embodiments.

[0196] Fig.104 is a plan view of a carrier assembly 400 having a substrate 450 located within a sample area 406. The substrate 450 can be a flow cell having one or more flow channels. For example, in the illustrated embodiment, the flow cell 450 has four flow channels 452 formed within a flow cell body 460 of the flow cell 450. Each flow channel 452 has an imaging segment 458 extending between a first port 454 and a second port 456. The first and second ports 454, 456 are openings or holes in the flow cell body 460. In the illustrated embodiment, the first port 454 is an inlet and the second port 456 is an outlet. However, in other embodiments, the first port 454 can be an outlet and the second port 456 can be an inlet. It is also shown that the flow channel 452 is linear and the imaging segments 458 of the flow channel 452 extend parallel to each other. However, in other embodiments, the flow channel 452 can extend along a non-linear path and / or can extend in non-parallel directions relative to each other.

[0197] In the illustrated embodiment, the adapter plate 420 is removed from the sample area 406. The frame body 404 or an optional adapter plate (not shown) can include an element (not shown) that extends into the sample area 406 and provides a resting surface for the flow cell 450, such that the frame body 404 prevents the flow cell 450 from passing through the sample area 406. The flow cell body 460 includes an outer body edge 462. The outer body edge 462 is configured to engage at least a portion of the inner frame edge 412 of the frame body 404. In some embodiments, the flow cell 450 can be sized and shaped relative to the inner frame edge 412 so that the flow cell 450 can be movable along the XY plane within the sample area 406.

[0198] refer to Fig. 9 and Fig.10 , frame body 404 includes apertures 464, 465, 466. In some embodiments where sample area 406 includes a window, apertures 464-466 open to the window. Apertures 464-466 are sized and shaped to receive corresponding datums 474, 475, 476 of a system stage (not shown). Apertures 464-466 receive corresponding datums 474-476 through second body side 410. Datums 474-476 may be aligned with datums 324-326 ( Figure 7) are similar or identical. The datum 476 is configured to stop the movement of the adapter plate 420 or, alternatively, the flow cell along the Y axis. The datums 474, 475 are configured to stop the movement of the adapter plate 420 or, alternatively, the flow cell along the X axis. The holes 464-466 are sized to be larger than the corresponding datums 474-476 to allow the frame body 404 to slide along the base surface during the positioning operation. Therefore, the datums 474-476 are configured to align the flow cell 450 at a specified position, or, alternatively, to align the adapter plate 420 and, therefore, the substrate 434 at a specified position. At the specified position, the flow cell 450 can be positioned for imaging and for aligning the flow channel 452 with the manifold port of the system stage (not shown). Each of the first and second ports 454, 456 of the flow cell 450 can be aligned with the corresponding manifold port. At the specified position, the substrate 434 is not fluidically coupled to any one of the corresponding manifold ports. In some embodiments, base 434 and / or adapter plate 420 may seal the manifold ports.

[0199] To position substrate 450 on the system stage, substrate 450 may be positioned within sample area 406 or the window. Sample area 406 may be sized larger than substrate 450 to allow for some movement of substrate 450 along the XY plane. Substrate 450 may engage one or more surfaces of frame body 404 that prevent substrate 450 from freely moving through window 406. When carrier assembly 400 is positioned on the system stage, fiducials 474-476 may be advanced through corresponding apertures 464-466. Alignment mechanism 330 ( Figure 7 ) can be activated to move the frame body 404 along the XY plane. More specifically, the movable arm can engage the outer frame edge 414 and provide an alignment force 437 that moves (e.g., shifts) the frame body 404 along the XY plane. When the frame body 404 moves along the XY plane, the base 450 engages the datums 474-476 and prevents the base 450 from moving further along the XY plane. The frame body 404 can move relative to the base 450 until the base 450 engages the inner frame edge 412 and prevents the frame body 404 from moving further. Therefore, the base 450 can have a specified position relative to the objective lens for detecting light signals.

[0200] To position the substrate 434 on the system stage, the adapter plate 420 can be positioned within the sample area 406 of the frame body 404. For example, the adapter plate 420 can be coupled to the second body side 410 ( Figure 8 ), so that a portion of the adapter plate 420 is disposed within the window 406. The substrate 434 can be loaded into the receiving portion 426 before the adapter plate 420 is positioned within the sample area 406 or after the adapter plate 420 is positioned within the sample area 406. For example, Fig.11A portion of a carrier assembly 400 is shown in which a substrate 434 is engaged with a datum block 440 and retained within a receiving portion 426. The datum block 440 is located within a retaining recess 480 defined at least in part by the inner plate edge 424. The datum block 440 includes an engagement surface 482 extending into the receiving portion 426 and is configured to engage the substrate 434 therein. The datum block 440 is configured to move relative to the receiving portion 426 or the adapter plate 420 to allow the substrate 434 to be freely positioned within the receiving portion 426. For example, the datum block 440 can be pressed so that the engagement surface 482 is located within the plate body 421 and not within the receiving portion 426. When the substrate 434 is loaded into the receiving portion 426 or after the substrate 434 is loaded into the receiving portion 426, the datum block 440 can be released to allow the engagement surface 482 to engage the substrate edge 438. The engagement surface 482 can be shaped so that the datum block 440 pushes the substrate 434 along the Y axis. The base 434 can be held between the datum block 440 and a portion of the inner panel edge 424. In an exemplary embodiment, the retaining mechanism 418 includes a spring that holds the datum block 440 in a biased position. However, alternative retaining mechanisms can be used.

[0201] Return to Fig. 9 , when substrate 434 is located in the receiving plate 420 and is held by the receiving plate 420, the carrier assembly 400 can be loaded onto the system stage. When the carrier assembly 400 is located on the system stage, the benchmark 474-476 can advance through the corresponding hole 464-466. As described above, the alignment mechanism can be activated to move the frame body 404 along the XY plane. When the frame body 404 moves along the XY plane, the receiving plate 420 engages the benchmark 474-476, which prevents the receiving plate 420 from moving further along the XY plane. In some embodiments, the frame body 404 can move relative to the receiving plate 420 until the receiving plate 420 engages the inner frame edge 412 and prevents the frame body 404 from moving further. Therefore, the receiving plate 420 can have a fixed position relative to the object lens, and therefore the substrate 434 can have a specified position relative to the object lens for detecting light signals.

[0202] As described herein, in alternative embodiments, the adapter plate 420 can have a fixed position relative to the frame body 404. For example, the adapter plate 420 can be removably secured to the frame body 404 such that the adapter plate 420 does not shift or move relative to the frame body 404. Alternatively, the frame body 404 and the adapter plate 420 can be part of the same unitary structure.

[0203] Fig.12 5 is a perspective view of a carrier assembly 500 according to an embodiment. The carrier assembly 500 may include a carrier assembly 400 ( Figure 8) with similar or identical features and elements. The carrier assembly 500 can be used with an assay system such as Figure 1 The carrier assembly 500 includes a support frame 502. The support frame 502 includes a frame body 504 that defines a sample area 506. The frame body 504 includes first and second body sides 508, 510. In the illustrated embodiment, the sample area 506 forms a receiving portion or space for receiving a substrate. It is also shown that the inner frame edge 512 of the frame body 504 defines holes 564, 565 and 566 of the frame body 504 that are open to the sample area 506. The holes 564-566 are sized and shaped to receive a reference (not shown) for aligning the flow cell during a positioning operation.

[0204] The frame body 504 includes an inner frame edge 512 and also an outer frame edge 514. The inner frame edge 512 can define a sample area 506. The outer frame edge 514 defines the perimeter of the frame body 504 and is configured to engage an alignment feature (not shown) of an optical system. The carrier assembly 500 includes an adapter plate 520 having a plate body 521. In the illustrated embodiment, the adapter plate 520 is located within the sample area 506. The adapter plate 520 spans the entire sample area 506, except for the passage or through hole 522 and the holes 564-566.

[0205] In some embodiments, the adapter plate 520 and the support frame 502 are separate components. In such embodiments, at least a portion of the adapter plate 520 can extend beside or engage the second body side 510 of the frame body 504. The board body 521 includes an inner board edge 524. The inner board edge 524 defines a receiving portion 526 for the adapter plate 520. The board body 521 also includes a substrate or chip platform 528 within the receiving portion 526. The chip platform 528 includes a platform surface 530, which is configured to have a substrate 534 located thereon. The board body 521 also includes a recess 532.

[0206] Fig.12 526, the adapter plate 520 includes a retaining mechanism 518 coupled to the plate body 521. The retaining mechanism 518 is configured to engage the substrate 534 when the substrate 534 is located within the receiving portion 526 to retain the substrate 534 in a fixed position relative to the adapter plate 520. The retaining mechanism 518 includes a movable reference block 540 operably coupled to a spring 541. The spring 541 is configured to urge the substrate 534 along the Y-axis to retain the substrate 534 between the reference block 540 and the inner plate edge 524. In the illustrated embodiment, the reference block 540 can be pulled away from the receiving portion 526 to allow the substrate 534 to be positioned therein.

[0207] In some embodiments, when base 534 is located on adapter plate 520 and when it can be similar to base 450 ( Fig.10 ) is located on the adapter plate 520, the adapter plate 520 can be coupled to the frame body 504. For example, the adapter plate 520 may include fluid openings 581, 582, 583 and 584. The fluid openings 581, 582 are located at one end 586 of the adapter plate 520, and the fluid openings 583, 584 are located at the opposite end 588 of the adapter plate 520. The fluid openings 583, 584 are located on opposite sides of the retaining mechanism 518. The fluid openings 581-584 allow a manifold port (not shown) of a manifold (or system stage) to enter the flow pool. For example, a nozzle can extend through the fluid openings 581-584 and engage a port of the flow pool.

[0208] Fig.13 5 is a plan view of a carrier assembly 500 positioned on a system stage 550. The system stage 550 includes a plurality of datums 574-576 protruding from a base surface 578 of the system stage 550. The second body side 510 ( Fig.12 ) engages base surface 578. During imaging operation, first body side 508 faces objective lens (not shown). Holes 564-566 of support frame 502 open to second body side 510 and extend from second body side 510 toward first body side 508. In the illustrated embodiment, holes 564-566 extend completely through support frame 502. However, in other embodiments, holes 564-566 may be recesses that extend only partially into support frame 502. Holes 564-566 receive corresponding datums 574-576.

[0209] In some embodiments, the adapter plate 520 is movable (e.g., slidable) relative to the frame body 504. In other embodiments, the adapter plate 520 has a fixed position relative to the frame body 504. The fluid openings can also receive nozzles of the manifold when the carrier assembly 500 is on a system table. As shown, the receiving portion 526 is centrally located so that the fluid openings 581, 582 and the fluid openings 583, 584 are located on opposite ends of the receiving portion 526. However, the receiving portion 426 ( Figure 8 ) is not located at the center. Instead, receiving portion 426 is located closer to one side than the other side. Receiving portion 426 is located farther from the corresponding reference than receiving portion 526. Fig.13 540. As also shown in FIG. 54, datum block 576 can engage datum block 540. In an exemplary embodiment, datum block 576 can facilitate pressing datum block 540 into substrate 534. Substrate 534 can be held between datum block 540 and one or more portions of inner panel edge 524.

[0210] Fig.14A5 is a cross-section of a portion of the carrier assembly 500 showing the sample region 506 and the receiving portion 526 in greater detail. As shown, the adapter plate 520 is coupled to the support frame 502 and is located within the sample region 506. The inner frame edge 512 defines a substrate receiving recess 542 (indicated by a dashed rectangular box) located above the adapter plate 520 and above the receiving portion 526. The substrate receiving recess 542 is sized and shaped to receive a first planar substrate, such as a flow cell 450. The inner plate edge 524 defines a receiving portion 526. The receiving portion 526 is sized and shaped to receive a substrate 534, which is also planar and sized to be smaller than the first planar substrate. The receiving portion 526 resides at least partially below the substrate receiving recess 542. In some embodiments, the receiving portion 526 is at least one of: coincident with a receiving plane 546 that intersects the inner frame edge 512 or located below the receiving plane 546. In the illustrated embodiment, the receiving portion 526 is located below the receiving plane 546. The receiving plane 546 extends parallel to the XY plane formed by the X and Y axes. Although the receiving portion 526 is located below the receiving plane 546, it should be understood that a portion of the substrate 534 can be located within the substrate receiving recess 542 during imaging operations.

[0211] Fig. 14B A flow cell 560 and an open-face substrate 570 are shown side by side. The flow cell 560 has a flow channel 562 defined between two internal channel surfaces 564, 566. In the illustrated embodiment, the open-face substrate 570 includes a microarray of features 572 (such as beads), wherein each feature has a specified address (among the features in the microarray) and a specified chemical (e.g., nucleic acid). A table or database can associate each address with a corresponding chemical. The features 572 are located along a substrate surface 574.

[0212] The carrier assembly described herein is configured to hold different types of substrates, such as a flow cell 560 and an open-face substrate 570, so that the desired surface or area to be imaged is located within the imaging zone 580 of the optical system. The imaging zone 580 can represent a generally flat volume within which the optical system can be focused. The generally flat volume can have an X dimension, a Y dimension, and a Z dimension. The X and Y dimensions can be several millimeters or more. The Z dimension can be within 1000 microns or less. More specifically, the Z dimension can be 900 microns or less, 800 microns or less, 700 microns or less, 600 microns or less, or 500 microns or less. In a specific embodiment, the Z dimension can be 400 microns or less, 300 microns or less, or 200 microns or less. In a more specific embodiment, the Z dimension can be 90 microns or less, 80 microns or less, 70 microns or less, or 60 microns or less. In a more specific embodiment, the Z dimension can be 50 microns or less, 40 microns or less, 30 microns or less, 20 microns or less, or 10 microns or less.

[0213] In some embodiments, at least one of the substrate surface 574 and the interior channel surfaces 564, 566 can be positioned within the imaging region 580 by a carrier assembly (not shown). The carrier assembly can be similar or identical to any of the carrier assemblies described herein. Thus, each of the open-face substrate 570 and the flow cell 560 can be inspected by an optical system. Fig. 14B As shown, the substrate surface 574 and the channel surface 564 are coplanar. In other embodiments, the substrate surface 574 may be coplanar with the channel surface 566. In other embodiments, the substrate surface 574 may not be coplanar with any channel surface. The substrate surface 574 can be offset along the Z axis with the corresponding channel surface by a specified maximum amount ΔZ. The maximum amount ΔZ can be, for example, 100 microns or less, 90 microns or less, 80 microns or less, 70 microns or less, 60 microns or less, 50 microns or less, 40 microns or less, 30 microns or less, 20 microns or less or 10 microns or less. However, in other embodiments, the maximum amount ΔZ of the offset can be greater. In the illustrated embodiment, the open face substrate 570 has a thickness greater than the thickness of the flow cell 560. In other embodiments, the thickness of the flow cell 560 can be greater than the thickness of the open face substrate 570. In other embodiments, the thickness can be substantially equal.

[0214] Fig.15 and Fig.164 is a plan view of substrates 450, 434, which are respectively referred to as flow cells and open-face substrates hereinafter. Flow cell 450 includes four flow channels 452A, 452B, 452C, 452D extending parallel to each other along the Y axis. In optional embodiments, more or fewer flow channels may be used. Flow channels 452A-452D are aligned so that each flow channel starts and ends at substantially the same axial position along the Y axis. Open-face substrate 434 includes microarray 448. Microarray 448 includes a plurality of array sections 621-628, each of which includes a plurality of characteristic strips or passages 630. In the illustrated embodiment, microarray 448 includes eight (8) array sections, each of which has five (5) characteristic strips. However, in other embodiments, more or fewer array sections may be used. In other embodiments, each array section may include more or fewer characteristic strips. In the illustrated embodiment, the array sections are separated from each other. In other embodiments, microarray 448 comprises one continuous array without separate array sections.

[0215] Fig.15 and Fig.16 Also shown are imaging zones 600, 620, respectively, which may be similar or identical to imaging zone 580. Imaging zones 600, 620 represent three-dimensional zones from which light signals may be detected by the optical system from flow cell 450 and open-face substrate 434, respectively. Different assay protocols may be configured (e.g., programmed) to image the respective zones. In some embodiments, the imaging zone represents the sum of volumes that may be scanned by the optical system for the respective substrates. In certain embodiments, imaging zone 600 may completely overlap imaging zone 620. In other embodiments, imaging zones 600, 620 may include non-overlapping portions. Imaging zones 600, 620 are typically flat zones with a small Z dimension. The optical system may include a reader head similar to read head 300 ( Figure 6 ) of a reading head or carrier (not shown). The optical system may include six microfluorometers (not shown) having, among other things, six objective lenses (not shown). Each objective lens is configured to scan a corresponding sub-area.

[0216] As described herein, one or more different types of substrates can be maintained in the same imaging area of ​​the optical system. For example, a first carrier assembly having a first type of substrate on a system stage can be replaced with a second carrier assembly on the system stage. The second carrier assembly can have a second type of substrate. Each of the substrates of the first and second carrier assemblies can be maintained so that the corresponding samples are located in the same imaging area. Therefore, although the imaging areas 600, 620 are described separately below, it should be understood that the imaging areas can overlap each other at least in part. For example, a sample along a second substrate (e.g., a microarray of features) can be located in the same imaging area for a different first substrate (e.g., a flow cell).

[0217] Each objective of the microfluorometer can have a field of view (FOV) corresponding to the area that can be imaged or captured by the objective in a single image. Fig.15 and Fig.16 Six FOVs 611-616 are shown. The optical system is configured to move the objective lens relative to the corresponding substrate to obtain multiple images. The optical system is a point-and-shoot optical system in which several different images are captured to cover the entire imaging area. In other embodiments, the optical system can be a line scan or point scan optical system. Fig.15 In FIG. 6 , each of FOVs 611-616 is configured to move along a portion of a first flow channel and then along a portion of a second flow channel. After the imaging operation, all four flow channels may be completely (or nearly completely) imaged. Fig.16 In the embodiment, only two FOVs 611, 612 are moved along the microarray to obtain multiple images of the microarray. In some embodiments, one or more FOVs not used for imaging the substrate can be used to image an identification code 640 (eg, a barcode) identifying the type of substrate.

[0218] As an example, during a first imaging operation, the read head may move along the flow cell 450. As the read head moves relative to the system stage, each of the objective lenses may detect an optical signal from a corresponding FOV. Fig.15As shown, the imaging area 600 is formed by six separate sub-areas 601-606. Each of the sub-areas 601-606 represents a portion of the imaging area 600 that can be imaged by one of the corresponding FOVs. For example, the read head can move along the Y axis. FOVs 611-613 can obtain multiple images of flow channel 452A, and FOVs 614-616 can obtain multiple images of flow channel 452C. In some embodiments, the read head can be paused intermittently so that the flow cell 450 and the read head have a substantially fixed position relative to each other when the image is obtained. In other embodiments, the read head may not be paused and can be continuously moved along the flow cell 450. Due to the number of microfluorometers and the position of the corresponding FOVs, the entire length of the flow channels 452A and 452C can be imaged after the read head moves about 1 / 3 of the length of the flow channel. The light signal emitted from the flow cell can be detected by a corresponding image sensor (e.g., a CMOS imager). Therefore, the two flow channels can be imaged concurrently or simultaneously.

[0219] In some embodiments, the FOVs 611-616 are sized so that the width of the FOV along the X-axis is less than the width of the corresponding flow channel. In such embodiments, the imaging of the flow channels 452A, 452C can be repeated. For example, the optical system can move the FOVs 611-616 along the X-axis by an increment so that the FOVs remain within the flow channels 452A, 452C, but at different X positions. The FOVs 611-616 can then be moved again along the Y-axis to image another strip of the flow channels 452A, 452C. The process of incrementally moving the FOV along the X-axis and imaging along the Y-axis can be repeated multiple times until the entire flow channels 452A, 452C are imaged. In other embodiments, the FOVs 611-616 are large enough to capture the entire width of the flow channels 452A, 452C, so that only one stage of moving the FOVs 611-616 along the Y-axis is necessary.

[0220] The readhead may then be moved along the X-axis so that FOVs 611-613 are positioned for imaging flow channel 452B and FOVs 614-616 are positioned for imaging flow channel 452D. The readhead may then be moved along the Y-axis. FOVs 611-613 may obtain multiple images of flow channel 452B and FOVs 614-616 may obtain multiple images of flow channel 452D. In some embodiments, the readhead may be temporarily paused so that the flow cell 450 and the readhead have a substantially fixed position relative to each other while the images are being obtained. Due to the number of microfluorometers and the position of the corresponding FOVs, each of flow channels 452B and 452D may be imaged after the readhead has moved approximately 1 / 3 of the length of the flow channel. As discussed above, the FOV may be incrementally moved along the X-axis and flow channels 452B, 452D may be imaged again until the entire desired portion of the flow channel is imaged.

[0221] Thus, during a first imaging protocol in which the readhead detects light signals from the flow cell, the readhead is configured to move a specified distance along the Y-axis (e.g., approximately 1 / 3 of the length of the flow channel) and a short distance along the X-axis to optionally reposition the FOV within the same flow channel and then position the FOV in an adjacent flow channel.

[0222] The image data obtained from the flow cell 450 can be transmitted and / or processed by the detection data analysis module of the measurement system. Optionally, the measurement system can then detect light signals from different surfaces of the flow cell. For example, the light signal can be detected from the top surface of the flow channel during a first imaging session and from the bottom surface during a second imaging session. In some embodiments, the optical system (or optical train) can be modified between the first and second imaging sessions.

[0223] During the second imaging operation, the read head may be scanned along the open face substrate 434. Unlike the first imaging operation, the second imaging operation may utilize only two microfluorometers for detecting light signals from the chemical substances. In the illustrated embodiment, the microarray 448 is imaged using only a microfluorometer associated with FOV 611 and a microfluorometer associated with FOV 612. More specifically, FOV 611 may be moved along each of the feature strips 630 for each of the array sections 621-624, and FOV 612 may be moved along each of the feature strips 630 for each of the array sections 625-628. While one feature strip 630 is being imaged through FOV 611, another feature strip 630 is being imaged through FOV 612. Thus, the two feature strips 630 may be imaged concurrently or simultaneously.

[0224] As indicated by the shading of FOVs 613-616, the microfluorometer associated with FOVs 613-616 does not capture an image of microarray 448. However, in some embodiments, one or more FOVs may capture an image (or multiple images) of identification code 640. For example, while FOVs 611, 612 are capturing images of microarray 448, FOV 613 may image identification code 640. The image of identification code 640 may be analyzed by the system to identify the type of microarray. In some embodiments, identification code 640 may include information about the microarray. For example, identification code 640 may identify the address and identity of a feature within a microarray. In other embodiments, identification code 640 may be used to determine the address and identity of a feature within a microarray by using, for example, a database. While Fig.16 The identification code 640 is shown at one particular location, but the identification code 640 may have other locations. For example, the identification code 640 may be located closer to the imaging area 620 along the array section 628. Alternatively, the identification code 640 may be located closer to the bottom edge of the open face substrate 434.

[0225] The image data obtained from the open face substrate 434 can be transmitted and / or processed by the detection data analysis module of the determination system. In any one of the first and second imaging operations, as described below, the image data can be digitally spliced ​​together. Alternatively, the image data may not be spliced ​​together. For example, each sub-area can be analyzed as a separate image.

[0226] Fig.17 650 according to an embodiment. The method 650 may be at least partially performed by, for example, the determination system 100 ( Figure 1 ) is performed or implemented by a measurement system of the optical system. Method 650 includes positioning a first carrier assembly on a system stage at 652. The system stage can be similar or identical to system stage 320. The carrier assembly can include a support frame having an inner frame edge defining a window of the support frame. The first carrier assembly can include a first substrate located within the window and surrounded by the inner frame edge. The first substrate has a sample thereon located within an imaging region of the optical system.

[0227] As an example, the first substrate can be a flow cell. If the first substrate is a flow cell, method 650 can also include flowing one or more fluids through a flow channel (or multiple flow channels) of the flow cell at 654. Flowing at 654 can be performed according to a predetermined order, wherein, for example, a first liquid is provided through the flow channel, followed by a second liquid, followed by a third liquid, and then by a fourth liquid. The liquid can be configured to perform a predetermined assay, such as an SBS assay. For example, the first liquid can be a solution comprising fluorescently labeled nucleotides, the second liquid can be a washing solution (e.g., a buffer solution), the third liquid can be a lysing solution, and the fourth liquid can be another washing solution.

[0228] At 656, an optical system can be used to detect an optical signal from the sample of the first substrate. In some embodiments, the detection at 656 can include irradiating the first substrate with an excitation light or multiple excitation lights. For example, the sample on the first substrate can include a fluorescent marker that provides light emission of a predetermined wavelength when excited by an excitation light of a predetermined wavelength. For embodiments in which the first substrate is a flow cell, the detection at 656 can utilize the flow sorting of one or more fluids at 654. For example, during an SBS assay protocol, fluorescently labeled bases are sequentially added to the nucleic acids of each cluster. After each incorporation event, the sample can be excited and an optical signal can be detected from the sample.

[0229] The optical system can capture a series of images of each flow channel using one or more microfluorometers according to a first imaging scheme. The first assay scheme can include a first imaging scheme. The first assay scheme can be stored as an instruction set in one or more modules (e.g., a memory). The first imaging scheme includes a series of steps for moving the first substrate relative to the optical system and capturing a specified portion of the imaging area. For example, a sequence can include imaging a series of images along one strip of a flow channel, and then imaging a series of images along an adjacent strip of the same flow channel, as described herein. The sequence can also include moving the FOV to another flow channel and repeating the process for capturing images for another flow channel. As described above, the optical system can include a read head having multiple microfluorometers.

[0230] The method 650 may also include replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage at 658. The second carrier assembly may include a support frame and an adapter plate held by the support frame. The second carrier assembly may have a second substrate held by the adapter plate, the second substrate having a sample thereon. The second substrate may be, for example, an open-face substrate. The sample of the second substrate is located within an imaging region of the optical system.

[0231] At 658, the replacement may include replacing the entire first carrier assembly with a completely new second carrier assembly. However, in some embodiments, at 658, the replacement includes changing the configuration of the first carrier assembly such that an adapter plate is added to the support frame. In other words, the first and second carrier assemblies may use the same support frame, but the second carrier assembly may include an adapter plate coupled to the support frame. It should also be understood that at 658, the replacement may include removing the first carrier assembly from the system table and placing the second carrier assembly on the system table within a short period of time (e.g., within a few minutes), but may also include removing the first carrier assembly from the system table and placing the second carrier assembly on the system table after an extended period of time (e.g., several days).

[0232] At 660, an optical system may be used to detect an optical signal from a second substrate. As described above, at 660, detection may include exciting a fluorescent marker of a sample and detecting light emission therefrom. At 660, detection may include capturing a series of images of a second substrate using one or more microfluorometers according to a second assay (or imaging) scheme. The second assay scheme is different from the first assay scheme. The second assay scheme may be stored as an instruction set in one or more modules (e.g., a memory). The second assay scheme includes a sequence of steps for moving the second substrate relative to the optical system and capturing a specified portion of the imaging area. For example, the sequence may include imaging a series of images along a feature strip of a microarray, and subsequently imaging a series of images along an adjacent feature strip, as described herein. After detecting an optical signal from the second substrate, the second carrier assembly may be replaced with a third carrier assembly at 662. The third carrier assembly may include or may not include an adapter plate, and may or may not include a substrate similar to the substrate of the first carrier assembly or the substrate of the second carrier assembly.

[0233] Thus, the same assay system can be configured to perform different imaging schemes for detecting light signals from different types of substrates. Different imaging schemes can include different movements of the substrate relative to the objective lens or multiple objective lenses. For embodiments utilizing more than one objective lens or microfluorometer, it is contemplated that the imaging schemes utilize different numbers of available microfluorometers. For example, a first imaging scheme may utilize six microfluorometers out of a total of six available microfluorometers. However, a second imaging scheme may utilize only two of the available six microfluorometers.

[0234] In a first imaging scheme, the measuring system can control the objective lens and / or the system stage to image a first series of side-by-side discrete images along one axis (e.g., the Y axis) of a substrate surface (such as a channel surface of a flow cell). Alternatively, the measuring system can control the objective lens and / or the system stage to move the objective lens along the X axis and image a second series of side-by-side discrete images along one axis (e.g., the Y axis) of the substrate surface. The second series can be adjacent to the first series so that the images of the first and second series are adjacent to each other. After the substrate surface is imaged, the measuring system can control the objective lens and / or the system stage in a similar manner to image the separated substrate surface. After another substrate surface, the measuring system can control the objective lens and / or the system stage to flow the reagent through the flow channel. The imaging scheme can then be repeated. The image can be analyzed to determine the characteristics or properties of the sample. In a specific embodiment, the first imaging scheme can be used during the SB scheme. As described above, the first imaging scheme can include only one objective lens (or microfluorometer) or multiple objective lenses with predetermined positions relative to each other.

[0235] In the second imaging scheme, the measuring system can control the object lens and / or the system stage to image different types of substrates. For example, different types of substrates can include a microarray with multiple discrete sections. Optionally, each discrete section can include multiple discrete feature strips. In the second imaging scheme, the measuring system can control the object lens and / or the system stage to image the side-by-side discrete images of the first series along an axis (e.g., X-axis) of the substrate surface. More specifically, the discrete images of the first series can belong to the first feature strip of the microarray. The measuring system can then control the object lens and / or the system stage to move the object lens to another feature strip along the Y-axis. The side-by-side discrete images of the second series can be generated along the X-axis. The second series can be adjacent to the first series, but the first and second series may not be adjacent to each other.

[0236] Figure 18-21 A stitching operation is shown, where images captured from adjacent areas of a substrate surface (e.g., a substrate surface having a microarray) can be combined or stitched together to provide a complete representation of the substrate surface. The complete representation can be a data representation that provides the location (e.g., address or absolute coordinates) and signal value of each feature. Alternatively, the complete representation can be a combined image comprising multiple images stitched together. The stitching operation can be used to form, for example, a microarray 448 ( Fig. 9 ). However, it is contemplated that the data representation may belong to other microarrays, such as random arrays or ordered arrays of nucleic acid clusters. The splicing operation is a method that can be performed by an assay system or another computing system within a commercially reasonable period of time. The splicing operation may be stored as an instruction set in a memory. The splicing operation may form part of an assay protocol (such as the second assay protocol described above).

[0237] Fig.18An image 700 according to one embodiment is shown. The image 700 may show, for example, a portion of a characteristic strip of a microarray. Fig.18 Also shown is an enlarged portion 702 of image 700. Image 700 includes a dense array of pixels, each of which represents or corresponds to a light intensity from a microarray. More specifically, the features of the microarray can provide light emissions detected by a corresponding image sensor. In a particular embodiment, the features are fluorescently labeled so that when excited by an excitation light, the features provide light emissions. The features of the microarray can have a specified order so that each feature has a known address relative to other features of the microarray.

[0238] Fig.19 7 is an enlarged view of an image 700 showing a feature locator 704 of a microarray. Each image may have a known position relative to the substrate surface captured within the image. Each image also has a known area. Fig.19 Also shown are individual pixels 706, where each pixel is a square with uniform light intensity. After obtaining an image of the microarray, the stitching operation may include identifying the location of features within the image. Fig.19 , each of the feature locators 704 is represented by a circle. Note that the feature locators 704 are not part of the image 700. Furthermore, the stitching operation does not require the feature locators 704 to be located relative to the image. Instead, each of the feature locators 704 represents an identified or determined location of a corresponding feature within the microarray shown within the image 700. The feature locators 704 (or the location of the features) can be determined by analyzing the image 700. More specifically, the features (e.g., beads) have a known size and shape and a known order or arrangement relative to each other within the microarray. For example, in the illustrated embodiment, the features are beads arranged in a hexagonal array. Using the known arrangement and size and shape of the features, the light intensity of the pixels can be analyzed to determine the location of the feature locators 704, or more specifically, the features within the image 700.

[0239] The stitching operation can also include determining the signal value for each of the features in the microarray. The signal value for each feature can be based on the light intensity of the pixel of the feature locator 704 corresponding to the corresponding feature. In the illustrated embodiment, each of the features can correspond to multiple pixels. For example, the feature locator 704' surrounds two complete pixels and eleven parts of other pixels. Some of the other pixels are mainly located in the feature locator 704', and some of the other pixels are mostly not in the feature locator 704'. The stitching operation can, for example, determine the signal value by adding the light intensity of the complete pixel and the light intensity of the other pixels. The score can be based on the number of corresponding pixels in the feature locator 704'. In other words, the pixels that are only partially in the feature locator can be weighted. Although a method for determining the signal value is described herein, it should be understood that there are multiple other formulas for determining the signal value based on the light intensity of the pixel associated with a specific feature.

[0240] A series of images captured by the optical system may include overlapping portions of the microarray. More specifically, the assay protocol may be configured to capture overlapping images so that the overlapping images can be stitched together in a subsequent analysis. In particular, the overlapping portions within two adjacent images may be used to align or stitch adjacent images. In some embodiments, the stitching operation includes stitching images to each other to generate a larger image that includes the entire microarray or a portion of the microarray (such as a segment or a characteristic strip). However, in exemplary embodiments (such as with respect to Fig. 20 and Fig.21 In the embodiment described herein, the stitching operation stitches (ie, combines) the data representations of the portions of the microarray captured within the image. Stitching the data representations together may be less computationally intensive than stitching the images of the microarray.

[0241] Fig. 20 and Fig.21 A stitching operation is schematically shown with respect to a series of data representations. Each data representation corresponds to one of the images captured by the optical system. The stitching operation can stitch (or combine) multiple data representations 711-715. Each data representation includes a subarray of data features 716. Each data feature 716 corresponds to one of the features of the microarray. Fig.16, each data feature 716 has a position relative to other data features 716 within the same data representation or subarray. For example, each position can be represented by an address having a column number and a row number. In other embodiments, each address can be an X, Y coordinate. Although not shown, each data feature 716 can have a signal value assigned to it, which is based on the light intensity associated with the corresponding feature of the microarray. Each of the data representations 711-715 can be generated by identifying the position of the feature and determining the signal value of the corresponding feature as described above. The microarray can have a known pattern or arrangement so that each of the data features 716 can have a known position relative to other data features.

[0242] like Fig. 20 As shown, each of the data representations 711-715 can include data features 716 corresponding to the features of the microarray also represented by the data features 716 of the adjacent data representations. In other words, the images represented by the data representations 711-715 overlap each other. The data features 716 represented by more than one data representation are located in the overlapping portion 720. However, due to the tolerance of the determination system, the amount of overlap between two adjacent images is unknown. The embodiment set forth herein is configured to compare the signal values ​​of the data features 716 in the adjacent data representations to identify the data features 716 and to combine the data representations together.

[0243] In some embodiments, the concatenation operation may include comparing data features 716 of one or more columns of a first data representation with data features 716 of one or more columns of an adjacent second data representation. More specifically, signal values ​​of data features 716 of one or more columns of the first data representation may be compared with signal values ​​of data features 716 of one or more columns of the second data representation. Optionally, the signal values ​​may be normalized before comparing the signal values.

[0244] As an example, data representation 711 has column 721 of data feature 716. Column 721 is the rightmost column of data representation 711. Data representation 712 has column 722A of data feature 716. Column 722A is the leftmost column of data representation 712. An embodiment may calculate a correlation value using the signal value of data feature 716 of column 721 and the signal value of data feature 716 of column 722A. If the correlation value meets a specified threshold, columns 721, 722A may be designated as overlapping columns representing the same feature of a microarray. If the correlation value does not meet a specified threshold, a splicing operation may compare column 721 to another column of data representation 712.

[0245] In certain embodiments, the stitching operation may compare more than one column of data representations 711 with more than one column of data representations 712. Again, a correlation value may be determined. If the correlation value meets a specified threshold, the data representations 711, 712 of the multiple columns are designated as overlapping columns representing the same feature of the microarray. If the correlation value does not meet the specified threshold, the stitching operation may compare more columns of each of the data representations 711, 712. The specified threshold may be, for example, 60% or greater.

[0246] The comparison operation may be repeated for each pair of adjacent data representations. For example, in the illustrated embodiment, comparison operations are also performed between data representations 712 and 713, between data representations 713 and 714, and between data representations 714 and 715. Thus, the data representations may be concatenated with one another to form a complete representation of a microarray (or a portion of a microarray, such as a characteristic stripe). Fig.21 711-715. As shown, the data representation between two data representations undergoes two comparison operations. The data representation at the end of the microarray undergoes only one comparison operation.

[0247] When spliced ​​to each other, the data representations can be combined to provide a complete representation of the microarray (or a discrete portion of the microarray, such as a segment or feature strip). The splicing operation can include comparing the number of features within the complete representation to the expected number of features (e.g., the known number of features in the microarray). If the number of features within the complete representation is equal to the expected number of features in the microarray, the assay system can analyze the features to determine a property or characteristic of the sample.

[0248] The complete representation may include the absolute coordinates for each feature and the signal value for each feature. Thus, the stitching operation may allow the location of one feature in a first image to be determined relative to the location of another feature in an image that is not adjacent to the first image. By knowing the location of each feature within the microarray, the chemical species immobilized at the feature may be identified, and the signal value of the feature may be used to determine a property or characteristic of the sample. In certain embodiments, the microarray may be used for genotyping.

[0249] although Fig. 20 and Fig.21Only five overlapping data representations are shown, but it should be understood that embodiments can analyze fewer or more data representations. For example, in some embodiments, the determination system can capture 13 images for each feature strip of the microarray. The 13 images can be stitched together by a stitching operation. In some embodiments, the number of columns within the overlap between two adjacent data representations can be from about 1% of the columns to about 20% of the columns within each data representation. For example, if each data representation includes 400 columns of data features, the overlap can include 4 to about 80 columns. In a specific embodiment, the number of columns within the overlap can be from about 2% of the columns to about 15% of the columns within each data representation.

[0250] like Fig. 22 As shown, a method 800 is provided, which includes a series of images of overlapping portions of a microarray of features captured at 802. Each of the features has a designated probe molecule fixed thereto. The microarray has a target analyte attached thereto. The method 800 also includes analyzing the light intensity associated with the corresponding features in the image at 804 and determining a data representation of the image. The data representation has a corresponding subarray of data features based on the corresponding features of the microarray. Each of the data features has a corresponding position relative to other data features and a signal value based on one or more light intensities. The method 800 also includes combining the data representations of adjacent images based on the comparison of the signal values ​​of the data features of the data representations of adjacent images at 806, thereby generating a data representation of the microarray. The method also includes analyzing the data representation of the microarray at 808 to determine the properties or characteristics of the sample.

[0251] In an embodiment, a method is provided, which includes positioning a first carrier assembly on a system stage. The first carrier assembly includes a support frame having an inner frame edge defining a window of the support frame. The first carrier assembly includes a removable first substrate, which is located within the window and surrounded by the inner frame edge. The first substrate has a sample thereon that is located within an imaging zone of an optical system. The method also includes using the optical system to detect an optical signal from the sample of the first substrate according to a first imaging scheme. The method also includes replacing the first carrier assembly with a second carrier assembly on the system stage. The second carrier assembly has a removable second substrate. The second substrate has a sample thereon that is located within an imaging zone of the optical system, wherein the first and second substrates are different types of substrates. The method also includes using the optical system to detect an optical signal from the sample of the second substrate according to a second imaging scheme that is different from the first imaging scheme. Optionally, the first imaging scheme and / or the second imaging scheme are automated.

[0252] In one aspect, each of the first and second carrier assemblies includes a hole extending into the corresponding carrier assembly. When the corresponding carrier assembly is located on the system stage, the hole receives a corresponding datum of the system stage. The second carrier assembly includes an adapter plate that holds the second substrate. The datum engages the first substrate when the first carrier assembly is located on the system stage and engages the adapter plate when the second carrier assembly is located on the system stage.

[0253] In another aspect, the optical system includes an objective lens, wherein detecting the light signal from the first substrate includes moving the objective lens and the first substrate relative to each other, and wherein detecting the light signal from the second substrate includes moving the objective lens and the second substrate relative to each other. The optical system detects the light signal from the first substrate along a first imaging area. The optical system detects the light signal from the second substrate along a second imaging area. The first and second imaging areas are different in size, wherein the first and second imaging schemes include automatically moving the objective lens along different paths relative to the first and second substrates, respectively.

[0254] In another aspect, the second carrier assembly includes a retaining mechanism including a movable reference block. The method also includes pressing the reference block, positioning the second substrate on the second carrier assembly, and releasing the reference block. The reference block engages with the second substrate to retain the second substrate on the second carrier assembly, wherein the reference block does not retain the first substrate relative to the first carrier assembly.

[0255] In another aspect, the first and second substrates have different thicknesses and first and second substrate surfaces, respectively, wherein detecting optical signals from the first and second substrates comprises detecting optical signals from the first and second substrate surfaces, respectively. The first and second substrate surfaces are in a common plane or offset by 100 microns or less.

[0256] In another aspect, the second substrate includes a microarray of features, and detecting the optical signal from the second substrate includes a series of images of overlapping portions of the microarray of the capture features. Each of the features has a designated probe molecule fixed thereto. The microarray has a target analyte attached thereto. The method also includes analyzing the light intensity associated with the corresponding features in the image and determining a data representation of the image. The data representation has a corresponding subarray of data features based on the corresponding features of the microarray. Each of the data features has a corresponding position relative to other data features and a signal value based on one or more light intensities. The method also includes combining the data representations of adjacent images based on a comparison of the signal values ​​of the data features of the data representations of adjacent images, thereby generating a data representation of the microarray. The method also includes analyzing the data representation of the microarray to determine the properties or characteristics of the sample.

[0257] In another aspect, the first substrate is a flow cell. Optionally, the flow cell includes a flow channel extending between an inlet and an outlet of the flow cell. The inlet and outlet are fluidly coupled to a manifold for flowing liquid through the flow channel. Optionally, the flow cell includes a plurality of flow channels extending between respective inlets and outlets of the flow cell. The inlet and outlet are fluidly coupled to a manifold for flowing liquid through the flow channel.

[0258] In another aspect, the method further comprises repeatedly flowing the reagents through the flow cell to perform a sequencing by synthesis (SBS) protocol.

[0259] In another aspect, the first and second imaging schemes include moving the objective lens and / or the system stage relative to each other along different paths.

[0260] In another aspect, the second substrate is an open-face substrate having a biological or chemical substance fixed to the outer surface of the open-face substrate. Optionally, the open-face substrate includes a microarray along the outer surface. Optionally, the microarray includes a plurality of characteristic strips extending parallel to each other. Each of the characteristic strips has an array of reaction sites.

[0261] In another aspect, each of the first and second carrier components includes a hole extending into the corresponding carrier component. When the corresponding carrier component is located on the system stage, the hole receives the corresponding reference. Optionally, the first substrate engages the reference and the second substrate does not engage the reference.

[0262] In another aspect, the first substrate is larger than the second substrate.

[0263] In another aspect, the optical system includes an objective lens. The step of detecting the light signal from the first substrate includes moving the objective lens and the first substrate relative to each other. The step of detecting the light signal from the second substrate includes moving the objective lens and the second substrate relative to each other.

[0264] In another aspect, the optical system detects light signals from the first substrate along a first imaging zone. The optical system detects light signals from the second substrate along a second imaging zone. The first and second imaging zones are different in size.

[0265] In another aspect, the first and second imaging schemes include automatically moving the objective lens relative to the first and second substrates, respectively, along different paths.

[0266] In another aspect, the first and second carrier assemblies engage the system stage in substantially the same manner.

[0267] In an embodiment, a method is provided, which includes positioning a first carrier assembly on a system stage. The first carrier assembly includes a support frame having an inner frame edge defining a window of the support frame. The first carrier assembly includes a first substrate located within the window and surrounded by the inner frame edge. The first substrate has a sample thereon that is located within an imaging area of ​​an optical system. The method also includes detecting an optical signal from the sample of the first substrate using the optical system and replacing the first carrier assembly with a second carrier assembly on the system stage. The second carrier assembly includes a support frame and an adapter plate coupled to the support frame. The second carrier assembly has a second substrate held by the adapter plate, which has a sample thereon. The sample of the second substrate is located within the imaging area of ​​the optical system. The method also includes detecting an optical signal from the sample of the second substrate using the optical system.

[0268] In another aspect, each of the first carrier component and the second carrier component includes a hole extending into the corresponding carrier component, and when the corresponding carrier component is located on the system table, the hole receives a corresponding reference of the system table, which engages the first base when the first carrier component is located on the system table and engages the mounting plate when the second carrier component is located on the system table.

[0269] In another aspect, the optical system includes an objective lens, wherein detecting an optical signal from a first substrate includes moving the objective lens and the first substrate relative to each other, wherein detecting an optical signal from a second substrate includes moving the objective lens and the second substrate relative to each other, wherein the optical system detects the optical signal from the first substrate along a first imaging area, and the optical system detects the optical signal from the second substrate along a second imaging area, the first imaging area and the second imaging area are different in size, wherein the first imaging scheme and the second imaging scheme include automatically moving the objective lens relative to the first substrate and the second substrate, respectively, along different paths.

[0270] In another aspect, the second carrier assembly includes a retaining mechanism including a movable reference block, the method further comprising pressing the reference block to position the second substrate on the second carrier assembly, and releasing the reference block, the reference block engaging with the second substrate to retain the second substrate on the second carrier assembly, wherein the reference block does not retain the first substrate relative to the first carrier assembly.

[0271] In another aspect, the first substrate and the second substrate have different thicknesses and have a first substrate surface and a second substrate surface, respectively, wherein detecting the optical signal from the first substrate and the second substrate comprises detecting the optical signal from the first substrate surface and the second substrate surface, respectively, the first substrate surface and the second substrate surface being in a common plane or offset by 100 microns or less. The second substrate comprises a microarray of features, and detecting the optical signal from the second substrate comprises capturing a series of images of overlapping portions of the microarray of features, each of the features having a designated probe molecule fixed thereto, the microarray having a target analyte attached thereto; the method further comprises: analyzing the light intensity associated with the corresponding feature in the image and determining a data representation of the image, the data representation having a corresponding subarray of data features based on the corresponding feature of the microarray, each of the data features having a corresponding position relative to other data features and a signal value based on one or more of the light intensities; and combining the data representations of adjacent images based on a comparison of the signal values ​​of the data features of the data representations of adjacent images, thereby generating a data representation of the microarray; analyzing the data representation of the microarray to determine a property or characteristic of the sample.

[0272] In another aspect, the first substrate is a flow cell. Optionally, the flow cell includes a flow channel extending between an inlet and an outlet of the flow cell. The inlet and the outlet are fluidly coupled to a manifold for flowing liquid through the flow channel. Optionally, the flow cell includes a plurality of flow channels extending between respective inlets and outlets of the flow cell. The inlet and the outlet are fluidly coupled to a manifold for flowing liquid through the flow channel. Optionally, the flow channels extend parallel to each other through the imaging area.

[0273] In another aspect, the method includes repeatedly flowing reagents through a flow cell to perform a sequencing by synthesis (SBS) protocol.

[0274] In another aspect, the second substrate is an open faced substrate having a biological or chemical substance immobilized to an outer surface of the open faced substrate. Optionally, the open faced substrate comprises a microarray along the outer surface.

[0275] In another aspect, the first substrate is larger than the second substrate.

[0276] In another aspect, the support frame of the first carrier assembly and the support frame of the second carrier assembly are the same support frame.

[0277] In another aspect, the support frame of the first carrier assembly and the support frame of the second carrier assembly are different support frames having respective outer edges defining the same perimeter.

[0278] In another aspect, the first base is slidable within the window along an XY plane extending parallel to an edge of the inner frame, and wherein the adapter plate is slidable within the window along the XY plane.

[0279] In another aspect, the system stage includes a plurality of fiducials. During positioning and replacement operations, the fiducials engage the first substrate and engage the adapter plate.

[0280] In another aspect, the adapter plate includes an inner plate edge defining a receiving portion. A second substrate is disposed within the receiving portion and engages the plate edge.

[0281] In another aspect, the optical system includes an objective lens. The step of detecting the light signal from the first substrate includes moving the objective lens and the first substrate relative to each other. The step of detecting the light signal from the second substrate includes moving the objective lens and the second substrate relative to each other.

[0282] In another aspect, the optical system detects light signals from the first substrate along a first imaging zone. The optical system detects light signals from the second substrate along a second imaging zone. The first and second imaging zones are different in size.

[0283] In another aspect, samples of the first and second substrates are located in different sections of the window.

[0284] In another aspect, the step of replacing the first carrier assembly with the second carrier assembly includes removing the first substrate from the support frame and positioning the second substrate within the adapter plate.

[0285] In another aspect, the second carrier assembly includes a retaining mechanism including a movable reference block disposed within a portion of the receiving portion. The method includes pressing the reference block, positioning the second substrate within the receiving portion, and releasing the reference block. The reference block engages with the second substrate to retain the second substrate in the receiving portion. Optionally, the retaining mechanism includes a bias spring that provides a spring force for retaining the second substrate within the receiving portion.

[0286] In an embodiment, a carrier assembly is provided, which includes a support frame having an inner frame edge defining a window of the support frame. The carrier assembly also includes an adapter plate coupled to the support frame and located within the window. The adapter plate includes a plate body having an inner plate edge defining a receiving portion for receiving a substrate having a size smaller than the window. The inner plate edge also defines a retaining recess open to the receiving portion. The carrier assembly also includes a movable reference block located within the retaining recess. The reference block is movable between a retracted position and an engaged position. The reference block is configured to engage the substrate when the reference block is in the engaged position and press the substrate against the opposing surface of the adapter plate to retain the substrate in the receiving portion.

[0287] In one aspect, the adapter plate extends parallel to the XY plane and faces in a direction along the Z axis. The datum block provides a retention force oriented along the XY plane.

[0288] In another aspect, the receiving portion is at least one of: coincident with a receiving plane that intersects an edge of the inner frame or located below a receiving plane.

[0289] In another aspect, the inner frame edge defines an aperture that opens to the window. The aperture is configured to receive the reference when the carrier assembly is located on the system stage. Optionally, the support frame includes a first and a second body side. The first body side is configured to face the objective lens during imaging operation, and the second body side is configured to be located on the base surface during imaging operation. The aperture of the support frame opens to the second body side and extends from the second body side toward the first body side.

[0290] In another aspect, the adapter plate is slidable within the window along the XY plane.

[0291] In another aspect, the adapter plate includes an opening that opens to the receiving portion.

[0292] In another aspect, the receiving portion is sized and shaped to receive a planar chip or slider.

[0293] In an embodiment, a carrier assembly is provided that includes a support frame having an inner frame edge defining a window of the support frame. The carrier assembly also includes an adapter plate coupled to the support frame and positioned within the window. The inner frame edge defines a substrate receiving recess positioned above the adapter plate. The substrate receiving recess is configured to receive a first planar substrate. The adapter plate includes a plate body having an inner plate edge that defines a receiving portion for receiving a second planar substrate having a smaller size than the first planar substrate. The receiving portion resides at least partially below the substrate receiving recess.

[0294] In another aspect, the carrier assembly includes a datum block movable between a retracted position and an engaged position. The datum block is configured to engage the substrate and press the substrate against an opposing surface of the adapter plate to retain the substrate within the receiving portion when the datum block is in the engaged position.

[0295] Optionally, the adapter plate extends parallel to the XY plane and faces in a direction along the Z axis. The datum block provides a retention force oriented along the XY plane.

[0296] In another aspect, the inner frame edge defines an aperture that opens to the window. The aperture is configured to receive a fiducial when the carrier assembly is positioned on the system stage.

[0297] Optionally, the support frame includes a first and a second body side. The first body side is configured to face the objective lens during imaging operation, and the second body side is configured to be located on the base surface during imaging operation. The hole of the support frame opens to the second body side and extends from the second body side toward the first body side.

[0298] In another aspect, the adapter plate is slidable within the window along the XY plane.

[0299] In another aspect, the receiving portion is sized and shaped to receive a planar chip or slider.

[0300] In another aspect, the adapter plate includes a fluid opening that provides access to the substrate receiving recess.

[0301] In another aspect, at least one of the fluid openings is located at a first end of the adapter plate and at least one of the fluid openings is located at an opposing second end of the adapter plate.

[0302] In one aspect, a measurement system is provided, which includes a system stage having a base extending parallel to an XY plane and a plurality of references coupled to the base. The reference includes a protrusion extending away from the base along a Z axis perpendicular to the XY plane. The measurement system also includes an optical system, which includes an objective lens. The objective lens is configured to move relative to the system stage along the XY plane. The measurement system also includes a fluid control system, which is configured to control the flow of one or more fluids through the flow cell when the flow cell is mounted on the system stage. The measurement system also includes a system controller, which is configured to control the fluid control system and the optical system to perform different first and second measurement schemes with the first and second samples, respectively. During the first measurement scheme, the system controller commands the fluid control system to guide the one or more fluids through the flow cell on the system stage, and commands the optical system to detect the light signal from the first sample on the flow cell. During the second measurement scheme, the system controller commands the optical system to detect the light signal from the second sample on the open surface substrate on the system stage without causing the fluid to flow through the second sample.

[0303] In one aspect, the first assay protocol is a sequencing by synthesis (SBS) protocol and the second assay protocol comprises imaging a microarray.

[0304] In another aspect, the assay system further comprises a carrier sensor configured to detect a type of a carrier assembly mounted to the system stage. The assay system is configured to issue a notification when the carrier assembly does not match the selected assay protocol.

[0305] In another aspect, an assay system includes a carrier assembly having a support frame defining a window. The support frame is configured to couple to an adapter plate extending across and covering the window.

[0306] In an embodiment, a method is provided for capturing a series of images of overlapping portions of a microarray of features. Each of the features has a designated probe molecule fixed thereto. The microarray has a target analyte attached thereto. The method also includes analyzing the light intensity associated with the corresponding features in the image to determine a data representation of the image. The data representation has a corresponding subarray of data features based on the corresponding features of the microarray. Each of the data features has a corresponding position relative to other data features and a signal value based on one or more light intensities. The method also includes combining the data representations of adjacent images based on a comparison of the signal values ​​of the data features of the data representations of adjacent images, thereby generating a data representation of the microarray. The method also includes analyzing the data representation of the microarray to determine a property or characteristic of the sample.

[0307] In one aspect, each of the data representations includes multiple columns of features. The comparison includes comparing the signal value of a column of one data representation with the signal value of a column of an adjacent data representation. The method includes calculating a correlation value based on the comparison. If the correlation value meets a specified threshold, the columns are designated as overlapping columns with the same feature.

[0308] In some aspects, each of the data representations includes multiple columns of features. The comparison includes comparing the signal values ​​of multiple columns of one data representation with the signal values ​​of multiple columns of an adjacent data representation. Optionally, the method includes calculating a correlation value based on the comparison. If the correlation value meets a specified threshold, the columns are designated as overlapping columns with the same features.

[0309] In some aspects, the combining operation is repeated for each pair of adjacent images, thereby generating a data representation of the microarray.

[0310] In some aspects, the data representation of the microarray is analyzed after comparing the number of features within the data representation of the microarray to the expected number of features.

[0311] In some aspects, the features of the microarray have known sizes and shapes and a known order or arrangement relative to each other within the microarray.

[0312] In some aspects, each of the features corresponds to a plurality of pixels in the respective image.

[0313] It will be understood that the above description is intended to be illustrative and not restrictive. For example, the above embodiments (and / or aspects thereof) can be used in combination with each other. In addition, in order to adapt to specific circumstances or materials, many modifications can be made to the embodiments without departing from the scope of the present invention. Although the specific components and processes described herein are intended to define the parameters of various embodiments, they are by no means restrictive and are exemplary embodiments. Many other embodiments will be obvious to those skilled in the art after examining the above description. The scope of the present invention should therefore be determined with reference to the attached claims together with the full range of equivalents to which such claims are entitled. In the attached claims, the terms "including" and "in which" are used as the plain English equivalents of the corresponding terms "comprising" and "wherein". In addition, in the claims, the terms "first", "second" and "third" etc. are used only as marks and are not intended to impose numerical requirements on their objects. Furthermore, claim limitations are not drafted in means-plus-function terms and are not intended to be interpreted pursuant to 35 USC § 112, Section 6 unless and until such claim limitation expressly uses the phrase "means for" followed by a recitation of the function without further structure.

Claims

1. A measurement system comprising: a system stage having a base surface extending parallel to an XY plane and a plurality of fiducials coupled to the base surface, the fiducials including protrusions extending away from the base surface along a Z axis perpendicular to the XY plane; an optical system comprising an objective lens configured to move relative to the system stage along the XY plane; a fluid control system configured to control the flow of one or more fluids through the flow cell when the flow cell is mounted on the system stage; as well as a system controller configured to control the fluid control system and the optical system to perform different first and second assay protocols with a first sample and a second sample, respectively, wherein during the first assay protocol, the system controller commands the fluid control system to direct one or more fluids through the flow cell on the system stage and commands the optical system to detect an optical signal from the first sample on the flow cell, and wherein during the second assay protocol, the system controller commands the optical system to detect an optical signal from the second sample on an open-face substrate on the system stage without flowing fluid through the second sample.

2. The measuring system according to claim 1, wherein The first assay protocol is a sequencing by synthesis (SBS) protocol, and the second assay protocol includes imaging a microarray.

3. The assay system of claim 1, further comprising a carrier sensor configured to detect a type of carrier assembly mounted to the system station, wherein the assay system is configured to issue a notification when the carrier assembly does not match a selected assay protocol.

4. The assay system of claim 1, further comprising a carrier assembly having a support frame defining a window, the support frame configured to be coupled to an adapter plate extending across and covering the window.

5. A method for imaging a sample for biological or chemical analysis, comprising: capturing a series of images of overlapping portions of a microarray of features, each of the features having a designated probe molecule immobilized thereto, the microarray having a target analyte attached thereto; analyzing light intensities associated with corresponding features in the image, and determining a data representation of the image having a corresponding subarray of data features based on the corresponding features of the microarray, each of the data features having a corresponding position relative to the other data features and a signal value based on one or more of the light intensities; as well as combining data representations of adjacent images based on a comparison of signal values ​​of data features of the data representations of adjacent images to generate a data representation of the microarray; The data representation of the microarray is analyzed to determine a property or characteristic of the sample.

6. The method of claim 5, wherein: Each of the data representations of the image includes multiple columns of the data features, and wherein the comparison includes comparing the signal value of a column of one data representation with the signal value of a column of an adjacent data representation, wherein the method includes calculating a correlation value based on the comparison, and if the correlation value meets a specified threshold, then the column of the one data representation and the column of the adjacent data representation are designated as overlapping columns with the same features.

7. The method of claim 5, wherein: Each of the data representations of the image includes multiple columns of the data features, and wherein the comparison includes comparing signal values ​​of multiple columns of one data representation with signal values ​​of multiple columns of an adjacent data representation, wherein the method includes calculating a correlation value based on the comparison, and if the correlation value meets a specified threshold, then the multiple columns of the one data representation and the multiple columns of the adjacent data representation are designated as overlapping columns with the same features.

8. The method of claim 5, wherein: The combining operation is repeated for each pair of adjacent images, thereby generating a data representation of the microarray.

9. The method of claim 5, wherein: Analysis of the data representation of the microarray is performed after comparing the number of features within the data representation of the microarray to the expected number of features.

10. The method of claim 5, wherein: The features of the microarray have known sizes and shapes and a known order or arrangement relative to each other within the microarray.

11. The method of claim 5, wherein: Each of the features corresponds to a plurality of pixels in a corresponding image.

Images