Patent Publication Number: US-2022226819-A1

Title: Systems, methods, and apparatuses to image a sample for biological or chemical analysis

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     The present application is a continuation of U.S. patent application Ser. No. 16/255,546, filed Jan. 23, 2019, which is a divisional of U.S. application Ser. No. 14/550956 (now U.S. Pat. No. 10,220,386), filed Nov. 22, 2014, which is a continuation of U.S. application Ser. No. 13/273,666 (Now U.S. Pat. No. 8,951,781), filed on Oct. 14, 2011, which relates to and claims the benefit of U.S. Provisional Application Nos. 61/431,425, filed on Jan. 10, 2011; U.S. Provisional Application No. 61/431,429, filed on Jan. 10, 2011; U.S. Provisional Application No. 61/431,439, filed on Jan. 11, 2011; U.S. Provisional Application No. 61/431,440, filed on Jan. 11, 2011; U.S. Provisional Application No. 61/438,486, filed on Feb. 1, 2011; U.S. Provisional Application No. 61/438,567, filed on Feb. 1, 2011; U.S. Provisional Application No. 61/438,530, filed on Feb. 1, 2011, the content of each of which is incorporated by reference herein in its entirety and for all purposes. 
    
    
     BACKGROUND OF THE INVENTION 
     Embodiments of the present invention relate generally to biological or chemical analysis and more particularly, to assay systems having fluidic devices, optical assemblies, and/or other apparatuses that may be used in detecting desired reactions in a sample. 
     Various assay protocols used for biological or chemical research are concerned with performing a large number of controlled reactions. In some cases, the controlled reactions are performed on support surfaces. The desired reactions may then be observed and analyzed to help identify properties or characteristics of the chemicals involved in the desired reaction. For example, in some protocols, a chemical moiety that includes an identifiable label (e.g., fluorescent label) may selectively bind to another chemical moiety under controlled conditions. These chemical reactions may be observed by exciting the labels with radiation and detecting light emissions from the labels. The light emissions may also be provided through other means, such as chemiluminescence. 
     Examples of such protocols include DNA sequencing. In one sequencing-by-synthesis (SBS) protocol, clusters of clonal amplicons are formed through bridge PCR on a surface of a flow channel. After generating the clusters of clonal amplicons, the amplicons may be “linearized” to make single stranded DNA (sstDNA). A series of reagents is flowed into the flow cell to complete a cycle of sequencing. Each sequencing cycle extends the sstDNA by a single nucleotide (e.g., A, T, G, C) having a unique fluorescent label. Each nucleotide has a reversible terminator that allows only a single-base incorporation to occur in one cycle. After nucleotides are added to the sstDNAs clusters, an image in four channels is taken (i.e., one for each fluorescent label). After imaging, the fluorescent label and the terminator are chemically cleaved from the sstDNA and the growing DNA strand is ready for another cycle. Several cycles of reagent delivery and optical detection can be repeated to determine the sequences of the clonal amplicons. 
     However, systems configured to perform such protocols may have limited capabilities and may not be cost-effective. Thus, there is a general need for improved systems, methods, and apparatuses that are capable of performing or being used during assay protocols, such as the SBS protocol described above, in a cost-effective, simpler, or otherwise improved manner. 
     BRIEF DESCRIPTION OF THE INVENTION 
     In accordance with one embodiment, a fluidic device for analyzing samples is provided. The fluidic device includes a flow cell having inlet and outlet ports and a flow channel extending therebetween. The flow cell is configured to hold a sample-of-interest. The fluidic device also includes a housing having a reception space that is configured to receive the flow cell. The reception space is sized and shaped to permit the flow cell to float relative to the housing. The fluidic device also includes a gasket that is coupled to the housing. The gasket has inlet and outlet passages and comprises a compressible material. The gasket is positioned relative to the reception space so that the inlet and outlet ports of the flow cell are approximately aligned with the inlet and outlet passages of the gasket, respectively. 
     In another embodiment, a removable cartridge configured to hold and facilitate positioning a flow cell for imaging is provided. The cartridge includes a removable housing that has a reception space configured to hold the flow cell substantially within an object plane. The housing includes a pair of housing sides that face in opposite directions. The reception space extends along at least one of the housing sides so that the flow cell is exposed to an exterior of the housing through said at least one of the housing sides. The cartridge also includes a cover member that is coupled to the housing and includes a gasket. The gasket has inlet and outlet passages and comprises a compressible material. The gasket is configured to be mounted over an exposed portion of the flow cell when the flow cell is held by the housing. 
     In yet another embodiment, a method of positioning a fluidic device for sample analysis is provided. The method includes positioning a removable fluidic device on a support surface of an imaging system. The device has a reception space, a flow cell located within the reception space, and a gasket. The flow cell extends along an object plane in the reception space and is floatable relative to the gasket within the object plane. The method also includes moving the flow cell within the reception space while on the support surface so that inlet and outlet ports of the flow cell are approximately aligned with inlet and outlet passages of the gasket. 
     In another embodiment, a method of positioning a fluidic device for sample analysis is provided. The method includes providing a fluidic device having a housing that includes a reception space and a floatable flow cell located within the reception space. The housing has recesses that are located immediately adjacent to the reception space. The method also includes positioning the fluidic device on a support structure having alignment members. The alignment members are inserted through corresponding recesses. The method also includes moving the flow cell within the reception space. The alignment members engage edges of the flow cell when the flow cell is moved within the reception space. 
     In another embodiment, a fluidic device holder is provided that is configured to orient a sample area with respect to mutually perpendicular X, Y, and Z-axes. The device holder includes a support structure that is configured to receive a fluidic device. The support structure includes a base surface that faces in a direction along the Z-axis and is configured to have the device positioned thereon. The device holder also includes a plurality of reference surfaces in respective directions along an XY-plane and an alignment assembly that includes an actuator and a movable locator arm that is operatively coupled to the actuator. The locator arm has an engagement end. The actuator moves the locator arm between retracted and biased positions to move the engagement end toward and away from the reference surfaces. The locator arm is configured to hold the device against the reference surfaces when the locator arm is in the biased position. 
     In another embodiment, a fluidic device holder is provided that includes a support structure having a loading region for receiving a fluidic device. The support structure includes a base surface that partially defines the loading region and is configured to have the device positioned thereon. The device holder includes a cover assembly that is coupled to the support structure and is configured to be removably mounted over the device. The cover assembly includes a cover housing having housing legs and a bridge portion that joins the housing legs. The housing legs extend in a common direction and have a viewing space that is located therebetween. The viewing space is positioned above the loading region. 
     In another embodiment, a method for orienting a sample area with respect to mutually perpendicular X, Y, and Z-axes is provided. The method includes providing an alignment assembly that has a movable locator arm having an engagement end. The locator arm is movable between retracted and biased positions. The method also includes positioning a fluidic device on a base surface that faces in a direction along the Z-axis and between a plurality of reference surfaces that face in respective directions along an XY-plane. The device has a sample area. The method also includes moving the locator arm to the biased position. The locator arm presses the device against the reference surfaces such that the device is held in a fixed position. 
     In yet another embodiment, an optical assembly is provided that includes a base plate having a support side and a component-receiving space along the support side. The component-receiving space is at least partially defined by a reference surface. The optical assembly also includes an optical component having an optical surface that is configured to reflect light or transmit light therethrough. The optical assembly also includes a mounting device that has a component retainer and a biasing element that is operatively coupled to the retainer. The retainer holds the optical component so that a space portion of the optical surface faces the reference surface and a path portion of the optical surface extends beyond the support side into an optical path. The biasing element provides an alignment force that holds the optical surface against the reference surface. In particular embodiments, the component-receiving space is a component cavity extending a depth into the base plate from the support side of the base plate. The optical and reference surfaces can have predetermined contours that are configured to position the optical surface in a predetermined orientation. 
     In another embodiment, a method of assembling an optical train is provided. The method includes providing a base plate that has a support side and a component-receiving space along the support side. The component-receiving space is at least partially defined by a reference surface. The method also includes inserting an optical component into the component-receiving space. The optical component has an optical surface that is configured to reflect light or transmit light therethrough. The optical surface has a space portion that faces the reference surface and a path portion that extends beyond the support side into an optical path. The method also includes providing an alignment force that holds the optical surface against the reference surface. In particular embodiments, the component-receiving space is a component cavity extending a depth into the base plate from the support side of the base plate. The optical and reference surfaces can have predetermined contours that are configured to position the optical surface in a predetermined orientation. 
     In another embodiment, an optical imaging system is provided that includes an object holder to hold and move an object and a detector to detect optical signals from the object at a detector surface. The imaging system also includes an optical train that is configured to direct the optical signals onto the detector surface. The optical train has an object plane that is proximate to the object holder and an image plane that is proximate to the detector surface. The optical train includes a mirror that is rotatable between an imaging position and a focusing position. The imaging system also includes an image analysis module that is configured to analyze a test image detected at the detector surface when the mirror is in the focusing position. The test image has an optimal degree-of-focus at a focused location in the test image. The focused location in the test image is indicative of a position of the object with respect to the object plane. The object holder is configured to move the object toward the object plane based on the focused location. 
     In another embodiment, a method for controlling focus of an optical imaging system is provided. The method includes providing an optical train that is configured to direct optical signals onto a detector surface. The optical train has an object plane that is proximate to an object and an image plane that is proximate to the detector surface. The optical train includes a mirror that is rotatable between an imaging position and a focusing position. The method also includes rotating the mirror to the focusing position and obtaining a test image of the object when the mirror is in the focusing position. The test image has an optimal degree-of-focus at a focused location in the test image. The focused location is indicative of a position of the object with respect to the object plane. The method also includes moving the object toward the object plane based on the focused location. 
     In another embodiment, an optical imaging system is provided that includes a sample holder configured to hold a flow cell. The flow cell includes a flow channel having a sample area. The imaging system also includes a flow system that is coupled to the flow cell and configured to direct reagents through the flow channel to the sample area. The imaging system also includes an optical train that is configured to direct excitation light onto the sample area and first and second light sources. The first and second light sources have fixed positions with respect to the optical train. The first and second light sources provide first and second optical signals, respectively, for exciting the biomolecules. The imaging system also includes a system controller that is communicatively coupled to the first and second light sources and to the flow system. The controller is configured to activate the flow system to flow the reagents to the sample area and activate the first and second light sources after a predetermined synthesis time period. The light sources can be, for example, lasers or semiconductor light sources (SLSs), such as laser diodes or light emitting diodes (LEDs). 
     In another embodiment, a method of performing a biological assay is provided. The method includes flowing reagents through a flow channel having a sample area. The sample area includes biomolecules that are configured to chemically react with the reagents. The method also includes illuminating the sample area with first and second light sources. The first and second light sources provide first and second optical signals, respectively. The biomolecules provide light emissions indicative of a binding reaction when illuminated by the first or second light sources. The method also includes detecting the light emissions from the sample area. The light sources can be, for example, lasers or semiconductor light sources (SLSs), such as a laser diodes or light emitting diodes (LEDs). 
     In another embodiment, a flow cell is provided that includes a first layer that has a mounting surface and an outer surface that face in opposite directions and that define a thickness therebetween. The flow cell also includes a second layer having a channel surface and an outer surface that face in opposite directions and that define a thickness therebetween. The second layer has a grooved portion that extends along the channel surface. The channel surface of the second layer is secured to the mounting surface. The flow cell also includes a flow channel that is defined by the grooved portion of the channel surface and a planar section of the mounting surface. The flow channel includes an imaging portion. The thickness of the second layer is substantially uniform along the imaging portion and is configured to transmit optical signals therethrough. The thickness of the first layer is substantially uniform along the imaging portion and is configured to permit uniform transfer of thermal energy therethrough. 
     In another embodiment, a light source module is provided that includes a module frame having a light passage and a light source that is secured to the module frame and oriented to direct optical signals through the light passage along an optical path. The light source module also includes an optical component that is secured to the module frame and has a fixed position and predetermined orientation with respect to the light source. The optical component is located within the light passage such that the optical component is within the optical path. 
     In another embodiment, an excitation light module is provided that includes a module frame and first and second semiconductor light sources (SLSs) that are secured to the module frame. The first and second SLSs have fixed positions with respect to each other. The first and second SLSs are configured to provide different excitation optical signals. The excitation light module also includes an optical component that is secured to the module frame and has a fixed position and predetermined orientation with respect to the first and second SLSs. The optical component permits the optical signals from the first SLS to transmit therethrough and reflects the optical signals from the second SLS. The reflected and transmitted optical signals are directed along a common path out of the module frame. 
     In one embodiment, a method of performing a biological or chemical assay is provided. The method includes establishing a fluid connection between a fluidic device having a sample area and a reaction component storage unit having a plurality of different reaction components for conducting one or more assays. The reaction components include sample-generation components and sample-analysis components. The method also includes generating a sample at the sample area of the fluidic device. The generating operation includes flowing different sample-generation components to the sample area and controlling reaction conditions at the sample area to generate the sample. The method also includes analyzing the sample at the sample area. The analyzing operation includes flowing at least one sample-analysis component to the sample area. Said at least one sample-analysis component reacts with the sample to provide optically detectable signals indicative of an event-of-interest. The generating and analyzing operations are conducted in an automated manner by the assay system. 
     In another embodiment, an assay system is provided that includes a fluidic device holder that is configured to hold a fluidic device and establish a fluid connection with the fluidic device. The assay system also includes a fluidic network that is configured to fluidicly connect the fluidic device to a reaction component storage unit. The assay system also includes a fluidic control system that is configured to selectively flow fluids from the storage unit through the fluidic device. Furthermore, the assay system includes a system controller that has a fluidic control module. The fluidic control module is configured to instruct the fluidic control system to (a) flow different sample-generation components from the storage unit to the sample area and control reaction conditions at the sample area to generate a sample; and (b) flow at least one sample-analysis component from the storage unit to the sample area. Said at least one sample-analysis component is configured to react with the sample to provide optically detectable signals indicative of an event-of-interest. The assay system also includes an imaging system that is configured to detect the optically detectable signals from the sample. The system controller is configured to automatically generate the sample and analyze the sample by selectively controlling the fluidic device holder, the fluidic control system, and the imaging system. 
     In another embodiment, a method of performing a biological or chemical assay is provided. The method includes: (a) providing a fluidic device having a sample area and a reaction component storage unit having a plurality of different reaction components for conducting one or more assays, the reaction components including sample-generation components and sample-analysis components; (b) flowing sample generation components according to a predetermined protocol to generate a sample at the sample area; (c) selectively controlling reaction conditions at the sample area to facilitate generating the sample; (d) flowing sample-analysis components to the sample area; and (e) detecting optical signals emitted from the sample area, the optical signals being indicative of an event-of-interest between the sample-analysis components and the sample; wherein (b)-(e) are conducted in an automated manner. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
         FIG. 1  is a block diagram of an assay system for performing biological or chemical assays formed in accordance with one embodiment. 
         FIG. 2  is a side view of a workstation configured to perform biological or chemical assays in accordance with one embodiment. 
         FIG. 3  is a front view of the workstation of  FIG. 2 . 
         FIG. 4  is a diagram of a fluidic network formed in accordance with one embodiment. 
         FIG. 5  is a perspective view of a flow cell formed in accordance with one embodiment. 
         FIG. 6  is a cross-section of the flow cell shown in  FIG. 5  taken along the line  6 - 6  in  FIG. 5 . 
         FIG. 7  is a plan view of the flow cell of  FIG. 5 . 
         FIG. 8  is an enlarged view of a curved segment of a flow channel. 
         FIG. 9  is a perspective view of a fluidic device formed in accordance with one embodiment. 
         FIG. 10  is another perspective view of the fluidic device of  FIG. 9 . 
         FIG. 11  is a cross-section of the fluidic device of  FIG. 9  taken along the lines  11 - 11  in  FIG. 9 . 
         FIG. 12  is a perspective view of a fluidic device formed in accordance with another embodiment. 
         FIG. 13  is a perspective view of the fluidic device of  FIG. 12 . 
         FIG. 14  is a plan view of a fluidic device formed in accordance with one embodiment. 
         FIG. 15  is a side perspective view of the fluidic device of  FIG. 14 . 
         FIG. 16  is a partially exploded view of a device holder formed in accordance with one embodiment. 
         FIG. 17  is a perspective view of the assembled holder of  FIG. 16 . 
         FIG. 18  is a perspective view of a support structure that may be used in the holder of  FIG. 16 . 
         FIG. 19  is a top plan view of the holder of  FIG. 16 . 
         FIG. 20  is a perspective view of the holder of  FIG. 16  having a cover assembly in an open position. 
         FIG. 21  is an enlarged plan view of the holder of  FIG. 16 . 
         FIG. 22  is a perspective view of a cover assembly that may be used in the holder of  FIG. 16 . 
         FIG. 23  is a cross-section of the cover assembly taken along the line  23 - 23  shown in  FIG. 22 . 
         FIG. 24  is a perspective view of a flow system that may be used with the holder of  FIG. 16 . 
         FIG. 25  is a block diagram of a method of positioning a fluidic device for sample analysis in accordance with one embodiment. 
         FIG. 26  is a block diagram illustrating a method of positioning a fluidic device for sample analysis in accordance with one embodiment. 
         FIG. 27  is a block diagram illustrating a method for orienting a sample area in accordance with one embodiment. 
         FIG. 28  is a perspective view of a fluid storage system formed in accordance with one embodiment. 
         FIG. 29  is a side cross-section of the fluid storage system of  FIG. 28 . 
         FIG. 30  is a perspective view of a removal assembly that may be used with the fluid storage system of  FIG. 28 . 
         FIG. 31  is a perspective view of a reaction component tray formed in accordance with one embodiment. 
         FIG. 32  is a top plan view of the tray shown in  FIG. 31 . 
         FIG. 33  is a side view of the tray shown in  FIG. 31 . 
         FIG. 34  is a front view of the tray shown in  FIG. 31 . 
         FIG. 35  is a side cross-section of a component well that may be used with the tray of  FIG. 31 . 
         FIG. 36  is a bottom perspective view of the component well of  FIG. 35 . 
         FIG. 37  is a perspective view of a component well that may be used with the tray of  FIG. 31 . 
         FIG. 38  is a diagram of an optical imaging system in accordance with one embodiment. 
         FIG. 39  is a perspective view of a motion-control system in accordance with one embodiment. 
         FIG. 40  is a perspective view of components that may be used with the motion-control system of  FIG. 39 . 
         FIG. 41  is a perspective view of an optical base plate that may be used in the imaging system of  FIG. 38 . 
         FIG. 42  is a plan view of the base plate of  FIG. 41 . 
         FIG. 43  is a perspective view of an optical component formed in accordance with one embodiment that may be used in the imaging system of  FIG. 38 . 
         FIG. 44  is a cut-away perspective view of the optical component of  FIG. 43 . 
         FIG. 45  is a front view of the optical component of  FIG. 43 . 
         FIG. 46  is a side view of the optical component of  FIG. 43  during a mounting operation. 
         FIG. 47  is a block diagram illustrating a method of assembling an optical train in accordance with one embodiment. 
         FIG. 48  is a perspective view of a light source module formed in accordance with one embodiment. 
         FIG. 49  is a side view of the light source module of  FIG. 48 . 
         FIG. 50  is a plan view of the light source module of  FIG. 48 . 
         FIG. 51  is a plan view of an image-focusing system in accordance with one embodiment. 
         FIG. 52  is a perspective view of a rotatable mirror assembly that may be used in the image-focusing system of  FIG. 51 . 
         FIG. 53  is a schematic diagram of a rotatable mirror in an imaging position that may be used in the image-focusing system of  FIG. 51 . 
         FIGS. 54 and 55  illustrate sample images that may be obtained by the image-focusing system of  FIG. 51 . 
         FIG. 56  is a schematic diagram of the rotatable mirror of  FIG. 53  in a focusing position. 
         FIGS. 57 and 58  illustrate test images that may be obtained by the image-focusing system of  FIG. 51 . 
         FIG. 59  is a block diagram illustrating a method for controlling focus of an optical imaging system. 
         FIG. 60  illustrates a method for performing an assay for biological or chemical analysis. 
         FIG. 61  illustrates a method for performing an assay for biological or chemical analysis. 
     
    
    
     DETAILED DESCRIPTION OF THE INVENTION 
     Embodiments described herein include various systems, methods, assemblies, and apparatuses used to detect desired reactions in a sample for biological or chemical analysis. In some embodiments, the desired reactions provide optical signals that are detected by an optical assembly. The optical signals may be light emissions from labels or may be transmission light that has been reflected or refracted by the sample. For example, embodiments may be used to perform or facilitate performing a sequencing protocol in which sstDNA is sequenced in a flow cell. In particular embodiments, the embodiments described herein can also perform an amplification protocol to generate a sample-of-interest for sequencing. 
     As used herein, a “desired reaction” includes a change in at least one of a chemical, electrical, physical, and optical property or quality of a substance that is in response to a stimulus. For example, the desired reaction may be a chemical transformation, chemical change, or chemical interaction. In particular embodiments, the desired reactions are detected by an imaging system. The imaging system may include an optical assembly that directs optical signals to a sensor (e.g., CCD or CMOS). However, in other embodiments, the imaging system may detect the optical signals directly. For example, a flow cell may be mounted onto a CMOS sensor. However, the desired reactions may also be a change in electrical properties. For example, the desired reaction may be a change in ion concentration within a solution. 
     Exemplary reactions include, but are not limited to, chemical reactions such as reduction, oxidation, addition, elimination, rearrangement, esterification, amidation, etherification, cyclization, or substitution; binding interactions in which a first chemical binds to a second chemical; dissociation reactions in which two or more chemicals detach from each other; fluorescence; luminescence; chemiluminescence; and biological reactions, such as nucleic acid replication, nucleic acid amplification, nucleic acid hybridization, nucleic acid ligation, phosphorylation, enzymatic catalysis, receptor binding, or ligand binding. The desired reaction can also be addition or elimination of a proton, for example, detectable as a change in pH of a surrounding solution or environment. 
     The stimulus can be at least one of physical, optical, electrical, magnetic, and chemical. For example, the stimulus may be an excitation light that excites fluorophores in a substance. The stimulus may also be a change in a surrounding environment, such as a change in concentration of certain biomolecules (e.g., enzymes or ions) in a solution. The stimulus may also be an electrical current applied to a solution within a predefined volume. In addition, the stimulus may be provided by shaking, vibrating, or moving a reaction chamber where the substance is located to create a force (e.g., centripetal force). As used herein, the phrase “in response to a stimulus” is intended to be interpreted broadly and include more direct responses to a stimulus (e.g., when a fluorophore emits energy of a specific wavelength after absorbing incident excitation light) and more indirect responses to a stimulus in that the stimulus initiates a chain of events that eventually results in the response (e.g., incorporation of a base in pyrosequencing eventually resulting in chemiluminescence). The stimulus may be immediate (e.g., excitation light incident upon a fluorophore) or gradual (e.g., change in temperature of the surrounding environment). 
     As used herein, the phrase “activity that is indicative of a desired reaction” and variants thereof include any detectable event, property, quality, or characteristic that may be used to facilitate determining whether a desired reaction has occurred. The detected activity may be a light signal generated in fluorescence or chemiluminescence. The detected activity may also be a change in electrical properties of a solution within a predefined volume or along a predefined area. The detected activity may be a change in temperature. 
     Various embodiments include providing a reaction component to a sample. As used herein, a “reaction component” or “reactant” includes any substance that may be used to obtain a desired reaction. For example, reaction components include reagents, enzymes, samples, other biomolecules, and buffer solutions. The reaction components are typically delivered to a reaction site (e.g., area where sample is located) in a solution or immobilized within a reaction site. The reaction components may interact directly or indirectly with the substance of interest. 
     In particular embodiments, the desired reactions are detected optically through an optical assembly. The optical assembly may include an optical train of optical components that cooperate with one another to direct the optical signals to an imaging device (e.g., CCD, CMOS, or photomultiplier tubes). However, in alternative embodiments, the sample region may be positioned immediately adjacent to an activity detector that detects the desired reactions without the use of an optical train. The activity detector may be able detect predetermined events, properties, qualities, or characteristics within a predefined volume or area. For example, an activity detector may be able to capture an image of the predefined volume or area. An activity detector may be able detect an ion concentration within a predefined volume of a solution or along a predefined area. Exemplary activity detectors include charged-coupled devices (CCD&#39;s) (e.g., CCD cameras); photomultiplier tubes (PMT&#39;s); molecular characterization devices or detectors, such as those used with nanopores; microcircuit arrangements, such as those described in U.S. Pat. No. 7,595,883, which is incorporated herein by reference in the entirety; and CMOS-fabricated sensors having field effect transistors (FET&#39;s), including chemically sensitive field effect transistors (chemFET), ion-sensitive field effect transistors (ISFET), and/or metal oxide semiconductor field effect transistors (MOSFET). 
     As used herein, the term “optical components” includes various elements that affect the propagation of optical signals. For example, the optical components may at least one of redirect, filter, shape, magnify, or concentrate the optical signals. The optical signals that may be affected include the optical signals that are upstream from the sample and the optical signals that are downstream from the sample. In a fluorescence-detection system, upstream components include those that direct excitation radiation toward the sample and downstream components include those that direct emission radiation away from the sample. Optical components may be, for example, reflectors, dichroics, beam splitters, collimators, lenses, filters, wedges, prisms, mirrors, detectors, and the like. Optical components also include bandpass filters, optical wedges, and optical devices similar to those described herein. 
     As used herein, the term “optical signals” or “light signals” includes electromagnetic energy capable of being detected. The term includes light emissions from labeled biological or chemical substances and also includes transmitted light that is refracted or reflected by optical substrates. Optical or light signals, including excitation radiation that is incident upon the sample and light emissions that are provided by the sample, may have one or more spectral patterns. For example, more than one type of label may be excited in an imaging session. In such cases, the different types of labels may be excited by a common excitation light source or may be excited by different excitation light sources at different times or at the same time. Each type of label may emit optical signals having a spectral pattern that is different from the spectral pattern of other labels. For example, the spectral patterns may have different emission spectra. The light emissions may be filtered to separately detect the optical signals from other emission spectra. 
     As used herein, when the term “different” is used with respect to light emissions (including emission spectra or other emission characteristics), the term may be interpreted broadly to include the light emissions being distinguishable or differentiable. For example, the emission spectra of the light emissions may have wavelength ranges that at least partially overlap so long as at least a portion of one emission spectrum does not completely overlap the other emission spectrum. Different emission spectra may also have the same or similar wavelength ranges, but have different intensities that are differentiable. Different optical signals can be distinguished based on different characteristics of excitation light that produces the optical signals. For example, in fluorescence resonance energy transfer (FRET) imaging, the light emissions may be the same but the cause (e.g., excitation optical signals) of the light emissions may be different. More specifically, a first excitation wavelength can be used to excite a donor fluorophore of a donor-acceptor pair such that FRET results in emission from the acceptor and excitation of the acceptor directly will also result in emission from the acceptor. As such, differentiation of the optical signals can be based on observation of an emission signal in combination with identification of the excitation wavelength used to produce the emission. Different light emissions may have other characteristics that do not overlap, such as emission anisotropy or fluorescence lifetime. Also, when the light emissions are filtered, the wavelength ranges of the emission spectra may be narrowed. 
     The optical components may have fixed positions in the optical assembly or may be selectively moveable. As used herein, when the term “selectively” is used in conjunction with “moving” and similar terms, the phrase means that the position of the optical component may be changed in a desired manner. At least one of the locations and the orientation of the optical component may be changed. For example, in particular embodiments, a rotatable mirror is selectively moved to facilitate focusing an optical imaging system. 
     Different elements and components described herein may be removably coupled. As used herein, when two or more elements or components are “removably coupled” (or “removably mounted,” and other like terms) the elements are readily separable without destroying the coupled components. For instance, elements can be readily separable when the elements may be separated from each other without undue effort, without the use of a tool (i.e. by hand), or without a significant amount of time spent in separating the components. By way of example, in some embodiments, an optical device may be removably mounted to an optical base plate. In addition, flow cells and fluidic devices may be removably mounted to a device holder. 
     Imaging sessions include a time period in which at least a portion of the sample is imaged. One sample may undergo or be subject to multiple imaging sessions. For example, one sample may be subject to two different imaging sessions in which each imaging session attempts to detect optical signals from one or more different labels. As a specific example, a first scan along at least a portion of a nucleic acid sample may detect labels associated with nucleotides A and C and a second scan along at least a portion of the sample may detect labels associated with nucleotides G and T. In sequencing embodiments, separate sessions can occur in separate cycles of a sequencing protocol. Each cycle can include one or more imaging session. In other embodiments, detecting optical signals in different imaging sessions may include scanning different samples. Different samples may be of the same type (e.g., two microarray chips) or of different types (e.g., a flow cell and a microarray chip). 
     During an imaging session, optical signals provided by the sample are observed. Various types of imaging may be used with embodiments described herein. For example, embodiments described herein may utilize a “step and shoot” procedure in which regions of a sample area are individually imaged. Embodiments may also be configured to perform at least one of epi-fluorescent imaging and total-internal-reflectance-fluorescence (TIRF) imaging. In other embodiments, the sample imager is a scanning time-delay integration (TDI) system. Furthermore, the imaging sessions may include “line scanning” one or more samples such that a linear focal region of light is scanned across the sample(s). Some methods of line scanning are described, for example, in U.S. Pat. No. 7,329,860 and U.S. Pat. Pub. No. 2009/0272914, each of which the complete subject matter is incorporated herein by reference in their entirety. Imaging sessions may also include moving a point focal region of light in a raster pattern across the sample(s). In alternative embodiments, imaging sessions may include detecting light emissions that are generated, without illumination, and based entirely on emission properties of a label within the sample (e.g., a radioactive or chemiluminescent component in the sample). In alternative embodiments, flow cells may be mounted onto an imager (e.g., CCD or CMOS) that detects the desired reactions. 
     As used herein, the term “sample” or “sample-of-interest” includes various materials or substances of interest that undergo an imaging session where optical signals from the material or substance are observed. In particular embodiments, a sample may include biological or chemical substances of interests and, optionally, an optical substrate or support structure that supports the biological or chemical substances. As such, a sample may or may not include an optical substrate or support structure. As used herein, the term “biological or chemical substances” may include a variety of biological or chemical substances that are suitable for being imaged or examined with the optical systems described herein. For example, biological or chemical substances include biomolecules, such as nucleosides, nucleic acids, polynucleotides, oligonucleotides, proteins, enzymes, polypeptides, antibodies, antigens, ligands, receptors, polysaccharides, carbohydrates, polyphosphates, nanopores , organelles, lipid layers, cells, tissues, organisms, and biologically active chemical compound(s) such as analogs or mimetics of the aforementioned species. Other chemical substances include labels that can be used for identification, examples of which include fluorescent labels and others set forth in further detail below. 
     Different types of samples may include different optical substrates or support structures that affect incident light in different manners. In particular embodiments, samples to be detected can be attached to one or more surfaces of a substrate or support structure. For example, flow cells may include one or more flow channels. In flow cells, the flow channels may be separated from the surrounding environment by top and bottom layers of the flow cell. Thus, optical signals to be detected are projected from within the support structure and may transmit through multiple layers of material having different refractive indices. For example, when detecting optical signals from an inner bottom surface of a flow channel and when detecting optical signals from above the flow channel, the optical signals that are desired to be detected may propagate through a fluid having an index of refraction, through one or more layers of the flow cells having different indices of refraction, and through the ambient environment having a different index of refraction. 
     As used herein, a “fluidic device” is an apparatus that includes one or more flow channels that direct fluid in a predetermined manner to conduct desired reactions. The fluidic device is configured to be fluidicly coupled to a fluidic network of an assay system. By way of example, a fluidic device may include flow cells or lab-on-chip devices. Flow cells generally hold a sample along a surface for imaging by an external imaging system. Lab-on-chip devices may hold the sample and perform additional functions, such as detecting the desired reaction using an integrated detector. Fluidic devices may optionally include additional components, such as housings or imagers, that are operatively coupled to the flow channels. In particular embodiments, the channels may have channel surfaces where a sample is located, and the fluidic device can include a transparent material that permits the sample to be imaged after a desired reaction occurs. 
     In particular embodiments, the fluidic devices have channels with microfluidic dimensions. In such channels, the surface tension and cohesive forces of the liquid flowing therethrough and the adhesive forces between the liquid and the surfaces of the channel have at least a substantial effect on the flow of the liquid. For example, a cross-sectional area (taken perpendicular to a flow direction) of a microfluidic channel may be about 10 μm 2  or less. 
     In alternative embodiments, optical imaging systems described herein may be used to scan samples that include microarrays. A microarray may include a population of different probe molecules that are attached to one or more substrates such that the different probe molecules can be differentiated from each other according to relative location. An array can include different probe molecules, or populations of the probe molecules, that are each located at a different addressable location on a substrate. Alternatively, a microarray can include separate optical substrates, such as beads, each bearing a different probe molecule, or population of the probe molecules, that can be identified according to the locations of the optical substrates on a surface to which the substrates are attached or according to the locations of the substrates in a liquid. Exemplary arrays in which separate substrates are located on a surface include, without limitation, a BeadChip Array available from Illumina®, Inc. (San Diego, Calif.) or others including beads in wells such as those described in U.S. Pat. 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 a surface include those set forth in US 2005/0227252; WO 05/033681; and WO 04/024328, each of which is hereby incorporated by reference. 
     Any of a variety of microarrays known in the art can be used. A typical microarray contains sites, sometimes referred to as features, each having a population of probes. The population of probes at each site is typically homogenous having a single species of probe, but in some embodiments the populations can each be heterogeneous. Sites or features of an array are typically discrete, being separated. The separate sites can be contiguous or they can have spaces between each other. The size of the probe sites and/or spacing between the sites can vary such that arrays can be high density, medium density or lower density. High density arrays are characterized as having sites separated by less than about 15 μm. Medium density arrays have sites separated by about 15 to 30 μm, while low density arrays have sites separated by greater than 30 μm. An array useful in the invention can have sites that are separated by less than 100 μm, 50 μm, 10 μm, 5 μm, 1 μm, or 0.5 μm. An apparatus or method of an embodiment of the invention can be used to image an array at a resolution sufficient to distinguish sites at the above densities or density ranges. 
     Further examples of commercially available microarrays that can be used include, for example, an Affymetrix® GeneChip® microarray or other microarray synthesized in accordance with techniques sometimes referred to as VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) technologies 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; 5,974,164; 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. A spotted microarray can also be used in a method according to an embodiment of the invention. An exemplary spotted microarray is a CodeLink™ Array available from Amersham Biosciences. Another microarray that is useful is one that is manufactured using inkjet printing methods such as SurePrint™ Technology available from Agilent Technologies. 
     The systems and methods set forth herein can be used to detect the presence of a particular target molecule in a sample contacted with the microarray. This can be determined, for example, based on binding of a labeled target analyte to a particular probe of the microarray or due to a target-dependent modification of a particular probe to incorporate, remove, or alter a label at the probe location. Any one of several assays can be used to identify or characterize targets 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, each of which is hereby incorporated by reference. 
     Furthermore, optical systems described herein may 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 Mar. 30, 2007 and/or to include various components and assemblies as described in International Publication No. WO 2009/042862, entitled “Fluorescence Excitation and Detection System and Method”, filed Sep. 26, 2008, both of which the complete subject matter are incorporated herein by reference in their entirety. In particular embodiments, optical systems can include various components and assemblies as described in U.S. Pat. No. 7,329,860 and WO 2009/137435, of which the complete subject matter is incorporated herein by reference in their entirety. Optical systems can also include various components and assemblies as described in U.S. patent application Ser. No. 12/638,770, filed on Dec. 15, 2009, of which the complete subject matter is incorporated herein by reference in its entirety. 
     In particular embodiments, methods, and optical systems described herein may be used for sequencing nucleic acids. For example, sequencing-by-synthesis (SBS) protocols are particularly applicable. In SBS, a plurality of fluorescently labeled modified nucleotides are used to sequence a plurality of clusters of amplified DNA (possibly millions of clusters) present on the surface of an optical substrate (e.g., a surface that at least partially defines a channel in a flow cell). The flow cells may contain nucleic acid samples for sequencing where the flow cells are placed within the appropriate flow cell holders. The samples for sequencing can take the form of single nucleic acid molecules that are separated from each other so as to be individually resolvable, amplified populations of nucleic acid molecules in the form of clusters or other features, or beads that are attached to one or more molecules of nucleic acid. Accordingly, sequencing can be carried out on an array such as those set forth previously herein. The nucleic acids can be prepared such that they comprise an oligonucleotide primer adjacent to an unknown target sequence. To initiate the first SBS sequencing cycle, one or more differently labeled nucleotides, and DNA polymerase, etc., can be flowed into/through the flow cell by a fluid flow subsystem (not shown). Either a single type of nucleotide can be added at a time, or the nucleotides used in the sequencing procedure can be specially designed to possess a reversible termination property, thus allowing each cycle of the sequencing reaction to occur simultaneously in the presence of several types of labeled nucleotides (e.g. A, C, T, G). The nucleotides can include detectable label moieties such as fluorophores. Where the four nucleotides are mixed together, the polymerase is able to select the correct base to incorporate and each sequence is extended by a single base. Nonincorporated nucleotides can be washed away by flowing a wash solution through the flow cell. One or more lasers may excite the nucleic acids and induce fluorescence. The fluorescence emitted from the nucleic acids is based upon the fluorophores of the incorporated base, and different fluorophores may emit different wavelengths of emission light. A deblocking reagent can be added to the flow cell to remove reversible terminator groups from the DNA strands that were extended and detected. The deblocking reagent can then be washed away by flowing a wash solution through the flow cell. The flow cell is then ready for a further cycle of sequencing starting with introduction of a labeled nucleotide as set forth above. The fluidic and detection steps can be repeated several times to complete a sequencing run. Exemplary sequencing methods are described, for example, in Bentley et al., Nature 456:53-59 (2008), WO 04/018497; U.S. Pat. No. 7,057,026; WO 91/06678; WO 07/123744; U.S. Pat. Nos. 7,329,492; 7,211,414; 7,315,019; 7,405,281, and US 2008/0108082, each of which is incorporated herein by reference. 
     In some embodiments, nucleic acids can be attached to a surface and amplified prior to or during sequencing. For example, amplification can be carried out using bridge amplification to form nucleic acid clusters on a surface. Useful bridge amplification methods are described, for example, in U.S. Pat. No. 5,641,658; U.S. Patent Publ. No. 2002/0055100; U.S. Pat. No. 7,115,400; U.S. Patent Publ. No. 2004/0096853; U.S. Patent Publ. No. 2004/0002090; U.S. Patent Publ. No. 2007/0128624; and U.S. Patent Publ. No. 2008/0009420. Another useful method for amplifying nucleic acids on a surface is rolling circle amplification (RCA), for example, as described in Lizardi et al., Nat. Genet. 19:225-232 (1998) and US 2007/0099208 A1, each of which 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), WO 05/010145, or U.S. Patent Publ. Nos. 2005/0130173 or 2005/0064460, each of which is incorporated herein by reference in its entirety. 
     Other sequencing techniques that are applicable for use of the methods and systems set forth herein are pyrosequencing, nanopore sequencing, and sequencing by ligation. Exemplary pyrosequencing techniques and samples that are particularly useful are described in U.S. Pat. Nos. 6,210,891; 6,258,568; 6,274,320 and Ronaghi, Genome Research 11:3-11 (2001), each of which is incorporated herein by reference. Exemplary nanopore techniques and samples that are also useful are described in Deamer et al., Acc. Chem. Res. 35:817-825 (2002); Li et al., Nat. Mater. 2:611-615 (2003); Soni et al., Clin Chem. 53:1996-2001 (2007) Healy et al., Nanomed. 2:459-481 (2007) and Cockroft et al., J. am. Chem. Soc. 130:818-820; and U.S. Pat. No. 7,001,792, each of which is incorporated herein by reference. In particular, these methods utilize repeated steps of reagent delivery. An instrument or method set forth herein can be configured with reservoirs, valves, fluidic lines and other fluidic components along with control systems for those components in order to introduce reagents and detect optical signals according to a desired protocol such as those set forth in the references cited above. Any of a variety of samples can be used in these systems such as substrates having beads generated by emulsion PCR, substrates having zero-mode waveguides, substrates having integrated CMOS detectors, substrates having biological nanopores in lipid bilayers, solid-state substrates having synthetic nanopores, and others known in the art. Such samples are described in the context of various sequencing techniques 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. 
     Exemplary labels that can be detected in accordance with various embodiments, for example, when present on or within a support structure include, but are not limited to, a chromophore; luminophore; fluorophore; optically encoded nanoparticles; particles encoded with a diffraction-grating; electrochemiluminescent label such as Ru(bpy) 32+ ; or moiety that can be detected based on an optical characteristic. Fluorophores that may be useful include, for example, fluorescent lanthanide complexes, including those of Europium and Terbium, fluorescein, rhodamine, tetramethylrhodamine, eosin, erythrosin, coumarin, methyl-coumarins, pyrene, Malacite green, Cy3, Cy5, stilbene, Lucifer Yellow, Cascade Blue™, Texas Red, alexa dyes, phycoerythin, bodipy, and others known in the art such as those described in Haugland, Molecular Probes Handbook, (Eugene, Oreg.) 6th Edition; The Synthegen catalog (Houston, Tex.), Lakowicz, Principles of Fluorescence Spectroscopy, 2nd Ed., Plenum Press New York (1999), or WO 98/59066, each of which is hereby incorporated by reference. In some embodiments, the one pair of labels may be excitable by a first excitation wavelength and another pair of labels may be excitable by a second excitation wavelength. 
     Although embodiments are exemplified with regard to detection of samples that include biological or chemical substances supported by an optical substrate, it will be understood that other samples can 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, and the like. Examples of some of the applications include microscopy, satellite scanners, high-resolution reprographics, fluorescent image acquisition, analyzing and sequencing of nucleic acids, DNA sequencing, sequencing-by-synthesis, imaging of microarrays, imaging of holographically encoded microparticles and the like. 
       FIG. 1  is a block diagram of an assay system  100  for biological or chemical analysis formed in accordance with one embodiment. In some embodiments, the assay system  100  is a workstation that may be similar to a bench-top device or desktop computer. For example, at least a majority of the systems and components for conducting the desired reactions can be within a common housing  117  of the assay system  100 . In other embodiments, the assay system  100  includes one or more components, assemblies, or systems that are remotely located from the assay system  100  (e.g., a remote database). The assay system  100  may include various components, assemblies, and systems (or sub-systems) that interact with each other to perform one or more predetermined methods or assay protocols for biological or chemical analysis. 
     For example, the assay system  100  includes a system controller  102  that may communicate with the various components, assemblies, and systems (or sub-systems) of the assay system  100 . As shown, the assay system  100  has an optical assembly  104 , an excitation source assembly  106 , a detector assembly  108 , and a fluidic device holder  110  that supports one or more fluidic devices  112  having a sample thereon. The fluidic device may be a flow cell, such as the flow cell  200  described below, or the fluidic device  112  may be the fluidic device  300  described below. 
     In some embodiments, the optical assembly  104  is configured to direct incident light from the excitation source assembly  106  onto the fluidic device(s)  112 . The excitation source assembly  106  may include one or more excitation light sources that are configured to excite labels associated with the sample. The excitation source assembly  106  may also be configured to provide incident light that is reflected and/or refracted by the samples. As shown, the samples may provide optical signals that include light emissions  116  and/or transmission light  118 . The device holder  110  and the optical assembly  104  may be moved relative to each other. In some embodiments, the device holder  110  includes a motor assembly  132  that moves the fluidic device  112  with respect to the optical assembly  104 . In other embodiments, the optical assembly  104  may be moved in addition to or alternatively to the device holder  110 . The optical assembly  104  may also be configured to direct the light emissions  116  and/or transmission light  118  to the detector assembly  108 . The detector assembly  108  may include one or more imaging detectors. The imaging detectors may be, by way of example only, CCD or CMOS cameras, or photomultiplier tubes. 
     Also shown, the assay system  100  may include a fluidic control system  134  to control the flow of fluid throughout a fluidic network  135  (indicated by the solid lines) of the assay system  100 . The fluidic control system  134  may deliver reaction components (e.g., reagents) or other fluids to the fluidic device  112  during, for example, a sequencing protocol. The assay system  100  may also include a fluid storage system  136  that is 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 fluid. The temperature control system  138  may also generally regulate a temperature of the assay system  100  using, for example, thermal modules, heat sinks, and blowers. 
     Also shown, the assay system  100  may include a user interface  140  that interacts with the user. For example, the user interface  140  may include a display  142  to display or request information from a user and a user input device  144  to receive user inputs. In some embodiments, the display  142  and the user input device  144  are the same device (e.g., touchscreen). As will be discussed in greater detail below, the assay system  100  may communicate with various components to perform the desired reactions. The assay system  100  may also be configured to analyze the detection data to provide a user with desired information. 
     The fluidic control system  134  is configured to direct and regulate the flow of one or more fluids through the fluidic network  135 . The fluidic control system  134  may include, for example, pumps and valves that are selectively operable for controlling fluid flow. The fluidic network  135  may be in fluid communication with the fluidic device  112  and the fluid storage system  136 . For example, select fluids may be drawn from the fluid storage system  136  and directed to the fluidic device  112  in a controlled manner, or the fluids may be drawn from the fluidic device  112  and directed toward, for example, a waste reservoir in the fluid storage system  136 . Although not shown, the fluidic control system  134  may also include flow sensors that detect a flow rate or pressure of the fluids within the fluidic network. The sensors may communicate with the system controller  102 . 
     The temperature control system  138  is configured to regulate the temperature of fluids at different regions of the fluidic network  135 , the fluid storage system  136 , and/or the fluidic device  112 . For example, the temperature control system  138  may include a thermocycler  113  that interfaces with the fluidic device  112  and controls the temperature of the fluid that flows along the fluidic device  112 . Although not shown, the temperature control system  138  may include sensors to detect the temperature of the fluid or other components. The sensors may communicate with the system controller  102 . 
     The fluid storage system  136  is in fluid communication with the fluidic device  112  and may store various reaction components or reactants that are used to conduct the desired reactions therein. The fluid storage system  136  may store fluids for washing or cleaning the fluidic network  135  or the fluidic device  112  and also for diluting the reactants. For example, the fluid storage system  136  may include various reservoirs to store reagents, enzymes, other biomolecules, buffer solutions, aqueous, and non-polar solutions, and the like. Furthermore, the fluid storage system  136  may also include waste reservoirs for receiving waste products. 
     The device holder  110  is configured to engage one or more fluidic devices  112 , for example, in at least one of a mechanical, electrical, and fluidic manner. The device holder  110  may hold the fluidic device(s)  112  in a desired orientation to facilitate the flow of fluid through the fluidic device  112  and/or imaging of the fluidic device  112 . 
     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 array (FPGAs), logic circuits, and any other circuit or processor capable of executing functions described herein. The above examples are exemplary only, and are thus not necessarily intended to limit the definition and/or meaning of the term system controller. In the exemplary embodiment, the system controller  102  executes a set of instructions that are stored in one or more storage elements, memories, or modules in order to at least one of obtain and analyze detection data. Storage elements may be in the form of information sources or physical memory elements within the assay system  100 . 
     The set of instructions may include various commands that instruct the assay system  100  to perform specific operations such as the methods and processes of the various embodiments described herein. The set of instructions 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 memory for execution by a computer, including RAM memory, ROM memory, EPROM memory, EEPROM memory, and non-volatile RAM (NVRAM) memory. The above memory types are exemplary only, and are thus not limiting as to the types of memory usable for storage of a computer program. 
     The software may be in various forms such as system software or application software. Further, the software may be in the form of a collection of separate programs, or a program module within a larger program or a portion of a program module. The software also may include modular programming in the form of object-oriented programming. After obtaining the detection data, the detection data may be automatically processed by the assay system  100 , processed in response to user inputs, or processed in response to a request made by another processing machine (e.g., a remote request through a communication link). 
     The system controller  102  may be connected to the other components or sub-systems of the assay system  100  via communication links (indicated by dashed lines). The system controller  102  may also be communicatively connected to off-site systems or servers. The communication links may be hardwired or wireless. The system controller  102  may receive user inputs or commands, from the user interface  140 . The user input device  144  may include a keyboard, mouse, a touch-screen panel, and/or a voice recognition system, and the like. Alternatively or in addition, the user input device  144  may also be the display  142 . 
       FIG. 1  also illustrates a block diagram of the system controller  102 . In one embodiment, the system controller  102  includes one or more processors or modules that can communicate with one another. The system controller  102  is illustrated conceptually as a collection of modules, but may be implemented utilizing any combination of dedicated hardware boards, DSPs, processors, etc. Alternatively, the system controller  102  may be implemented utilizing an off-the-shelf PC with a single processor or multiple processors, with the functional operations distributed between the processors. As a further option, the modules described below may be implemented utilizing a hybrid configuration in which certain modular functions are performed utilizing dedicated hardware, while the remaining modular functions are performed utilizing an off-the-shelf PC and the like. The modules also may be implemented as software modules within a processing unit. 
     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 the 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 the other systems. Also, the modules  151 - 158  may communicate with the system control module  150  through the other modules. 
     The plurality of modules  151 - 158  include system modules  151 - 153  that communicate with the sub-systems. The fluidic control module  151  may communicate with the fluidic control system  134  to control the valves and flow sensors of the fluidic network  135  for controlling the flow of one or more fluids through the fluidic network  135 . The fluid storage module  152  may notify the user when fluids are low or when the waste reservoir must be replaced. The fluid storage module  152  may also communicate with the temperature control module  153  so that the fluids may be stored at a desired temperature. 
     The plurality of modules  151 - 158  may also include an image analysis module  158  that receives and analyzes the detection data (e.g., image data) from the detector assembly  108 . The processed detection data may be stored for subsequent analysis or may be transmitted to the user interface  140  to display desired information to the user. Protocol modules  155 - 157  communicate with the system control module  150  to control the operation of the sub-systems when conducting predetermined assay protocols. The protocol modules  155 - 157  may include sets of instructions for instructing the assay system  100  to perform specific operations pursuant to predetermined protocols. 
     The protocol module  155  may be configured to issue commands for generating a sample within the fluidic device  112 . For example, the protocol module  155  may direct the fluid storage system  136  and the temperature control system  138  to generate the sample in a sample area. In one particular embodiment, the protocol module  155  may issue commands to perform bridge PCR where clusters of clonal amplicons are formed on localized areas within a channel (or lane) of a flow cell. 
     The protocol module  156  may be a sequencing-by-synthesis (SBS) module configured to issue various commands for performing sequencing-by-synthesis processes. In some embodiments, the SBS module  156  may also process detection data. After generating the amplicons through bridge PCR, the SBS module  156  may provide instructions to linearize or denature the amplicons to make sstDNA and to add a sequencing primer such that the sequencing primer may be hybridized to a universal sequence that flanks a region of interest. Each sequencing cycle extends the sstDNA by a single base and is accomplished by modified DNA polymerase and a mixture of four types of nucleotides delivery of which can be instructed by the SBS module  156 . The different types of nucleotides have unique fluorescent labels, and each nucleotide has a reversible terminator that allows only a single-base incorporation to occur in each cycle. After a single base is added to the sstDNA, the SBS module  156  may instruct a wash step to remove nonincorporated nucleotides by flowing a wash solution through the flow cell. The SBS module  156  may further instruct the excitation source assembly and detector assembly to perform an image session(s) to detect the fluorescence in each of the four channels (i.e., one for each fluorescent label). After imaging, the SBS module  156  may instruct delivery of a deblocking reagent to chemically cleave the fluorescent label and the terminator from the sstDNA. The SBS module  156  may instruct a wash step to remove the deblocking reagent and products of the deblocking reaction. Another similar sequencing cycle may follow. In such a sequencing protocol, the SBS module  156  may instruct the fluidic control system  134  to direct a flow of reagent and enzyme solutions through the fluidic device  112 . 
     In some embodiments, the SBS module  157  may be configured to issue various commands for performing the steps of a pyrosequencing protocol. Pyrosequencing detects the release of inorganic pyrophosphate (PPi) as particular nucleotides are incorporated into the nascent strand (Ronaghi, M. et al. (1996) “Real-time DNA sequencing using detection of pyrophosphate release.” Analytical Biochemistry 242(1), 84-9; Ronaghi, M. (2001) “Pyrosequencing sheds light on DNA sequencing.” Genome Res. 11(1), 3-11; Ronaghi, M. et al. (1998) “A sequencing method based on real-time pyrophosphate.” Science 281(5375), 363; U.S. Pat. Nos. 6,210,891; 6,258,568 and 6,274,320, the disclosures of which are incorporated herein by reference in their entireties. In pyrosequencing, released PPi can be detected by being immediately converted to adenosine triphosphate (ATP) by ATP sulfurylase, and the level of ATP generated is detected via luciferase-produced photons. In this case, the fluidic device  112  may include millions of wells where each well has a single capture bead having clonally amplified sstDNA thereon. Each well may also include other smaller beads that, for example, may carry immobilized enzymes (e.g., ATP sulfurylase and luciferase) or facilitate holding the capture bead in the well. The SBS module  157  may be configured to issue commands to the fluidic control module  151  to run consecutive cycles of fluids that carry a single type of nucleotide (e.g., 1st cycle: A; 2nd cycle: G; 3rd cycle: C; 4th cycle: T; 5th cycle: A; 6th cycle: G; 7th cycle: C; 8th cycle: T; and on). When a nucleotide is incorporated into the DNA, pyrophosphate is released thereby instigating a chain reaction where a burst of light is generated. The burst of light may be detected by a sample detector of the detector assembly. Detection data may be communicated to the system control module  150 , the image analysis module  158 , and/or the SBS module  157  for processing. The detection data may be stored for later analysis or may be analyzed by the system controller  102  and an image may be sent to the user interface  140 . 
     In some embodiments, the user may provide user inputs through the user interface  140  to select an assay protocol to be run by the assay system  100 . In other embodiments, the assay system  100  may automatically detect the type of fluidic device  112  that has been inserted into the device holder  110  and confirm with the user the assay protocol to be run. Alternatively, the assay system  100  may offer a limited number of assay protocols that could be run with the determined type of fluidic device  112 . The user may select the desired assay protocol, and the assay system  100  may then perform the selected assay protocol based on preprogrammed instructions. 
       FIGS. 2 and 3  illustrate a workstation  160  formed in accordance with one embodiment that is configured for biological and chemical analysis of a sample. As shown, the workstation  160  is oriented with respect to mutually perpendicular X, Y, and Z-axes. In the illustrated embodiment, a gravitational force g extends parallel to the Z-axis. The workstation  160  may include a workstation casing  162  (or workstation housing) that is shown in phantom in  FIGS. 2 and 3 . The casing  162  is configured to hold the various elements of the workstation  160 . For example, the workstation  160  may include similar elements as described above with respect to the assay system  100  ( FIG. 1 ). As shown, the workstation  160  has an optical deck  164  having a plurality of optical components mounted thereto. The optical components may be part of an optical assembly, such as the optical assembly  602  described with reference to  FIG. 38  et al. The optical deck  164  may have a fixed position with respect to the casing  162 . 
     The workstation  160  may also include a sample deck  166  that is movably coupled to the optical deck  164 . The sample deck  166  may have a slidable platform  168  that supports a fluidic device thereon having a sample-of-interest. In the illustrated embodiment, the fluidic device is the fluidic device  300  that is described in greater detail below. The platform  168  is configured to slide with respect to the optical deck  166  and, more specifically, with respect to an imaging lens of the optical assembly  602 . To this end, the platform  168  may slide bi-directionally along the X-axis so that the fluidic device  300  may be positioned on the sample deck  166  and so that the imaging lens may slide over the fluidic device  300  to image the sample therein. In other embodiments, the platform  168  may be stationary and the sample deck  166  may slide bi-directionally along the X-axis to position the fluidic device  300  with respect to an imaging lens of the optical assembly  602 . Thus, the platform and sample deck can be moveable relative to each other due to movement of the sample deck, platform, or both. 
     Also shown, the workstation  160  may include a user interface  172 , a computing system  174  ( FIG. 2 ), and fluid storage units  176  and  178  ( FIG. 4 ). The user interface  172  may be a touchscreen that is configured to display information to a user and also receive user inputs. For example, the touchscreen may receive commands to perform predetermined assay protocols or receive inquiries from the user. The computing system  174  may include processors and modules, such as the system controller  102  and the modules  151 - 158  described with reference to  FIG. 1 . The fluid storage units  176  and  178  may be part of a larger fluid storage system. The fluid storage unit  176  may be for collecting waste that results from performing the assays and the fluid storage unit  178  may include a buffer solution. 
       FIG. 4  is a diagram of a fluidic network  552  that may be used in the workstation  160  ( FIG. 2 ). As used herein, fluids may be liquids, gels, gases, or a mixture of thereof. Also, a fluid can be a mixture of two or more fluids. The fluidic network  552  may include a plurality of fluidic components (e.g., fluid lines, pumps, flow cells or other fluidic devices, manifolds, reservoirs) configured to have one or more fluids flowing therethrough. As shown, the fluidic network  552  includes a plurality of fluidic components  553 - 561  interconnected through fluid lines (indicated by the solid lines). In the illustrated embodiment, the fluidic network  552  includes a buffer solution container  553 , a reagent tray  554 , a multi-port valve  555 , a bypass valve  556 , a flow rate sensor  557 , a flow cell  558 , another flow rate sensor  559 , a pump  560 , and a waste reservoir  561 . Fluid flow directions are indicated by arrows along the fluid lines. In addition to the fluidic components  553 - 561 , the fluidic network may also include other fluidic components. 
     The reagent tray  554  may be similar to the reaction component tray (or reaction component storage unit)  1020  described in greater detail below. The tray  1020  may include various containers (e.g., vials or tubes) containing reaction components for performing assays with embodiments described herein. Operation of the multi-port valve  555  may be controlled by an assay system, such as the assay system  100 , to selectively flow different fluids, including mixtures thereof, to the flow cell  558 . The flow cell  558  may be the flow cell  200  or the fluidic device  300 , which are described in greater detail below, or other suitable fluidic devices. 
       FIGS. 5-60 , which are described in greater detail below, illustrate various elements (e.g., components, devices, assemblies, systems, and the like) and methods that may be used with the workstation  160 . These elements may cooperate with one another in imaging a sample, analyzing the detection data, and providing information to a user of the workstation  160 . However, the following elements and methods may also be used independently, in other apparatuses, or with other apparatuses. For example, the flow cell  200  and the fluidic device  300  may be used in other assay systems. The optical assembly  602  (and elements thereof) may be used for examining other items, such as microcircuits. Furthermore, the device holder  400  may be used to hold other fluidic devices, such as lab-on-chip devices. Assay systems with these devices may or may not be include an optical assembly to detect the desired reactions. 
       FIGS. 5-7  illustrate a flow cell  200  formed in accordance with one embodiment. As shown in  FIGS. 5-7 , the flow cell  200  is oriented relative to the X, Y, and Z-axes. The flow cell  200  is configured to hold a sample-of-interest  205  in a flow channel  206 . The sample  205  is illustrated as a plurality of DNA clusters that can be imaged during a SBS protocol, but other samples may be used in alternative embodiments. Although only the single U-shaped flow channel  206  is illustrated, alternative embodiments may include flow cells having multiple flow channels with differently shaped paths. The flow cell  200  may be in fluid communication with a fluidic system (not shown) that is configured to deliver reagents to the sample  205  in the flow channel  206 . In some embodiments, the sample  205  may provide detectable characteristics (e.g., through fluorescence or chemiluminescence) after desired reactions occur. For instance, the flow cell  200  may have one or more sample areas or regions (i.e., areas or regions where the sample  205  is located) from which optical signals are emitted. In some embodiments, the flow cell  200  may also be used to generate the sample  205  for performing a biological or chemical assay. For example, the flow cell  200  may be used to generate the clusters of DNA before the SBS protocol is performed. 
     As shown in  FIGS. 5-7 , the flow cell  200  can include a first layer  202  and a second layer  204  that are secured together and define the flow channel  206  therebetween. The first layer  202  has a mounting surface  208  and an outer or exterior surface  210  ( FIGS. 5 and 6 ). The mounting and outer surfaces  208  and  210  face in opposite directions along the Z-axis and define a thickness Ti ( FIGS. 5 and 6 ) therebetween. The thickness T 1  is substantially uniform along an XY-plane, but may vary in alternative embodiments. The second layer  204  has a channel surface  212  ( FIG. 6 ) and an outer or exterior surface  214 . The channel and outer surfaces  212  and  214  face in opposite directions along the Z-axis and define a thickness T 2  ( FIG. 6 ) therebetween. 
     Also shown in  FIG. 5 , the first layer  202  has a dimension or length L 1  measured along the X-axis and another dimension or width W 1  measured along the Y-axis. In some embodiments, the flow cell  200  may be characterized as a microdevice. Microdevices may be difficult to hold or move by an individual&#39;s hands. For example, the length L 1  of the flow cell  200  may be about 100 mm, or about 50 mm, or less. In particular embodiments, the length L 1  is about 30 mm or less. In some embodiments, the width W 1  may be about 35 mm, or about 25 mm or less or, more particularly, the width W 1  may be about  15  mm or less. Furthermore, a combined or total height H T  shown in  FIG. 7  (e.g., a sum of thicknesses T 1  and T 2 ) may be about 10 mm, or about 5 mm or less. More specifically, the height H T  may be about 2 mm or about 1.5 mm or less. 
     The flow cell  200  includes edges  231 - 234  that are linear in the illustrated embodiment. Edges  231  and  233  are spaced apart by the width W 1  and extend the length Li of the flow cell  200 . Edges  232  and  234  are spaced apart by the length L 1  and extend along the width W 1 . Also shown, the second layer  204  may have a dimension or length L 2  measured along the X-axis and another dimension or width W 2  measured along the Y-axis. In the illustrated embodiment, the edges  231 - 234  define a perimeter of the flow cell  200  and extend along a common cell plane that extends parallel to the XY-plane. Also shown, the second layer  204  may have edges  241 - 244  that are similarly oriented as the edges  231 - 234  as shown in  FIG. 5 . 
     In the illustrated embodiment, the width W 1  is substantially greater than the width W 2 , and the second layer  204  is positioned on only a portion of the mounting surface  208 . As such, the mounting surface  208  includes exposed grip portions  208 A and  208 B on opposite sides of the second layer  204 . The width W 2  extends between the grip portions  208 A and  208 B. The flow cell  200  may also have cell sides  256  and  258  that face in opposite directions along the Z-axis. In the illustrated embodiment, the cell side  256  includes the grip portions  208 A and  208 B and the exterior surface  214 , and the cell side  258  includes the exterior surface  210 . Also shown, the flow cell  200  may extend lengthwise between opposite first and second cell ends  246  and  248 . In the illustrated embodiment, the edges  232  and  242  are substantially flush with respect to each other at the first cell end  246 , and the edges  234  and  244  are substantially flush with respect to each other at the opposite second cell end  248 . 
     As shown in  FIG. 6 , the second layer  204  has at least one grooved portion  216  that extends along the channel surface  212 . In the illustrated embodiment, the channel surface  212  is etched to form the grooved portion  216 , but the grooved portion  216  may be formed by other processes, such as machining the channel surface  212 . To assemble the flow cell  200 , the channel surface  212  of the second layer  204  is mounted onto and secured to the mounting surface  208  of the first layer  202 . For example, the channel and mounting surfaces  212  and  208  may be bonded together using an adhesive (e.g., light-activated resin) that prevents leakage from the flow cell  200 . In other embodiments, the channel and mounting surfaces  212  and  208  may be secured together by other adhesives or mechanically interlocked and/or held together. Thus, the first layer  202  is configured to cover the grooved portion  216  of the second layer  204  to form the flow channel  206 . In the illustrated embodiment, the grooved portion  216  may be a single continuous groove that extends substantially the length L 2  toward the first end, curves, and then extends substantially the length L 2  toward the second end. Thus, the flow channel  206  may be substantially U-shaped. 
     In  FIGS. 5-7  the sample  205  is shown as being located along only the mounting surface  208 . However, in other embodiments, the sample  205  may be located on any surface that defines the flow channel  206 . For instance, the sample  205  may also be located on the mating surface  212  of the grooved portion  216  that partially defines the flow channel  206 . 
     In the illustrated embodiment, the flow channel  206  may include a plurality of channel segments  250 - 252 . Different channel segments may have different dimensions with respect to the immediately upstream or downstream channel segment. In the illustrated embodiment, the flow channel  206  may include a channel segment  250 , which may also be referred to as the imaging segment  250 . The channel segment  250  may have a sample area that is configured to be imaged by an imaging system (not shown). The flow channel  206  may also have channel segments  251  and  252 , which may also be referred to as non-imaging segments  250  and  252 . As shown, the channel segments  250  and  252  extend parallel to each other through the flow cell  200 . The channel segments  251  and  252  of the flow channel  206  may be sized and shaped relative to the channel segment  250  to control the flow of fluid and gases that may flow therethrough. 
     For example,  FIG. 7  also illustrates cross-sections C 1 -C 3  of the channel segments  250 - 252 , respectively, that are taken perpendicular to a flow direction F 1 . In some embodiments, the cross-sections C 1 -C 3  may be differently sized (i.e., different cross-sectional areas) to control the flow of fluid through the flow channel  206 . For example, the cross-section C 1  is greater in size than the cross-sections C 2  and C 3 . More specifically, the channel segments  250 - 252  of the flow channel  206  may have a substantially equal height H 1  measured between the grooved portion  216  of the channel surface  212  ( FIG. 6 ) and the mounting surface  208 . However, the channel segments  250 - 252  of the flow channel  206  may have different widths W 3 -W 5 , respectively. The width W 3  is greater than the widths W 4  and W 5 . The channel segment  251  may constitute a curved or elbow segment that fluidicly joins the channel segments  250  and  252 . The cross-section C 3  is smaller than the cross-sections C 1  and C 2 . For example, the width W 5  is less than the widths W 3  and W 4 . 
       FIG. 8  is an enlarged view of the curved segment  251  and portions of the channel segments  250  and  252 . As described above, the channel segments  250  and  252  may extend parallel to each other. Within the flow channel  206 , it may be desirable to have a uniform flow across the sample area. For example, the fluid may include stream portions F 2 -F 4 . Dimensions of the channel segments  250 - 252  may be configured so that the stream portions F 2 -F 4  have substantially equal flow rates across the sample area. In such embodiments, different sections or portions of the sample  205  ( FIG. 5 ) may have a substantially equal amount of time to react with reaction components within the fluid. 
     To this end, the curved segment  251  of the flow channel  206  may have a non-continuous contour that fluidicly joins the channel segments  250  and  252 . For example, as shown in  FIG. 8 , the curved segment  251  may include a tapering portion  270 , an intermediate portion  276 , and a downstream portion  278 . As shown, the tapering portion  270  has a width W 5A  that gradually reduces in size. More specifically, the curved segment  251  may include sidewalls  272  and  274  that extend inward toward each other at a substantially equal angle. The intermediate portion  276  curves from the tapering portion  270  to the downstream portion  278 . The intermediate portion  276  has a width W 5B  that reduces in size and then begins to increase in size. The downstream portion  278  has a substantially uniform width W 5 c throughout and extends along a substantially linear path from the intermediate portion  276  to the channel segment  252 . In other words, the sidewalls  272  and  274  may extend parallel to each other throughout the downstream portion  278 . 
     Returning to  FIG. 7 , the flow cell  200  includes inlet and outlet ports  222  and  224 , respectively. The inlet and outlet ports  222  and  224  are formed only through the second layer  204 . However, in alternative embodiments, the inlet and outlet ports  222  and  224  may be formed through only the first layer  202  or through both layers  202  and  204 . The flow channel  206  is in fluid communication with and extends between the inlet and outlet ports  222  and  224 . In particular embodiments, the inlet and outlet ports  222  and  224  are located proximate to each other at the cell end  248  of the flow cell  200  (or proximate to the edges  234  and  244 ). For example, a spacing  282  that separates the inlet and outlet ports  222  and  224  may be approximately equal to the width W 3 . More specifically, the spacing  282  may be about 3 mm, about 2 mm, or less. Furthermore, the channel segments  250  and  252  may be separated by a spacing  280 . The spacing  280  may be less than the width W 3  of the channel segment  250  or, more particularly, less than the width W 4  of the channel segment  252 . Thus, a path of the flow channel  206  may be substantially U-shaped and, in the illustrated embodiment, have a non-continuous contour along the curved segment  251 . 
     In alternative embodiments, the flow channel  206  may have various paths such that the inlet and outlet ports  222  and  224  have different locations in the flow cell  200 . For example, the flow channel may form a single lane that extends from the inlet port at one end of the flow cell to the outlet port at the opposite end of the flow cell. 
     With respect to  FIG. 6 , in some embodiments, the thickness T 2  ( FIG. 6 ) of the second layer  204  is substantially uniform along the imaging portion  250 . The uniform thickness T 2  along the imaging portion  250  may be configured to transmit optical signals therethrough. Furthermore, the thickness Ti of the first layer  202  is substantially uniform along the imaging portion  250  and configured to permit uniform transfer of thermal energy therethrough into the flow channel  206 . 
       FIGS. 9-11  illustrate a fluidic device  300  formed in accordance with one embodiment. For illustrative purposes, the fluidic device  300  is oriented with respect to the mutually perpendicular X, Y, and Z-axes shown in  FIGS. 9 and 10 .  FIGS. 9 and 10  are perspective views of the fluidic device  300 . As shown in  FIGS. 9 and 10 , the fluidic device  300  includes a cartridge (or flow cell carrier)  302  and the flow cell  200 . The cartridge  302  is configured to hold the flow cell  200  and facilitate orienting the flow cell  200  for an imaging session. 
     In some embodiments, the fluidic device  300  and the cartridge  302  may be removable such that the cartridge  302  may be removed from an imaging system (not shown) by an individual or machine without damage to the fluidic device  300  or cartridge  302 . For example, the cartridge  302  may be configured to be repeatedly inserted and removed into the imaging system without damaging the cartridge  302  or rendering the cartridge  302  unsuitable for its intended purpose. In some embodiments, the fluidic device  300  and the cartridge  302  may be sized and shaped to be handheld by an individual. Furthermore, the fluidic device  300  and the cartridge  302  may be sized and shaped to be carried by an automated system. 
     As shown in  FIGS. 9 and 10 , the cartridge  302  may include a housing or carrier frame  304  and a cover member  306  that is coupled to the housing  304 . The housing  304  has housing or carrier sides  303  and  305  that face in opposite directions along the Z-axis and have a height H 2  (shown in  FIG. 11 ) extending therebetween. As shown in  FIG. 9 , the housing  304  includes a bridge member  324  at a loading end  316  of the fluidic device  300  and a base member  326  at an opposite receiving end  318  of the fluidic device  300 . The housing  304  also includes a pair of spaced apart leg extensions  328  and  330  that extend between the bridge and base members  324  and  326 . The bridge member  324  extends between and joins the leg extensions  328  and  330 . The bridge member  324  may include a recess  321  (shown in  FIG. 10 ) that opens to an exterior of the fluidic device  300 . As shown in  FIG. 9 , the leg extensions  328  and  330  may have a plurality of grip members  371 - 374  that are configured to grip the cell side  256  of the flow cell  200 . 
     Also shown in  FIG. 9 , the fluidic device  300  may have a device window  315  that passes entirely through the cartridge  302  along the Z-axis. In the illustrated embodiment, the device window  315  is substantially framed by the bridge member  324 , the cover member  306 , and the leg extensions  328  and  330 . The device window  315  includes a reception space  308  and a plurality of recesses  320  and  322  that are immediately adjacent to the reception space  308 . The reception space  308  is configured to receive the flow cell  200 . When the flow cell  200  is positioned within the reception space  308 , the flow cell  200  is exposed to an exterior of the fluidic device  300  such that the flow cell  200  may be viewed or directly engaged along the housing side  303  and also the housing side  305 . For example, the cell side  258  (also shown in  FIG. 11 ) that faces in an opposite direction along the Z-axis relative to the cell side  256 . The cell side  256  may be viewed by the imaging system or directly engaged by another component along the housing side  303 . Likewise, the cell side  258  may be viewed by the imaging system or directly engaged by another component along the housing side  305 . 
     With respect to  FIGS. 9 and10 , the cover member  306  may include a cover body  340  and a gasket  342  that are coupled to each other. The gasket  342  includes inlet and outlet passages  346  and  344  (shown in  FIG. 9 ) that are located proximate to one another. In the illustrated embodiment, the cover body  340  and the gasket  342  are co-molded into a unitary structure. When formed, the cover body  340  and the gasket  342  may have different compressible properties. For example, in particular embodiments, the gasket  342  may comprise a material that is more compressible than material of the cover body  340 . However, in alternative embodiments, the cover body  340  and the gasket  342  may be separate parts that are coupled together (e.g., mechanically or using an adhesive). In other embodiments, the cover body  340  and the gasket  342  may be different portions or regions of a single continuous structure. 
     The cover member  306  may be movably coupled to the housing  304 . For example, the cover member  306  may be rotatably coupled to the base member  326  of the housing  304 . In such embodiments, the gasket  342  is rotatable about an axis of rotation R 1  between a mounted position (shown in  FIG. 9 ) and a disengaged position (shown in  FIG. 10 ). In other embodiments in which the cover member  306  is movably coupled to the housing  304 , the cover member  306  may be detachable from the housing  304 . For example, when attached to the housing  304 , the detachable cover member may be in a mounted position that is similar to the mounted position as shown in  FIG. 9 . 
     When unattached to the housing  304 , the detachable cover member may be completely removed in a disengaged position. 
     Also shown in  FIG. 10 , the housing  304  may define a cartridge cavity  338  ( FIG. 10 ) that is accessible when the cover member  306  is in the disengaged position. In some embodiments, an identification transmitter  336  may be positioned within the cartridge cavity  338 . The identification transmitter  336  is configured to communicate information about the flow cell  200  to a reader. For example, the identification transmitter  336  may be an RFID tag. The information provided by the identification transmitter  336  may, for example, identify the sample in the flow cell  200 , a lot number of the flow cell or sample, a date of manufacture, and/or the assay protocol to be performed when the flow cell  200  is inserted into the imaging system. The identification transmitter  336  may communicate other information as well. 
       FIG. 11  is a cross-section of the fluidic device  300  viewed along the Y-axis. In some embodiments, the reception space  308  is sized and shaped relative to the flow cell  200  so that the flow cell  200  is retained in the space, but in at least some configurations may float therein. As used herein, the term “float” and like terms includes the component being permitted to move a limited distance in at least one direction (e.g., along the X, Y, or Z-axes). For example, the flow cell  200  may be capable of shifting within the reception space  308  along the XY-plane. The flow cell  200  may also be capable of moving in a direction along the Z-axis within the reception space  308 . Furthermore, the flow cell  200  can also be capable of slightly rotating within the reception space  308 . In particular embodiments, the housing  304  permits the flow cell  200  to shift, move, and slightly rotate within the reception space  308  with respect to any of the X, Y, and Z-axes. 
     In some embodiments, the reception space  308  may also be characterized as the space that the fluidic device  300  allows the flow cell  200  to move freely within when the fluidic device  300  is holding the flow cell  200 . Thus, dimensions of the reception space  308  may be based upon positions of reference surfaces of the fluidic device  300  that can directly engage the flow cell  200 . The reference surfaces may be surfaces of the housing  304  or the cover member  306 , including the gasket  342 . For example,  FIG. 11  illustrates a plurality of reference surfaces  381 - 387 . The references surfaces  381  and  382  of the grip members  371  and  372 , respectively, and the reference surface  383  of the gasket  342  may limit movement of the flow cell  200  beyond a predetermined level when the flow cell  200  is held within the reception space  308 . The reference surface  384  of the gasket  342  and the reference surface  385  of the bridge member  324  may limit movement of the flow cell  200  along the XY-plane. Furthermore, the reference surfaces  386  and  387  of the bridge member  324  and the cover member  306 , respectively, may also limit movement of the flow cell  200  along the Z-axis. However, the references surfaces  381 - 387  are exemplary only and the fluidic device  300  may have other reference surfaces that limit movement of the flow cell  200 . 
     To assemble the fluidic device  300 , the flow cell  200  may be loaded into the reception space  308 . For example, the flow cell  200  may be advanced toward the device window  315  along the housing side  305 . The edge  234  ( FIG. 5 ) may be advanced between the grip members  372  and  373  and the gasket  342 . The cell side  256  may then be rotated toward the grip members  371 - 374  so that the grip members  371 - 374  interface the cell side  256 . The edge  232  ( FIG. 5 ) may then be moved toward the bridge member  324  and, more specifically, the reference surface  385  of the bridge member  324 . In some embodiments, the bridge member  324  may be deflected or bent to provide more space for positioning the cell end  246  ( FIG. 5 ) thereon. When the flow cell  200  is loaded into the cartridge  302 , the housing  304  and the cover member  306  may effectively grip the perimeter of the flow cell  200  such that the flow cell  200  is confined to move only within the reception space  308 . 
     In alternative embodiments, the cell end  246  may be first inserted positioned by the bridge member  324  and then the gasket  342 . In other embodiments, the flow cell  200  may approach the housing side  303 . The grip members  371 - 374  may have tapered or beveled surfaces that permit the flow cell  200  to be snapped into position within the reception space  308 . 
     Before, after, or during the loading of the flow cell  200 , the cover member  306  may be moved to the disengaged position so that the identification transmitter  336  ( FIG. 10 ) may be positioned with the cartridge cavity  338  ( FIG. 10 ). When the gasket  342  is in the mounted position, the inlet and outlet passages  346  and  344  may have a predetermined location and orientation with respect to the housing  304  and the reception space  308 . The gasket  342  may be mounted over the flow cell  200  along an exposed portion of the flow cell  200  (i.e., the cell side 256 ). The inlet and outlet passages  346  and  344  may be generally aligned with the inlet and outlet ports  224  and  222  ( FIG. 5 ). 
     However, it should be noted that the illustrated fluidic device  300  is only one particular embodiment, and the fluidic device  300  may have different configurations in alternative embodiments. For example, in alternative embodiments, the flow cell  200  may not be exposed to the exterior of the fluidic device  300  along each of the housing sides  303  and  305 . Instead, the flow cell  200  may be exposed to the exterior along only one of the housing sides (e.g., the housing side  303 ). Furthermore, in alternative embodiments, the cover member  306  may not be rotatably coupled to the housing  304 . For example, the cover member  306  may be entirely detachable. 
       FIGS. 12-15  illustrate fluidic devices  900  and  920  formed in accordance with alternative embodiments that may also be used in assay systems, such as the assay system  100  ( FIG. 1 ) and the workstation  160  ( FIG. 2 ). The fluidic devices  900  and  920  may include similar features as the fluidic device  300 . For example, as shown, in  FIGS. 12 and 13 , the fluidic device  900  may include a cartridge (or flow cell carrier)  902  and the flow cell  200 . The cartridge  902  is configured to hold the flow cell  200  and facilitate orienting the flow cell  200  for an imaging session. The cartridge  902  includes a housing  904  and a cover member  906  that is movably mounted to the housing  904 . The cover member  906  is in the mounted position in  FIG. 12  and the disengaged position in  FIG. 13 . 
     Also shown in  FIGS. 12 and 13 , the fluidic device  900  may include a sealing member  910  that covers the inlet and outlet ports  222  and  224  ( FIG. 13 ) of the flow cell  200 . In some embodiments, the sealing member  910  is configured to facilitate retaining fluid within the flow channel  206  so that the sample  205  ( FIG. 5 ) within the flow channel  206  remains in a fluid environment. However, in some embodiments, the sealing member  910  may be configured to prevent unwanted materials from entering the flow channel  206 . As shown in  FIGS. 12 and 13 , the sealing member  910  is a single piece of tape that extends between the cell ends  246  and  248  ( FIG. 13 ). An overhang portion  912  may extend away from the cell end  246 . In alternative embodiments, the sealing member  910  may be more than one piece of tape (e.g., one piece of tape for each of the inlet and outlet ports  222  and  224 ) or the sealing member  910  may be other elements capable of covering the inlet and outlet ports  222  and  224 . For example, the sealing member  910  could include plugs. 
     In some embodiments, the sealing member  910  covers the inlet and outlet ports  222  and  224  when the fluidic device  900  is not mounted to an assay system. For example, the sealing member  910  may be used when the fluidic device  900  is being stored or transported, or when a sample is being grown or generated within the flow cell  200 . In such instances, the sealing member  910  may be secured to the flow cell  200  and the housing  904  as shown in  FIG. 13 . More specifically, the sealing member  910  may couple to and extend along the cell side  256  and cover the inlet and outlet ports  222  and  224 . The sealing member  910  may also couple to a base member  914  of the housing  904 . The cover member  906  may then be moved to the mounted position as shown in  FIG. 12  such that the sealing member  910  is sandwiched between the inlet and outlet ports  222  and  224  and the cover member  906 . The cover member  906  may facilitate preventing the sealing member  910  from being inadvertently removed. In alternative embodiments, the sealing member  910  may cover inlet and outlet passages  916  and  918  of the cover member  906 . 
       FIGS. 14 and 15  illustrate the fluidic device  920 , which may also have similar features as the fluidic devices  300  and  900 . As shown, the fluidic device  920  includes a cartridge (or flow cell carrier)  922  and the flow cell  200 . The cartridge  922  includes a housing  924  and a cover member  925  that is movably mounted to the housing  924 . The cover member  925  is only shown in the mounted position in  FIGS. 14 and 15 . The housing  924  and the cover member  925  may be similar to the housings  204  and  904  and the cover member  306  and  906  described above. 
     However, the housing  924  may also include fin projections  926  and  928 . The fin projections  926  and  928  are sized and shaped to be gripped by an individual or robotic device, such as when the fluidic device  920  is being inserted in or removed from a device holder (not shown). In some embodiments, the fin projections  926  and  928  may prevent the cover assembly (not shown) from moving to the closed position if the fluidic device  920  is not properly positioned. The fin projections  926  and  928  may include tactile features  927  and  929  that are configured to be gripped by the individual. In the illustrated embodiment, the fin projections  926  and  928  are located at a receiving end  930  of the fluidic device  920 . The cover member  925  may extend between the fin projections  926  and  928 . However, the fin projections  926  and  928  may have other locations along the cartridge  902 . 
       FIGS. 16-24  show various features of a fluidic device holder  400  formed in accordance with one embodiment.  FIG. 16  is a partially exploded view of the holder  400 . When assembled, the holder  400  may be used to hold the fluidic device  300  ( FIG. 9 ) and the flow cell  200  ( FIG. 5 ) in a desired orientation during an imaging session. Furthermore, the holder  400  may provide an interface between the fluidic device  300  and the imaging system (not shown) in which the holder  400  may be configured to direct fluids through the flow cell  200  and provide or remove thermal energy from the flow cell  200 . Although the holder  400  is shown as holding the fluidic device  300 , the holder  400  may be configured to hold other fluidic devices, such as lab-on-chip devices or flow cells without cartridges. 
     As shown in  FIG. 16 , the holder  400  may include a removable cover assembly  404  and a support structure  402 . In some embodiments, the holder  400  may also include a plate structure  406  and a movable platform  408 . The plate structure  406  is operatively coupled to the cover assembly  404  and includes an opening  410  therethrough. Likewise, the platform  408  includes an opening  412  therethrough. The support structure  402  may include a heat sink  414  and a thermal module (or thermocycler)  416  that is mounted onto the heat sink  414 . The thermal module  416  includes a base portion  418  and a pedestal  420 . When the holder  400  is assembled, the support structure  402 , the platform  408 , and the plate structure  406  are stacked with respect to each other. As such, the opening  412  is sized and shaped to receive the base portion  418 , and the opening  410  is sized and shaped to receive the pedestal  420 . When assembled, the cover assembly  404  may be operatively coupled to the plate structure  406  and the support structure  402 . 
       FIG. 17  shows the assembled holder  400 . In the illustrated embodiment, a panel  424  is positioned over the plate structure  406  ( FIG. 16 ). As shown in  FIGS. 16 and 17 , the cover assembly  404  includes a cover housing  435  that is coupled to the plate structure  406 . The cover housing  435  may be substantially U-shaped having a pair of spaced apart housing legs  436  and  438  that extend in a common direction. The housing legs  436  and  438  may be rotatably coupled to the plate structure  406  at joints  437  and  439 . The cover housing  435  may also include a bridge portion  440  that extends between and joins the housing legs  436  and  438 . In this manner, the cover assembly  404  may be configured to provide a viewing space  442  ( FIG. 17 ). The viewing space  442  may be sized and shaped to permit an imaging lens (not shown) to move in a direction Dx ( FIG. 17 ) along and over the flow cell  200 . 
     In the illustrated embodiment, the cover assembly  404  is movable relative to the plate structure  406  or support structure  402  between an open position (shown in  FIG. 16 ) and a closed position (shown in  FIG. 17 ). In the open position, the cover assembly  404  is withdrawn or retracted to permit access to a loading region  422  (shown in  FIG. 18 ) of the holder  400  so that the fluidic device  300  may be removed from or inserted into the loading region  422 . In the closed position, the cover assembly  404  is mounted over the fluidic device  300 . In particular embodiments, the cover assembly  404  establishes a fluid connection with the fluidic device  300  in the closed position and presses the flow cell  200  against the support structure  402 . 
     As shown in  FIG. 16 , in some embodiments, the holder  400  includes a coupling mechanism  450  to facilitate holding the cover assembly  404  in the closed position. For example, the coupling mechanism  450  may include an operator-controlled element  452  that includes a button  453  that is coupled to a pair of latch openings  456  and  458 . The coupling mechanism  450  also includes a pair of latch ends  454  and  455  that project away from a mating face  460  of the cover housing  435 . The cover housing  435  may be biased into the open position by spring elements  464  and  466 . When the cover assembly  404  is moved into the closed position by an individual or machine, the latch ends  454  and  455  are inserted into the latch openings  456  and  458 , respectively, and grip the operator-controlled element  452 . To move the cover assembly  404  into the open position, the individual or machine may actuate the button  453  by, for example, pushing the button  453  inward. Since the cover housing  435  is biased by the spring elements  464  and  466 , the cover housing  435  is rotated away from the panel  424  ( FIG. 17 ) about the joints  437  and  439 . 
     In alternative embodiments, the coupling mechanism  450  may include other elements to facilitate holding the cover assembly  404  in the closed position. For example, the latch ends  454  and  455  may be replaced by magnetic elements or elements that form an interference fit with openings. 
       FIG. 18  is an isolated perspective view of thermal module  416  and the heat sink  414  of the support structure  402 . The thermal module  416  may be configured to control a temperature of the flow cell  200  for predetermined periods of time. For example, the thermal module  416  may be configured to raise the temperature of the flow cell  200  so that DNA in the sample may denature. Furthermore, the thermal module  416  may be configured to remove thermal energy thereby lowering the temperature of the flow cell  200 . As shown, the pedestal  420  includes a base surface  430  that is sized and shaped to interface with the flow cell  200  ( FIG. 5 ). The base surface  430  faces in a direction along the Z-axis. The pedestal  420  may also include a plurality of alignment members  431 - 433  that are positioned around the base surface  430 . In the illustrated embodiment, the alignment members  431 - 433  have fixed positions with respect to the base surface  430 . The alignment members  431 - 433  have corresponding reference surfaces that are configured to engage the flow cell  200  and facilitate positioning the flow cell  200  for imaging. For example, the reference surfaces of the alignment members  431 - 433  may face in respective directions along the XY-plane and, as such, may be configured to limit movement of the flow cell  200  along the XY-plane. The support structure  402  may include at least a portion of the loading region  422 . The loading region  422  may be partially defined by the base surface  430  and the reference surfaces of the alignment members  431 - 433 . 
       FIGS. 19 and 20  illustrate an alignment assembly  470  that may be used with the holder  400  in accordance with one embodiment.  FIG. 19  is a plan view of the holder  400  in which the cover housing  435  is shown in phantom to illustrate the alignment assembly  470 .  FIG. 20  is a perspective view of the holder  400  in which the cover assembly  404  is in the open position. (In both  FIGS. 19 and 20 , the panel  424  ( FIG. 17 ) has been removed for illustrative purposes.) 
     The fluidic device  300  is loaded into the loading region  422  in  FIGS. 19 and 20 . When the fluidic device  300  is loaded, the flow cell  200  is placed onto the base surface  430  ( FIG. 18 ) and the alignment members  432 ,  433 , and  431  are advanced through the recesses  320 ,  322 , and  321  ( FIGS. 9 and 10 ) of the cartridge  302 . More specifically, the device window  315  ( FIG. 9 ) along the housing side  305  may be sized and shaped to be greater than a perimeter of the base surface  430 . As such, the cartridge  302  or housing  304  may be allowed to fall around the base surface  430 , but the flow cell  200  is prevented from falling by the base surface  430 . In this manner, the cell side  258  of the flow cell  200  may be pressed against the base surface  430  so that the thermal module  416  may control a temperature of the flow cell  200 . When the flow cell  200  is mounted on the base surface  430 , the reference surfaces  381 - 383  ( FIG. 11 ) of the cartridge  302  are pressed against the cell side  256  ( FIG. 1111 ). At this time, a cell plane of the flow cell  200  that extends along the sample  205  may be substantially aligned with an object plane of the imaging system. 
     In the illustrated embodiment, when the fluidic device  300  is loaded into the loading region  422 , an identification reader of the assay system may detect information from the identification transmitter  336  ( FIG. 10 ). For example, the holder  400  may include an identification reader (not shown) in the plate structure  406  proximate to the identification transmitter  336 . The identification reading may occur before the cover assembly  404  is mounted onto the fluidic device  300 . 
     With reference to  FIGS. 19 and 20 , the alignment assembly  470  includes various elements that cooperate together in orienting and positioning the flow cell  200  for imaging. For example, the alignment assembly  470  includes a movable locator arm  472  and an actuator  474  that is operatively coupled to the locator arm  472 . As shown, the actuator  474  includes a lever  476  and a pin element  478  that is coupled to the cover housing  435 . In the illustrated embodiment, the lever  476  is rotatable about an axis of rotation R 2  ( FIG. 19 ). The lever  476  may be L-shaped having a first extension  480  configured to engage the pin element  478  and a second extension  482  configured to engage the locator arm  472 . The locator arm  472  is also rotatable about an axis of rotation R 3  ( FIG. 19 ) and includes a finger  484  having an engagement end  486 . The alignment assembly  470  also includes a biasing element  490  (e.g., a coil spring) that engages the finger  484 . The engagement end  486  is configured to engage the cartridge  302  of the fluidic device  300 . In alternative embodiments, the engagement end  486  may be configured to directly engage the flow cell  200 . 
     The alignment assembly  470  is in an engaged arrangement in  FIG. 19  and in a withdrawn arrangement in  FIG. 20 . The locator arm  472  is in a retracted position when the alignment assembly  470  is in the withdrawn arrangement and in a biased position when the alignment assembly  470  is in the engaged arrangement. To align the flow cell  200  in the loading region  422 , the alignment assembly  470  is changed from the withdrawn arrangement to the engaged arrangement. For example, when the cover housing  435  is moved to the open position shown in  FIG. 20 , the pin element  478  engages the first extension  480  of the lever  476  causing the lever  476  to rotate about the axis R 2  in a counter-clockwise direction (as shown in  FIG. 19 ). The cover housing  435  may be maintained in the open position by the spring elements  464  and  466  ( FIG. 16 ). When the lever  476  is rotated, the second extension  482  rotates about the axis R 2  and engages the locator arm  472 . The locator arm  472  is rotated about the axis R 3  in a clockwise direction (as shown in  FIG. 19 ). When the locator arm  472  is rotated, the locator arm  472  is moved to the retracted position. When moved to the retracted position, the engagement end  486  is moved away from the reference surfaces of the alignment members  431 - 433 . 
     To change the alignment assembly  470  from the withdrawn arrangement to the engaged arrangement, the cover housing  435  may be rotated toward the fluidic device  300  and mounted over the flow cell  200 . When the cover housing  435  is moved toward the fluidic device  300 , the pin element  478  is rotated away from the first extension  480  of the lever  476 . When the second extension  482  moves away from the locator arm  472 , potential energy stored in the biasing element  490  may cause the locator arm  472  to rotate in a counter-clockwise direction such that the engagement end  486  presses against the cartridge  302 . As such, the locator arm  472  is moved to the biased position. When moved to the biased position, the engagement end  486  is moved toward the reference surfaces of the alignment members  431 - 433 . 
       FIG. 21  is an enlarged plan view of the fluidic device  300  in the loading region  422  when the engagement end  486  of the locator arm  472  is pressed against the cartridge  302 . The engagement end  486  may be configured to move within the XY-plane between the retracted and biased positions. When the engagement end  486  is moved toward the biased position and presses against the cartridge  302 , the engagement end  486  provides a force Fxy against the cartridge  302 . The cartridge  302  may shift along the XY-plane and/or press the flow cell  200  against the reference surfaces of the alignment members  431 - 433 . The force Fxy has an X-component and a Y-component. The X-component may press the flow cell  200  against the alignment member  431 , and the Y-component may press the flow cell  200  against the alignment members  432  and  433 . As such, the alignment member  431  may stop movement of the flow cell  200  in a direction along the X-axis, and the alignment members  432  and  433  may stop movement of the flow cell  200  in a direction along the Y-axis. 
     Before the alignment assembly  470  is changed to the engaged arrangement, the inlet and outlet passages  346  and  344  of the cover member  306  may be approximately aligned with the inlet and outlet ports  224  and  222  ( FIG. 7 ), respectively, of the flow cell  200 . After the alignment assembly  470  is changed to the engaged arrangement, the inlet and outlet passages  346  and  344  are effectively (or operatively) aligned with the inlet and outlet ports  224  and  222  so that fluid may effectively flow therethrough. 
     Accordingly, the cover assembly  404  may be operatively coupled to the alignment assembly  470  such that one step or action causes the alignment assembly  470  to engage the fluidic device  300 . More specifically, as the cover assembly  404  is mounted over the device in the closed position, the actuator  474  moves the locator arm  472  to the biased position. In the biased position, the locator arm  472  holds the flow cell  200  against the reference surfaces of the alignment members  431 - 433  in a fixed position along the XY-plane. When the cover assembly  404  is in the closed position, the viewing space  442  ( FIG. 17 ) may be located over the flow cell  200  so that an imaging lens may move along the flow cell  200  to image the flow channel  206 . As the cover assembly  404  is moved to the open position, the actuator  474  moves the locator arm  472  to the retracted position. However, in the illustrated embodiment, the flow cell  200  remains in position when the locator arm  472  is retracted. Accordingly, the flow cell  200  may be floatable relative to various elements. For example, the flow cell  200  may be floatable with respect to the cover member  306  and the gasket  342  when the cover member  306  is in the mounted position. The flow cell  200  may also be floatable relative to the cover assembly  404  and the base surface  430 . 
     In some embodiments, the alignment assembly  470  and the cover assembly  404  may operate at a predetermined sequence. For example, in particular embodiments, the locator arm  472  is configured to hold the flow cell  200  against the alignment members  431 - 433  in the fixed position before the cover assembly  404  reaches the closed position. When the cover assembly  404  reaches the closed position, the cover assembly  404  may facilitate pressing the flow cell  200  against the base surface  430  and also pressing the inlet and outlet passages  346  and  344  against the inlet and outlet ports  224  and  222 . Generally, the alignment assembly  470  can be configured to position the flow cell  200  in the x and y dimensions after the base surface  430  positions the flow cell  200  in the z dimension. Alternatively, an alignment assembly can be configured to position the flow cell  200  first in the x and y dimensions and then in the z dimension. Thus, alignment in the x, y and z dimensions can occur sequentially and in various orders in response to a single step or motion carried out by a user. 
     In alternative embodiments, the alignment assembly  470  may not be operatively coupled to the cover assembly  404  as described above. Instead, the alignment assembly  470  and the cover assembly  404  may operate independently from each other. As such, an individual may be required to perform a plurality of steps to align the flow cell  200  and fluidicly couple the flow cell  200 . For example, the alignment assembly  470  can be separately actuated by an individual thereby moving the locator arm  472  to align the flow cell  200 . After the flow cell  200  is aligned, the individual may then lower the cover assembly  404  onto the flow cell  200 . Furthermore, the alignment assembly  470  may comprise additional and/or other components than those described above. 
       FIG. 22  is an isolated perspective view of the cover assembly  404  in the closed position.  FIG. 22  illustrates dimensions of the viewing space  442 . As shown, the cover housing  435  may have a top surface  492 . The viewing space  442  may have a depth D P  that is measured from the top surface  492  to the fluidic device  300  or the flow cell  200 . The viewing space  442  may also have a width W 6  measured along the Y-axis and a length L 6  measured along the X-axis. The dimensions of the viewing space  442  may be sized so that an imaging lens (not shown) may move therethrough over the flow cell  200 . More specifically, an imaging lens may enter the viewing space  442  through an access opening  443  and move in a direction along the X-axis over the flow cell  200 . 
       FIG. 23  is a cross-section of the cover assembly  404  taken along the line  23 - 23  in  FIG. 22 . In the illustrated embodiment, the cover assembly  404  may include a plurality of compression arms  494  and  496 . The compression arms  494  and  496  are configured to provide respective compressive forces Fci and FC 2  against the housing side  303  of the fluidic device  300 . In the illustrated embodiment, the compression arms  494  and  496  press against the cartridge  302 . However, in alternative embodiments, the compression arms  494  and  496  may press against the flow cell  200 . 
     The compressive forces Fci and FC 2  press the housing  304  of the fluidic device  300  thereby pressing the cell side  256  ( FIG. 9 ) of the flow cell  200  against the thermal module  416 . As such, the flow cell  200  may maintain intimate contact with the base surface  430  for transferring thermal energy therebetween. In the illustrated embodiment, the compression arms  494  and  496  operate independently of each other. For example, each of the compression arms  494  and  496  is operatively coupled to respective compression springs  495  and  497 . 
     As shown in  FIG. 23 , the compression arms  494  and  496  extend toward the viewing space  442  and the loading region  422 . The compression arms  494  and  496  may engage the housing side  303  when the cover assembly  404  is moved to the closed position. As the compression arms  494  and  496  press against the housing side  303 , resistance from the housing side  303  may cause the compression arms  494  and  496  to rotate about axes R 4  and R 5 . Each of the compression springs  495  and  497  may resist the rotation of the respective compression arm thereby providing the corresponding compressive force Fc against the housing side  303 . Accordingly, the compression arms  494  and  496  are independently biased relative to each other. 
       FIG. 24  is an isolated perspective view of a flow assembly  500  of the cover assembly  404  ( FIG. 16 ). The flow assembly  500  includes a manifold body  502  and upstream and downstream flow lines  504  and  506 . As shown in  FIG. 16 , the manifold body  502  may extend between the housing legs  436  and  438 . Returning to  FIG. 24 , the flow lines  504  and  506  are mechanically and fluidicly coupled to the manifold body  502  at body ports  508  and  510 , respectively. The flow lines  504  and  506  also include line ends  514  and  516  that are configured to be inserted into the inlet and outlet passages  346  and  344  of the gasket  342 . 
     As shown in  FIG. 24 , the flow assembly  500  is in a mounted position with respect to the gasket  342 . In the mounted position, the line ends  514  and  516  are inserted into the inlet and outlet passages  346  and  344 , respectively, so that fluid may flow through the flow cell  200 . Furthermore, in the mounted position, the flow assembly  500  may press the gasket  342  ( FIG. 9 ) against the flow cell  200  so that the fluid connection is effectively sealed. To this end, the flow assembly  500  may include biasing springs  520  and  522 . The biasing springs  520  and  522  are configured to press against an interior of the cover housing  435  ( FIG. 16 ) and provide a force F C3  against the gasket  342 . The coupling mechanism  450  ( FIG. 16 ) may facilitate maintaining the seal against the gasket  342 . 
     Accordingly, the cover assembly  404  may press against the housing  304  of the fluidic device  300  at three separate compression points. More specifically, the gasket  342  may constitute a first compression point P 1  (shown in  FIG. 24 ) when engaged by the line ends  514  and  516 , and the compression arms  494  and  496  may contact the fluidic device  300  at second and third compression points P 2  and P 3  (shown in  FIG. 23 ). As shown in  FIGS. 22-24 , the three compression points P 1 -P 3  are distributed about the flow cell  200 . Moreover, the cover assembly  404  independently provides the compressive forces F C1 -F C3  at the compression points P 1 -P 3 . As such, the cover assembly  404  may be configured to provide a substantially uniform compressive force against the fluidic device  300  so that the flow cell  200  is uniformly pressed against the base surface  430  and the fluidic connection is sealed from leakage. 
       FIG. 25  is a block diagram of a method  530  of positioning a fluidic device for sample analysis. The method  530  includes positioning at  532  a removable fluidic device on a base surface. The fluidic device may be similar to the fluidic device  300  described above. For example, the fluidic device may include a reception space, a flow cell located within the reception space, and a gasket. The flow cell may extend along an object plane in the reception space and be floatable relative to the gasket within the object plane. The method  530  also includes moving the flow cell at  534  within the reception space while on the base surface so that inlet and outlet ports of the flow cell are approximately aligned with inlet and outlet passages of the gasket. The moving operation  534  may include actuating a locator arm to press the flow cell against alignment members. 
       FIG. 26  is a block diagram illustrating a method  540  of positioning a fluidic device for sample analysis. The fluidic device  300  may be similar to the fluidic device  300  described above. The method  540  includes providing a fluidic device at  542  having a device housing that includes a reception space and a floatable flow cell located within the reception space. The device housing may include recesses that are located immediately adjacent to the reception space. The method also includes positioning at  544  the fluidic device on a support structure having alignment members. The alignment members may be inserted through corresponding recesses. Furthermore, the method  540  may include moving the flow cell at  546  within the reception space. When the flow cell is moved within the reception space, the alignment members may engage edges of the flow cell. The moving operation  546  may include actuating a locator arm to press the flow cell against the alignment members. 
       FIG. 27  is a block diagram illustrating a method  550  for orienting a sample area with respect to mutually perpendicular X, Y, and Z-axes. The method  550  includes providing an alignment assembly at  552 . The alignment assembly may be similar to the alignment assembly  470  described above. More specifically, the alignment assembly may include a movable locator arm that has an engagement end. The locator arm may be movable between retracted and biased positions. The method  550  also includes positioning a fluidic device at  554  on a base surface that faces in a direction along the Z-axis and between a plurality of reference surfaces that face in respective directions along an XY-plane. Furthermore, the method  550  may include moving at  556  the locator arm to the biased position. The locator arm can press the device against the reference surfaces such that the device is held in a fixed position. 
       FIGS. 28-37  illustrate various features of a fluid storage system  1000  ( FIG. 28 ). The storage system  1000  is configured to store and regulate a temperature of various fluids that may be used during predetermined assays. The storage system  1000  may be used by the workstation  160  ( FIG. 2 ) and enclosed by the casing  162  ( FIG. 3 ). As shown in  FIG. 28 , the storage system  1000  includes an enclosure  1002  having a base shell (or first shell)  1004  and a top shell (or second shell)  1006  that are coupled together and define a system cavity  1008  therebetween. The enclosure  1002  may also include a system door  1010  that is configured to open and provide access to the system cavity  1008 . Also shown, the storage system  1000  may include a temperature-control assembly  1012  that is coupled to a rear of the enclosure  1002  and a elevator drive motor  1014  that is located on the top shell  1006 . 
       FIG. 29  is a side cross-section of the storage system  1000  and illustrates the system cavity  1008  in greater detail. The storage system  1000  may also include a reaction component tray (or reaction component storage unit)  1020  and a fluid removal assembly  1022  that includes an elevator mechanism  1024 . The tray  1020  is configured to hold a plurality of tubes or containers for storing fluids. The elevator mechanism  1024  includes the drive motor  1014  and is configured to move components of the removal assembly  1022  bi-directionally along the Z-axis. In  FIG. 29 , the tray  1020  is located in a fluid-removal position such that fluid held by the tray  1020  may be removed and delivered to, for example, a fluidic device for performing a desired reaction or for flushing the flow channels of the fluidic device. 
     Also shown, the temperature-control assembly  1012  may project into the system cavity  1008 . The temperature-control assembly  1012  is configured to control or regulate a temperature within the system cavity  1008 . In the illustrated embodiment, the temperature-control assembly  1012  includes a thermo-electric cooling (TEC) assembly. 
       FIG. 30  is a perspective view of the removal assembly  1022 . As shown, the removal assembly  1022  may include a pair of opposing guide rails  1032  and  1034 . The opposing guide rails  1032  and  1034  are configured to receive and direct the tray  1020  to the fluid-removal position shown in  FIG. 29 . The guide rails  1032  and  1034  may include projected features or ridges  1035  that extend longitudinally along the guide rails  1032  and  1034 . The guide rails  1032  and  1034  are configured to be secured to the base shell  1004  ( FIG. 28 ). The removal assembly  1022  also includes support beams (or uprights)  1036  and  1038  that extend in a direction along the Z-axis. A guide plate  1040  of the removal assembly may be coupled to the support beams  1036  and  1038  at an elevated distance D Z  and project therefrom along the XY-plane. In the illustrated embodiment, the guide plate  1040  is affixed to the support beams  1036  and  1038 . 
     The elevator mechanism  1024  includes structural supports  1041  and  1042 , a lead screw  1044  that extends between the structural supports  1041  and  1042 , and a stage assembly  1046  that includes a transport platform  1048 . The structural supports  1041  and  1042  are secured to opposite ends of the support beams  1036  and  1038  and are configured to support the elevator mechanism  1024  during operation. Threads of the lead screw  1044  are operatively coupled to the stage assembly  1046  such that when the lead screw  1044  is rotated, the stage assembly  1046  moves in a linear direction along the Z-axis (indicated by the double arrows). 
     The transport platform  1048  is configured to hold an array of sipper tubes  1050 . The sipper tubes  1050  may be in fluid communication with a system pump (not shown) that is configured to direct a flow of fluid through the sipper tubes  1050 . As shown, the sipper tubes  1050  include distal portions  1052  that are configured to be inserted into component wells  1060  (shown in  FIG. 31 ) of the tray  1020 . The distal portions  1052  extend through corresponding openings  1053  of the guide plate  1040 . 
     The elevator mechanism  1024  is configured to move the sipper tubes  1050  between withdrawn and deposited levels. At the deposited level (shown in  FIGS. 50 and 51 ), the distal portions  1052  of the sipper tubes  1050  are inserted into the component wells  1060  to remove fluid thereform. At the withdrawn level, the distal portions  1052  are completely removed from the tray  1020  such that the tray  1020  may be removed from the system cavity  1008  ( FIG. 28 ) without damage to the sipper tubes  1050  or the tray  1020 . More specifically, when the drive motor  1014  rotates the lead screw  1044 , the stage assembly  1046  moves along the Z-axis in a direction that is determined by a rotational direction of the lead screw  1044 . Consequently, the transport platform  1048  moves along the Z-axis while holding the sipper tubes  1050 . If the transport platform  1048  advances toward the guide plate  1040 , the distal portions  1052  slide through the corresponding openings  1053  of the guide plate  1040  toward the tray  1020 . The guide plate  1040  is configured to prevent distal portions  1052  from becoming misaligned with the component wells  1060  before the distal portions  1052  are inserted therein. When the elevator mechanism  1024  moves the stage assembly  1046  away from the guide plate  1040 , a distance (ΔZ) between the transport platform  1048  and the guide plate  1040  increases until the distal portions  1052  are withdrawn from the component wells  1060  of the tray  1020 . 
       FIG. 30  illustrates additional features for operating the elevator mechanism  1024 . For example, the stage assembly  1046  may also include a guide pin  1058  (also shown in  FIG. 29 ) that is affixed to and extends from the transport platform  1048  in a direction that is parallel to the sipper tubes  1050 . The guide pin  1058  also extends through a corresponding opening  1053  of the guide plate  1040 . In the illustrated embodiment, the guide pin  1058  extends a greater distance than the sipper tubes  1050  so that the guide pin  1058  reaches the tray  1020  before the sipper tubes  1050  are inserted into the component wells  1060 . Thus, if the tray  1020  is misaligned with respect to the sipper tubes  1050 , the guide pin  1058  may engage the tray  1020  and adjust the position of the tray  1020  so that the component wells  1060  are properly aligned with the corresponding sipper tubes  1050  before the sipper tubes  1050  are inserted therein. 
     In addition to the above, the removal assembly  1022  may include a position sensor  1062  and a location sensor (not shown). The position sensor  1062  is configured to receive a flag  1063  (shown in  FIG. 34 ) of the tray  1020  to determine that the tray  1020  is present in the system cavity  1008  ( FIG. 28 ) and at least approximately aligned for receiving the sipper tubes  1050 . The location sensor may detect a flag  1064  of the stage assembly  1046  to determine a level of the stage assembly  1046 . If the flag  1064  has not reached a threshold level along the Z-axis, the location sensor may communicate with the workstation  160  (or other assay system) to notify the user that the tray  1020  is not ready for removal. The workstation  160  could also prevent the user from opening the system door  1010 . 
     Furthermore, when the distal portions  1052  of the sipper tubes  1050  are initially inserted into the component wells  1060 , the sipper tubes  1050  may pierce protective foils that cover the component wells  1060 . In some instances, the foils may grip the sipper tubes  1050 . When the sipper tubes  1050  are subsequently withdrawn from the corresponding component wells  1060 , the gripping of the protective foils may collectively lift the tray  1020 . However, in the illustrated embodiment, the ridges  1035  are configured to grip a tray base  1070  ( FIG. 31 ) and prevent the tray base  1070  from being lifted in a direction along the Z-axis. For example, the ridges  1035  may grip a lip  1071  of the tray base  1070 . 
       FIGS. 31-34  illustrate different views of the tray  1020 . The tray  1020  is configured to hold a plurality of component wells  1060 . The component wells  1060  may include various reaction components, such as, but not limited to, one or more samples, polymerases, primers, denaturants, linearization mixes for linearizing DNA, enzymes suitable for a particular assay (e.g., cluster amplification or SBS), nucleotides, cleavage mixes, oxidizing protectants, and other reagents. In some embodiments, the tray  1020  may hold all fluids that are necessary to perform a predetermined assay. In particular embodiments, the tray  1020  may hold all reaction components necessary for generating a sample (e.g., DNA clusters) within a flow cell and performing sample analysis (e.g., SBS). The assay may be performed without removing or replacing any of the component wells  1060 . 
     The component wells  1060  include rectangular component wells  1060 A (shown in  FIGS. 35-36 ) and tubular component wells  1060 B (shown in  FIG. 37 ). The tray  1020  includes a tray base  1070  and a tray cover  1072  coupled to the tray base  1070 . As shown in  FIGS. 31 and 32 , the tray cover  1072  includes a handle  1074  that is sized and shaped to be gripped by a user of the tray  1020 . The tray cover  1072  may also include a grip recess  1076  that is sized and shaped to receive one or more fingers of the user. 
     As shown in  FIGS. 31 and 32 , the tray cover  1072  may include a plurality of tube openings  1080  that are aligned with corresponding component wells  1060 . The tube openings  1080  may be shaped to direct the sipper tubes  1050  (exemplary sipper tubes  1050  are shown in  FIG. 31 ) into the corresponding component wells  1060 . As shown in  FIG. 32 , the tray cover  1072  also includes a pin opening  1082  that is sized and shaped to receive the guide pin  1058 . The guide pin  1058  is configured to provide minor adjustments to the position of the tray  1020  if the guide pin  1058  approaches and enters the pin opening  1082  in a misaligned manner. Also shown, the tray  1020  may include an identification tag  1084  along a surface of the tray cover  1072 . The identification tag  1084  is configured to be detected by a reader to provide the user with information regarding the fluids held by the component wells  1060 . 
     As shown in  FIGS. 33 and 34 , the tube openings  1080  are at least partially defined by rims  1086  that project from a surface  1073  of the tray cover  1072 . The rims  1086  project a small distance away from the surface  1073  to prevent inadvertent mixing of fluids that are accidentally deposited onto the tray cover  1072 . Likewise, the identification tag  1084  may be attached to a raised portion  1088  of the tray cover  1072 . The raised portion  1088  may also protect the identification tag  1084  from inadvertently contacting fluids. 
       FIG. 35  shows a side cross-sectional view of the component well  1060 A, and  FIG. 36  shows a bottom perspective view of the component well  1060 A. As shown, the component well  1060 A includes opposite first and second ends  1091  and  1092  and a reservoir  1090  ( FIG. 35 ) extending therebetween. The reservoir  1090  has a depth D R  ( FIG. 35 ) that increases as the reservoir  1090  extends from the second end  1092  to the first end  1091 . The component well  1060 A is configured to receive the sipper tube  1050  in a deeper portion of the reservoir  1090 . As shown in  FIG. 36 , the component well  1060 A includes a plurality of projections  1094  along an exterior surface that are configured to rest upon a surface of the tray base  1070 . 
       FIG. 37  is a perspective view of the component well  1060 B. As shown, the component well  1060 B may also include a plurality of projections  1096  around an exterior surface of the component well  1060 B. The component well  1060 B extends along a longitudinal axis  1097  and has a profile that tapers as the component well  1060 B extends longitudinally to a bottom  1098 . The bottom  1098  may have a substantially planar surface. 
       FIG. 61  illustrates a method  960  for performing an assay for biological or chemical analysis. In some embodiments, the assay may include a sample generation protocol and a sample analysis protocol. For example, the sample generation protocol may include generating clusters of DNA through bridge amplification and the sample analysis protocol may include sequencing-by-synthesis (SBS) analysis using the clusters of DNA. The sample generation and sample analysis operations may be conducted within a common assay system, such as the assay system  100  or the workstation  160 , and without user intervention between the operations. For instance, a user may be able to load a fluidic device into the assay system. The assay system may automatically generate a sample for analysis and carry out the steps for performing the analysis. 
     With respect to  FIG. 61 , the method  960  includes establishing at  962  a fluid connection between a fluidic device having a sample area and a reaction component storage unit having a plurality of different reaction components. The reaction components may be configured for conducting one or more assays. The fluidic device may be, for example, the fluidic device  300  or the flow cell  200  described above. In some embodiments, the sample area includes a plurality of reaction components (e.g., primers) immobilized thereon. The storage unit may be, for example, the storage unit  1020  described above. The reaction components may include sample-generation components that are configured to be used to generate the sample, and sample-analysis components that are configured to be used to analyze the sample. In particular embodiments, the sample-generation components include reaction components for performing bridge amplification as described above. Furthermore, in particular embodiments, the sample-analysis components include reaction components for performing SBS analysis as described above. 
     The method  960  also includes generating at  964  a sample at the sample area of the fluidic device. The generating operation  964  may include flowing different sample-generation components to the sample area and controlling reaction conditions at the sample area to generate the sample. For example, a thermocycler may be used to facilitate hybridizing nucleic acids. However, isothermal methods can be used if desired. Furthermore, a flow rate of the fluids may be controlled to permit hybridization or other desired chemical reactions. In particular embodiments, the generating operation  964  includes conducting multiple bridge-amplification cycles to generate a cluster of DNA. 
     An exemplary protocol for bridge amplification can include the following steps. A flow cell is placed in fluid communication with a reaction component storage unit. The flow cell includes one or more surfaces to which are attached pairs of primers. A solution having a mixture of target nucleic acids of different sequences is contacted with a solid support. The target nucleic acids can have common priming sites that are complementary to the pairs of primers on the flow cell surface such that the target nucleic acids bind to a first primer of the pairs of primers on the flow cell surface. An extension solution containing polymerase and nucleotides can be introduced to the flow cell such that a first amplification product, which is complementary to the target nucleic acid, is formed by extension of the first primer. The extension solution can be removed and replaced with a denaturation solution. The denaturation solution can include chemical denaturants such as sodium hydroxide and/or formamide. The resulting denaturation conditions release the original strand of the target nucleic acid, which can then be removed from the flow cell by removing the denaturation solution and replacing it with the extension solution. In the presence of the extension solution the first amplification product, which is attached to the support, can then hybridize with a second primer of the primer pairs attached to the flow cell surface and a second amplification product comprising an attached nucleic acid sequence complementary to the first amplification product can be formed by extension of the second primer. Repeated delivery of the denaturation solution and extension solution can be used to form clusters of the target nucleic acid at discrete locations on the surface of the flow cell. Although the above protocol is exemplified using chemical denaturation, it will be understood that thermal denaturation can be carried out instead albeit with similar primers and target nucleic acids. Further description of amplification methods that can be used to produce clusters of immobilized nucleic acid molecules is provided, for example, in U.S. Pat. No. 7,115,400; U.S. Publication No. 2005/0100900; WO 00/18957; or WO 98/44151, each of which is incorporated by reference herein. 
     The method  960  also includes analyzing at  966  the sample at the sample area. Generally, the analyzing operation  966  may include detecting any detectable characteristic at the sample area. In particular embodiments, the analyzing operation  966  includes flowing at least one sample-analysis component to the sample area. The sample-analysis component may react with the sample to provide optically detectable signals that are indicative of an event-of-interest (or desired reaction). For example, the sample-analysis components may be fluorescently-labeled nucleotides used during SBS analysis. When excitation light is incident upon the sample having fluorescently-labeled nucleotides incorporated therein, the nucleotides may emit optical signals that are indicative of the type of nucleotide (A, G, C, or T), and the imaging system may detect the optical signals. 
     A particularly useful SBS protocol exploits modified nucleotides having removable  3 ′ blocks, for example, as described in WO 04/018497, US 2007/0166705A1 and U.S. Pat. No. 7,057,026, each of which is incorporated herein by reference. Repeated cycles of SBS reagents can be delivered to a flow cell having target nucleic acids attached thereto, for example, as a result of the bridge amplification protocol set forth above. The nucleic acid clusters can be converted to single stranded form using a linearization solution. The linearization solution can contain, for example, a restriction endonuclease capable of cleaving one strand of each cluster. Other methods of cleavage can be used as an alternative to restriction enzymes or nicking enzymes, including inter alia chemical cleavage (e.g., cleavage of a diol linkage with periodate), cleavage of abasic sites by cleavage with endonuclease (for example ‘USER’, as supplied by NEB, Ipswich, Mass., USA, part number M5505S), by exposure to heat or alkali, cleavage of ribonucleotides incorporated into amplification products otherwise comprised of deoxyribonucleotides, photochemical cleavage or cleavage of a peptide linker. After the linearization step a sequencing primer can be delivered to the flow cell under conditions for hybridization of the sequencing primer to the target nucleic acids that are to be sequenced. 
     The flow cell can then be contacted with an SBS extension reagent having modified nucleotides with removable  3 ′ blocks and fluorescent labels under conditions to extend a primer hybridized to each target nucleic acid by a single nucleotide addition. Only a single nucleotide is added to each primer because once the modified nucleotide has been incorporated into the growing polynucleotide chain complementary to the region of the template being sequenced there is no free 3′-OH group available to direct further sequence extension and therefore the polymerase cannot add further nucleotides. The SBS extension reagent can be removed and replaced with scan reagent containing components that protect the sample under excitation with radiation. Exemplary components for scan reagent are described in US publication US 2008/0280773 A1 and US Ser. No. 13/018,255, each of which is incorporated herein by reference. The extended nucleic acids can then be fluorescently detected in the presence of scan reagent. Once the fluorescence has been detected, the 3′ block may be removed using a deblock reagent that is appropriate to the blocking group used. Exemplary deblock reagents that are useful for respective blocking groups are described in WO04018497, US 2007/0166705A1 and U.S. Pat. No. 7,057,026, each of which is incorporated herein by reference. The deblock reagent can be washed away leaving target nucleic acids hybridized to extended primers having 3′ OH groups that are now competent for addition of a further nucleotide. Accordingly the cycles of adding extension reagent, scan reagent, and deblock reagent, with optional washes between one or more of the steps, can be repeated until a desired sequence is obtained. The above cycles can be carried out using a single extension reagent delivery step per cycle when each of the modified nucleotides has a different label attached thereto, known to correspond to the particular base. The different labels facilitate discrimination between the bases added during each incorporation step. Alternatively, each cycle can include separate steps of extension reagent delivery followed by separate steps of scan reagent delivery and detection, in which case two or more of the nucleotides can have the same label and can be distinguished based on the known order of delivery. 
     Continuing with the example of nucleic acid clusters in a flow cell, the nucleic acids can be further treated to obtain a second read from the opposite end in a method known as paired end sequencing. Methodology for paired end sequencing are described in PCT publication WO07010252, PCT application Serial No. PCTGB2007/003798 and US patent application publication US 2009/0088327, each of which is incorporated by reference herein. In one example, a series of steps may be performed as follows; generate clusters as set forth above, linearize as set forth above, hybridize a first sequencing primer and carry out repeated cycles of extension, scanning and deblocking, also as set forth above, “invert” the target nucleic acids on the flow cell surface by synthesizing a complementary copy, linearize the resynthesized strand, hybridize a first sequencing primer and carry out repeated cycles of extension, scanning and deblocking, also as set forth above. The inversion step can be carried out be delivering reagents as set forth above for a single cycle of bridge amplification. 
     Although the analyzing operation has been exemplified above with respect to a particular SBS protocol, it will be understood that other protocols for sequencing any of a variety of other molecular analyses can be carried out as desired. Appropriate modification of the apparatus and methods to accommodate various analyses will be apparent in view of the teaching set forth herein and that which is known about the particular analysis method. 
     In some embodiments, the method  960  is configured to be conducted with minimal user intervention. The generating and analyzing operations  964  and  966  may be conducted in an automated manner by an assay system. For example, in some cases, a user may only load the fluidic device and the storage unit and activate the assay system to perform the method  960 . In some embodiments, during the generating and analyzing operations  964  and  966 , the storage unit and the fluidic device remain in fluid communication from a beginning of the generating operation and throughout the analyzing operation until the sample is sufficiently analyzed. In other words, the fluidic device and the storage unit may remain in fluid communication from before the sample is generated until after the sample is analyzed. In some embodiments, the fluidic device is continuously held by the device holder from a beginning of the generating operation and throughout the analyzing operation until the sample is sufficiently analyzed. During such time, the device holder and an imaging lens may be automatically moved with respect to each other. The storage unit and the fluidic device may remain in fluid communication when the fluidic device and the imaging lens are automatically moved with respect to each other. In some embodiments, the assay system is contained within a workstation housing and the generating and analyzing operations  964  and  966  are conducted exclusively within the workstation housing. 
       FIG. 38  is a schematic illustration of an optical imaging system  600  formed in accordance with one embodiment. The imaging system  600  includes an optical assembly  602 , a light source (or excitation light) module or assembly  604 , a flow cell  606  having a sample area  608 , and imaging detectors  610  and  612 . The light source module  604  includes first and second excitation light sources  614  and  616  that are configured to illuminate the sample area  608  with different excitation spectra. In particular embodiments, the first and second excitation light sources  614  and  616  comprise first and second semiconductor light sources (SLSs). SLSs may include light-emitting diodes (LEDs) or laser diodes. However, other light sources may be used in other embodiments, such as lasers or arc lamps. The first and second SLSs may have fixed positions with respect to the optical assembly  602 . 
     As shown, the optical assembly  602  may include a plurality of optical components. For example, the optical assembly  602  may include lenses  621 - 627 , emission filters  631 - 634 , excitation filters  635  and  636 , and mirrors  641 - 645 . The plurality of optical components are arranged to at least one of (a) direct the excitation light toward the sample area  608  of the flow cell  606  or (b) collect emission light from the sample area  608 . Also shown, the imaging system  600  may also include a flow system  652  that is in fluid communication with the flow cell  606  and a system controller  654  that is communicatively coupled to the first and second excitation light sources  614  and  616  and the flow system  652 . The controller  654  is configured to activate the flow system  652  to flow reagents to the sample area  608  and activate the first and second SLSs after a predetermined time period. 
     For example,  FIG. 60  illustrates a method  900  for performing an assay for biological or chemical analysis. In particular embodiments, the assay may include a sequencing-by-synthesis (SBS) protocol. The method  900  includes flowing reagents through a flow channel of a flow cell at  902 . The flow cell may have a sample area that includes a sample with biomolecules configured to chemically react with the reagents. The method  900  also includes illuminating the sample area at  904  with first and second semiconductor light sources (SLSs). The first and second SLSs provide first and second excitation spectra, respectively. The biomolecules of the sample may provide light emissions that are indicative of a binding reaction when illuminated by the first or second SLSs. Furthermore, the method  900  includes detecting the light emissions from the sample area at  906 . Optionally, the method  900  may include moving the flow cell at  908  relative to an imaging lens and repeating the illuminating and detecting operations  904  and  906 . The steps shown in  FIG. 60  and exemplified above can be repeated for multiple cycles of a sequencing method. 
       FIGS. 39 and 40  illustrate various features of a motion-control system  700  formed in accordance with one embodiment that may be used with the imaging system  600 . The motion-control system  700  includes an optical base plate  702  and a sample deck  708  that is movably coupled to the base plate  702 . As shown, the base plate  702  has a support side  704  and a bottom side  705 . The support and bottom sides  704  and  705  face in opposite directions along the Z-axis. The base plate  702  is configured to support a majority of the optical components of the optical assembly  602  ( FIG. 38 ) on the support side  704 . The base plate  702  and the sample deck  708  may be movably coupled to each other by an intermediate support  715  and a face plate  722  such that the sample holder  650  may substantially rotate about the X and Y axes, shift along the Y axis, and slide along the X axis. 
       FIG. 40  is an isolated perspective view of the intermediate support  715 , a motor assembly  724 , and a movable platform  726  of the sample deck  708  ( FIG. 39 ). The motor assembly  724  is operatively coupled to the platform  726  and is configured to slide the platform  726  bi-directionally along the X-axis. As shown, the intermediate support  715  includes a tail end  728  and an imaging end  730 . The intermediate support  715  may include pins  746  and  748  proximate to the imaging end  730  that project away from each other along the Y-axis. Proximate to the imaging end  730 , the intermediate support  715  may include a lens opening  750  that is sized and shaped to allow the imaging lens  623  ( FIG. 38 ) to extend therethrough. In the illustrated embodiment, the pins  746  and  748  have a common line  755  extending therethrough that also extends through the lens opening  750 . 
     Returning to  FIG. 39 , the platform  726  is coupled to the bottom side  705  through the intermediate support  715 . Accordingly, a weight of the sample deck  708  may be supported by the base plate  702 . Furthermore, the motion-control system  700  may include a plurality of alignment devices  733 ,  735 ,  737 , and  739  that are configured to position the sample holder  650 . In the illustrated embodiment, the alignment devices  733 ,  735 ,  737 , and  739  are micrometers. The alignment device  733  is operatively coupled to the tail end  728  of the intermediate support  715 . When the alignment device  733  is activated, the tail end  728  may be moved in a direction along the Z-axis. Consequently, the intermediate support  715  may rotate about the pins  746  and  748  ( FIG. 40 ) or, more specifically, about the line  755 . When the alignment devices  735  and  737  are activated, the sample holder  650  may shift along the Y-axis as directed. When the alignment device  739  is activated, the sample holder  650  may rotate about an axis of rotation R 7  that extends parallel to the X-axis. 
       FIGS. 41-42  show a perspective view and plan view, respectively, of the optical base plate  702  that may be used with the imaging system  600  ( FIG. 38 ). In some embodiments of the imaging system  600 , one or more of the optical components  621 - 627 ,  631 - 636 , and  641 - 645  ( FIG. 38 ) can have a fixed position in the optical assembly  602  such that the fixed (or static) optical component does not move during operation of the imaging system  600 . For example, the base plate  702  is configured to support a plurality of optical components and other parts of the imaging system  600 . As shown, the base plate  702  constitutes a substantially unitary structure having a support side (or surface)  704  that faces in a direction along the Z-axis. In the illustrated embodiment, the support side  704  is not continuously smooth, but may have various platforms  716 - 718 , depressions (or receiving spaces)  719 - 721 , and component-receiving spaces  711 - 714  that are located to arrange the optical assembly  602  in a predetermined configuration. As shown in  FIG. 42 , each of the component-receiving spaces  711 - 714  has respective reference surfaces  781 - 784 . In some embodiments, the reference surfaces  781 - 784  can facilitate orienting and holding corresponding optical components in desired positions. 
       FIGS. 43 and 44  show a front perspective view and a cutaway rear perspective view, respectively, of an optical device  732 . As shown in  FIG. 43 , the optical device  732  is oriented relative to mutually perpendicular axes  791 - 793 . The axis  791  may extend along a gravitational force direction and/or parallel to the Z-axis illustrated above. In particular embodiments, the optical device  732  is configured to be positioned within the component-receiving space  713  ( FIG. 43 ) of the base plate  702  (only a portion of the base plate  702  is shown in  FIGS. 43 and 44 ). 
     The component-receiving space  713  has one or more surfaces that define an accessible spatial region where an optical component may be held. These one or more surfaces may include the reference surface(s) described below. In the illustrated embodiment, the component-receiving space  713  is a component cavity of the base plate  701  that extends a depth within the base plate  702 . However, the base plate  702  may form the component-receiving space in other manners. For example, in a similar way that the base plate  702  may form a cavity, the base plate  702  may also have one or more raised platforms including surfaces that surround and define the component-receiving space. Accordingly, the base plate  702  may be shaped to partially or exclusively provide the component-receiving space. The base plate  702  may include the reference surface. In alternative embodiments, sidewalls may be mounted on the base plate  702  and configured to define the spatial region. Furthermore, other optical devices mounted to the base plate  702  may define the component-receiving spaces. As used herein, when an element “defines” a component-receiving space, the element may exclusively define the component-receiving space or may only partially define the component-receiving space. 
     The optical device  732  can be removably mounted to the base plate  702  in the component-receiving space  713 , but may be configured to remain in a fixed position during operation of the imaging system. However, in alternative embodiment, the optical device  732  is not positioned within the component-receiving space  713 , but may be positioned elsewhere, such as on a platform of the support side  704 . In the illustrated embodiment, the optical device  732  includes a mounting device  734  and an optical component  736  that is configured to reflect and/or transmit light therethrough. The mounting device  734  is configured to facilitate holding the optical component  736  in a desired orientation and also removably mount the optical component  736  to the base plate  702 . The mounting device  734  includes a component retainer  738  and a biasing element  740  that is operatively coupled to the retainer  738 . 
     In the illustrated embodiment, the optical component  736  comprises an optical filter that transmits optical signals therethrough while filtering for a predetermined spectrum. However, other optical components may be used in alternative embodiments, such as lenses or mirrors. As shown, the optical component  736  may include optical surfaces  742  and  744  that face in opposite directions and define a thickness T 3  of the optical component  736  therebetween. As shown, the optical surfaces  742  and  744  may be continuously smooth and planar surfaces that extend parallel to each other such that the thickness T 3  is substantially uniform. However, the optical surfaces  742  and  744  may have other contours in alternative embodiments. The optical component  736  may have a plurality of component edges  751 - 754  ( FIG. 43 ) that define a perimeter or periphery. The periphery surrounds the optical surfaces  742  and  744 . As shown, the periphery is substantially rectangular, but other geometries may be used in alternative embodiments (e.g., circular). 
     The retainer  738  facilitates holding the optical component  736  in a desired orientation. In the illustrated embodiment, the retainer  738  is configured to engage the optical surface  742  and extend around at least a portion of the periphery to retain the optical component  736 . For example, the retainer  738  may include a wall portion  756  and a frame extension  758  that extends from the wall portion  756  along the periphery of the optical component  736  (e.g., the component edge  752  ( FIG. 43 )). In the illustrated embodiment, the frame extension  758  may form a bracket that limits movement of the optical component  736 . More specifically, the frame extension  758  may include a proximal arm  760  and a distal arm  762 . The proximal arm  760  extends from the wall portion  756  along the component edge  752  and the axis  791 . The distal arm  762  extends from the proximal arm  760  along the component edge  751 . The distal arm  762  includes a projection or feature  764  that extends toward and engages the optical component  736 . Also shown, the retainer  738  may include a grip member  766  that is located opposite the frame extension  758 . The grip member  766  and the frame extension  758  may cooperate in limiting movement of the optical component  736  along the axis  793 . The retainer  738  may grip a portion of the periphery of the optical component  736 . 
     As shown in  FIGS. 43 and 44 , the wall portion  756  is configured to engage the optical surface  742 . For example, the wall portion  756  has a mating surface  770  ( FIG. 43 ) that faces the optical component  736 . In some embodiments, the wall portion  756  includes a plurality of orientation features  771 - 773  ( FIG. 43 ) along the mating surface  770 . The orientation features  771 - 773  are configured to directly engage the optical surface  742  of the optical component  736 . When the orientation features  771 - 773  directly engage the optical surface  742 , the optical surface  742  (and consequently the optical component  736 ) is positioned in a desired orientation with respect to the retainer  738 . As shown in  FIG. 43 , the reference surface  783  of the component-receiving space  713  also includes a plurality of orientation features  761 - 763 . The orientation features  761 - 763  are configured to directly engage the optical surface  744 . Furthermore, the orientation features  761 - 763  may be arranged such that each of the orientation features  761 - 763  generally opposes a corresponding one of the orientation features  771 - 773 . 
     Also shown in  FIG. 44 , the wall portion  756  has a non-mating surface  774  that faces in an opposite direction with respect to the mating surface  770  ( FIG. 43 ). The wall portion  756  includes an element projection  776  that extends away from the non-mating surface  774  and the optical component  736 . The biasing element  740  is configured to couple to the element projection  776 . In the illustrated embodiment, the element projection  776  and the biasing element  740  extend into a slot  778  of the component-receiving space  713 . The slot  778  is sized and shaped to receive the biasing element  740 . The slot  778  has an element surface  780  that engages the biasing element  740 . 
       FIG. 45  shows an isolated front view of the optical device  732 , and  FIG. 46  shows how the optical device  732  may be removably mounted to the base plate  702 . To removably mount the optical component  736 , the optical component  736  may be positioned within a component-receiving space  789  of the mounting device  734  that is generally defined by the wall portion  756  ( FIG. 46 ), the frame extension  758 , and the grip member  766 . In particular embodiments, when the optical component  736  is positioned within the mounting device  734 , the optical component  736  is freely held within the component-receiving space  789 . For instance, the optical component  736  may not form an interference fit with the retainer  738 . Instead, during a mounting operation, the optical component  736  may be held within the component-receiving space  789  by the wall portion  756 , the frame extension  758 , the grip member  766  and, for example, an individual&#39;s hand. However, in alternative embodiments, the optical component  736  may form an interference fit with the retainer  738  or may be confined within a space that is defined only by the retainer  738 . 
     With respect to  FIG. 46 , during the mounting operation, the biasing element  740  may be initially compressed so that the mounting device  734  may clear and be inserted into the component-receiving space  713 . For example, the biasing element  740  may be compressed by an individual&#39;s finger to reduce the size of the optical device  732 , or the biasing element  740  may be compressed by first pressing the biasing element  740  against the element surface  780  and then advancing the retainer  738  into the component-receiving space  713 . Once the optical device  732  is placed within the component-receiving space  713 , the stored mechanical energy of the compressed biasing element  740  may move the retainer  738  and the optical component  736  toward the reference surface  783  until the optical surface  744  directly engages the reference surface  783 . More specifically, the optical surface  744  may directly engage the orientation features  761 - 763  ( FIG. 43 ) of the reference surface  783 . As shown in  FIG. 46 , when the optical component  736  is mounted, a small gap Gi may exist between the optical surface  742  and the mating surface  770  ( FIG. 43 ) because of the orientation features  771 - 773  ( FIG. 43 ), and a small gap G 2  may exist between the optical surface  744  and the reference surface  783  because of the orientation features  761 - 763  ( FIG. 43 ). 
     In the mounted position, the biasing element  740  provides an alignment force FA that holds the optical surface  744  against the reference surface  783 . The optical and reference surfaces  744  and  783  may be configured to position the optical component  736  in a predetermined orientation. The alignment force FA is sufficient to hold the optical component  736  in the predetermined orientation throughout operation of the imaging system. In other words, the mounting device  734  and the reference surface  783  may prevent the optical component  736  from moving in a direction along the axis  792 . Furthermore, in the mounted position, the projection  764  ( FIG. 43 ) may press against the component edge  751  ( FIG. 43 ) to prevent the optical component  736  from moving in a direction along the axis  791 . The frame extension  758  and the grip member  766  may prevent or limit movement of the optical component  736  in a direction along the axis  793 . Accordingly, the component-receiving space  713  and the mounting device  734  may be configured with respect to each other to hold the optical component  736  in a predetermined orientation during imaging sessions. 
     As shown in  FIG. 45 , when the optical component  736  is in the mounted position, a space portion  798  of the optical surface  744  may face and interface with the reference surface  783 , and a path portion  799  of the optical surface  744  may extend beyond the support side  704  into an optical path taken by optical signals. Also shown in  FIG. 46 , the component-receiving space  713  may extend a depth Dc into the base plate  702  from the support side  704 . 
     The biasing element  740  may comprise any elastic member capable of storing mechanical energy to provide the alignment force FA. In the illustrated embodiment, the elastic member comprises a coil spring that pushes the optical surface  744  against the reference surface  783  when compressed. However, in alternative embodiments, the elastic member and the component-receiving space may be configured such that the elastic member pulls the optical surface against the reference surface when extended. For example, a coil spring may have opposite ends in which one end is attached to the element surface in a slot that extends from the reference surface and another end is attached to the retainer. When the coil spring is extended, the coil spring may provide an alignment force that pulls the optical component against the reference surface. In this alternative embodiment, a rubber band may also be used. 
     In alternative embodiments, the mounting device  734  may be used to affix the optical component  736  to the base plate  702  using an adhesive. More specifically, the optical component  736  may be held against the reference surface  783  by the mounting device  734 . An adhesive may be deposited into the gap G 2  between the optical surface  744  and the reference surface  783 . After the adhesive cures, the mounting device  734  may be removed while the optical component  736  remains affixed to the reference surface  783  by the adhesive. 
       FIG. 47  is a block diagram illustrating a method  800  of assembling an optical train. The method  800  includes providing an optical base plate at  802  that has a component-receiving space. The base plate and the component-receiving space may be similar to the base plate  702  and the component-receiving space  713  described above. The method  800  also includes inserting an optical component at  804  into the component-receiving space. The optical component may be similar to the optical component  736  described above and include an optical surface that is configured to reflect or transmit light therethrough. The optical surface may have a space portion that faces a reference surface of the component-receiving space and a path portion that extends beyond the support side into an optical path. The method  800  also includes providing an alignment force at  806  that holds the optical surface against the reference surface to orient the optical component. The optical and reference surfaces may be configured to hold the optical component in a predetermined orientation when the alignment force is provided. In some embodiments, the method  800  may also include removing the optical component at  808  and, optionally, inserting a different optical component at  810  into the component-receiving space. The different optical component may have the same or different optical qualities. In other words, the different optical component may be a replacement that has the same optical qualities or the different optical component may have different optical qualities. 
       FIGS. 48 and 49  provide a perspective view and a side view, respectively, of the light source (or excitation light module)  604 . As used herein, a light source module includes one or more light sources (e.g., lasers, arc lamps, LEDs, laser diodes) that are secured to a module frame and also includes one or more optical components (e.g., lenses or filters) that are secured to the module frame in a fixed and predetermined position with respect to said one or more light sources. The light source modules may be configured to be removably coupled within an imaging system so that a user may relatively quickly install or replace the light source module. In particular embodiments, the light source module  604  constitutes a SLS module  604  that includes the first and second SLSs  614  and  616 . As shown, the SLS module  604  includes a module frame  660  and a module cover  662 . A plurality of imaging components may be secured to the module frame  660  in fixed positions with respect to each other. For example, the first and second SLSs  614  and  616 , the excitation filter  635 , and the lenses  624  and  625  may be mounted onto the module frame  660 . In addition, the SLS module  604  may include first and second heat sinks  664  ( FIGS. 48 ) and  666  that are configured to transfer thermal energy from the first and second SLSs  614  and  616 , respectively. 
     The SLS module  604  and the module frame  660  may be sized and shaped such that an individual could hold the SLS module  604  with the individual&#39;s hands and readily manipulate for installing into the imaging system  600 . As such, the SLS module  604  has a weight that an adult individual could support. 
     The SLS module  604  is configured to be placed within the module-receiving space  719  ( FIG. 41 ) and removably coupled to the base plate  702  ( FIG. 41 ). As shown, the module frame  660  has a plurality of sides including a mounting side  670  and an engagement face  671  ( FIG. 48 ). In the illustrated embodiment, the module frame  660  is substantially rectangular or block-shaped, but the module frame  660  may have other shapes in alternative embodiments. The mounting side  670  is configured to be mounted to the base plate  702  within the module-receiving space  719 . As such, at least a portion of the module-receiving space  719  may be shaped to receive and hold the SLS module  604 . Similar to the component-receiving space  713 , the module-receiving space  719  may be defined by one or more surfaces that provide an accessible spatial region where the SLS module  604  may be held. The surface(s) may be of the base plate  702 . For example, in the illustrated embodiment, the module-receiving space  719  is a depression of the base plate  702 . The mounting side  670  may have a contour that substantially complements the base plate  702  and, more specifically, the module-receiving space  719 . For example, the mounting side  670  may be substantially planar and include a guidance pin  672  ( FIG. 49 ) projecting therefrom that is configured to be inserted into a corresponding hole (not shown) in the base plate  702 . The guidance pin  672  may be a fastener (e.g., screw) configured to facilitate removably coupling the module frame  660  to the base plate  702 . In particular embodiments, the guidance pin  672  is inserted into the base plate  702  at a non-orthogonal angle. As shown in  FIG. 49 , the heat sink  666  may be coupled to the module frame  660  such that an offset  676  exists from the mounting side  670  to the heat sink  666 . 
     The module frame  660  may include first and second light passages  682  and  684  that intersect each other at a passage intersection  685 . The SLSs  614  and  616  may be secured to the module frame  660  and have fixed positions with respect to each other. The SLSs  614  and  616  are oriented such that optical signals are substantially directed along optical paths through the respective light passages  682  and  684  toward the passage intersection  685 . The optical paths may be directed toward the excitation filter  635 . In the illustrated embodiment, the optical paths are perpendicular to one another until reaching the excitation filter  635 . The excitation filter  635  is oriented to reflect at least a portion of the optical signals generated by the SLS  616  and transmit at least a portion of the optical signals generated by the SLS  614 . As shown, the optical signals from each of the SLSs  614  and  616  are directed along a common path and exit the SLS module  604  through a common module window  674 . The module window  674  extends through the engagement face  671 . 
       FIG. 50  is a plan view of the SLS module  604  mounted onto the base plate  702 . In the illustrated embodiment, the SLS module  604  is configured to rest on the base plate  702  such that the gravitational force g facilitates holding the SLS module  604  thereon. As such, the SLS module  604  may provide an integrated device that is readily removed or separated from the optical assembly  600 . For example, after removing a housing (not shown) of the assay system or after receiving access to the optical assembly, the SLS module  604  may be grabbed by an individual and removed or replaced. When the SLS module  604  is located on the base plate  702 , the engagement face  671  may engage an optical device  680 . The optical device  680  may be adjacent to the module window  674  such that the optical signals generated by the SLS module  604  are transmitted through the optical device  680 . 
     Although the illustrated embodiment is described as using an SLS module with first and second SLSs, excitation light may be directed onto the sample in other manners. For example, the SLS module  604  may include only one SLS and another optical component (e.g., lens or filter) having fixed positions with respect to each other in a module frame. Likewise, more than two SLSs may be used. In a similar manner, light modules may include only one laser or more than two lasers. 
     However, embodiments described herein are not limited to only having modular excitation systems, such as the SLS module  604 . For example, the imaging system  600  may use a light source that is not mounted to a module frame. More specifically, a laser could be directly mounted to the base plate or other portion of the imaging system or may be mounted to a frame that, in turn, is mounted within the imaging system. 
     Returning to  FIG. 38 , the imaging system  600  may have an image-focusing system  840  that includes the object or sample holder  650 , an optical train  842 , and the imaging detector  610 . The optical train  842  is configured to direct optical signals from the sample holder  650  (e.g., light emissions from the sample area  608  of the flow cell  606 ) to a detector surface  844  of the imaging detector  610 . As shown in  FIG. 38 , the optical train  842  includes the optical components  623 ,  644 ,  634 ,  633 ,  621 ,  631 , and  642 . The optical train  842  may include other optical components. In the illustrated configuration, the optical train  842  has an object or sample plane  846  located proximate to the sample holder  650  and an image plane  848  located proximate to the detector surface  844 . The imaging detector  610  is configured to obtain object or sample images at the detector surface  844 . 
     In some embodiments, the image-focusing system  840  is configured to move the image plane  848  relative to the detector  610  and capture a test image. More specifically, the image plane  848  may be moved such that the image plane  848  extends in a non-parallel manner with respect to the detector surface  844  and intersects the detector surface  844 . A location of the intersection may be determined by analyzing the test image. The location may then be used to determine a degree-of-focus of the imaging system  600 . In particular embodiments, the image-focusing system  840  utilizes a rotatable mirror that is operatively coupled to an actuator for moving the rotatable mirror. However, the image-focusing system  840  may move other optical components that direct the optical signals to the detector surface  844 , or the image-focusing system  840  may move the detector  610 . In either case, the image plane  848  may be relatively moved with respect to the detector surface  844 . For example, the image-focusing system  840  may move a lens. 
     In particular embodiments, the imaging detector  610  is configured to obtain test images using a rotatable mirror  642  to determine a degree-of-focus of the imaging system  600 . As a result of the determined degree-of-focus, the imaging system  600  may move the sample holder  650  so that the object or sample is located within the sample plane  846 . For example, the sample holder  650  may be configured to move the sample area  608  in a z-direction a predetermined distance (as indicated by Az). 
       FIG. 51  is a plan view that illustrates several of the components in the image-focusing system  840 . As shown, the image-focusing system  840  includes a rotatable mirror assembly  850  that includes the mirror  642 , a mounting assembly  852  having the mirror  642  mounted thereon, and an actuator or rotation mechanism  854  that is configured to rotate the mounting assembly  852  and the mirror  642  about an axis of rotation R 6 . The mirror  642  is configured to reflect optical signals  863  that are received from the sample area  608  ( FIG. 38 ) toward the imaging detector  610  and onto the detector surface  844 . In the illustrated embodiment, the mirror  642  reflects the optical signals  863  directly onto the detector surface  844  (i.e., there are no intervening optical components that redirect the optical signals  863 ). However, in alternative embodiments, there may be additional optical components that affect the propagation of the optical signals  863 . 
     In the illustrated embodiment, the image-focusing system  840  also includes positive stops  860  and  862  that are configured to prevent the mirror  642  from rotating beyond predetermined rotational positions. The positive stops  860  and  862  have fixed positions with respect to the axis R 6 . The mounting assembly  852  is configured to pivot about the axis R 6  between the positive stops  860  and  862  depending upon whether sample images or test images are being obtained. Accordingly, the mirror  642  may be rotated between a test position (or orientation) and an imaging position (or orientation). By way of example only, the mirror  642  may be rotated from approximately 5° to approximately 12° about the axis R 6  between the different rotational positions. In particular embodiments, the mirror  642  may be rotated approximately 8° about the axis R 6 . 
       FIG. 52  is a perspective view of the mirror assembly  850 . As shown, the mounting assembly  852  includes an interior frame  864  and a support bracket  866 . The interior frame  864  is configured to couple to the mirror  642  and also to the support bracket  866 . The interior frame  864  and the support bracket  866  may interact with each other and a plurality of set screws  868  to provide minor adjustments to the orientation of the mirror  642 . As such, the mounting assembly  852  may constitute a gimbal mirror mount assembly. Also shown, the mounting assembly  852  is coupled to the rotation mechanism  854 . In the illustrated embodiment, the rotation mechanism  854  comprises a direct drive motor. However, a variety of alternative rotation mechanisms may be used, such as direct current (DC) motors, solenoid drivers, linear actuators, piezoelectric motors, and the like. Also shown in  FIG. 52 , the positive stop  860  may have a fixed position with respect to the rotation mechanism  854  and the axis R 6 . 
     As discussed above, the rotation mechanism  854  is configured to rotate or pivot the mirror  642  about the axis R 6 . As shown in  FIG. 52 , the mirror  642  has a geometric center C that extends along the axis R 6 . The geometric center C of the mirror  642  is offset with respect to the axis R 6 . In some embodiments, the rotation mechanism  854  is configured to move the mirror  642  between the test position and imaging position in less than  500  milliseconds. In particular embodiments, the rotation mechanism  854  is configured to move the mirror  642  between the test position and imaging position in less than  250  milliseconds or less than  160  milliseconds. 
       FIG. 53  is a schematic diagram of the mirror  642  in the imaging position. As shown, the optical signals  863  from the sample area  608  ( FIG. 38 ) are reflected by the mirror  642  and directed toward the detector surface  844  of the imaging detector  610 . Depending upon the configuration of the optical train  842  and the z-position of the sample holder  610 , the sample area  608  may be sufficiently in-focus or not sufficiently in-focus (i.e., out-of-focus).  FIG. 53  illustrates two image planes  848 A and  848 B. The image plane  848 A substantially coincides with the detector surface  844  and, as such, the corresponding sample image has an acceptable or sufficient degree-of-focus. However, the image plane  848 B is spaced apart from the detector surface  844 . Accordingly, the sample image obtained when the image plane  848 B is spaced apart from the detector surface  844  may not have a sufficient degree-of-focus. 
       FIGS. 54 and 55  illustrate sample images  870  and  872 , respectively. The sample image  870  is the image detected by the imaging detector  610  when the image plane  848 A coincides with the detector surface  844 . The sample image  872  is the image detected by the imaging detector  610  when the image plane  848 B does not coincide with the detector surface  844 . (The sample images  870  and  872  include clusters of DNA that provide fluorescent light emissions when excited by predetermined excitation spectra.) As shown in  FIGS. 54 and 55 , the sample image  870  has an acceptable degree-of-focus in which each of the clusters along the sample image  870  is clearly defined, and the sample image  872  does not have an acceptable degree-of-focus in which each of the clusters is clearly defined. 
       FIG. 56  is a schematic diagram of the mirror  642  in the focusing position. As shown, the mirror  642  in the focusing position has been rotated about the axis R 6  an angle  0 . Again, the optical signals  863  from the sample area  608  ( FIG. 38 ) are reflected by the mirror  642  and directed toward the detector surface  844  of the imaging detector  610 . However, the optical train  842  in  FIG. 56  is arranged so that the image plane  848  has been moved with respect to the detector surface  844 . More specifically, the image plane  848  does not extend parallel to the detector surface  844  and, instead, intersects the detector surface  844  at a plane intersection PI. While the mirror  642  is in the focusing position, the imaging system  600  may obtain a test image of the sample area  608 . As shown in  FIG. 56 , the plane intersections PI may occur at different locations on the detector surface  844  depending upon the degree to which the sample area  608  is in-focus during an imaging session. 
     For example,  FIGS. 57 and 58  illustrate test images  874  and  876 , respectively. The test image  874  represents the image obtained when the sample area  608  is in-focus, and the test image  876  represents the image obtained when the optical train  842  is out-of-focus. As shown, the test image  874  has a focused region or location FL 1  that is located a distance XD 1  away from a reference edge  880 , and the test image  876  has a focused region or location FL 2  that is located a distance XD 2  away from a reference edge  880 . The focused locations FL 1  and FL 2  may be determined by an image analysis module  656  ( FIG. 38 ). 
     To identify the focused locations FL 1  and FL 2  in the test images  874  and  876 , the image analysis module  656  may determine the location of an optimal degree-of-focus in the corresponding test image. More specifically, the analysis module  656  may determine a focus score for different points along the x-dimension of the test images  874  and  876 . The analysis module  656  may calculate the focus score at each point based on one or more image quality parameters. Examples of image quality parameters include image contrast, spot size, image signal to noise ratio, and the mean-square-error between pixels within the image. By way of example, when calculating a focus score, the analysis module  656  may calculate a coefficient of variation in contrast within the image. The coefficient of variation in contrast represents an amount of variation between intensities of the pixels in an image or a select portion of an image. As a further example, when calculating a focus score, the analysis module  656  may calculate the size of a spot derived from the image. The spot can be represented as a Gaussian spot and size can be measured as the full width half maximum (FWHM), in which case smaller spot size is typically correlated with improved focus. 
     After determining the focused location FL in the test image, the analysis module  656  may then measure or determine the distance XD that the focused location FL is spaced apart or separated from the reference edge  880 . The distance XD may then be correlated to a z-position of the sample area  608  with respect to the sample plane  846 . For example, the analysis module  656  may determine that the distance XD 2  shown in  FIG. 58  corresponds to the sample area  608  be located a distance Az from the sample plane  846 . As such, the sample holder  650  may then be moved the distance Az to move the sample area  608  within the sample plane  846 . Accordingly, the focused locations FL in test images may be indicative of a position of the sample area  608  with respect to the sample plane  846 . As used herein, the phrase “being indicative of a position of the object (or sample) with respect to the object (or sample) plane” includes using the factor (e.g., the focused location) to provide a more suitable model or algorithm for determining the distance Az. 
       FIG. 59  is a block diagram illustrating a method  890  for controlling focus of an optical imaging system. The method  890  includes providing an optical train at  892  having a rotatable mirror that is configured to direct optical signals onto a detector surface. The detector surface may be similar to the detector surface  844 . The optical train may have an object plane, such as the sample plane  846 , that is proximate to an object. The optical train may also have an image plane, such as the image plane  848 , that is proximate to the detector surface. The rotatable mirror may be rotatable between an imaging position and a focusing position. 
     The method  890  also includes rotating the mirror at  894  to the focusing position and obtaining a test image of the object at  896  when the mirror is in the focusing position. The test image may have an optimal degree-of-focus at a focused location. The focused location may be indicative of a position of the object with respect to the object plane. Furthermore, the method  890  may also include moving the object at  898  toward the object plane based on the focused location. 
     It is to be understood that the above description is intended to be illustrative, and not restrictive. For example, the above-described embodiments (and/or aspects thereof) may be used in combination with each other. In addition, many modifications may be made to embodiments without departing from the of the scope invention in order to adapt a particular situation or material. While the specific components and processes described herein are intended to define the parameters of the various embodiments, they are by no means limiting and are exemplary embodiments. Many other embodiments will be apparent to those of skill in the art upon reviewing the above description. The scope of the invention should, therefore, be determined with reference to the appended claims, along with the full scope of equivalents to which such claims are entitled. In the appended claims, the terms “including” and “in which” are used as the plain-English equivalents of the respective terms “comprising” and “wherein.” Moreover, in the following claims, the terms “first,” “second,” and “third,” etc. are used merely as labels, and are not intended to impose numerical requirements on their objects. Further, the limitations of the following claims are not written in means-plus-function format and are not intended to be interpreted based on 35 U.S.C. § 112, sixth paragraph, unless and until such claim limitations expressly use the phrase “means for” followed by a statement of function void of further structure.