BACKGROUND

Various protocols used for biological or chemical research include the execution of a large number of controlled reactions. The reactions may be carried out in accordance with a predetermined protocol by automated systems that have, for example, suitable fluidics, optics, and electronics. The systems may be used, for example, to generate a biological or chemical product for subsequent use or to analyze a sample to detect certain properties/characteristics of the sample. When analyzing a sample in some cases, a chemical moiety that includes an identifiable label (e.g., fluorescent label) may be delivered to a chamber where the sample is located and selectively bind to another chemical moiety of the sample. These chemical reactions may be observed or confirmed by exciting the labels with radiation and detecting light emissions from the labels. Such light emissions may also be provided through other means, such as chemiluminescence.

Some known systems use a fluidic device, such as a flowcell, that includes a flow channel (e.g., interior chamber) defined by one or more interior surfaces of the flowcell. The reactions may be carried out along the interior surfaces. The flowcell is typically positioned proximate to an optical assembly that includes a device for imaging the sample within the flow channel. The optical assembly may include an objective lens and/or a solid state imaging device (e.g., CCD or CMOS). In some cases, an objective lens is not used and the solid state imaging device is positioned immediately adjacent to the flowcell for imaging the flow channel.

Before imaging the flow channel, it may be necessary to conduct a number of reactions with the sample. For example, in one sequencing-by-synthesis (SBS) technique, one or more surfaces of the flow channel have arrays of nucleic acid clusters (e.g., clonal amplicons) that are formed through bridge PCR. After generating the clusters, the nucleic acids are “linearized” to provide single stranded DNA (sstDNA). To complete a cycle of sequencing, a number of reaction components are flowed into the flow channel according to a predetermined schedule. For example, each sequencing cycle includes flowing one or more nucleotides (e.g., A, T, G, C) into the flow channel for extending the sstDNA by a single base. A reversible terminator attached to the nucleotides may ensure that only a single nucleotide is incorporated by the sstDNA per cycle. Each nucleotide has a unique fluorescent label that emits a color when excited (e.g., red, green, blue, and the like) that is used to detect the corresponding nucleotide. With the newly-incorporated nucleotides, an image of numerous clusters is taken in four channels (i.e., one for each fluorescent label). After imaging, another reaction component is flowed into the flow channel to chemically cleave the fluorescent label and the reversible terminator from the sstDNA. The sstDNA is then ready for another cycle. Accordingly, a number of different reaction components are provided to the flow channel for each cycle. A single sequencing session may include numerous cycles, such as 100, 300, or more.

The fluids that include the reaction components are typically held in a storage device (e.g., tray or cartridge) in which different fluids are stored in different reservoirs. Due to the number of reaction components and the large number of cycles, the total volume of fluid that is used during one session can be quite large. In fact, for some applications, it is impractical to supply the total volume of reaction components in a single cartridge. For such applications, it may be necessary to use a larger system, multiple systems, or to execute numerous sessions with a single system. These solutions can be costly, inconvenient, or unreasonable in some circumstances.

DEFINITIONS

All literature and similar material cited in this application, including, but not limited to, patents, patent applications, articles, books, treatises, and web pages, regardless of the format of such literature and similar materials, are expressly incorporated by reference in their entirety. In the event that one or more of the incorporated literature and similar materials differs from or contradicts this application, including but not limited to defined terms, term usage, described techniques, or the like, this application controls.

As used herein, the following terms have the meanings indicated.

Examples described herein include various systems, methods, assemblies, and apparatuses used to detect desired reactions in a sample for biological or chemical analysis. In some examples, 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, examples may be used to perform or facilitate performing a sequencing protocol in which sstDNA is sequenced in a flow cell. In particular examples, the examples described herein can also perform an amplification protocol to generate a sample-of-interest for sequencing.

Examples herein enable desired reactions to occur where the desired reactions include 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 examples, 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 examples, 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.

Various examples 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 the 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 examples, 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 examples, 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 (COD's) (e.g., CCD cameras); photomultiplier tubes (PMT'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'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 “illumination element” and “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.

The illumination element and/or 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 examples, a rotatable mirror is selectively moved to facilitate focusing an optical imaging system.

Analysis operations (also referred to as 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 examples, separate sessions can occur in separate cycles of a sequencing protocol. Each cycle can include one or more imaging session. In other examples, 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 analysis operation, optical signals provided by the sample are observed. Various types of imaging may be used with examples described herein. For example, examples described herein may utilize a “step and shoot” procedure in which regions of a sample area are individually imaged. Examples may also be configured to perform at least one of epi-fluorescent imaging and total-internal-reflectance-fluorescence (TIRF) imaging. In other examples, 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 examples, 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 examples, 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 examples, 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 examples, 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.

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 examples, 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 examples, 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, pluralities 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. Non-incorporated 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 U.S. 2008/0108082, each of which is incorporated herein by reference.

In some examples, 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 U.S. 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 U.S. 2005/0042648; U.S. 2005/0079510; U.S. 2005/0130173; and WO 05/010145, each of which is incorporated herein by reference.

Exemplary labels that can be detected in accordance with various examples, 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 examples, 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 examples 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 examples 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 micro-particles and the like.

SUMMARY

In accordance with examples herein, a cartridge assembly for use with a fluidics analysis instrument is provided. The cartridge assembly comprises housing, including a flow cell chamber to receive a flow cell, and a well plate having liquid wells to receive desired amounts of liquids. The well plate includes a valve station, a pump station and a fluidics analysis station. The well plate includes channels associated with the wells, the valve station, pump station and fluidics analysis station. A pump assembly is provided on the well plate at the pump station. The pump assembly manages fluid flow through the channels between the pump station and the fluidics analysis station. A rotary valve assembly is positioned on the well plate at the valve station. The rotary valve assembly includes a rotor shaft and rotor valve positioned to rotate about a rotational axis and to selectively couple the wells to the pump station. The rotor shaft has a distal end exposed through the housing. The rotor shaft includes a dual spline configuration at the distal end thereof. The dual spline configuration has first and second sets of splines. The first set of splines forms a drive interface and the second set of splines forms a position encoding interface. The position encoding interface is utilized by the valve drive assembly to track a position of the rotor shaft.

Optionally, the first set of splines represent exterior splines extending about an exterior of the distal end, wherein lateral sides of adjacent splines are separated by a first predetermined spline to spline spacing. The spline to spline spacing corresponds to a spline pattern on a drive shaft of a valve drive assembly. The second set of splines may represent interior splines formed about an interior of a cavity provided at the distal end of the rotor shaft. The interior splines may have lateral sides that are angled such that adjacent lateral sides form a predetermined non-parallel angle with respect to one another. The adjacent lateral sides may merge at a bottom to form pockets to receive mating splines on a drive shaft of the valve drive assembly.

Optionally, the rotor valve may be mounted to a proximal end of the rotor shaft through a coupling flange. The coupling flange may allow a predetermined amount of tilting movement between the rotor valve and rotor shaft. The rotor valve may include a rotor base having one or more ribs positioned about a proximal end of the rotor shaft. The coupling flange may be held between the ribs and the proximal end of the rotor shaft. The rotor valve may include well plate engaging face having a central port and a radial port. The rotor valve may include a channel oriented to extend in a radial direction outward from the central port to the radial port.

Optionally, the central port may be aligned to correspond with a rotational axis of the rotor shaft and align with a central feed port in the well plate. The rotor valve may rotate about the rotational axis to align the radial port with a corresponding well port. The rotary valve may include a well plate engaging face formed with an interface ring thereon. The interface ring may extend about a perimeter of the well plate engaging face. The cartridge assembly may further comprise a valve cap including an interior cavity to rotatably receive the rotary valve. The valve cap may include one or more latch arms to secure the valve cap to the wells and downward against the well plate. A biasing element may be within the interior cavity and may apply a biasing force against the rotary valve to maintain a sealed interface between ports in the rotary valve and ports in the well plate.

Optionally, the pump assembly may include a plunger having a drive end and a biasing surface located at opposite ends of the plunger. The drive end and biasing surface may be exposed at upper and lower surfaces of the housing such that corresponding unidirectional drive and biasing forces are applied thereto in connection with moving the plunger in a reciprocating motion. The plunger may have a drive arm and a plunger arm joined with one another through a bridge segment in a U-shape and may be formed together in a monolithic structure. The drive and plunger arms may be received within support posts located on the well plate. The plunger may comprise a plunger arm and plunger element that are molded together from different materials. The plunger element may be formed on a leading end of the plunger arm. The plunger element may move within the corresponding support post to form high and low pressure states at the pumping station.

Optionally, the pump station may include a channel segment functionally divided into a preparation segment, a discharge segment and a pump work segment, all of which are formed continuous with one another to support fluid flow in either direction. The pump station may include a work area sandwiched between a pair of pinch valves located upstream and downstream of the work area. The pump assembly may comprise a plunger aligned with the work area. The plunger may reciprocally move toward and away from the work area to introduce high and low pressure states. The pump assembly may further comprise push pins aligned with the pinch valves. The push pins may be alternately moved to open and close the pinch valves. A piercer unit may be provided in the housing and positioned proximate to the wells. The piercer unit may include a piercer element. The piercer unit may be moved to a piercing position where the piercer element pierces a cover for the corresponding well.

Optionally, the housing may include a cover having a piercer access opening that provides an instrument access to an upper end of the piercer unit. The piercer unit may include a body that is shaped in a conical tubular manner with a lower platform, an intermediate segment and an upper flange, at least one of the lower platforms or upper flange including piercing elements distributed in a predetermined manner. The piercing elements may be arranged to align with the wells on the well plate. A piercer unit may have a platform that fits over the rotor shaft. The platform may include indexing features that engage mating features on the rotary valve assembly to locate the piercer unit in a predetermined rotational orientation with respect to the rotor shaft in order to align piercer elements with corresponding wells.

Optionally, the well plate may include well transition ports arranged in a predetermined pattern corresponding to the rotary valve assembly. The well plate may include well discharge ports aligned with corresponding wells. The well plate may include well discharge channels extending between corresponding well discharge ports and well transition ports. The well plate may include a base having top and bottom surfaces, at least one of which includes the channels. The channels may include open sided channels. The base may be joined to a backing layer to close the open sided channels. The well plate may include an optical interface window, provided within the optical analysis station. A top side of the well plate may include an insertion limit element to engage an illumination element on an instrument. The insertion limit element may represent one or more ribs that are provided about the optical interface window. The ribs may define a Z-tolerance between an illumination element and the optical interface window.

In accordance with examples herein, a fluidics system is provided comprising a cartridge assembly that has a housing that includes an illumination chamber and a well plate. The well plate is maintained within the housing and has liquid wells to receive desired amounts of liquids. The well plate includes a fluidics analysis station aligned with the illumination chamber. The well plate includes an interface window and interface ports located at the fluidics analysis station. A flow cell cartridge has a frame that contains an analysis circuit therein. The frame includes a flow cell window aligned with the analysis circuit. The frame includes flow cell ports that are fluidly coupled to an active area in the analysis circuit. The housing includes a flow cell chamber to receive the flow cell cartridge. The flow cell chamber to position the flow cell cartridge at the fluidics analysis station with the flow cell window and ports aligned with the corresponding interface window and ports, respectively.

Optionally, the flow cell chamber may include side rails and end stop, at least one of which has an end limit to position the flow cell cartridge, when in a fully loaded position, at a predetermined datum point such that the flow cell window and ports aligned with the corresponding interface window and ports, respectively. The flow cell chamber may include a biasing arm that may be oriented to extend along at least one of the side rails. The biasing arm may extend inward toward the flow cell chamber and to apply a lateral biasing force upon the flow cell cartridge to maintain the flow cell cartridge at the predetermined datum point. The biasing arm may include a latch element positioned to fit with a notch provided in a lateral side of the flow cell cartridge. The latch element may maintain the flow cell cartridge at an X datum point relative to an XYZ coordinate system (as described herein).

Optionally, the flow cell cartridge may include top and bottom frames. The top frame may include the flow cell window and ports. The top frame may include a rib extending upward from the top frame by a predetermined height to define a Z datum point relative to an XYZ coordinate system. The flow cell cartridge may include gaskets formed in a monolithic manner from an elastomer material. The well plate may include a valve station, pump station and interface channels. The interface channels may provide a first fluidic path between the valve station and one of the interface ports and a second fluidic path between the pump station and one of the interface ports. The illumination chamber may be oriented to extend along an illumination axis that may extend through the interface window, flow cell window and the active area within the analysis circuit.

