CN202379991U - Nucleic acid sequencing system - Google Patents

Abstract

The utility model relates to a nucleic acid sequencing system. The nucleic acid sequencing system comprises an object stage (a), a fluid storage system (b), a flow system (c), a light exciting module (d), a detector (e) and an optical system (f), wherein the object stage (a) comprises a support structure, a plurality of reference planes and an alignment assembly; the fluid storage system (b) comprises a shell, a temperature control assembly and a fluid transfer assembly; the flow system (c) is used for guiding a sequencing reagent from the fluid storage system (b) to the position of a support structure which is used for accommodating a dismountable fluid jetting device; the light exciting module (d) comprises a first semiconductor light source, a second semiconductor light source and an optical part; and the optical system (f) is used for guiding light which is excited by the light exciting module to the position of the support structure which is used for accommodating the dismountable fluid jetting device.

Description

Nucleic acid sequencing system

Technical field

Embodiment of the present invention relates generally to be used for the mensuration system of bioanalysis, relates more specifically to be used to measure the system and the parts thereof of nucleic acid.

Background technology

The various mensuration schemes that are used for biological or chemical research relate to carries out a large amount of controlled reactions.In some cases, said controlled reaction carries out on stayed surface.Can observe and analyze said required reaction then, to help to confirm the attribute or the characteristic of chemical related in the said required reaction.For example, in some versions, under controlled condition, the chemical constitution part that comprises discernible mark (for example fluorescent mark) can optionally be bonded to another chemical constitution part.The light emission that also detects from said mark through the said mark of radiation excitation can observe these chemical reactions.Also can said light emission be provided through other modes (like chemoluminescence).

The example of this type scheme comprises dna sequencing.In order-checking (SBS) scheme, on the surface of flow passage, form the clonal expansion submanifold while synthesizing at one through bridge-type PCR.After generating said clonal expansion submanifold, can be with said amplicon " linearizing ", to produce single stranded DNA (sstDNA).A series of reagent is flowed into flow cell, to accomplish the order-checking circulation.Each order-checking cycles through the fluorescently-labeled mononucleotide (for example A, T, G, C) with uniqueness and extends said sstDNA.Each Nucleotide has the reversible terminator that only allows the single base of the interior generation of a circulation to mix.After Nucleotide is added to said sstDNA bunch, imaging (that is, each fluorescent mark is) in four passages.After the imaging, said fluorescent mark and said terminator quilt are from said sstDNA chemical cracking, and ever-increasing DNA chain prepares to be used for another circulation.Can repeat the reagent of several cycles and carry and optical detection, to confirm the sequence of said clonal expansion.

Yet being configured to the system that carries out these schemes maybe be limited in one's ability and possibly not meet cost benefit.Therefore, generally need can be cost-benefit to have, more easy or otherwise improved mode carry out mensuration scheme (SBS scheme as indicated above) or can be used in improved system, the method and apparatus of said mensuration scheme process.

Summary of the invention

According to an embodiment, be provided for the fluidic hardware of analytic sample.Said fluidic hardware comprises flow cell with entrance and exit and the flow passage that extends betwixt.Said flow cell is configured to and holds relevant sample.Said fluidic hardware also comprises shell, and said shell has and is configured to the spatial accommodation that holds said flow cell.Said spatial accommodation is by allowing sized and the moulding unsteady with respect to said shell of said flow cell.Said fluidic hardware also comprises the packing ring that is coupled to said shell.Said packing ring has the entrance and exit passage and comprises compressible material.Said packing ring is with respect to said spatial accommodation setting, so as the said entrance and exit of said flow cell respectively with the said entrance and exit passage rough alignment of said packing ring.

In another embodiment, provide a kind of being configured to hold and be convenient to be provided with dismountable chuck (cartridge) that flow cell is carried out to picture.Said chuck comprises dismountable shell, and said dismountable shell has to be configured to said flow cell is remained on the spatial accommodation in the object plane substantially.Said shell comprises a pair of towards rightabout shell surface.Said spatial accommodation extends along at least one of said shell surface, so that said flow cell is exposed to the outside of said shell through at least one of said shell surface.Said chuck also comprises the lid member that is coupled to said shell and comprises packing ring.Said packing ring has the entrance and exit passage and comprises compressible material.Said gasket arrangements is for when said flow cell during by said outer casing supporting, and said packing ring is installed in the top of the expose portion of said flow cell.

In another embodiment still, a kind of method that is provided for the fluidic hardware of sample analysis is provided.Said method is included on the stayed surface of imaging system dismountable fluidic hardware is set.Said device comprises spatial accommodation, is positioned at the flow cell and the packing ring of said spatial accommodation.Said flow cell can float along extension of the object plane in the said spatial accommodation and the said packing ring inner with respect to said object plane.Said method also is included in the said spatial accommodation but on said stayed surface, moves said flow cell, so that the entrance and exit passage rough alignment of the entrance and exit of said flow cell and said packing ring.

In another embodiment, a kind of method that is provided for the fluidic hardware of sample analysis is provided.Said method comprises provides the fluidic hardware with shell, said shell to comprise spatial accommodation and the relocatable flow cell that is positioned at said spatial accommodation.Said shell has and the tight adjacent groove of said spatial accommodation.Said method also comprises said fluidic hardware is arranged on the supporting structure with alignment members.Said alignment members is inserted into through corresponding grooves.Said method also comprises the said flow cell that moves in the said spatial accommodation.When said flow cell moved in said spatial accommodation, said alignment members meshed the edge of said flow cell.

In another embodiment, a kind of fluidic hardware support is provided, said fluidic hardware support is configured to respect to orthogonal X, Y and Z axle location sample area.Said device support comprises and is configured to the supporting structure of holding fluidic hardware.Said supporting structure comprises the basal plane of the said Z-direction towards the edge and is configured to said device fixing on it.Said device support also comprise a plurality of along the XY plane reference plane of direction and comprise actuator and operationally be coupled to the alignment components of the movably registration arm of said actuator separately.Said registration arm has end of engagement.Said actuator moves said registration arm between withdrawal and offset position, with towards with move said end of engagement away from said reference plane.When said registration arm was in said offset position, said registration arm was configured to the said device of supporting against said reference plane.

In another embodiment, a kind of fluidic hardware support is provided, said fluidic hardware support comprises having the supporting structure that is written into the zone that is used to hold fluidic hardware.Said supporting structure comprise partly limit said be written into the zone basal plane and be configured on it said device setting.Said device support comprises the cap assemblies that is coupled to said supporting structure and is configured to be removably installed in the top of said device.Said cap assemblies comprises and covers shell that said lid shell has shell leg and the bridging part that is connected said shell leg.Said shell leg is with the extension of common direction and have the therebetween space of watching.The said space of watching is positioned at said being written on the zone.

In another embodiment, a kind of method that is used for respect to orthogonal X, Y and Z axle location sample area is provided.Said method comprises provides alignment components, and said alignment components comprises the movably registration arm with end of engagement.Said registration arm be the withdrawal and offset position between movably.Said method also be included in towards along on the basal plane of the direction of said Z axle and a plurality of towards between the reference plane of direction fluidic hardware being set separately along the XY planar.Said device has sample area.Said method comprises that also mobile said registration arm is to said offset position.Said registration arm is pressed in said device on the said reference plane, so that said device is maintained at the fixed position.

In another embodiment still, a kind of optical module is provided, said optical module comprises base plate, said base plate has bearing surface and along the parts spatial accommodation of said bearing surface.Said parts spatial accommodation is limited reference plane at least in part.Said optical module also comprises optics, said optics have be configured to reflected light or the transmission light pass optical surface wherein.Said optical module also comprises installing device, and said installing device has component holder and operationally is coupled to the biasing element of said retainer.Said retainer keeps said optics, so that the space segment of said optical surface is towards said reference plane and the path part of said optical surface extends beyond said bearing surface and gets into light path.Said biasing element provides the aligning power of said optical surface against said reference plane.In concrete embodiment, said parts spatial accommodation is the parts chamber that extends into said base plate from the said bearing surface degree of depth of said base plate.Said optical surface and reference plane can have the predetermined profile that said optical surface is set by pre-determined direction that is configured to.

The method of a kind of assembling optical system (optical train) is provided in another embodiment.Said method comprises the base plate that the parts spatial accommodation with the said bearing surface of bearing surface and edge is provided.Said parts spatial accommodation is limited reference plane at least in part.Said method also comprises inserts into said parts spatial accommodation with optics.Said optics also comprise have be configured to reflected light or the transmission light pass optical surface wherein.Said optical surface has towards the space segment of said reference plane and extends beyond the path part that said bearing surface gets into light path.Said method also comprises to be provided the aligning power of said optical surface against said reference plane.In concrete embodiment, said parts spatial accommodation is the parts chamber that extends into said base plate from the said bearing surface degree of depth of said base plate.Said optical surface and reference plane can have the predetermined profile that said optical surface is set by pre-determined direction that is configured to.

In another embodiment, a kind of optical imaging system is provided, said optical imaging system comprises the subject support of fixing and mobile object and detects the detector from the optical signal of the object of detector surface.Said imaging system also comprises and is configured to the optical system of the said optical signal of guiding on the said detector surface.Said optical system has the object plane of closing on said subject support and the plane of delineation that closes on said detector surface.Said optical system is included in rotatable mirror between image space and the focal position.Said imaging system also comprises image analysis module, and when said mirror was in said focal position, said image analysis module was configured to analysis at the detected test pattern of said detector surface.Said test pattern has best focal power (degree-of-focus) at the focal position of said test pattern.Indicate the position of said object at the said focal position of said test pattern with respect to said object plane.Said subject support is configured to based on said focal position and moves said object towards said object plane.

In another embodiment, a kind of method of controlling the focus of optical imaging system is provided.Said method comprises providing and is configured to the optical system of direct light signal on the detector surface.Said optical system has the object plane of closing on object and the plane of delineation that closes on said detector surface.Said optical system is included in rotatable mirror between image space and the focal position.Said method also comprises the said mirror of rotation to said focal position, and when said mirror during at said focal position, obtains the test pattern of said object.Said test pattern has best focal power at the focal position of said test pattern.Said focal position is indicated the position of said object with respect to said object plane.Said method also comprises based on said focal position and moves said object towards said object plane.

In another embodiment, a kind of optical imaging system is provided, said optical imaging system comprises the sample holder that is configured to the supporting flow cell.Said flow cell comprises the flow passage with sample area.Said imaging system also comprises and is coupled to said flow cell and is configured to guiding reagent through the said flow passage flow system of said sample area extremely.Said imaging system comprises that also being configured to guiding exciting light arrives the optical system and first and second light sources on the said sample area.Said first and second light sources have the fixed position with respect to said optical system.Said first and second light sources are provided for exciting first and second optical signals of biomolecules respectively.Said imaging system also comprises the central controller that is coupled to said first and second light sources and said flow system communicatedly.Said unit is configured to and starts said flow system so that said reagent flows into said sample area and is configured to after predetermined generated time section, activates said first and second light sources.Said light source can be, for example, and laser or semiconductor light source (SLS) (like laser diode or photodiode (LED))

In another embodiment, a kind of method of carrying out biological assay is provided.Said method comprises the flow passage that reagent is flow through have sample area.Said sample area comprises the biomolecules that is configured to said reagent generation chemical reaction.Said method also comprises with the said sample area of first and second light source irradiation.Said first and second light sources provide first and second optical signals respectively.When by said first or secondary light source when irradiation, said biomolecules provides the light emission of indication association reaction.Said method also comprises the said light emission of detection from said sample area.Said light source can be, for example, and laser or semiconductor light source (SLS) (like laser diode or photodiode (LED)).

In another embodiment, a kind of flow cell is provided, said flow cell comprises having towards reverse direction and limit the installation surface of a thickness and the first layer of outside surface betwixt.Said flow cell also comprises having towards reverse direction and limit the channel surface of a thickness and the second layer of outside surface betwixt.The said second layer has the groove part that extends along said channel surface.The said channel surface of the said second layer is fixed on said installation surface.Said flow cell also comprises the flow passage that the planar section the said groove part of said channel surface and said installation surface limits.Said flow passage comprises imaging moiety.The said thickness of the said second layer along said imaging moiety substantially evenly and be configured to transmitting optical signal and pass wherein.The said thickness of said the first layer along said imaging moiety substantially evenly and be configured to allow heat energy evenly transmission pass wherein.

In another embodiment, a kind of light source module is provided, said light source module comprises the module frame with optical channel and is fixed to said module frame and the directed light source that passes through said optical channel with the direct light signal along light path.Said light source module also comprises and is fixed to said module frame and has with respect to the fixed position of said light source and the optics of pre-determined direction.Said optics is placed in the said optical channel, so that said optics is in said light path.

In another embodiment, a kind of exciting light module is provided, first and second semiconductor light sources (SLS) that said exciting light module comprises module frame and is fixed to said module frame.Said first and second SLS have fixed position relative to each other.Said first and second SLS are configured to the optical excitation signal that provides different.Said exciting light module also comprises and is fixed to said module frame and has with respect to the fixed position of said first and second SLS and the optics of pre-determined direction.Said optics allows to pass wherein and reflect the optical signal from said the 2nd SLS from the optical signal transmission of a said SLS.The optical signal of said reflection and transmission is directed leaving said module frame along a common path.

In one embodiment, a kind of biological or chemical method for measuring of carrying out is provided.Said method is included in the fluidic hardware with sample area and has and sets up fluid between the reacted constituent storage unit of reacted constituent that a plurality of different being used to carry out one or more mensuration and connect.Said reacted constituent comprises that sample generates composition and sample analysis composition.The said sample area that said method also is included in said fluidic hardware generates sample.Said generating run comprises makes different samples generate the reaction conditions that composition flows into said sample area and controls said sample area, to generate said sample.Said method also comprises the said sample of analyzing said sample area.Said analysis operation comprises makes at least a sample analysis composition flow into said sample area.Said at least a sample analysis composition and said sample react, with detectable signal on the optics that the indication dependent event is provided.Said generation and analysis operation carry out with automated manner through said mensuration system.

In another embodiment, a kind of mensuration system is provided, said mensuration system comprises and is configured to the supporting fluidic hardware and sets up the fluidic hardware support that is connected with the fluid of said fluidic hardware.Said mensuration system also comprises and is configured to the fluidic networks that said fluidic hardware fluid is connected to the reacted constituent storage unit.Said mensuration system also comprises being configured to optionally fluid is flowed into the jet control system through said fluidic hardware from said storage unit.In addition, said mensuration system comprises the central controller with jet control module.Said jet control module is configured to the said jet control system of order (a) so that different samples generates reaction conditions that composition flows into said sample area and control said sample area from said storage unit to generate sample; And (b) so that at least a sample analysis composition flows into said sample area from said storage unit.Said at least a sample analysis composition is configured to said sample and reacts, with detectable signal on the optics that the indication dependent event is provided.Said mensuration system also comprises and is configured to the imaging system of detection from detectable signal on the said optics of said sample.Said central controller is configured to through optionally controlling said fluidic hardware support, said jet control system and said imaging system to generate automatically said sample and analyze said sample.

In another embodiment, a kind of biological or chemical method for measuring of carrying out is provided.Said method comprises: fluidic hardware with sample area (a) is provided and has the reacted constituent storage unit that the reacted constituent of one or more detections is carried out in a plurality of different being used to, said reacted constituent comprises that sample generates composition and sample analysis composition; (b) make sample generate composition according to predetermined scheme and flow into, to generate sample in said sample area; (c) optionally control the reaction conditions of said sample area, so that generate said sample; (d) make the sample analysis composition flow into said sample area; And (e) detecting the optical signal that sends from said sample area, said optical signal is indicated the dependent event between said sample analysis composition and the said sample; Wherein (b)-(e) carries out with automated manner.

Description of drawings

Fig. 1 is the block diagram that carries out the mensuration system that biological or chemical measures according to embodiment being used to of forming.

Fig. 2 is the side-view that is configured to the workstation that carries out biological or chemical mensuration according to an embodiment.

Fig. 3 is the frontview of the said workstation of Fig. 2.

Fig. 4 is the figure according to the fluidic networks of an embodiment formation.

Fig. 5 is the skeleton view according to the flow cell of an embodiment formation.

Fig. 6 is the cross-sectional view of the said flow cell shown in Figure 5 got along the line 6-6 among Fig. 5.

Fig. 7 is the plat of the said flow cell of Fig. 5.

Fig. 8 is the enlarged view of the bending section of flow passage.

Fig. 9 is the skeleton view according to the fluidic hardware of an embodiment formation.

Figure 10 is another skeleton view of the said fluidic hardware of Fig. 9.

Figure 11 is the cross-sectional view of the said fluidic hardware of Fig. 9 of being got along the line 11-11 among Fig. 9.

Figure 12 is the skeleton view according to the fluidic hardware of another embodiment formation.

Figure 13 is the skeleton view of the said fluidic hardware of Figure 12.

Figure 14 is the plat according to the fluidic hardware of an embodiment formation.

Figure 15 is the side perspective view of the said fluidic hardware of Figure 14.

Figure 16 is the part exploded view according to the device support of an embodiment formation.

Figure 17 is the skeleton view of the assembling bracket of Figure 16.

Figure 18 is the skeleton view of supporting structure that can be used for the said support of Figure 16.

Figure 19 is the plan view from above of the said support of Figure 16.

Figure 20 is the said perspective views of supports according of Figure 16 that has cap assemblies at aperture position.

Figure 21 is the amplification plat of the said support of Figure 16.

Figure 22 is the skeleton view of cap assemblies that can be used for the said support of Figure 16.

Figure 23 is the cross-sectional view of the said cap assemblies got along line 23-23 shown in Figure 22.

Figure 24 is the skeleton view of the flow system that can use with the said support of Figure 16.

Figure 25 is a kind of block diagram of method of the fluidic hardware that is provided for sample analysis according to an embodiment.

Figure 26 is the block diagram of the method for a kind of fluidic hardware that is provided for sample analysis according to an embodiment of explanation.

Figure 27 is a kind of block diagram that is used to locate the method for sample area according to an embodiment of explanation.

Figure 28 is the skeleton view according to the fluid storage system of an embodiment formation.

Figure 29 is the cross-sectional side view of the said fluid storage system of Figure 28.

Figure 30 is the skeleton view that pipettes assembly that can use with the said fluid storage system of Figure 28.

Figure 31 is the skeleton view according to the reacted constituent pallet of an embodiment formation.

Figure 32 is the plan view from above of said pallet shown in Figure 31.

Figure 33 is the side-view of said pallet shown in Figure 31.

Figure 34 is the frontview of said pallet shown in Figure 31.

Figure 35 is the cross-sectional side view in the composition hole that can use with the said pallet of Figure 31.

Figure 36 is the bottom perspective view in the said composition hole of Figure 35.

Figure 37 is the skeleton view in the composition hole that can use with the said pallet of Figure 31.

Figure 38 is the figure according to the optical imaging system of an embodiment.

Figure 39 is the skeleton view according to the mobile control system of an embodiment.

Figure 40 is the skeleton view of the parts that can use with the said mobile control system of Figure 39.

Figure 41 is the skeleton view of optical backplane that can be used for the said imaging system of Figure 38.

Figure 42 is the plat of the said base plate of Figure 41.

Figure 43 is the skeleton view according to the optics of the said imaging system that can be used for Figure 38 of an embodiment formation.

Figure 44 is the broken-open perspective view of the said optics of Figure 43.

Figure 45 is the frontview of the said optics of Figure 43.

Figure 46 is the side-view of the said optics of Figure 43 in the install operation process.

Figure 47 is a kind of block diagram that assembles the method for optical system according to an embodiment of explanation.

Figure 48 is the skeleton view according to the light source module of an embodiment formation.

Figure 49 is the side-view of the said light source module of Figure 48.

Figure 50 is the plat of the said light source module of Figure 48.

Figure 51 is the plat according to the image focusing system of an embodiment.

Figure 52 is the skeleton view of rotatable mirror assembly that can be used for the said image focusing system of Figure 51.

Figure 53 is the synoptic diagram of the rotatable mirror that is positioned at image space that can be used for the said image focusing system of Figure 51.

Figure 54 and Figure 55 illustrate the sample image that can obtain through the said image focusing system of Figure 51.

Figure 56 is the synoptic diagram of said rotatable mirror that is positioned at Figure 53 of focal position.

Figure 57 and the 58th illustrates the test pattern that can obtain through the said image focusing system of Figure 51.

Figure 59 is the block diagram of the method for a kind of focus that is used to control optical imaging system of explanation.

Figure 60 explains a kind of method that is used to carry out the biological or chemical assay determination.

Figure 61 explains a kind of method that is used to carry out the biological or chemical assay determination.

Embodiment

Embodiment as herein described comprises various system, method, assembly and the devices that are used for the required reaction of sample that biological or chemical analyzes in order to detection.In some embodiments, said required reaction provides the optical signal that detects through optical module.Said optical signal can be from the light emission of mark or can be by said sample reflection or refractive transmitted light.For example, embodiment can be used for carrying out or be convenient to carry out the order-checking scheme that sstDNA wherein checks order in flow cell.In concrete embodiment, embodiment as herein described also can be carried out the amplification scheme, the associated sample that is used to check order with generation.

As used herein, " required reaction " comprises at least one the variation of stimulation being made chemistry, electricity, physics and optical property or the quality of the material of response.For example, said required reaction can be chemical transformation, chemical transformation or chemical action.In concrete embodiment, said required reaction is detected by imaging system.Said imaging system can comprise the optical module that optical signal is guided to transmitter (like CCD or CMOS).Yet in the mode of other enforcements, said imaging system can directly detect said optical signal.For example, flow cell can be installed on the cmos sensor.Yet said required reaction also can be the variation in electric property.For example, said required reaction can be the variation of ionic concn in the solution.

Exemplary reaction includes but not limited to chemical reaction (like reduction, oxidation, addition, elimination, rearrangement, esterification, amidation, etherificate, cyclisation or replacement); Keying action, wherein first chemical is bonded to second chemical; Dissociation reaction, wherein two or more chemical is separated from each other; Fluorescence; Luminous; Chemoluminescence; And biological respinse (combining) like nucleic acid replication, nucleic acid amplification, nucleic acid hybridization, nucleic acid connection, phosphorylation, enzymatic action, receptors bind or part.Said required reaction also can be, for example, detects and is the addition or the elimination of the proton of the variation of solution or environment PH on every side.

Said stimulation can be following at least one: physics, optical, electricity, magnetics with chemistry.For example, said stimulation can be the exciting light that excites fluorophore in the material.Said stimulation also can be the variation of surrounding environment, like the concentration change of some biomolecules in the solution (like enzyme or ion).Said stimulation also can be the electric current that is applied to solution in the preparatory defined volume.In addition, said stimulation can provide through rocking, vibrate or move the residing reaction chamber of said material, with generation power (for example centripetal force).As used herein; Work done in the manner of a certain author extensive interpretation that phrase " is made response to stimulation " and comprise to stimulation make more directly the reaction (for example; After absorbing the incident exciting light; Fluorophore sends the energy of specific wavelength) and owing to said stimulation startup finally causes a series of incidents of said response and more indirect reaction (for example, in the tetra-sodium order-checking, introduce alkali, finally cause chemoluminescence) is made in stimulation.Said stimulation can be (for example, incident exciting light on the fluorophore) or progressive (for example, the temperature variation of surrounding environment) immediately.

As used herein, phrase " is indicated the activity of required reaction " and variant comprises available so that whether definite required reaction takes place any can detected incident, attribute, quality or characteristic.Said detected activity can be the optical signal that generates in fluorescence or the chemoluminescence.Said detected activity also can be in the preparatory defined volume or along the electric property variation of the solution of localized area in advance.Said detected activity can be a variation of temperature.

Various embodiments comprise provides reacted constituent to sample.As used herein, " reacted constituent " or " reactant " comprises any material that can be used for obtaining required reaction.For example, reacted constituent comprises reagent, enzyme, sample, other biological molecule and buffering solution.Said reacted constituent be delivered to usually in the solution reaction site (for example, the residing zone of sample) or in the reaction site internal fixingization.Said reacted constituent can directly or indirectly react with relevant material.

In concrete embodiment, through the said required reaction of optical module optical detection.Said optical module can comprise the optical system that cooperatively interacts with the optics that said optical signal guided to image device (for example CCD, CMOS or PM).Yet in substituting embodiment, said sample area can be set to be close to the activity detector that detects said required reaction and do not use optical system.Said activity detector can have the ability to detect foregone conclusion spare, attribute, quality or characteristic in preparatory defined volume or the zone.For example, activity detector can have the ability to catch the image in said preparatory defined volume or zone.Activity detector can be had the ability to detect in the solution of preparatory defined volume or along the ionic concn of localized area in advance.Exemplary activity detector comprises charge-coupled device (CCD) (for example CCD camera); PM (PMT); Characterization of molecules equipment or detector (like those said characterization of molecules equipment or detectors that uses with nanoporous); The microcircuit device (for example U.S. Patent number 7,595, those microcircuit devices of 883 descriptions, the full content of said patent is incorporated this paper into way of reference); And CMOS system transmitter with field-effect transistor (FET) (comprising chemical sensitive field effect transistor (chemFET), ion-sensitive field effect transistor (ISFET) and/or MOSFET (MOSFET)).

As used herein, term " optics " comprises the various elements that influence lightray propagation.For example, said optics can have following at least one function: reboot, filtration, moulding, amplification or concentrated said optical signal.Maybe affected said optical signal comprise from the optical signal at the said sample upper reaches with from the optical signal in said sample downstream.In fluorescence detecting system, upstream components comprises that those directs excitation radiation are towards the parts of said sample and components downstream comprises the parts of those directs excitation radiation away from said sample.Optics can be, for example, and reverberator, dichroscope, beam splitter, collimator, lens, wave filter, chock, prism, mirror, detector or the like.Optics also comprise BPF., wedge and with the similar optics of those devices as herein described.

As used herein, term " optical signal " comprises the electromagnetic energy that can be detected.Said term comprises from the light emission of the biological or chemical material of mark and also comprises the transmitted light by optical base-substrate refraction or reflection.Optical signal includes exciting radiation that is incident upon on the said sample and the light emission that is provided by said sample, and said optical signal can have one or more spectral patterns.For example, in the imaging stage, can excite the mark more than a type.In this case, dissimilar marks can pass through the common excitation light source excites, perhaps in different time or at one time through different excitation light source excites.Every type mark can send the optical signal that its spectral pattern is different from other marks.For example, said spectral pattern can have distinct transmit spectrum.Said light emission can be by filtering, to detect the optical signal from other emmission spectrum respectively.

As used herein, term " different " uses to light emission (comprising emmission spectrum or other emission characteristics), and said term can broadly be interpreted as and comprise recognizable or differentiable light emission.For example, said photoemissive emmission spectrum can have partly overlapping at least wavelength region, as long as at least a portion of a kind of emmission spectrum is incomplete and other emmission spectrum is overlapping.Distinct transmit spectrum also can have identical or similar wavelength region, but has different recognizable intensity.Different characteristics based on the exciting light that produces said optical signal can be distinguished different optical signals.For example, in FRET (FRET) imaging, said light emission can be identical, but the said photoemissive origin cause of formation (for example optical excitation signal) may be different.More specifically, first excitation wavelength can be used for the right donor fluorophore of excited donor-acceptor, and exciting also of said acceptor will directly cause the emission from said acceptor so that FRET causes from the emission of said acceptor.Just in this point, distinguishing of said optical signal can be based on the observation to transmitting, and combine the affirmation in order to the said emission wavelength that produces said emission.Different light emission can have other nonoverlapping characteristics, like emission anisotropy or fluorescence lifetime.In addition, when said light emission during by filtering, the wavelength region of said emmission spectrum can be dwindled.

Said optics can have the fixed position in optical module, maybe can be optionally movably.As used herein, term " optionally " uses with " moving " and similar term, and said phrase refers to that the position of said optics can be changed in a desired manner.The position of said optics and at least one of direction can be changed.For example, in concrete embodiment, rotatable mirror is optionally moved, so that the focusing optical imaging system.

Different element as herein described and parts can be by removably couplings.As used herein, when two or more elements or parts quilt " removably coupling " (or " removably installing " and other similar terms), said element can not destroyed said coupled parts by separation easily.For example, when element can be easily separated from one another and without OVEREXERTION, tool using (promptly using hand) or do not spend in the separation of great amount of time at said parts not, said element can be easily separable.For instance, in some embodiments, optics can removably be mounted to optical backplane.In addition, flow cell and fluidic hardware can removably be mounted to the device support.

The imaging stage comprises the time period that the part at least of wherein said sample is formed images.A kind of sample can experience or stand a plurality of imaging stages.For example, a kind of sample can stand two different imaging stages, and wherein each imaging stage attempts to detect from one or more optical signals of isolabeling not.As a concrete example, can detect the mark relevant with C and scan along second of the part at least of said sample and can detect and mark that Nucleotide G and T are correlated with Nucleotide A along first scanning of the part at least of nucleic acid samples.In the order-checking embodiment, in the independent circulation of order-checking scheme can take place the independent stage.Each circulation can comprise one or more imaging stages.In other embodiments, can comprise the scanning different samples in different imaging stage sensed light signal.Different samples can be identical type (for example two micro-array chips) or different types (for example flow cell and micro-array chip).

During the imaging stage, the optical signal of observing said sample provide.Various types of imagings can be used with embodiment as herein described.For example, embodiment as herein described can utilize " step-scan " method, and the each several part coverlet of sample area alone becomes picture in said method.Embodiment also can be configured at least one that carry out to fall to penetrating fluorescence imaging and total internal reflection fluorescent (TIRF) imaging.In other embodiments, the sample imager is to postpone integrated (TDI) system sweep time.In addition, the said imaging stage can comprise " line scanning " one or more samples, so that the whole said sample of the line focus domain scanning of light.The description of some line scanning methods is shown in, for example, U.S. Patent number 7,329,860 with U.S. Patent Publication number 2009/0272914, wherein the complete theme of each is all incorporated this paper into way of reference.The imaging stage can comprise that also the point focusing district that moves light with grating mode crosses over said sample.In substituting embodiment, the imaging stage can comprise detect unglazed according to the time and the light emission that generates based on the emitting performance (radioactivity in the for example said sample or chemoluminescence composition) of the mark in the said sample fully.In substituting embodiment, flow cell can be installed on the imager (like CCD or CMOS) that detects said required reaction.

As used herein, term " sample " or " associated sample " comprise various relevant material or the material that experiences the imaging stage, and in the said imaging stage, observation is from the optical signal of said material or material.In concrete embodiment, sample can comprise and relevant biological or chemical material and alternatively supports the optical substrate or the supporting structure of said biological or chemical material.Just in this point, sample can comprise or can not comprise optical substrate or supporting structure.As used herein, term " biological or chemical material " can comprise the various biological or chemical materials that are suitable for optical system imaging as herein described or check.For example; The biological or chemical material comprises biomolecules, like nucleosides, nucleic acid, polynucleotide, oligonucleotide, protein, enzyme, polypeptide, antibody, antigen, part, acceptor, polysaccharide, glucide, polyphosphate, nanoporous, organoid, lipid layer, cell, tissue, organism and bioactive compounds (like the analogue or the mimetic of above-mentioned kind).Other chemical substances comprise the mark that can be used to identify, and its example comprises other marks that fluorescent mark and hereinafter further detail.

Dissimilar samples can comprise influences substrate of the different optical of incident light or supporting structure in a different manner.In concrete embodiment, sample to be detected can be connected to one or more surfaces of substrate or supporting structure.For example, flow cell can comprise one or more flow passages.In flow cell, said flow passage can be through top layer and the bottom and the surrounding environment separation of said flow cell.Therefore, optical signal projection to be detected also can be transmitted through having a plurality of material layers of different refractivity from the inside of said supporting structure.For example; When detecting, hope that said optical signal to be detected can be propagated fluid through having a kind of specific refractory power, through the different specific refractory power of having of said flow cell one or more layers and through having a kind of surrounding environment of different refractivity from the optical signal of the inner bottom surface of flow passage and when detecting from the optical signal above the said flow passage.

As used herein, " fluidic hardware " is a kind ofly to comprise that one or more fluidic flow passages that guide in a predetermined manner are to carry out the device of required reaction.Said fluidic hardware be configured to by jet be coupled to the fluidic networks of mensuration system.For instance, fluidic hardware can comprise flow cell or chip lab (lab-on-chip) equipment.Usually, flow cell along the surface bearing sample with through the imaging of outside imaging system.Chip lab equipment can support sample and carry out extra function, as utilizes integrated detector to detect said required reaction.Fluidic hardware can also comprise other parts that operationally are coupled to said flow passage alternatively, like shell or imager.In concrete embodiment, said passage can have the channel surface that is provided with sample, and said fluidic hardware can comprise the transparent material that allows said sample that the back imaging takes place in required reaction.

In concrete embodiment, said fluid device has the passage of microfluid size.In such passage, the bounding force between the surface of the surface tension pass liquid wherein of flowing and force of cohesion and said liquid and said passage has materially affect to said liquid mobile at least.For example, the cross-sectional area of microfluidic channel (perpendicular to the flow direction intercepting) can be about 10 μ m ²Or it is littler.

In substituting embodiment, optical imaging system as herein described can be used for scanning the sample with microarray.A microarray can comprise a different set of probe molecule that is connected to one or more substrates, comes so that said different probe molecule can be distinguished from each other according to relative position.An array can comprise different probe molecules, or on the same group probe molecule not, and wherein each is positioned at addressed location different in the substrate.Alternatively; A microarray can comprise independent optical substrate (like pearl); Each carries a different probe molecule; Or a different set of probe molecule, said probe molecule can perhaps be discerned according to the position of said substrate in liquid according to the position of the above substrate of surface that is connected with said optical substrate.Wherein independent substrate is set at lip-deep exemplary array and includes but not limited to, (San Diego comprises the array of pearl in BeadChip array CA) or other holes from Inc.; Being described in the patent No. like those is 6,266,459,6; 355,431,6,770; 441,6,859,570 and 7; 622,294 USP; And the PCT publication No. is the array in the patent of WO 00/63437, and each of said patent incorporated this paper into way of reference.Other have the particulate array comprises that those are set forth in US 2005/0227252, WO 05/033681 and WO 04/024328 (wherein each incorporates this paper into way of reference) array from the teeth outwards.

Can use any of various microarraies known in the art.Typical microarray comprises site (also being called as functional component sometimes), and each has one group of probe.Probe groups on each site has the probe of single variety usually, is homogeneity, but in some embodiments, and each can be heterogeneous in said group.The site of array or functional component normally discrete, be spaced.Independent site can be a successive, and perhaps they can have at interval each other.The size and/or the spacing between the said site of said probe site can be different, so that array can be high-density, middle density or than low density.The characteristics of high density arrays are that the site is at interval less than about 15 μ m.The site of middle density array is about 15 to 30 μ m at interval, and the site of low density array is at interval greater than 30 μ m.Be used for array of the present invention and can have the site of interval less than 100 μ m, 50 μ m, 10 μ m, 5 μ m, 1 μ m or 0.5 μ m.The device of embodiment of the present invention or method can be used to make array image-forming with the resolving power in the site that is enough to distinguish above-mentioned density or density range.

The further example of operable commercially available microarray comprises, for example

Microarray or other are according to being called as VLSIPS sometimes ^TMThe method synthetic microarray of (ultra-large immobilized polymer is synthetic) technology, as, for example the patent No. is 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, described in 591 the USP (wherein each incorporates this paper into way of reference).The point-like microarray also can be used in the method according to the embodiment of the present invention.Exemplary point-like microarray is the CodeLink from Amersham Biosciences ^TMArray.Another useful microarray is that a kind of use ink jet printing method is (from the SurePrint of Agilent Technologies ^TMTechnology) microarray of making.

The said system and method that this paper sets forth can be used for detecting the existence of concrete target molecule in the sample of said microarray contact.This can, for example based on the combination of the concrete probe of the target analyte of mark to said microarray or since the target spot dependency of concrete probe revise to confirm, to mix, to remove or to change the mark of said probe location.Several kinds of any in detecting can be used for utilizing microarray (as, for example publication No. is described in 2003/0108867,2003/0108900,2003/0170684,2003/0207295 or 2005/0181394 the U.S. Patent application (wherein each incorporates this paper into way of reference)) identification or characterize target spot.

In addition, optical system as herein described can be illustrated as and comprise various parts and the assembly described in the PCT application PCT/US07/07991 that is entitled as " System and Devices for Sequence by Synthesis Analysis " that submitted on March 30th, 2007 and/or comprise that the international publication number that is entitled as " Fluorescence Excitation and Detection System and Method " like submission on September 26th, 2008 is various parts and the assembly (the complete theme integral body of said two applications is incorporated this paper into way of reference) described in the international application of WO 2009/042862.In concrete embodiment, optical system can comprise like U.S. Patent number 7,329,860 with various parts and the assembly described in the WO 2009/137435 (its complete theme integral body is incorporated this paper into way of reference).Optical system can comprise that also like the application number of submitting on December 15th, 2009 be various parts and the assembly described in 12/638,770 the USP (its complete theme integral body is incorporated this paper into way of reference).

In concrete embodiment, method as herein described and optical system can be used for nucleic acid sequencing.For example, order-checking (SBS) scheme is particularly suitable while synthesizing.In SBS, a plurality of fluorescently-labeled modified ribonucleotides are used to a plurality of DNA amplifications that the surface (for example in flow cell, limiting the surface of passage at least in part) to optical substrate go up to exist bunch (maybe in 1,000,000 bunch) order-checking.Said flow cell can comprise the nucleic acid samples that is used to check order, and wherein said flow cell is placed in the suitable flow cell support.The said sample that is used to check order can present the form of single nucleic acid molecule; Said single nucleic acid molecule is separated each other; So that as bunch or the nucleic acid molecule crowd that can split separately, increase of other characteristic formps, perhaps be connected to the pearl of one or more nucleic acid molecule.Therefore, can on the array of setting forth, check order such as those preceding text.Nucleic acid can be prepared as it and comprise Oligonucleolide primers with unknown target sequence position adjacent.Begin SBS order-checking circulation, the Nucleotide of one or more not isolabelings and archaeal dna polymerase etc. can flow into/flow through said flow cell through fluid flow subsystem (not shown).The Nucleotide of single type can once be added; The Nucleotide that perhaps in the order-checking process, uses can be specifically designed as has reversible terminated attribute, thereby allows in the presence of the labeled nucleotide (like A, C, T, G) of several types, each round-robin sequencing reaction to take place simultaneously.Said Nucleotide can comprise detectable mark part, like fluorophore.When said four kinds of Nucleotide mixed, said polysaccharase can select correct alkali mixing, and each sequence is extended through single base.Uncorporated Nucleotide can be washed off through making washing lotion flow through said flow cell.One or more laser apparatus can excite nucleic acid and bring out fluorescence.The fluorescence that said nucleic acid sends is based on the fluorophore of the alkali that is mixed, and different fluorophores can send the emission light of different wave length.Deblocking reagent can be added to said flow cell, to remove reversible terminator group from the DNA chain that is extended and detects.Then, said deblocking reagent can be washed off through making washing lotion flow through said flow cell.Said flow cell is ready for use on the order-checking circulation of the introducing that further starts from aforesaid labeled nucleotide then.Jet can be repeated repeatedly with the detection step, to accomplish the order-checking operation.The description of exemplary sequence measurement is shown in, people such as Bentley for example, and Nature 456:53-59 (2008), WO 04/018497; US 7,057, and 026; WO 91/06678; WO 07/123744; US 7,329, and 492; US 7,211, and 414; US 7,315, and 019; US 7,405,281 with US 2008/0108082, wherein each incorporates this paper into way of reference.

In some embodiments, nucleic acid can the order-checking before or during be attached to the surface and the amplification.For example, can use bridge-type to increase, to form nucleic acid bunch from the teeth outwards.The description of useful bridge-type amplification method is shown in; For example; U.S. Patent number 5,641,658, U.S. Patent Publication 2002/0055100, U.S. Patent number 7; 115,400, U.S. Patent Publication 2004/0096853, U.S. Patent Publication 2004/0002090, U.S. Patent Publication 2007/0128624 and U.S. Patent Publication 2008/0009420.Another is useful, and be used to the to increase method of lip-deep nucleic acid is rolling circle amplification (RCA), for example, and like people such as Lizardi, described in Nat.Genet.19:225-232 (1998) and the US2007/0099208 A1 (wherein each incorporates this paper into way of reference).Emulsion PCR also can use on the pearl; For example; Like people such as Dressman, described in Proc.Natl.Acad.Sci.USA100:8817-8822 (2003), WO 05/010145 or the U.S. Patent Publication 2005/0130173 or 2005/0064460 (wherein the full content of each is incorporated this paper into way of reference).

Other are applicable to that the sequencing technologies of the purposes of the said method and system that this paper sets forth is tetra-sodium order-checking, nanoporous order-checking and connection method order-checking.Useful especially exemplary tetra-sodium sequencing technologies and sample are described in US 6,210, and 891, US 6,258,568, US 6,274,320 and Ronaghi, Genome Research 11:3-11 (2001) (wherein each incorporates this paper into way of reference).Also useful exemplary nano hole technology and sample are described in people such as Deamer, Acc.Chem.Res.35:817-825 (2002); People such as Li, Nat.Mater.2:611-615 (2003); People such as Soni, people such as Clin Chem.53:1996-2001 (2007), Healy, people such as Nanomed.2:459-481 (2007) and Cockroft, J.am.Chem.Soc.130:818-820; And US 7,001,792 (wherein each incorporates this paper into way of reference).Particularly, these methods are utilized multiple reagent delivery step.Instrument or the configurable system that storage, valve, jet line and other fluidic component is arranged and be used for those parts of method that this paper proposes are with introducing reagent and according to required scheme (those schemes that propose in the for example aforesaid reference) sensed light signal.Any these systems that is used in the various samples, for example have the pearl that generates through emulsion PCR substrate, have zero mode waveguide substrate, have the substrate of integrated CMOS detector, in double-layer of lipoid, have the substrate in biological nano hole, solid substrate and other substrates known in the art with synthesis of nano hole.These samples are described in the various sequencing technologies backgrounds in the reference mentioned above and further are described in US2005/0042648, US 2005/0079510, US 2005/0130173 and WO 05/010145 (wherein each incorporates this paper into way of reference).

Can be to be detected according to different embodiment the exemplary indicia of (for example, above being present in supporting structure or when inner) include but not limited to the nanoparticle of chromophoric group, luminophor, fluorophore, optical encoding, with the mark of the particle of diffraction grating coding, electrochemiluminescence (like Ru (bpy) ³²⁺) or the part that can be detected based on optical characteristics.Can comprise by useful fluorophore, for example fluoresce lanthanide mixture (mixture that comprises those europiums and terbium), resorcinolphthalein, rhodamine, tetramethyl-rhodamine, eosin, tetraiodofluorescein, tonka bean camphor, methylcoumarin, pyrene, malachite green, Cy3, Cy5, toluylene, fluorescent yellow (Lucifer Yellow), Cascade Blue ^TM, Texas Red, alexa dyestuff, phycoerythrin, fluorine boron is glimmering and other fluorophores known in the art, like those at Haugland, Molecular Probes Handbook, (Eugene, OR) 6th Edition; The Synthegen catalog (Houston; TX.), Lakowicz, Principles of Fluorescence Spectroscopy; The fluorophore of describing among the 2nd Ed., Plenum Press New York (1999) or WO 98/59066 (wherein each incorporates this paper into way of reference).In some embodiments, a pair of mark can be by first excitation wavelength can excite and another can be excited by second excitation wavelength mark.

Though embodiment is about the example of the detection of the sample that comprises the biological or chemical material that is supported by optical substrate, is appreciated that other samples can be formed images through embodiment as herein described.Other exemplary samples include but not limited to biological sample (like cell or tissue), electronic chip (as in the computer processor employed those) or the like.Some examples of applications comprise microscope, satellite scanner, high resolving power duplicating, fluoroscopic image collection, foranalysis of nucleic acids and order-checking, dna sequencing, the order-checking while synthesizing, microarray imaging, the imaging of holographic encoding particulate or the like.

Fig. 1 is the block diagram that carries out the mensuration system 100 that biological or chemical analyzes according to embodiment being used to of forming.In some embodiments, said mensuration system 100 is the workstations that can be similar to bench device or desktop computer.For example, the great majority system and the parts that are used to carry out required reaction can be co-located in the shell 117 of said mensuration system 100 at least.In other embodiments, said mensuration system 100 comprises one or more parts, assembly or the system (for example remote data base) from the 100 long-range settings of said mensuration system.Said mensuration system 100 can comprise and interact with each otherly is used for the preordering methods that biological or chemical analyzes or various parts, assembly and the system (or subsystem) of the scheme of mensuration to carry out one or more.

For example, said mensuration system 100 comprises central controller 102, and said central controller 102 can be communicated with said various parts, assembly and the system (or subsystem) of said mensuration system 100.As shown in the figure, said mensuration system 100 has optical module 104, excitaton source assembly 106, detector module 108 and supports one or more fluidic hardware supports 110 that have the fluidic hardware 112 of sample on it.Said fluidic hardware can be a flow cell, and flow cell 200 as mentioned below, perhaps said fluidic hardware 112 can be fluidic hardwares 300 hereinafter described.

In some embodiments, said optical module 104 be configured to guiding from the incident light of said excitaton source assembly 106 on said fluidic hardware 112.Said excitaton source assembly 106 can comprise that one or more are configured to the excitation light source that excites the mark relevant with said sample.Said excitaton source assembly 106 also can be configured to be provided by said sample reflection and/or refractive incident light.As shown in the figure, said sample can provide the optical signal that comprises light emission 116 and/or transmitted light 118.Said device support 110 can move relative to each other with said optical module 104.In some embodiments, said device support 110 comprises the electric machine assembly 132 that moves said fluidic hardware 112 with respect to said optical module 104.In other embodiments, said optical module 104 can perhaps alternatively be moved to said device support 110 in addition.Said optical module 104 also can be configured to and guide said light emission 116 and/or transmitted light 118 to said detector module 108.Said detector module 108 can comprise one or more imaging detectors.Said imaging detector can be, just as giving an example CCD or CMOS camera, or PM.

Still as shown in the figure, said mensuration system 100 can comprise the jet control system 134 of the fluid flow of the whole fluidic networks 135 of control (solid line is represented).Said jet control system 134 can in, send reacted constituent (for example reagent) or other fluids during the for example order-checking scheme to said fluidic hardware 112.Said mensuration system 100 also can comprise and is configured to the temperature controlling system 138 depositing said mensuration 100 available fluidic fluid storage systems 136 of system and regulate said fluidic temperature.Said temperature controlling system 138 is usually also capable of using, and for example radiating module, scatterer and gas blower are regulated the temperature of said mensuration system 100.

Still as shown in the figure, said mensuration system 100 can comprise the user interface 140 with user interaction.For example, said user interface 140 can comprise that demonstration or request are from the indicating meter 142 of user's information and the user input device 144 of reception user input.In some embodiments, said indicating meter 142 is identical equipment (like touch-screen) with said user input device 144.As will do more detailed discussion hereinafter, said mensuration system 100 can with each members to carry out required reaction.Said mensuration system 100 also can be configured to analysis detecting data, to the user information needed to be provided.

Said jet control system 134 is configured to guiding and regulates one or more fluids through said fluidic networks 135.Said jet control system 134 can comprise, for example, optionally can operate and is used to control fluid mobile pump and valve.Said fluidic networks 135 can be communicated with said fluidic hardware 112 and said fluid storage system 136 fluids.For example; Selected fluid can be drawn from said fluid storage system 136 and with controlled way is directed to said fluidic hardware 112; Or said fluid can be drawn from said fluidic hardware 112 and be drawn towards, the litter receptacle in the for example said fluid storage system 136.Though show, said jet control system 134 also can comprise the flow sensor that detects said flow rate of fluid in the said fluidic networks or pressure.Said transmitter can be communicated with said central controller 102.

Said temperature controlling system 138 is configured to the fluid temperature (F.T.) of the different zones of regulating said fluidic networks 135, said fluid storage system 136 and/or said fluidic hardware 112.For example, said temperature controlling system 138 can comprise the thermo cycler 113 that engages and control the temperature of said fluidic hardware 112 flowing fluids in edge with said fluidic hardware 112.Though do not show that said temperature controlling system 138 can comprise the transmitter of the temperature of test fluid or miscellaneous part.Said transmitter can be communicated with said central controller 102.

Said fluid storage system 136 is communicated with said fluidic hardware 112 fluids and can stores various reacted constituents or the reactant that is used for carrying out required reaction among this paper.Said fluid storage system 136 can store the fluid that is used to clean or clean said fluidic networks 135 or said fluidic hardware 112 and also is used to dilute said reactant.For example, said fluid storage system 136 can comprise the various storages that are used for storing reagent, enzyme, other biological molecule, buffered soln, water and non-polar solution or the like.In addition, said fluid storage system 136 also can comprise the litter receptacle that is used to receive waste product.

Said device support 110 for example is configured to, and meshes one or more said fluidic hardwares 112 with in mechanical, electric and the fluid mode at least one.Said device support 110 can an expectation direction support said fluidic hardware 112 so that fluid flows through said fluidic hardware 112 and/or 112 imagings of said fluidic hardware.

Said central controller 102 can comprise any based on treater or based on the system of microprocessor, comprises using microcontroller, reduced instruction set computers machine (RISC), application specific integrated circuit (ASIC), field programmable gate array (FPGA), logical circuit and any other can carry out the system of the circuit or the treater of function as herein described.Top example only is exemplary, and therefore not necessarily is intended to limit the definition and/or the implication of said term system unit.In exemplary embodiment, said central controller 102 is carried out the instruction group that is stored in one or more storage unit, storer or module, so that realize detecting Data Acquisition and analysis at least one.Storage element can be the form of the physical memory element in information source or the said mensuration system 100.

Said instruction group can comprise that the said mensuration of various indications system 100 carries out the order of concrete operations (method of various embodiments as described herein and process).Said instruction group can be the form of software program.As used herein; Term " software " and " firmware " can exchange; And comprise and be stored in the storer any computer program of carrying out by computingmachine, said storer comprises RAM storer, ROM storer, eprom memory, eeprom memory, non-volatile ram (NVRAM) storer.Above type of memory only is exemplary, because of rather than to the restriction of the type of the storer that can be used for storing computer program.

Said software can be various forms, like system software or application software.In addition, said software can be the set of independent program, perhaps than the inner programmodule of large program or the part of programmodule.Said software also can comprise the modularization programming of the form of OOP.After detecting data, can handle, respond the user automatically through said mensuration system 100 and import the request handling or respond another handler and the make remote request of communication link (for example through) and handle said detection data.

Said central controller 102 can be connected to the miscellaneous part or the subsystem of said mensuration system 100 through communication link (dotted line is represented).Said central controller 102 also can be connected to remote system or server communicatedly.Said communication link can be a hardwired or wireless.Said central controller 102 can receive user's input or the order from said user interface 140.Said user input device 144 can comprise keyboard, mouse, touch panel and/or speech recognition system or the like.Alternatively or additionally, said user input device 144 also can be said indicating meter 142.

Fig. 1 also illustrates the block diagram of said central controller 102.In one embodiment, said central controller 102 comprises one or more treaters that can communicate with each other or module.Said central controller 102 illustrates in the conceptive set that is used as module, but can utilize the arbitrary combination of specialized hardware plate, DSP, treater etc. to realize.Alternatively, the said central controller 102 ready-made PCs that have uniprocessor or multi-processor capable of using are realized, and feature operation is distributed between the said treater.As further selection, module hereinafter described can utilize mixed configuration to realize, wherein certain module functional utilization specialized hardware is carried out, and remaining functions of modules is utilized ready-made PC to wait to carry out.The software module that said module also can be used as in the processing unit realizes.

Said central controller 102 can comprise a plurality of module 151-158 that are communicated with system control module 150.Said system control module 150 can be communicated with said user interface 140.Directly be communicated with though said module 151-158 is shown with said system control module 150, said module 151-158 also can be each other, with said user interface 140 or directly be communicated with other system.In addition, said module 151-158 can be communicated with said system control module 150 through other modules.

Said a plurality of module 151-158 comprises the system module 151-153 that is communicated with said subsystem.Said fluid control module 151 can be communicated with said jet control system 134, with valve and the flow sensor of controlling said fluidic networks 135, thereby controls one or more fluid flow through said fluidic networks 135.When the fluid step-down or when said litter receptacle must be changed, said fluid storage module 152 can be notified the user.Said fluid storage module 152 can also be communicated with said temperature control modules 153, so that said fluid can be stored under the ideal temperature.

Said a plurality of module 151-158 also can comprise reception and analyze the image analysis module 158 from the detection data (for example view data) of said detector module 108.Detection data after the processing can be stored for subsequent analysis maybe can be sent to said user interface 140 to show required information to the user.Scheme module 155-157 is communicated with said system control module 150, to control the running of said subsystem when the mensuration scheme of being scheduled to.Said scheme module 155-157 can comprise and is used to indicate said mensuration system 100 to carry out the instruction group of concrete operations according to predetermined scheme.

Said scheme module 155 can be configured to and be emitted in the order that generates sample in the said fluidic hardware 112.For example, said scheme module 155 can indicate said fluid storage system 136 and said temperature controlling system 138 in sample area, to generate sample.In a concrete embodiment, said scheme module 155 can be sent the order of carrying out bridge-type PCR, and wherein the clonal expansion submanifold is formed at the partial zones in the flow cell passage (or path).

Said scheme module 156 can be configured to send various execution check order while synthesizing process order while synthesizing the order-checking (SBS) module.In some embodiments, but also processing and detecting data of said SBS module 156.After generating said amplicon through bridge-type PCR; Said SBS module 156 can provide the instruction of carrying out said amplicon linearizing or sex change to produce sstDNA and to add sequencing primer, is positioned at the lateral universal sequence of domain of dependence so that said sequencing primer can hybridize to become.Each order-checking cycles through the said sstDNA of single-basic extension and accomplishes through modification archaeal dna polymerase and four kinds of mixture of ribonucleotides (it sends the indication that can receive said SBS module 156).Dissimilar Nucleotide has unique fluorescent mark, and each Nucleotide has the reversible terminator that only allows the single base of the interior generation of a circulation to mix.After single base was added into said sstDNA, said SBS module 156 can be sent the instruction of cleaning step, to remove uncorporated Nucleotide through making washing lotion flow through said flow cell.Said SBS module 156 can further indicate said excitaton source assembly and detector module to carry out the imaging stage in of said four passages, to detect fluorescence (being one of each fluorescent mark).After the imaging, said SBS module 156 can be indicated and sent deblocking reagent, with from said fluorescent mark of said sstDNA chemical chop and said terminator.Said SBS module 156 can be sent the instruction of cleaning step, to remove the product of said deblocking reagent and said deblocking reagent.Can carry out subsequently another kind of like order-checking circulation.In the sort sequencer scheme, said SBS module 156 can indicate said jet control system 134 guiding reagent and enzyme solution to flow through said fluidic hardware 112.

In some embodiments, said SBS module 157 can be configured to the order of sending various execution tetra-sodium order-checking scheme steps.When concrete Nucleotide is incorporated into nascent strand; The tetra-sodium order-checking detects the release (Ronaghi of inorganic pyrophosphate (PPi); M. wait the people. (1996) " Real-time DNAsequencing using detection of pyrophosphate release. " Analytical Biochem istry242 (1), 84-9; Ronaghi, M. (2001) " Pyrosequencing sheds light on DNAsequencing. " Genome Res.11 (1), 3-11; Ronaghi, people such as M.. (1998) " Asequencing method based on real-time pyrophosphate. " Science 281 (5375), 363; U.S. Patent number 6,210,891; U.S. Patent number 6,258,568 with U.S. Patent number 6,274,320, the full content of its disclosure is incorporated this paper into way of reference).In the tetra-sodium order-checking, the PPi of release can detect through being converted into ATP immediately by adenosine triphosphate adenosine monophosphate (ATP) sulfurylase, and the ATP level that generates detects through the photon that luciferase produces.In this case, said fluidic hardware 112 can comprise millions of holes, and wherein each hole has the single trapping pearl that has clonal expansion sstDNA above that.Each hole also can comprise other less pearls (for example portability immobilized enzyme (for example ATP sulfurylase and luciferase) or be convenient to said bead capture is remained on the pearl in the said hole).Said SBS module 157 can be configured to said fluid control module 151 and give an order, with fluidic circulation (for example, the 1st circulation: the A that carries single type Nucleotide continuously; The 2nd circulation: G; The 3rd circulation: C; The 4th circulation: T; The 5th circulation: A; The 6th circulation: G; The 7th circulation: C; The 8th circulation: T; Or the like).When Nucleotide was incorporated among the DNA, tetra-sodium was released, thereby caused Kettenreaktion, wherein produced the burst of light.The said burst of light can detect through the sample detector of said detector module.Detecting data can be communicated to said system control module 150, said image analysis module 158 and/or said SBS module 157 and handle.Said detection data can store and be used for later analysis and maybe can analyze and image can be sent to said user interface 140 through said central controller 102.

In some embodiments, the user can provide the user to import through said user interface 140, so that select will be by the mensuration scheme of said mensuration system 100 operations.In other embodiments, said mensuration system 100 can detect the type of the fluidic hardware 112 that is inserted into said device support 110 automatically and confirm mensuration scheme to be moved with the user.Alternatively, said mensuration system 100 can provide a limited number of mensuration schemes with fluidic hardware 112 operations of confirming type.The user can select required mensuration scheme, and said then mensuration system 100 can carry out selected mensuration scheme according to preprogrammed instruction.

Fig. 2 and 3 illustrates the workstation1 60 that is arranged to the biological and chemical analysis of sample according to an embodiment.As shown in the figure, said workstation1 60 is with respect to orthogonal X, Y and Z axle location.In the embodiment shown, terrestrial gravitation g is parallel to said Z axle extension.Said workstation1 60 can comprise workstation shell 162 (or workstation shell), and it is shown in the sectional view of Fig. 2 and Fig. 3.Said shell 162 is configured to the various elements that hold said workstation1 60.For example, said workstation1 60 can comprise the like about said mensuration system 100 (Fig. 1) as indicated above.As shown in the figure, said workstation1 60 has optical table 164, and said optical table 164 has a plurality of opticses that are mounted to it.Said optics can be the optical module part of (as wait said optical module of describing 602 according to Figure 38).Said optical table 164 can have the fixed position with respect to said shell 162.

Said workstation1 60 also can comprise the sample table 166 that is coupled to said optical table 164 movably.Said sample table 166 can have the sliding platform 168 that supports the fluidic hardware with relevant sample above that.In the embodiment shown, said fluidic hardware is the fluidic hardware of describing in more detail hereinafter 300.Said platform 168 be configured to respect to said optical table 164 and, more specifically, slide with respect to the imaging len of said optical module 602.For this reason, said platform 168 can be along the two-way slip of said X axle, so that said fluidic hardware 300 can be placed on the said sample table 166 and wherein the sample imaging so that said imaging len can slide above said fluidic hardware 300.In other embodiments, said platform 168 can be an immobilized and said sample table 166 can be provided with said fluidic hardware 300 with the imaging len with respect to said optical module 602 along the two-way slip of said X axle.Therefore, said platform and sample table can be relative to each other movably owing to said sample table, platform or both moving.

Still as shown in the figure, said workstation1 60 can comprise user interface 172, computing system 174 (Fig. 2) and fluid storage unit 176 and 178 (Fig. 4).Said user interface 172 can be to be configured to the user to show information and also receive the touch-screen that the user imports.For example, said touch-screen can receive and carry out predetermined mensuration scheme or receive the order from user's inquiry.Said computing system 174 can comprise treater and module, like said central controller 102 and the said module 151-158 that describes according to Fig. 1.Said fluid storage unit 176 and 178 can be the part of bigger fluid storage system.Said fluid storage unit 176 can be used for collecting carries out the refuse that said mensuration produces and said fluid storage unit 178 can comprise damping fluid.

Fig. 4 is the figure that can be used for the fluidic networks 552 of said workstation1 60 (Fig. 2).As used herein, fluid can be liquid, gel, gas or its mixture.In addition, fluid can be two or more mixtures of liquids.Said fluidic networks 552 can comprise a plurality of fluidic component (for example, fluid line, pump, flow cell or other fluidic hardwares, manifold, storage) that one or more fluids flow through that are configured to.As shown in the figure, said fluidic networks 552 comprises a plurality of fluidic component 553-561 (solid line is represented) through the fluid line interconnection.In the embodiment shown, said fluidic networks 552 comprises buffered soln container 553, reagent tray 554, multi-ported valve 555, by-pass valve 556, flow sensor 557, flow cell 558, another flow sensor 559, pump 560 and litter receptacle 561.The fluidic flow direction is represented through the arrow along said fluid line.Except said fluidic component 553-561, said fluidic networks also can comprise other fluidic component.

Said reagent tray 554 can be similar with reacted constituent pallet (or reacted constituent storage unit) 1020 that hereinafter is described in more detail.Said pallet 1020 can comprise the various containers (for example bottle or pipe) that are used for carrying out with embodiment as herein described the reacted constituent of measuring that comprise.The operation of said multi-ported valve 555 can be controlled by the mensuration system, like said mensuration system 100, flows into said flow cell 558 optionally to make different fluids (comprising its mixture).Said flow cell 558 can be said flow cell 200 or said fluidic hardware 300 (both are described hereinafter in more detail) or other suitable fluidic hardwares.

Fig. 5-60 (being described in more detail hereinafter) illustrates can be with the various elements (for example parts, equipment, assembly, system or the like) and the method for said workstation1 60 uses.These elements can be fitted to each other with the imaging sample, analyze said detection data and to the user of said workstation1 60 information is provided.Yet following element and method also can independently be used, in other devices, use or use with other devices.For example, said flow cell 200 and said fluidic hardware 300 can be used for other mensuration system.Said optical module 602 (and element) can be used for checking sundry item, like microcircuit.In addition, said device support 400 can be used to support other fluidic hardwares, like chip lab equipment.The mensuration system that has these equipment can comprise or not comprise optical module, to detect said required reaction.

Fig. 5-7 illustrates the flow cell 200 that forms according to an embodiment.Shown in Fig. 5-7, said flow cell 200 is with respect to said X, Y and Z axle location.Said flow cell 200 is configured to and in flow passage 206, keeps relevant sample 205.Said sample 205 is shown in a plurality of DNA bunches that can form images in the SBS scheme process, but other samples can be used in the substituting embodiment.Though single U-shaped flow passage 206 only is shown, substituting embodiment can comprise the flow cell with the moving passage of multithread that has difform path.Said flow cell 200 can be communicated with fluidic system (not shown) fluid, and said fluidic system is configured to the said sample 205 in delivery of agents to the said flow passage 206.In some embodiments, after required reaction took place, said sample 205 can provide detectable characteristic (for example through fluorescence or chemoluminescence).For example, said flow cell 200 can have one or more sample area or the part (be said sample 205 residing zone or parts) of optical signal from wherein sending.In some embodiments, said flow cell 200 also can be used for generating said sample 205, measures to carry out biological or chemical.For example, before said SBS scheme was carried out, said flow cell 200 can be used for generating said DNA bunch.

Shown in Fig. 5-7, said flow cell 200 can comprise the first layer 202 and the second layer 204 that is fixed together and limits said flow passage 206 betwixt.Said the first layer 202 has installation surface 208 and outer surface or outside surface 210 (Fig. 5 and 6).Said installation surface and outer surface 208 and 210 are along said Z axial plane in the opposite direction and thickness limited betwixt T ₁(Fig. 5 and 6).Said thickness T ₁Along the XY plane is uniformly substantially, but can be different in substituting embodiment.The said second layer 204 has channel surface 212 (Fig. 6) and outer surface or outside surface 214.Said channel surface and outer surface 212 and 214 are along said Z axial plane in the opposite direction and thickness limited betwixt T ₂(Fig. 6).

Still as shown in Figure 5, said the first layer 202 has along said X axle measured dimensions or length L ₁With another size or the width W measured along said Y axle ₁In some embodiments, said flow cell 200 is named as microdevice.Microdevice possibly be difficult to through individual's hand maintenance or move.For example, the said length L of said flow cell 200 ₁Can be about 100mm or about 50mm or littler.In concrete embodiment, said length L ₁Be about 30mm or littler.In some embodiments, said width W ₁Can be about 35mm or about 25mm or littler, more specifically, said width W ₁Can be about 15mm or littler.In addition, merging or overall height H shown in Figure 7 _T(thickness T for example ₁And T ₂Summation) can be about 10mm or about 5mm or littler.More specifically, said height H _TCan be about 2mm or about 1.5mm or littler.

Be linear edge 231-234 in the embodiment shown in said flow cell 200 is included in.Edge 231 and 233 is with said width W ₁Spaced apart and extend said flow cell 200 said length L ₁Edge 232 and 234 is with said length L ₁Spaced apart and along said width W ₁Extend.Still as shown in the figure, the said second layer 204 can have along said X axle measured dimensions or length L ₂With another size or the width W measured along said Y axle ₂In the embodiment shown, said edge 231-234 limits the periphery of said flow cell 200 and extends along being parallel to the plane, common pond of extending on said XY plane.Still as shown in the figure, the said second layer 204 can have like the similar localized edge 241-244 of said edge 231-234 (as shown in Figure 5).

In the embodiment shown, said width W ₁Substantially greater than said width W ₂, and the said second layer 204 only is placed on the part of said installation surface 208.Just in this point, said installation surface 208 comprises the retained part 208A and the 208B of exposure in the relative both sides of the said second layer 204.Said width W ₂Between said retained part 208A and 208B, extend.Said flow cell 200 also can have along said Z axial plane pond face 256 and 258 round about.In the embodiment shown, said pond face 256 comprises said retained part 208A and 208B and said outside surface 214, and said pond face 258 comprises said outside surface 210.Still as shown in the figure, said flow cell 200 can be between the relative first and second pond ends 246 and 248 longitudinal extension.In the embodiment shown, said edge 232 and 242 is at coplane and said edge 234 and 244 coplane each other substantially on the said second relative pond end 248 each other substantially on the said first pond end 246.

As shown in Figure 6, the said second layer 204 has at least one groove part 216 that extends along said channel surface 212.In the embodiment shown, said channel surface 212 is etched forming said trench portions 216, but said trench portions 216 can form through other technologies (as cutting said channel surface 212).For assembling said flow cell 200, the said channel surface 212 of the said second layer 204 is mounted and is fixed on the said installation surface 208 of said the first layer 202.For example, said channel surface and installation surface 212 and 208 can use the tackiness agent (for example photoactivation resin) that prevents from the leakage of said flow cell 200 to be bonded together.In other embodiments, said channel surface and installation surface 212 and 208 can be bonded together or mechanical interlocked and/or be fixed together through other tackiness agents.Therefore, said the first layer 202 be configured to cover the said second layer 204 said groove part 216 to form said flow passage 206.In the embodiment shown, said trench portions 216 can be to extend said length L substantially towards said first end ₂, bending is extended said length L towards said second end then substantially ₂Single successive groove.Therefore, said flow passage 206 can be a U-shaped substantially.

Fig. 5-7 shows that said sample 205 only is provided with along said installation surface 208.Yet in other embodiments, said sample 205 can be placed on the surface of the said flow passage 206 of any qualification.For instance, said sample 205 also can be placed on the matching surface 212 of the said trench portions 216 that partly limits said flow passage 206.

In the embodiment shown, said flow passage 206 can comprise a plurality of channel section 250-252.Different channel sections can have the different size with respect to the adjacent upper reaches or downstream passage section.In the embodiment shown, said flow passage 206 can comprise channel section 250 (it also can be called as imaging session 250).Said channel section 250 can have the sample area that is configured to through the imaging of imaging system (not shown).Said flow passage 206 also can have channel section 251 and 252 (it also can be called as non-imaging session 251 and 252).As shown in the figure, said channel section 250 and 252 extends parallel to each other through said flow cell 200.The said channel section 251 of said flow passage 206 and 252 can be pressed certain size with respect to said channel section 250 and make and moulding, possibly flow with control and pass fluid and gas flow wherein.

For example, Fig. 7 also illustrates said channel section 250-252 xsect C separately ₁-C ₃, it passes through perpendicular to flow direction F ₁Intercepting.In some embodiments, said xsect C ₁-C ₃Can be (being different sectional areas) of different sizes, with control fluid flowing through said flow passage 206.For example, said xsect C ₁Size greater than said xsect C ₂And C ₃More specifically, the said channel section 250-252 of said flow passage 206 can have the height H that equates substantially ₁, said height H ₁Measure between the said groove part 216 (Fig. 6) and said installation surface 208 of said channel surface 212.Yet the said channel section 250-252 of said flow passage 206 can have different widths W respectively ₃-W ₅Said width W ₃Greater than said width W ₄And W ₅ Said channel section 251 can constitute bending or the bend loss that jet ground connects said channel section 250 and 252.Said xsect C ₃Than said xsect C ₁And C ₂Less.For example, said width W ₅Less than said width W ₃And W ₄

Fig. 8 is the enlarged view of the said bending section 251 and the part of said channel section 250 and 252.As stated, said channel section 250 and 252 can extend parallel to each other.In said flow passage 206, perhaps need evenly flowing through said sample area.For example, said fluid can comprise stream part F ₂-F ₄The size of said channel section 250-252 can be configured, so that said stream part F ₂-F ₄In whole said sample area, has the flow velocity that equates substantially.In this type embodiment, the time that the different sections of said sample 205 or part (Fig. 5) can have equivalent substantially with the intravital reacted constituent reaction of said stream.

For this reason, the said bending section 251 of said flow passage 206 can have jet ground to connect discrete profile of said channel section 250 and 252.For example, as shown in Figure 8, said bending section 251 can comprise tapered section 270, middle portion 276 and downstream part 278.As shown in the figure, said tapered section 270 has the width W that size reduces gradually _5AMore specifically, said bending section 251 can comprise the sidewall 272 and 274 that extends internally toward each other with angle same substantially.Said middle portion 276 from said tapered section 270 to 278 bendings of said downstream part.The size that has said middle portion 276 reduces gradually, the size width W that begins to increase then _5BSaid downstream part 278 has substantially width W uniformly everywhere _5CAnd linear substantially path, edge extends to said channel section 252 from said middle portion 276.In other words, said sidewall 272 and 274 can extend parallel to each other and pass said downstream part 278.

Turn back to Fig. 7, said flow cell 200 includes an inlet and an outlet, and is respectively 222 and 224.Said entrance and exit 222 and 224 has only through the said second layer 204 formation.Yet in substituting embodiment, said entrance and exit 222 and 224 has only through said the first layer 202 or through said layer 202 and 204 both formation.Said flow passage 206 is communicated with said entrance and exit 222 and 224 fluids and extends therein.In concrete embodiment, end 248 adjoins (or adjoin with said edge 234 and 244) to said entrance and exit 222 and 224 each other in the said pond of said flow cell 200.The interval 282 of for example, separating said entrance and exit 222 and 224 can approximate said width W ₃More specifically, said interval 282 can be about 3mm, about 2mm approximately or still less.In addition, said channel section 250 and 252 can be spaced apart 280 fens and opens.Said interval 280 can be less than the said width W of said channel section 250 ₃Or more specifically, less than the said width W of said channel section 252 ₄Therefore, the path of said flow passage 206 can be substantially U-shaped and, in the embodiment shown, have the discrete profile along said bending section 251.

In substituting embodiment, said flow passage 206 can have different paths, so that said entrance and exit 222 has different positions with 224 in said flow cell 200.For example, said flow passage can form the unipath from the said entrance extension of said flow cell one end to the said outlet of said flow cell opposite end.

About Fig. 6, in some embodiments, the said thickness T of the said second layer 204 ₂Be uniform substantially (Fig. 6) along said imaging moiety 250.Said homogeneous thickness T along said imaging moiety 250 ₂Can be configured to transmitting optical signal passes wherein.In addition, the said thickness T of said the first layer 202 ₁Along said imaging moiety 250 is substantially uniformly and be configured to and allow heat energy to transmit equably to pass wherein to get into said flow passage 206.

Fig. 9-11 illustrates the fluidic hardware 300 that forms according to an embodiment.For illustrative purpose, said fluidic hardware 300 is with respect to the orthogonal X shown in Fig. 9 and 10, Y and Z axle location.Fig. 9 and 10 is skeleton views of said fluidic hardware 300.Shown in Fig. 9 and 10, said fluidic hardware 300 comprises chuck (or flow cell carrier) 302 and said flow cell 200.Said chuck 302 is configured to and holds said flow cell 200 and be convenient to locate the said flow cell 200 that is used to the stage of forming images.

In some embodiments, said fluidic hardware 300 can be dismountable with said chuck 302, so that said chuck 302 can be removed and do not damage said fluidic hardware 300 or chuck 302 from the imaging system (not shown) through individual or machine.For example, said chuck 302 can be configured to inserted and move to said imaging system repeatedly and not destroy said chuck 302 or make said chuck 302 be not suitable for its intended purposes.In some embodiments, said fluidic hardware 300 can be made also moulding with operated by the individual by certain size with said chuck 302.In addition, said fluidic hardware 300 can be made also moulding to be carried by automation system by certain size with said chuck 302.

Shown in Fig. 9 and 10, said chuck 302 can comprise shell or carrier frame 304 and the lid member 306 that is coupled to said shell 304.Said shell 304 has shell or along said Z axial plane round about and have betwixt a height H of extending ₂The carrier side 303 and 305 of (shown in figure 11).As shown in Figure 9, said shell 304 comprises bridge members 324 and comprises substructure member 326 at the relative receiving end 318 of said fluidic hardware 300 at the end 316 that is written into of said fluidic hardware 300.Said shell 304 also is included in a pair of isolated leg extn 328 and 330 that extends between said bridge members and substructure member 324 and 326.Said bridge members 324 is extended between said leg extn 328 and 330 and is connected said leg extn 328 and 330.Said bridge members 324 can comprise out the recess 321 (shown in figure 10) to the outside of said fluidic hardware 300.As shown in Figure 9, said leg extn 328 and 330 can have a plurality of clamping components 371-374 that are configured to the said pond face 256 of the said flow cell 200 of clamping.

Still as shown in Figure 9, said fluidic hardware 300 can have the device window 315 that passes completely through said chuck 302 along said Z axle.In the embodiment shown, said device window 315 is become with 330 frames by said bridge members 324, said lid member 306 and said leg extn 328 substantially.Said device window 315 comprises the recess 320 and 322 of spatial accommodation 308 and the said spatial accommodation 308 of a plurality of next-door neighbour.Said spatial accommodation 308 is configured to and holds said flow cell 200.In the time of in said flow cell 200 is placed in said spatial accommodation 308, said flow cell 200 is exposed to the outside of said fluidic hardware 300, so that said flow cell 200 can be in sight or be also had said shell surface 305 directly to be meshed along said shell surface 303.For example, the said Z axial plane in face 258 (also shown in figure 11) edge, said pond is to the opposite direction with respect to said pond face 256.Said pond face 256 can be seen or directly meshed along another parts of said shell surface 303 by said imaging system.Equally, said pond face 258 can be seen or directly meshed by another parts along said shell surface 305 by said imaging system.

About Fig. 9 and 10, said lid member 306 can comprise the lid 340 and packing ring 342 that intercouples.Said packing ring 342 comprises the entrance and exit passage 346 and 344 (as shown in Figure 9) that adjoins each other.In the embodiment shown, said lid 340 is co-molded to integral structure with said packing ring 342.After the formation, said lid 340 can have different compressible character with said packing ring 342.For example, in concrete embodiment, said packing ring 342 can comprise that the material than said lid 340 has more the material of compressible character.Yet, in substituting embodiment, said lid 340 with said packing ring 342 can be coupling in together (as mechanically or use tackiness agent) independent parts.In other embodiments, said lid 340 and said packing ring 342 can be single successive structure distinct portions or zone.

Said lid member 306 can be coupled to said shell 304 movably.For example, said lid member 306 can rotatably be coupled to the said substructure member 326 of said shell 304.In such embodiment, said packing ring 342 is the turning axle R that can center between installation site (as shown in Figure 9) and the disengaged position (shown in figure 10) ₁Rotation.Be coupled to movably in the embodiment of said shell 304 at other wherein said lid members 306, said lid member 306 can be dismountable from said shell 304.For example, when being connected to said shell 304, said dismountable lid member can be in the installation site that is similar to installation site as shown in Figure 9.When breaking away from said shell 304, said dismountable lid member can be removed at disengaged position fully.

Still shown in figure 10, said shell 304 can limit the chuck chamber 338 (Figure 10) that can get into during at said disengaged position when said lid member 306.In some embodiments, identification XMTR 336 can be placed in the said chuck chamber 338.Said identification XMTR 336 be configured to reception and registration about the information of said flow cell 200 to reader.For example, said identification XMTR 336 can be the RFID label.When said flow cell 200 is inserted into said imaging system; The information that said identification XMTR 336 is provided is passable; For example, discern the said sample in the said flow cell 200, a large amount of said flow cell or sample, date manufactured and/or mensuration schemes to be carried out.Said identification XMTR 336 also can be passed on other information.

Figure 11 is the cross-sectional view of the said fluidic hardware 300 looked along said Y axle.In some embodiments, said spatial accommodation 308 is pressed certain size with respect to said flow cell 200 and is made and moulding, so that said flow cell 200 is maintained in the said space, but some configuration can be floated therein at least.As used herein, term " float " and similarly term comprise parts and be allowed to move limited distance in a direction (for example along said X, Y or Z axle) at least.For example, said flow cell 200 can have the ability at said spatial accommodation 308 internal shifts along said XY plane.Said flow cell 200 also can have in said spatial accommodation 308 ability that moves along the direction of said Z axle.In addition, said flow cell 200 also can have the ability of in said spatial accommodation 308, rotating a little.In concrete embodiment, said shell 304 allow said flow cell 200 about any one of said X, Y and Z axle at said spatial accommodation 308 internal shifts, move and rotation a little.

In some embodiments, said spatial accommodation 308 also can be characterized as being such space: when said fluidic hardware 300 held said flow cell 200, said fluidic hardware 300 allowed said flow cell 200 to move freely therein.Therefore, the size of said spatial accommodation 308 can be based on the position of the reference plane of the said fluidic hardware 300 that can directly mesh said flow cell 200.Said reference plane can be said shell 304 or the surface that comprises the said lid member 306 of said packing ring 342.For example, Figure 11 illustrates a plurality of reference plane 381-387.In the time of in said flow cell 200 is housed inside said spatial accommodation 308, said clamping components 371 and 372 separately reference plane 381 and 382 and the reference plane 383 of said packing ring 342 can limit said flow cell 200 and exceed moving of predeterminated level.The said reference plane 384 of said packing ring 342 and the reference plane 385 of said bridge members 324 can limit said flow cell 200 and move along said XY planar.In addition, the reference plane 386 and 387 of said bridge members 324 and said lid member 306 also can limit said flow cell 200 moving along said Z axle.Yet said reference plane 381-387 is exemplary and said fluidic hardware 300 can have the reference plane that moves of other the said hydrogymnasium 200 of restriction.

Assemble said fluidic hardware 300, said flow cell 200 can be written into said spatial accommodation 308.For example, said flow cell 200 can move forward towards said device window 315 along said shell surface 305.Said edge 234 (Fig. 5) can said clamping components 372 and 373 and said packing ring 342 between move forward.Then, said pond face 256 can be towards said clamping components 371-374 rotation, so that said clamping components 371-374 engages said pond face 256.Then, said edge 232 (Fig. 5) towards said bridge members 324 and, more specifically, move towards the said reference plane 385 of said bridge members 324.In some embodiments, but said bridge members 324 deflections or crooked so that the space that more is used for being provided with said pond end 246 (Fig. 5) above that to be provided.When said flow cell 200 was written into said chuck 302, said shell 304 and said lid member 306 be the periphery of the said flow cell 200 of clamping effectively, so that said flow cell 200 is limited with only said spatial accommodation 308 inner moving.

In substituting embodiment, said pond end 246 inserts the location through said packing ring 342 then at first through said bridge members 324.In other embodiment, said flow cell 200 can close on said shell surface 303.Said clamping components 371-374 can have taper or the chamfered surface that allows said flow cell 200 to snap in the position in the said spatial accommodation 308.

Said flow cell 200 be written into preceding, be written into the back or be written into during, said lid member 306 can be moved into said disengaged position, so that said identification XMTR 336 (Figure 10) can be placed in the said chuck chamber 338 (Figure 10).When said packing ring 342 was in said installation site, said entrance and exit passage 346 and 344 can have predetermined position and the direction with respect to said shell 304 and said spatial accommodation 308.Said packing ring 342 can be installed in the top of said flow cell 200 along the expose portion (being said pond face 256) of said flow cell 200.Said entrance and exit passage 346 and 344 usually can be aimed at said entrance and exit 224 and 222 (Fig. 5).

But the fluidic hardware 300 shown in being to be noted that is a concrete embodiment just, and in substituting embodiment, said fluidic hardware 300 can have different configurations.For example, in substituting embodiment, said flow cell 200 can be not be exposed to the outside of said fluidic hardware 300 along each of said shell surface 303 and 305.On the contrary, said flow cell 200 can one (a for example said shell surface 303) along said shell surface be exposed to said outside.In addition, in substituting embodiment, said lid member 306 can rotatably be coupled to said shell 304.For example, said lid member 306 can be intactly dismountable.

Figure 12-15 illustrates the fluidic hardware 900 and 920 that also can be used for mensuration system (like said mensuration 100 (Fig. 1) of system and said workstation1 60 (Fig. 2)) that forms according to substituting embodiment.Said fluidic hardware 900 and 920 can comprise and said fluidic hardware 300 similar functional components.For example, as shown in the figure, in Figure 12 and 13, said fluidic hardware 900 can comprise chuck (or flow cell carrier) 902 and said flow cell 200.Said chuck 902 is configured to and keeps said flow cell 200 and be convenient to directed said flow cell 200 being used for the imaging stage.Said chuck 902 comprises shell 904 and the lid member 906 that is movably mounted said shell 904.Said lid member 906 is in installation site and the disengaged position among Figure 13 among Figure 12.

Still shown in Figure 12 and 13, said fluidic hardware 900 can comprise the said inlet entrance and exit 222 that covers said flow cell 200 and the sealing member 910 of 224 (Figure 13).In some embodiments, said sealing member 910 is configured to be convenient to fluid is retained in the said flow passage 206, so that the said sample 205 (Fig. 5) in the said flow passage 206 remains in the fluid environment.Yet in some embodiments, said sealing member 910 can be configured to and prevent that unwanted material from getting into said flow passage 206.Shown in Figure 12 and 13, said sealing member 910 is monolithic adhesive tapes that between said pond end 246 and 248 (Figure 13), extend.Sponson 912 can extend away from said pond end 246.In substituting embodiment, said sealing member 910 can be that a slice adhesive tape (for example said inlet entrance and exit 222 and 224 each each a slice adhesive tape) or said sealing member 910 can be other elements that can cover said inlet entrance and exit 222 and 224 incessantly.For example, said sealing member 910 can comprise stopper.

In some embodiments, when said fluidic hardware 900 was not installed to the mensuration system, said sealing member 910 covered said inlet entrance and exit 222 and 224.For example, when said fluidic hardware 900 is stored or transports or when just growth or when generating, said sealing member 910 can be used in said flow cell 200 of sample.In this case, said sealing member 910 can be fixed in said flow cell 200 and said shell 904, and is shown in figure 13.More specifically, said sealing member 910 can be coupled to face 256 extensions of the said pond of said pond face 256 and edge and cover said inlet entrance and exit 222 and 224.Said sealing member 910 also can be coupled to the substructure member 914 of said shell 904.Then, said lid member 906 can be moved to said installation site (shown in figure 12), so as said sealing member 910 be sandwiched in said inlet entrance and exit 222 and 224 and said lid member 906 between.Said lid member 906 can be convenient to prevent that said sealing member 910 from all of a sudden being removed.In substituting embodiment, said sealing member 910 can cover the inlet entrance and exit passage 916 and 918 of said lid member 906.

Figure 14 and Figure 15 illustrate said fluidic hardware 920, and said fluidic hardware 920 also can have and said fluidic hardware 300 and 900 similar functional components.As shown in the figure, said fluidic hardware 920 comprises chuck (or flow cell carrier) 922 and said flow cell 200.Said chuck 922 comprises shell 924 and the lid member 925 that is movably mounted said shell 924.Show 925 installation sites that are in Figure 14 and 15 of said lid member.Said shell 924 and said lid member 925 can with said shell 204 mentioned above with 904 and said lid member 206 and 906 similar.

Yet said shell 924 also can comprise fin-shaped ledge 926 and 928.Said fin-shaped ledge 926 and 928 press that certain size is made and moulding with by individual or robot device's clamping, for example, when said fluidic hardware 920 is inserted into the device support or when device support (not shown) removes.In some embodiments, if said fluidic hardware 920 not by reasonable placement, said fin-shaped ledge 926 and 928 can stop said cap assemblies (not shown) to move to closing position.Said fin-shaped ledge 926 and 928 can comprise and is configured to the feeling function parts 927 and 929 that gripped by the individual.In the embodiment shown, said fin-shaped ledge 926 and 928 is placed in the receiving terminal 930 of said fluidic hardware 920.Said lid member 925 can extend between said fin-shaped ledge.Yet said fin-shaped ledge 926 and 928 can have other positions along said chuck 902.

Figure 16-24 shows the various functional components of the fluidic hardware support 400 that forms according to an embodiment.Figure 16 is the part exploded view of said support 400.During assembling, said support 400 can be used to during the imaging stage, support said fluidic hardware 300 (Fig. 9) and said flow cell 200 (Fig. 5) by required orientation.In addition, said support 400 can provide interface between said fluidic hardware 300 and said imaging system (not shown), and wherein said support 400 can be configured to the guiding fluid through said flow cell 200 and provide or remove the heat energy from said flow cell 200.Though being shown as, said support 400 keeps said fluidic hardware 300, said support 400 to be configured to keeping other jet apparatus, like laboratory equipment on the chip or there is not the flow cell of chuck.

Shown in figure 16, said support 400 can comprise dismountable cap assemblies 404 and supporting structure 402.In some embodiments, said support 400 also can comprise plate structure 406 and platform 408 movably.Said plate structure 406 operationally is coupled to said cap assemblies 404 and comprises the opening 410 that passes wherein.Equally, said platform 408 comprises the opening 412 that passes wherein.Said supporting structure 402 can comprise scatterer 414 and be installed to the radiating module (or thermal cycler) 416 on the said scatterer 414.Said radiating module 416 comprises base part 418 and base 420.When the said support 400 of assembling, said supporting structure 402, said platform 408 and said plate structure 406 are piled up each other.Just in this point, said opening 412 by the sized of holding said base part 418 and moulding and said opening 410 by the sized of holding said base 420 and moulding.When assembling, said cap assemblies 404 can operationally be coupled to said plate structure 406 and said supporting structure 402.

Figure 17 illustrates the support of being assembled 400.In the embodiment shown, panel 424 is placed in the top of said plate structure 406 (Figure 16).Shown in Figure 16 and 17, said cap assemblies 404 comprises the cover housing 435 that is coupled to said plate structure 406.But said cover housing 435 U-shaped in general have a pair of isolated shell leg 436 and 438 that extends towards the common direction.Said shell leg 436 and 438 can rotatably be coupled to said plate structure 406 at binding site 437 and 439 places.Said cover housing 435 also can be included in the bridging portion 440 that extends and connect said shell leg 436 and 438 between said shell leg 436 and 438.So, said cap assemblies 404 can be configured to provide and watch space 442 (Figure 17).The said space 442 of watching can make also moulding to allow the imaging len (not shown) to move along said flow cell 200 and the direction Dx (Figure 17) above said flow cell 200 by certain size.

In the embodiment shown, said cap assemblies 404 be said relatively plate structure 406 or supporting structure 402 between open position (shown in figure 16) and make-position (shown in figure 17) movably.At said open position, said cap assemblies 404 is drawn back or is withdrawn to allow getting into regional 422 (shown in figure 18) of being written into of said support 400, so that said fluidic hardware 300 can be removed or be inserted into the said zone 422 that is written into from the said zone 422 that is written into.In said make-position, said cap assemblies 404 is installed to the top of said fluidic hardware 300.In concrete embodiment, said cap assemblies 404 is set up in said make-position and is connected with the fluid of said fluidic hardware 300 and said flow cell 200 is pressed on the said supporting structure 402.

Shown in figure 16, in some embodiments, said support 400 comprises coupling mechanism 450, so that keep said cap assemblies 404 in said make-position.For example, said coupling mechanism 450 can comprise the element 452 (it comprises the button 453 that is coupled to a pair of lock opening 456 and 458) that the operator controls.Said coupling mechanism 450 also comprises a pair of lock termination 454 and 455 of giving prominence to from the matching surface 460 of said cover housing 435.Said cover housing 435 can be biased into said open position through spring element 464 and 466.When said cap assemblies 404 during by individual or the said make-position of machine shift-in, said lock termination 454 and 455 is respectively inserted into said lock opening 456 and 458 and the element 452 of the said operator's control of clamping.Will be with the said open position of said cap assemblies 404 shift-ins, said individual or machine can pass through, and for example, inwardly press said button 453 and start said button 453.Because said cover housing 435 is biased through said spring element 464 and 466, said cover housing 435 rotates away from said panel 424 (Figure 17) around said binding site 437 and 439.

In substituting embodiment, said coupling mechanism 450 can comprise other elements, so that said cap assemblies 404 is remained on said make-position.For example, said lock termination 454 and 455 is replaceable is magnetics or forms the element of interference fit with opening.

Figure 18 is the radiating module 416 of said supporting structure 402 and the isolated skeleton view of said scatterer 414.Said radiating module 416 can be configured to the temperature at the said flow cell 200 of preset time section inner control.For example, said radiating module 416 can be configured to the temperature that improves said flow cell 200, so that the DNA in the said sample can sex change.In addition, said radiating module 416 can be configured to removal heat energy, thereby reduces the temperature of said flow cell 200.As shown in the figure, said base 420 comprises by certain size to be made and the basal plane 430 of moulding to engage with said flow cell 200 (Fig. 5).Said basal plane 430 is towards the direction along said Z axle.Said base 420 also can comprise a plurality of alignment members 431-433 that are provided with around said basal plane 430.In the embodiment shown, said alignment members 431-433 has the fixed position with respect to said basal plane 430.Said alignment members 431-433 has to be configured to accordingly and engages said flow cell 200 and be convenient to be provided with the reference plane that said flow cell 200 is used to form images.For example, the said reference plane of said alignment members 431-433 can be towards the said XY planar in edge direction separately, and just in this point, it can be configured to the said flow cell 200 of restriction and move along said XY planar.Said supporting structure 402 can comprise said at least a portion that is written into zone 422.The said zone 422 that is written into can partly be limited the said reference plane of said basal plane 430 and said alignment members 431-433.

Figure 19 and 20 illustrates can be with the alignment components 470 of said support 400 uses according to an embodiment.Figure 19 is the plat of said support 400, and wherein said cover housing 435 is shown so that said alignment components 470 to be shown with sectional view.Figure 20 is the skeleton view of said support 400, and wherein said cap assemblies 404 is in said open position.(in Figure 19 and 20 liang of figure, said panel 424 (Figure 17) is deleted, only supplies illustrative purposes.)

In Figure 19 and 20, said fluidic hardware 300 is written into said being written in the zone 422.When said fluidic hardware 300 is written into, said flow cell 200 is placed to that said basal plane 430 (Figure 18) is gone up and said alignment members 432,433 and 431 is advanced through the said recess 320,322 and 321 (Fig. 9 and 10) of said chuck 302.More specifically, can be along the said device window 315 (Fig. 9) of said shell surface 305 by sized and moulding greater than the periphery of said basal plane 430.Thus, said chuck 302 or shell 304 can be allowed to fall said basal plane 430 around, but said flow cell 200 is prevented from falling said basal plane 430 next doors.So, the said pond face 258 of said flow cell 200 can be crushed on the said basal plane 430, so that the temperature of the said flow cell 200 of said radiating module 416 may command.Be installed to 430 last times of said basal plane when said flow cell 200, the said reference plane 381-383 (Figure 11) of said chuck 302 is crushed on the said pond face 256 (Figure 11).At this moment, the plane, pond of the said flow cell 200 of said sample 205 extensions in edge can be aimed at the object plane of said imaging system substantially.

In the embodiment shown, saidly be written into regionally 422 the time when said fluidic hardware 300 is written into, the identification reader of said mensuration system can detect the information from said identification XMTR 336 (Figure 10).For example, said support 400 can comprise the identification reader (not shown) of closing on said identification XMTR 336, being positioned at said plate structure 406.Identification is read and can be occurred in before said cap assemblies 404 is installed on the said fluidic hardware 300.

With reference to Figure 19 and 20, said alignment components 470 comprises that common cooperation is with the directed and various elements of the said flow cell 200 in location to form images.For example, said alignment components 470 comprises registration arm 472 movably and operationally is coupled to the actuator 474 of said registration arm 472.As shown in the figure, said actuator 474 comprises bar 476 and the pin element 478 that is coupled to said cover housing 435.In the embodiment shown, said bar 476 is around turning axle R ₂(Figure 19) rotatable.Said bar 476 can be L shaped, has first extn 480 and second extn 482 that is configured to the said registration arm 472 of engagement that are configured to the said pin element 478 of engagement.Said registration arm 472 also is around turning axle R ₃(Figure 19) rotatable and comprise finger piece 484 with end of engagement 486.Said alignment components 470 also comprises the biasing element 490 (for example whisker) that meshes said finger piece 484.Said end of engagement 486 is configured to the said chuck 302 of the said fluidic hardware 300 of engagement.In substituting embodiment, said end of engagement 486 can be configured to the said flow cell 200 of direct engagement.

Said alignment components 470 is in engagement and arranges and in Figure 20, be in and draw back layout in Figure 19.When said alignment components 470 is in said drawing back when arranging, said registration arm 472 is in retracted position and when said alignment components 470 was in said engagement layout, said registration arm 472 was in offset position.Aim at said flow cell 200 in the zone 422 said being written into, said alignment components 470 arranges that from said drawing back changing to said engagement arranges.For example, when said cover housing 435 moves to said open position (shown in figure 20), said first extn 480 of the said bar 476 of said pin element 478 engagements makes said bar 476 by counterclockwise centering on said axle R ₂Rotation (shown in figure 19).Said cover housing 435 can be maintained at said open position through said spring element 464 and 466 (Figure 16).When said bar 476 rotated, said second extn 482 was around said axle R ₂Rotation is also meshed said registration arm 472.Said registration arm 472 is in the direction of the clock around said axle R ₃Rotation (shown in figure 19).When said registration arm 472 was rotated, said registration arm 472 was moved to said retracted position.When moving on to said retracted position, said end of engagement 486 moves away from the said reference plane of said alignment members 431-433.

Make said alignment components 470 arrange that from said drawing back being altered to said engagement arranges, said cover housing 435 can be towards the top that said fluidic hardware 300 rotates and be installed to said flow cell 200.When said cover housing 435 when said fluidic hardware 300 moves, said pin element 478 is away from said first extn 480 rotation of said bar 476.When said second extn 482 moved away from said registration arm 472, the potential energy that is stored in said biasing element 490 can cause said registration arm 472 by rotation counterclockwise, makes said end of engagement 486 be pressed on the said chuck 302.Just in this point, said registration arm 472 is moved to said offset position.When being moved to said offset position, said end of engagement 486 moves towards the said reference plane of said alignment members 431-433.

Figure 21 is that the said end of engagement 486 when said registration arm 472 is pressed in the said chuck said enlarged view that is written into fluidic hardware 300 described in the zone 422 of 302 last times.Said end of engagement 486 can be configured to and in said XY plane, move between said retracted position and the said offset position.When said end of engagement 486 moves and be pressed in 302 last times of said chuck towards said offset position, said end of engagement 486 provides the power F to said chuck 302 _XY Said chuck 302 can be pressed in the said reference plane of said alignment members 431-433 along said XY plane displacement and/or with said flow cell 200.Said power F _XYHave X component and Y component.Said X component can be pressed in said flow cell 200 on the said alignment members 431, and said Y component can be pressed in said flow cell 200 on said alignment members 432 and 433.Just in this point, said alignment members 431 can stop moving of the said X-direction in said flow cell 200 edges, and said alignment members 432 and 433 can stop said flow cell 200 moving along said Y direction.

Be altered to before said engagement arranges in said alignment components 470, the said inlet entrance and exit passage 346 of said lid member 306 and 344 can be respectively and said inlet entrance and exit 224 and 222 (Fig. 7) rough alignment of said flow cell 200.Be altered to after said engagement arranges in said alignment components 470, said inlet entrance and exit passage 346 and 344 with said inlet entrance and exit 224 and 222 effectively (or operationally) aim at pass wherein so that fluid can flow effectively.

Therefore, said cap assemblies 404 can operationally be coupled to said alignment components 470, so that step or action can make the said fluidic hardware 300 of said alignment components 470 engagements.More specifically, when said cap assemblies 404 was installed to the said device top that is in said make-position, said actuator 474 moved said registration arm 472 to said offset position.At said offset position, the said flow cell 200 of said registration arm 472 supportings is against the said reference plane of the said alignment members 431-433 that is in a fixed position along said XY plane.When said cap assemblies 404 was in said make-position, the said top of watching space 442 (Figure 17) can be placed in said flow cell 200 was so that imaging len can move with the said flow passage 206 that forms images along said flow cell 200.Along with said cap assemblies 404 moves to said open position, said actuator 474 moves to said retracted position with said registration arm 472.Yet in the embodiment shown, when said registration arm 472 was withdrawn, said flow cell 200 remained on original position.Therefore, said flow cell 200 can be relocatable with respect to various elements.For example, when said lid member 306 was in said installation site, said flow cell 200 can be relocatable with respect to said lid member 306 and said packing ring 342.Said flow cell 200 also can be relocatable with respect to said cap assemblies 404 and said basal plane 430.

In some embodiments, said alignment components 470 can be by predetermined sequential operation with said cap assemblies 404.For example, in concrete embodiment, before said cap assemblies 404 arrived said make-position, said registration arm 472 was configured to the said flow cell 200 of supporting against the said alignment members 431-433 that is in said fixed position.When said cap assemblies 404 arrived said make-position, said cap assemblies 404 can be convenient to said flow cell 200 is pressed on the said basal plane 430 and also said inlet entrance and exit passage 346 and 344 is pressed on said inlet entrance and exit 224 and 222.Usually, said basal plane 430 was located said flow cell 200 in the z dimension after, said alignment components 470 can be configured to the said flow cell 200 in location in x and y dimension.In addition, alignment components can be configured to and in x and y dimension, in the z dimension, locate said flow cell 200 earlier then.Therefore, the aligning in x, y and z dimension can respond single step or the action that the user takes and one after the other and by various orders takes place.

In substituting embodiment, said alignment components 470 can be not as indicated above operationally is coupled to said cap assemblies 404.On the contrary, said alignment components 470 can independently of one anotherly operate with said cap assemblies 404.Just in this point, perhaps the individual need carry out a plurality of steps to aim at said flow cell 200 and the said flow cell 200 of jet ground coupling.For example, said alignment components 470 can be started separately by the individual, thereby moves said registration arm 472 to aim at said flow cell 200.After said flow cell 200 was aimed at, said individual can reduce said cap assemblies 404 again to said flow cell 200.In addition, said alignment components 470 can comprise the extra and/or miscellaneous part except that above-mentioned those parts.

Figure 22 is the isolated skeleton view that is in the said cap assemblies 404 of said make-position.Figure 22 illustrates said size of watching space 442.As shown in the figure, said cover housing 435 can have top surface 492.Saidly watch the depth D that space 442 can have from said top surface 492 to said fluidic hardware 300 or said flow cell 200 records _PThe said space 442 of watching also can have the width W that records along said Y axle ₆With the length L that records along said X axle ₆The said length and width height in space 442 of watching can be made by certain size, moves above said flow cell 200 so that the imaging len (not shown) can be passed wherein.More specifically, imaging len can get into the said space 442 and mobile above said flow cell 200 along the direction of said X axle of watching through inspection window 443.

Figure 23 is the cross-sectional view of the said cap assemblies 404 got along the line 23-23 among Figure 22.In the embodiment shown, said cap assemblies 404 can comprise a plurality of compression arms 494 and 496.Said compression arm 494 and 496 is configured to the force of compression F that provides respectively to the said shell surface 303 of said fluidic hardware 300 _C1And F _C2In the embodiment shown, said compression arm 494 and 496 is pressed onto on the said chuck 302.Yet in substituting embodiment, said compression arm 494 and 496 can be pressed onto on the said flow cell 200.

Said force of compression F _C1And F _C2Push the said shell 304 of said fluidic hardware 300, thereby the said pond face 256 (Fig. 9) of said flow cell 200 is pressed onto on the said radiating module 416.Just in this point, said flow cell 200 can keep contacting closely with said basal plane 430, in order to transferring heat energy betwixt.In the embodiment shown, said compression arm 494 and 496 runnings independently of one another.For example, said compression arm 494 and 496 each operationally be coupled to compression spring 495 and 497 separately.

Shown in figure 23, said compression arm 494 and 496 extends towards said space 442 and the said zone 422 that is written into watched.When said cap assemblies 404 moves on to said make-position, said compression arm 494 and 496 engageable said shell surfaces 303.Because said compression arm 494 and 496 is pressed onto on the said shell surface 303, can make said compression arm 494 center on a R with 496 from the resistance of said shell surface 303 ₄And R ₅Rotation.In the said compression spring 495 and 497 each all can resist the rotation of compressing arm separately, thereby the corresponding force of compression F to said shell surface 303 is provided _CTherefore, the relative to each other independent biasing of said compression arm 494 and 496.

Figure 24 is the isolated skeleton view of the stream sending component 500 of said cap assemblies 404 (Figure 16).Said stream sending component 500 comprises manifold body 502 and upstream and downstream flow line 504 and 506.Shown in figure 16, said manifold body 502 can be extended between said shell leg 436 and 438.Turn back to Figure 24, said flow line 504 and 506 respectively body port 508 and 510 by mechanically and jet be coupled to said manifold body 502.Said flow line 504 and 506 also comprises and is configured to the said inlet entrance and exit passage 346 that is inserted into said packing ring 342 and 344 pipe end 514 and 516.

Shown in figure 24, said stream sending component 500 with respect to said packing ring 342 in the installation site.In said installation site, said pipe end 514 and 516 is inserted into said entrance and exit passage 346 and 344 respectively, passes said flow cell 200 so that fluid can flow.In addition, in said installation site, said stream sending component 500 can be pressed in said packing ring 342 (Fig. 9) on the said flow cell 200, so that fluid connects by sealing effectively.For this reason, said stream sending component 500 can comprise bias spring 520 and 522.Said bias spring 520 and 522 is configured to the inside that is pressed onto said cover housing 435 (Figure 16) and the power F to said packing ring 342 is provided _C3Said coupling mechanism 450 (Figure 16) can be so that keep the sealing to said packing ring 342.

Therefore, said cap assemblies 404 can be pressed onto on the said shell 304 of said fluidic hardware 300 three independent point of compression.More specifically, when by said pipe end 514 and 516 engagements, said packing ring 342 can constitute the first point of compression P ₁(shown in figure 24), and said compression arm 494 and 496 can be at the second and the 3rd point of compression P ₂And P ₃The said fluidic hardware 300 of (shown in figure 23) contact.Shown in Figure 22-24, said three point of compression P ₁-P ₃Distribute around said flow cell 200.In addition, said cap assemblies 404 is at said point of compression P ₁-P ₃Said force of compression F is provided independently _C1-F _C3Just in this point, said cap assemblies 404 can be configured to the uniform substantially force of compression that provides to said fluidic hardware 300, so that said flow cell 200 is pressed onto on the said basal plane 430 equably and jet connects by sealing with anti-leak.

Figure 25 is a kind of block diagram of localization method 530 of the fluidic hardware that is used for sample analysis.Said method 530 is included in dismountable fluidic hardware (seeing 532) is set on the basal plane.Said fluidic hardware can be similar to fluidic hardware mentioned above 300.For example, said fluidic hardware can comprise spatial accommodation, be positioned at the flow cell and the packing ring of said spatial accommodation.Said flow cell can and can be relocatable with respect to the said packing ring in the said object plane along the extension of the object plane in the said spatial accommodation.Said method 530 also is included in the said spatial accommodation but on said basal plane, moves said flow cell, so that the entrance and exit passage rough alignment (seeing 534) of the entrance and exit of said flow cell and said packing ring.Move operation 534 can comprise that the startup localizer arm is to be pressed onto said flow cell on the said alignment members.

Figure 26 is a kind of block diagram of localization method 540 of the fluidic hardware that is used for sample analysis.Said fluidic hardware can be similar to fluidic hardware mentioned above 300.Said method 540 comprises providing to have device outer case, comprise spatial accommodation and be positioned at the fluidic hardware (seeing 542) of relocatable flow cell of said spatial accommodation.Said device outer case can comprise the recess that is close to said spatial accommodation.Said method also comprises said fluidic hardware is arranged on the supporting structure with alignment members (sees 544).Said alignment members can be inserted into through corresponding recess.In addition, said method 540 can be included in and move said flow cell (seeing 546) in the said spatial accommodation.When said flow cell moved in said spatial accommodation, said alignment members can mesh the edge of said flow cell.Move operation 546 can comprise that the startup localizer arm is to be pressed onto said flow cell on the said alignment members.

Figure 27 is a kind of block diagram that is used for respect to the method 550 of orthogonal X, Y and Z axle location sample area of explanation.Said method 550 comprises provides alignment components (seeing 552).Said alignment components can be similar to alignment components mentioned above 470.More specifically, said alignment components can comprise the movably registration arm with end of engagement.Said registration arm can be the withdrawal and offset position between movably.Said method 550 also comprises fluidic hardware is arranged on towards along on the basal plane of the direction of said Z axle and be arranged on a plurality of towards along the XY planar separately between the reference plane of direction (seeing 554).In addition, said method 550 comprises that also mobile said registration arm is to said offset position (seeing 556).Said registration arm can be pressed onto said device on the said reference plane, so that said device is maintained at the fixed position.

Figure 28-37 illustrates the various functional components of fluid storage system 1000 (Figure 28).Said storage system 1000 is configured to the various fluids that can between predetermined test period, use of storage and regulates said fluidic temperature.Said storage system 1000 can be sealed through said workstation1 60 (Fig. 2) use and by said shell 162 (Fig. 3).Shown in figure 28, said storage system 1000 comprises shell 1002, and said shell 1002 has base shell (or first shell) 1004 and the top enclosure (or second shell) 1006 that is coupled and limits system chamber 1008 betwixt.Said shell 1002 also can comprise system door 1010, and said system door 1010 is configured to opens and provide the approach that gets into said system chamber 1008.Still as shown in the figure, said storage system 1000 can comprise the temperature-controlling module 1012 at the rear portion that is coupled to said shell 1002 and be set at the elevator drives motor 1014 on the said top enclosure 1006.

Figure 29 is the cross-sectional side view of said storage system 1000 and illustrates in greater detail said system chamber 1008.Said storage system 1000 also can comprise reacted constituent pallet (or reacted constituent storage unit) 1020 and comprise that the fluid of hoisting appliance 1024 pipettes assembly 1022.Said pallet 1020 is configured to and supports a plurality of be used to deposit fluidic pipeline or containers.Said hoisting appliance 1024 comprises said drive-motor 1014 and is configured to the parts that pipette assembly 1022 along the two-way mobile said fluid of said Z axle.In Figure 29, said pallet 1020 is positioned at fluid and pipettes the position, so that the fluid that said pallet 1020 keeps can be pipetted and be transported to, fluidic hardware for example is in order to carry out required reaction or in order to wash the said flow passage of said fluidic hardware.

Still as shown in the figure, said temperature-controlling module 1012 can be given prominence to and get into said system chamber 1008.Said temperature-controlling module 1012 is configured to control or regulates the temperature in the said system chamber 1008.In the embodiment shown, said temperature-controlling module 1012 comprises thermoelectric refrigeration (TEC) assembly.

Figure 30 is the said skeleton view that pipettes assembly 1022.As shown in the figure, the said assembly 1022 that pipettes can comprise a pair of relative guide rail 1032 and 1034.Said relative guide rail 1032 and 1034 is configured to reception and guides said pallet 1020 to said fluid to pipette the position, and is shown in figure 29.Said guide rail 1032 and 1034 can comprise along the outstanding functional component or the ridge 1035 of said guide rail 1032 and 1034 longitudinal extensions.Said guide rail 1032 and 1034 is configured to and is fixed in said base shell 1004 (Figure 28).The said assembly 1022 that pipettes also comprises the supporting beam (or column) 1036 and 1038 that extends along said Z-direction.The said guide plate 1040 that pipettes assembly can be with the distance B that raises _ZBeing coupled to said supporting beam 1036 and 1038 also stretches out along said XY plane thus.In the embodiment shown, said guide plate 1040 is fixed in said supporting beam 1036 and 1038.

Said hoisting appliance 1024 comprises structural supports 1041 and 1042, leading screw 1044 that between said structural supports 1041 and 1042, extends and the Stage microscope assembly 1046 that comprises delivery platform 1048.Said structural supports 1041 and 1042 is fixed in the two ends of said supporting beam 1036 and 1038 and is configured to and in operational process, supports said hoisting appliance 1024.The screw thread of said leading screw 1044 operationally is coupled to said Stage microscope assembly 1046, and when rotating with the said leading screw 1044 of box lunch, said Stage microscope assembly 1046 moves (being represented by double-headed arrow) along said Z axle by rectilinear direction.

Said delivery platform 1048 is configured to supporting suction pipe 1050 arrays.Said suction pipe 1050 can be configured to the systems pumps (not shown) fluid that the guiding fluid flow passes said suction pipe 1050 and be communicated with.As shown in the figure, said suction pipe 1050 comprises the distal portions 1052 that is configured to the composition hole 1060 (shown in figure 31) that is inserted into said pallet 1020.Said distal portions 1052 passes the respective openings 1053 of said guide plate 1040 and extends.

Said hoisting appliance 1024 is configured to be drawn back level and is transferring and move said suction pipe 1050 between the level.Said when transferring level (shown in Figure 50 and 51), the said distal portions 1052 of said suction pipe 1050 is inserted into said composition hole 1060 with from wherein pipetting fluid.When drawing back level, said distal portions 1052 is shifted out said pallet 1020 fully, so that said pallet 1020 can be moved out of said system chamber 1008 (Figure 28), and does not damage said suction pipe 1050 or said pallet 1020 said.More specifically, when the said leading screw 1044 of said drive-motor 1014 rotations, said Stage microscope assembly 1046 moves with the direction by the sense of rotation decision of said leading screw 1044 along said Z axle.Therefore, said transmission platform 1048 moves along said Z axle, supports said suction pipe 1050 simultaneously.If said delivery platform 1048 advances towards said guide plate 1040, said distal portions 1052 passes the respective openings 1053 of said guide plate 1040 and slides towards said pallet 1020.Said guide plate 1040 is configured to and prevents that distal portions 1052 from becoming no longer aim at said composition hole 1060 before it is inserted into said composition hole 1060.When said hoisting appliance 1024 moves apart said Stage microscope assembly 1046 on said guide plate 1040; It is big that distance between said delivery platform 1048 and the said guide plate 1040 (Δ Z) becomes, and draws back from the said composition hole 1060 of said pallet 1020 until said distal portions 1052.

Figure 30 illustrates the attachment feature that is used to move said hoisting appliance 1024.For example, said Stage microscope assembly 1046 also can comprise guide pin 1058 (still shown in figure 29), and said guide pin 1058 is fixed in said delivery platform 1048 and extends from said delivery platform 1048 with the direction that is parallel to said suction pipe 1050.Said guide pin 1058 also extends through the corresponding opening 1053 of said guide plate 1040.In the embodiment shown, said guide pin 1058 is bigger than the distance that said suction pipe 1050 extends, so that before said suction pipe 1050 is inserted into said composition hole 1060, said guide pin 1058 arrives said pallet 1020.Therefore; If said pallet 1020 is not aimed at respect to said suction pipe 1050; Said guide pin 1058 can mesh said pallet 1020 and adjust the position of said pallet 1020, so that said composition hole 1060 corresponding suction pipe 1050 of correct aligning before said suction pipe 1050 is inserted into wherein.

Except that mentioned above, the said assembly 1022 that pipettes can comprise position transducer 1062 and positioned sensor (not shown).Said position transducer 1062 is configured to the label 1063 (shown in figure 34) that receives said pallet 1020, with confirm said pallet 1020 be present in the said system chamber 1008 (Figure 28) and at least rough alignment in order to receive said suction pipe 1050.Said positioned sensor can detect the label 1064 of said Stage microscope assembly 1046, to confirm the level of said Stage microscope assembly 1046.If said label 1064 does not also reach threshold level along said Z axle, said positioned sensor can be linked up with said workstation1 60 (or other mensuration systems), does not prepare to remove to notify the said pallet 1020 of user.Said workstation1 60 can prevent that also the user from opening said system door 1010.

In addition, when the said distal portions 1052 of said suction pipe 1050 was inserted into said composition hole 1060 at first, said suction pipe 1050 can pierce through the protective foil that covers said composition hole 1060.In some cases, said paper tinsel can the said suction pipe 1050 of clamping.When said suction pipe 1050 subsequently when draw back in corresponding composition hole 1060, said pallet 1020 is lifted to power in the clamping of said protective foil together.Yet in the embodiment shown, said ridge 1035 is configured to holding tray base 1070 (Figure 31) and prevents that said basetray 1070 is lifted with the direction along said Z axle.For example, the lip 1071 that said ridge 1035 can the said basetray 1070 of clamping.

Figure 31-34 illustrates the different views of said pallet 1020.Said pallet 1020 is configured to a plurality of compositions of supporting hole 1060.Said composition hole 1060 can comprise various reacted constituents; For example, but be not limited only to one or more samples, polysaccharase, primer, denaturing agent, be used for linearizing DNA the linearizing mixture, be applicable to concrete mensuration (as bunch the amplification or a SBS) enzyme, Nucleotide, cleavage mixture, oxidation protection agent and other reagent.In some embodiments, said pallet 1020 can hold predetermined all the essential fluids of mensuration of execution.In concrete embodiment, said pallet 1020 can be contained in and generate sample (for example DNA bunch) in the flow cell and carry out all essential reacted constituents of sample analysis (for example SBS).Can under the situation that does not remove or change any described composition hole 1060, carry out said mensuration.

Said composition hole 1060 comprises quadratic component hole 1060A (shown in Figure 35-36) and tubulose composition hole 1060B (shown in figure 37).Said pallet 1020 comprises basetray 1070 and the pallet cover 1072 that is coupled to said basetray 1070.Shown in Figure 31 and 32, said pallet cover 1072 comprises handle 1074, and said handle 1074 is pressed certain size and made and moulding, with the user's handling by said pallet 1020.Said pallet cover 1072 also can comprise and grips recess 1076, said sized and the moulding that grips recess 1076 by the one or more fingers that hold said user.

Shown in Figure 31 and 32, said pallet cover 1072 can comprise a plurality of and corresponding composition hole 1060 aligned pores 1080.Said pore 1080 is plastic to guide said suction pipe 1050 (exemplary suction pipe 1050 is shown in figure 31) to get into corresponding composition hole 1060.Shown in figure 32, said pallet cover 1072 also comprises pin hole 1082, and said pin hole 1082 is by the sized of holding said guide pin 1058 and moulding.Said guide pin 1058 be configured to when said guide pin 1058 with non-alignment so near and when getting into said pin hole 1082, the slight adjustment to the position of said pallet 1020 is provided.Still as shown in the figure, said pallet 1020 can comprise along the identification tag 1084 on the surface of said pallet cover 1072.Said identification tag 1084 is configured to be read device and detects, so that the fluidic information of holding about said composition hole 1060 to be provided to said user.

Shown in Figure 33 and 34, said pore 1080 is limited at the 1073 outstanding edges 1086, surface from said pallet cover 1072 at least in part.Said edge 1086 mixes to prevent the accidental fluid that deposits on the said pallet cover 1072 from said surperficial 1073 outstanding segment distances accidentally.Equally, said identification tag 1084 can be attached to the bossing 1088 of said pallet cover 1072.Said bossing 1088 also can protect said identification tag 1084 to touch fluid accidentally.

Figure 35 shows the cross-sectional side view of said composition hole 1060A, and Figure 36 shows the bottom perspective view of said composition hole 1060A.As shown in the figure, said composition hole 1060A comprises the first relative end and second end 1091 and 1092 and the storage 1090 (Figure 35) that extends betwixt.Said storage 1090 has depth D _R(Figure 35), said depth D _RAlong with said storage 1090 extends to said first end 1091 and increases from said second end 1092.Said composition hole 1060A is configured to the darker part that said suction pipe 1050 is contained in said storage 1090.Shown in figure 36, said composition hole 1060A comprises a plurality of lip-deep protuberances 1094 that are configured to lean against said basetray 1070 along outside surface.

Figure 37 is the skeleton view of said composition hole 1060B.As shown in the figure, said composition hole 1060B also can comprise the protuberance 1096 of the outside surface of a plurality of said composition hole 1060B of centering on.Said composition hole 1060B longitudinally axle 1097 extends and has along with said composition hole 1060B extends lengthwise into bottom 1098 and tapered profile.Said bottom 1098 can have flat substantially surface.

Figure 61 explains a kind of method 960 that is used to carry out the biological or chemical assay determination.In some embodiments, said mensuration can comprise that sample generates scheme and sample analysis scheme.For example, said sample generates scheme and can comprise that generating DNA bunch and said sample analysis scheme through the bridge-type amplification can comprise and utilize order-checking (SBS) analysis while synthesize of said DNA bunch.Sample generates to operate to measure at common with sample analysis and carries out in system's (like said mensuration system 100 or said workstation1 60) and need not user intervention between the said operation.For example, the user can be written into said mensuration system with fluidic hardware.Said mensuration system can generate the sample that is used to analyze automatically and carry out the step of said analysis.

About Figure 61, said method 960 is included in the fluidic hardware with sample area and contains and sets up fluid between the reacted constituent storage unit of a plurality of differential responses compositions and connect (seeing 962).Said reacted constituent can be configured to and be used to carry out one or more mensuration.Said fluidic hardware can be, for example, and fluidic hardware 300 mentioned above or flow cell 200.In some embodiments, said sample area comprises a plurality of fixing reacted constituents (for example primer) on it.Said storage unit can be, for example, and storage unit 1020 mentioned above.Said reacted constituent can comprise being configured to and be used to generate the sample generation composition of said sample and be configured to the sample analysis composition that is used to analyze said sample.In concrete embodiment, said sample generates composition and comprises the reacted constituent that is used to carry out bridge-type amplification mentioned above.In addition, in concrete embodiment, said sample analysis composition comprises the reacted constituent that is used to carry out SBS analysis mentioned above.

The said sample area that said method 960 also is included in said fluidic hardware generates sample (seeing 964).Generating run 962 can comprise makes different samples generate reaction conditions that composition flows into said sample area and control said sample area to generate said sample.For example, thermal cycler can be used so that nucleic acid hybridization.Yet, if necessary, can use isothermal method.In addition, but said flow rate of fluid Be Controlled, to allow hybridization or other required chemical reactions.In concrete embodiment, said generating run 962 comprises and carries out a plurality of bridge-type amplification cycles, to generate DNA bunch.

The exemplary arrangement of bridge-type amplification can comprise following step.Flow cell is set up with reacted constituent storage unit fluid and is communicated with.Said flow cell comprises and has adhered to the right one or more surfaces of primer.The solution contact solid carrier that contains not homotactic target nucleic acid mixture.Said target nucleic acid can have the common priming site, and the lip-deep said primer of said priming site and said flow cell is to complementation, so that said target nucleic acid combines the first right primer of the lip-deep said primer of said flow cell.The extension solution that contains polysaccharase and Nucleotide can be introduced into said flow cell, so that formed by the extension of said first primer with target nucleic acid complementary first amplified production.Said extension solution can be removed and replace with denaturing soln.Said denaturing soln can comprise chemical denaturant, like sodium hydroxide and/or methane amide.Consequent sex change condition discharges the former chain of said target nucleic acid, and it then can be through removing said denaturing soln and removing from said flow cell with the replacement of said extension solution.In the presence of said extension solution; Said first amplified production that is adhered to said carrier then can with the second right primer hybridization of said primer that adheres to said flow cell surface, and second amplified production that comprises with the adherent nucleotide sequence of the said first amplified production complementary can extending to form through said second primer.Said denaturing soln and the conveying repeatedly of extending solution can be used for forming target nucleic acid bunch at the lip-deep discrete location of said flow cell.Though such scheme utilizes chemically denatured as demonstration, will understand and also can carry out thermally denature similar primer and target nucleic acid.The further describing of amplification method that can be used for producing the immobilized nucleic acids molecular clustering is provided in, and for example U.S. Patent number 7,115, and 400; US publication 2005/0100900, WO 00/18957 or WO98/44151 (wherein each incorporates this paper into way of reference).

Said method 960 also comprises the said sample (seeing 966) of analyzing said sample area.Usually, said analysis operation 966 can comprise any detectable characteristic that detects said sample area.In concrete embodiment, said analysis operation 966 comprises makes at least a sample analysis composition flow into said sample area.Said sample analysis composition can react with said sample, with detectable signal on the optics that indication dependent event (or required reaction) is provided.For example, said sample analysis composition can be the fluorescently-labeled Nucleotide that uses in the SBS analytic process.When exciting light incided on the said sample that mixes fluorescently-labeled Nucleotide therein, said Nucleotide can send the optical signal of indication Nucleotide type (A, G, C or T), and said imaging system can detect said optical signal.

The utilization of a kind of useful especially SBS scheme has the modified ribonucleotide of removable 3 ' end sealing, for example, and described in WO 04/018497, U.S. 2007/0166705A1 and the U.S. 7,057,026 (wherein each incorporates this paper into way of reference).SBS reagent can be transported to the flow cell that has adhered to target nucleic acid repeatedly circularly, for example, because the bridge-type that preceding text are set forth amplification scheme.Said nucleic acid bunch can use linearizing solution to be converted to the form of strand.Said linearizing solution can comprise, for example, and the restriction enzyme of a chain of each bunch of ability cracking.Concerning restriction enzyme or nickase, other cleavage method can be used as a kind of selection, comprises especially chemical cracking (for example with the periodate cleavage diol bond); Through with restriction endonuclease (NEB for example; Ipswich, the item number that MA, USA provide are ' USER ' of M5505S) cracking, through being exposed to the abasic site cracking that heat or alkali carry out; Mix in addition the cracking of the ribonucleotide of the amplified production of forming by deoxyribonucleotide, the photodestruction of peptide linker or cracking.After the linearizing step, to the condition of target nucleic acid to be checked order, said sequencing primer can be delivered to said flow cell in sequencing primer hybridization.

Said flow cell can contact with containing the modified ribonucleotide and the fluorescently-labeled SBS extension reagent that have removable 3 ' end sealing then under certain condition, will hybridize the primer extension to each target nucleic acid to add through mononucleotide.Have only a mononucleotide to be added into each primer; Because in case described modified ribonucleotide has been incorporated into and the ever-increasing polynucleotide chain of template zone complementary that is checking order; Just do not have to guide that further sequence extends is free 3 '-the OH group, so polysaccharase can not add more Nucleotide.Said SBS extends reagent and can remove and replace to contain the scanning reagent of the composition of the said sample of protection under radiation excitation.The description that is used to scan the exemplary composition of reagent is shown in u. s. published US 2008/0280773 A1 and United States serial 13/018,255 (wherein each incorporates this paper into way of reference).Then, in the presence of scanning reagent, the nucleic acid that fluoroscopic examination is extended.In case detected fluorescence, said 3 ' end sealing can use the deblocking reagent that is applicable to used blocking groups to remove.Can be used for the description of the exemplary deblocking reagent of blocking groups separately and be shown in WO04018497, US 2007/0166705A1 and US7057026 (wherein each incorporates this paper into way of reference).Said deblocking reagent can be washed off, lets target nucleic acid hybridization to the extension primer that contains 3 ' OH group, and said 3 ' OH group can add more Nucleotide now.Therefore, can repeat to add and extend reagent, scanning reagent and conciliate the circulation of closed reagent and between said step one or more, clean alternatively, until obtaining required sequence.When each of said modified ribonucleotide all has the different markers (alkali that its known correspondence is concrete) that adheres to it, can carry out above-mentioned circulation by the single reagent supplying step that extends of each recycle.Said different markers is convenient to distinguish that each mixes the alkali that adds during the step.Substituting ground; Each circulation can comprise independent extension reagent supplying step, succeeded by independent scanning reagent supplying step and detection, in this case; The two or more of said Nucleotide can have identical mark, and can distinguish based on known sequence of batching products.

Continue the example of flow cell amplifying nucleic acid bunch, said nucleic acid can be read to obtain second through the method that is called terminal pairing order-checking from the other end by further processing.The description of terminal pairing sequence measurement is shown in PCT and announces among WO07010252, PCT patent application serial numbers PCTGB2007/003798 and the U.S. Patent Application Publication US 2009/0088327 (wherein each incorporates this paper into quoting method).In one embodiment; It is following to carry out a series of step: such as preceding text elaboration generate bunch; Such as preceding text the elaboration linearizing; Still such as preceding text elaboration hybridization first sequencing primer and carry out round-robin extension repeatedly, scanning and deblocking, still as the elaboration of preceding text institute through synthesizing the lip-deep said target nucleic acid of the said flow cell of complementary copy " inversion ", linearizing resynthesis chain, hybridize first sequencing primer and carrying out round-robin extension repeatedly, scanning and deblocking.Said inversion step can such as preceding text elaboration be used for the amplification of single-cycle bridge-type through delivery of therapeutic agents and carry out.

Though said analysis operation about concrete SBS scheme such as preceding text as demonstration, understanding other any schemes of other kinds analysis of molecules that are used to check order can be carried out as required.The enlightenment that proposes in view of this paper and about the general knowledge of specific analytical method will be for the suitable modifications that adapts to the said apparatus and method that different analyses does will be conspicuous.

In some embodiments, said method 960 is configured under minimum user intervention, carry out.Said generating run and analysis operation 964 and 966 can carry out with automated manner through the mensuration system.For example, in some cases, the user can only be written into said fluidic hardware and said storage unit, and starts said mensuration system to carry out said method 960.In some embodiments; During said generating run and analysis operation 964 and 966; Said storage unit and said fluidic hardware begin and maintenance fluid connection during whole said analysis operation from said generating run, are fully analyzed until said sample.In other words, said fluidic hardware and said storage unit can all keep fluid to be communicated with after said sample analysis before said sample generates.In some embodiments, said fluidic hardware begins and during whole said analysis operation, is constantly supported by said device support from said generating run, is fully analyzed until said sample.During during this period of time, said device support and imaging len can relative to each other move automatically.When said device support and said imaging len relative to each other moved automatically, said storage unit and said fluidic hardware can keep fluid to be communicated with.In some embodiments, said mensuration system is included in the workstation shell and said generating run and analysis operation 964 and 966 carry out in the workstation shell independently.

Figure 38 is the synoptic diagram according to the optical imaging system 600 of an embodiment formation.Said imaging system 600 comprises optical module 602, light source (or exciting light) module or assembly 604, the flow cell 606 with sample area 608 and imaging detector 610 and 612.Said light source module 604 comprises first and second excitation light sources 614 and 616 that are configured to shine with different excitation spectrums said sample area 608.In concrete embodiment, said first and second excitation light sources 614 and 616 comprise first and second semiconductor light sources (SLS).SLS can comprise photodiode (LED) or laser diode.Yet, in other embodiment, can use other light sources, like laser or Jupiter.Said first and second SLS can have the fixed position with respect to said optical module 602.

As shown in the figure, said optical module 602 can comprise a plurality of opticses.For example, said optical module 602 can comprise lens 623-625, emission light-filter 631, exciting light strainer 635 and mirror 644 and 642.Said optical module 602 can have extra being used to guide said exciting light and/or said radiative optics (like lens, emission light or exciting light strainer, mirror or the like), and its Reference numeral is summarised as 621.Said a plurality of optics is configured to be used for following at least one: (a) the said exciting light of guiding is collected from the emission light of said sample area 608 towards the said sample area 608 of said flow cell 606 or (b).Still as shown in the figure, said imaging system 600 also can comprise the flow system 652 that is communicated with said flow cell 606 fluids and be coupled to said first and second excitation light sources 614 communicatedly and 616 with the central controller 654 of said flow system 652.Said unit 654 is configured to and starts said flow system 652 so that reagent flows into said sample area 608 and after the preset time section, activates said first and second SLS.

For example, Figure 60 explains a kind of method 900 that is used to carry out the biological or chemical assay determination.In concrete embodiment, said mensuration can comprise order-checking (SBS) scheme while synthesizing.Said method 900 comprises the flow passage (seeing 902) that makes reagent flow through flow cell.Said flow cell can have sample area, and said sample area comprises and has the sample that is configured to the biomolecules of said reagent generation chemical reaction.Said method 900 also comprises with first and second semiconductor light sources (SLS) shines said sample area (seeing 904).Said first and second SLS provide first and second excitation spectrums respectively.When being shone by the said first or the 2nd SLS, the said biomolecules of said sample can provide the light emission of indication association reaction.In addition, said method 900 comprises the said light emission (see 906) of detection from said sample area.Alternatively, said method 900 can comprise with respect to imaging len and moves said flow cell and repeat said irradiation and detecting operation 904 and 906 (seeing 908).Shown in Figure 60 and the step of above-illustrated can repeat, to carry out the repeatedly circulation of sequence measurement.

Figure 39 and Figure 40 illustrate the multiple functional component of the mobile control system 700 that forms according to embodiment, can use with said imaging system 600.Said mobile control system 700 comprises optical backplane 702 and is coupled to the sample table 708 of said optical backplane 702 movably.As shown in the figure, said sample table 702 has bearing surface 704 and bottom surface 705.The said Z axial plane in said bearing surface and bottom surface 704 and 705 edges is to opposite direction.The major part that said base plate 702 is configured to the said optics of said optical module 602 (Figure 38) is supported on the said bearing surface 704.Said base plate 702 can be to intercouple movably through intermediate supports 715 and panel 722 with said sample table 708, so that said sample holder 650 can slide along said y-axis shift position and along said X axle substantially around said X and the rotation of Y axle.

Figure 40 is the said intermediate supports 715, electric machine assembly 724 of said sample table 708 (Figure 39) and the isolated skeleton view of platform 726 movably.Said electric machine assembly 724 operationally is coupled to said platform 726 and is configured so that the two-way slip of the said platform 726 said X axles in edge.As shown in the figure, said intermediate supports 715 comprises tail end 728 and imaging end 730.Said intermediate supports 715 can comprise the pin 746 and 748 that closes on said imaging end 730 and give prominence to away from each other along said Y axle.Close on said imaging end 730, said intermediate supports 715 can comprise lens opening 750, and said lens opening 750 is by allowing said imaging len 623 (Figure 38) to extend through wherein sized and moulding.In the embodiment shown, said pin 746 and 748 all has the common line 755 that extends through wherein, and said line 755 also extends through said lens opening 750.

Turn back to Figure 39, said platform 726 is coupled to said bottom surface 705 through said intermediate supports 715.Therefore, the weight of said sample table 708 can be supported by said base plate 702.In addition, said mobile control system 700 can comprise a plurality of aligning devices 733,735,737 and 739 that are configured to the said sample holder 650 in location.In the embodiment shown, said aligning device 733,735,737 and 739 is a micrometrie scale.Said aligning device 733 operationally is coupled to the said tail end 728 of said intermediate supports 715.When said aligning device 733 was activated, said tail end 728 can move along the direction of said Z axle.Therefore, said intermediate supports 715 can center on said pin 746 and 748 (Figure 40), or more specifically, around said line 755 rotations.When said aligning device 735 and 737 was activated, said sample holder 650 can be by indication along said y-axis shift position.When said aligning device 739 was activated, said sample holder 650 can be around being parallel to the turning axle R that said X axle extends ₇Rotation.

Figure 41-42 illustrates the skeleton view and the plat of the said optical backplane 702 that can use with said imaging system 600 (Figure 38) respectively.In some embodiments of said imaging system 600; The one or more of said optics (Figure 38) can have the fixed position in said optical module 602, so that said fixing (or static) optics can not move in the operational process of said imaging system 600.For example, said base plate 702 is configured to the miscellaneous part that supports a plurality of opticses and said imaging system 600.As shown in the figure, said base plate 702 has constituted the incorporate substantially structure of the bearing surface (or surface) 704 that has towards the said Z-direction in edge.In the embodiment shown; Said bearing surface 704 is not continuously slick, but various platform 716-718, pit (or spatial accommodation) 719-721 and the parts spatial accommodation 711-714 that is set to arrange with predetermined configuration said optical module 602 can be arranged.Shown in figure 42, each of said spatial accommodation 711-714 has reference plane 781-784 separately.In some embodiments, said reference plane 781-784 can be convenient to corresponding optics location and remain on the desired position.

Figure 43 and Figure 44 illustrate the front perspective view and the rear portion broken-open perspective view of optics 732 respectively.Shown in figure 43, said optics 732 is with respect to orthogonal axle 791-793 location.Said axle 791 can be like the elaboration of preceding text institute along the terrestrial gravitation direction and/or be parallel to said Z axle extension.In concrete embodiment, said optics 732 is configured to be set in the said parts spatial accommodation 713 (Figure 43) of said base plate 702 (part of said base plate 702 only being shown at Figure 43 and Figure 44).

Said parts spatial accommodation 713 has one or more surfaces that qualification wherein can be held reached at the area of space of optics.These one or more surfaces can comprise the reference plane that is described below.In the embodiment shown, said parts spatial accommodation 713 is the parts chambeies at the said base plate 701 of said base plate 702 internal depth extension.Yet said base plate 702 can otherwise form said parts spatial accommodation.For example, can form the similar fashion in chamber with said base plate 702, said base plate 702 also can have the platform of one or more convexities, the platform of said convexity comprise around and limit the surface of said parts spatial accommodation.Therefore, said base plate 702 is plastic so that said parts spatial accommodation partly or ad hoc to be provided.Said base plate 702 can comprise said reference plane.In substituting embodiment, sidewall can be installed on the said base plate 702 and be configured to and limit said area of space.In addition, other optics that are mounted to said base plate 702 can limit said parts spatial accommodation.As used herein, when element " qualification " parts spatial accommodation, it maybe can be partly to limit said parts spatial accommodation that said element can ad hoc limit said parts spatial accommodation.

Said optics 732 can removably be mounted to the said base plate 702 in the said parts spatial accommodation 713, but can be configured in the operation of said imaging system, keep the fixed position.Yet in substituting embodiment, said optics 732 is not set at the inside of said parts spatial accommodation 713, but can be set at elswhere, on the platform of for example said bearing surface 704.In the embodiment shown, said optics 732 comprises installing device 734 and is configured to reflection and/or transmission ray and passes optics 736 wherein.Said installing device 734 is configured to be convenient to support said optics 736 and said optics 736 is mounted to said base plate 702 by required orientation.Said installing device 734 comprises component holder 738 and operationally is coupled to the biasing element 740 of said retainer 738.

In the embodiment shown, said optics 736 comprises that transmitting optical signal passes the spectral filter that wherein is filtered into predetermined spectrum simultaneously.Yet, in substituting embodiment, can use other optics, for example lens or mirror.As shown in the figure, said optics 736 can comprise that face limits the thickness T of said optics 736 in the opposite direction and betwixt ₃ Optical surface 742 and 744.As shown in the figure, said optical surface 742 and 744 can be to be parallel to each other the continuous slick plane of extending, and makes said thickness T ₃Even substantially.Yet in substituting embodiment, said optical surface 742 and 744 can have other profiles.Said optics 736 can have the edge-of-part 751-754 (Figure 43) of a plurality of qualification peripheries or periphery.Said peripheral ring is around said optical surface 742 and 744.As shown in the figure, said periphery is orthogonal substantially, but in substituting embodiment, can use other geometrical shapies (for example circular).

Said retainer 738 is convenient to support said optics 736 by required orientation.In the embodiment shown, said retainer 738 is configured to the said optical surface 742 of engagement and extends around at least a portion of said periphery, to keep said optics 736.For example, said retainer 738 can comprise the framework extension 758 that wall part 756 and the said periphery (for example said edge-of-part 752 (Figure 43)) from said wall part 756 along said optics 736 are extended.In the embodiment shown, said framework extension 758 can form the carriage that the said optics 736 of restriction moves.More specifically, said framework extension 758 can comprise proximal arm 760 and distal arm 762.Said proximal arm 760 extends from said wall part 756 said edge-of-parts 752 in edge and said axle 791.Said distal arm 762 extends along said edge-of-part 751 from said proximal arm 760.Said distal arm 762 comprises protuberance or the functional component 764 that extends and mesh said optics 736 towards said optics 736.Still as shown in the figure, said retainer 738 can comprise the clamping components 766 that places said framework extension 758 opposites.Said clamping components 766 can cooperate to limit said optics 736 with said framework extension 758 and moves along said axle 793.Said retainer 738 can the said optics 736 of clamping the part of said periphery.

Shown in Figure 43 and 44, said wall part 756 is configured to the said optical surface 742 of engagement.For example, said wall part 756 has the matching surface 770 (Figure 43) towards said optics 736.In some embodiments, said wall part 756 comprises a plurality of positioning function parts 771-773 (Figure 43) along said matching surface 770.Said positioning function parts 771-773 is configured to the said optical surface 742 of the said optics 736 of direct engagement.When said positioning function parts 771-773 directly meshed said optical surface 742, said optical surface 742 (thereby said optics 736) was provided with respect to said retainer 738 by required orientation.Shown in figure 43, the said reference plane 783 of said parts spatial accommodation 713 also comprises a plurality of positioning function parts 761-763.Said positioning function parts 761-763 is configured to the said optical surface 744 of direct engagement.In addition, said positioning function parts 761-763 can be arranged so that usually, each of said positioning function parts 761-763 and said positioning function parts 771-773 corresponding one relatively.

Still shown in figure 44, said wall part 756 has non-matching surface 774, and said non-matching surface 774 is towards the opposite direction with respect to said matching surface 770 (Figure 43).Said wall part 756 comprises the element protuberance 776 of extension away from said non-matching surface 774 and said optics 736.Said biasing element 740 is configured to and is coupled to said element protuberance 776.In the embodiment shown, said element protuberance 776 and said biasing element 740 extend into the groove 778 of said parts spatial accommodation 713.Said groove 778 is by the sized of holding said biasing element 740 and moulding.Said groove 778 has the element surface 780 of the said biasing element 740 of engagement.

Figure 45 illustrates the isolated frontview of said optics 732, and Figure 46 illustrates

How said optics 732 can removably be mounted to said base plate 702.Said optics 736 will removably be installed; Said optics 736 can be placed in the parts spatial accommodation 789 of said installing device 734, and said parts spatial accommodation 789 is generally limited said wall part 756 (Figure 46), said framework extension 758 and said clamping components 766.In concrete embodiment, in said optics 736 was placed in said installing device 734, said optics 736 freely was contained in the said parts spatial accommodation 789.For example, said optics 736 can not form interference fit with said retainer 738.On the contrary, in install operation process, said optics 736 can through said wall part 756, said framework extension 758, said clamping components 766 and, for example, staff is housed inside in the said parts spatial accommodation 789.Yet in substituting embodiment, said optics 736 can form in the space that interference fit only maybe can be limited in being limited said retainer 738 with said retainer 738.

About Figure 46, in said install operation process, said biasing element 740 can at first be compressed, so as said installing device 734 can through and be inserted into said parts and receive space 713.For example; Said biasing element 740 can be compressed through people's finger; Reducing the size of said optics 732, perhaps said biasing element 740 can through at first with said biasing element 740 be pressed onto on the said element surface 780, the said retainer 738 that moves forward then gets into said parts spatial accommodation 713 to be compressed.In case said optics 732 is placed in said parts and receives in the space 713; The mechanical energy of storage can move said retainer 738 towards said reference plane 783 with said optics 736 in the biasing element 740 of said compression, directly meshes said reference plane 783 until said optical surface 744.More specifically, said optical surface 744 can directly mesh the said positioning function parts 761-763 (Figure 43) of said reference plane 783.Shown in figure 46, when said optics 736 is installed, because can there be little clearance G in said positioning function parts 771-773 (Figure 43) between said optical surface 742 and said matching surface 770 (Figure 43) ₁, and because can there be little clearance G in said positioning function parts 761-763 (Figure 43) between said optical surface 774 and said reference plane 783 ₂

In said installation site, said biasing element 740 provides said optical surface 744 is pressed onto the aligning power F on the said reference plane 783 _ASaid optical surface and reference plane 744 and 783 can be configured to by predetermined orientation said optics 736 is set.Said aligning power F _ABe enough in the whole operation of said imaging system, keep said optics 736 by predetermined orientation.In other words, said installing device 734 can stop said optics 736 to move with the direction along said axle 792 with said reference plane 783.In addition, in said installation site, said protuberance 764 (Figure 43) can be pressed on the said edge-of-part 751 (Figure 43), moves with the direction along said axle 791 to stop said optics 736.Said framework extension 758 can stop or limit said optics 736 with said clamping components 766 and move with the direction along said axle 793.Therefore, said parts spatial accommodation 713 can relative to each other dispose with said installing device 734, during the imaging stage, to support said optics 736 by predetermined orientation.

Shown in figure 45; When said optics 736 is in said installation site; The space segment 798 of said optical surface 744 can be faced and engage said reference plane 783, and the path part 799 of said optical surface 744 can extend beyond the light path that said bearing surface 704 entering optical signals are got.Still shown in figure 46, said parts spatial accommodation 713 can extend depth D from said bearing surface 704 _CGet into said base plate 702.

Said biasing element 740 can comprise any can store mechanical can be so that said aligning power F to be provided _AElastic component.In the embodiment shown, said elastic component comprises whisker, then promotes said optical surface 744 when said whisker is compressed against said reference plane 783.Yet in substituting embodiment, said elastic component and said parts spatial accommodation can be configured, and make that the said optical surface of drawing was against said reference plane when said elastic component was stretched.For example, whisker can have relative two ends, and wherein an end is connected to the said element surface that is arranged in the groove that extends from said reference plane and the other end is connected to said retainer.When said whisker was stretched, said whisker can provide the aligning power of the said optics of drawing against said reference plane.In this substituting embodiment, also can use rubber item.

In substituting embodiment, said installing device 734 can be with the use tackiness agent said optics 736 being labelled to said base plate 702.More specifically, said optics 736 can bear against said reference plane 783 by said installing device 734.Tackiness agent can be deposited the said clearance G between said optical surface 744 and the said reference plane 783 ₂After said tackiness agent solidified, said installing device 734 can be removed, and said optics 736 still is labelled to said reference plane 783 through said tackiness agent.

Figure 47 is the block diagram of the said method 800 of explanation assembling optical system.Said method 800 comprises provides the optical backplane with parts spatial accommodation (seeing 802).Said base plate and said parts spatial accommodation can be similar with parts spatial accommodation 713 with base plate 702 mentioned above.Said method 800 also comprises inserts said parts spatial accommodation (seeing 804) with optics.Said optics is can be with optics mentioned above 736 similar and comprise and be configured to reflection or transmission ray passes optical surface wherein.Said optical surface can have the space segment and the path part that extends beyond said bearing surface entering light path towards the reference plane of said parts spatial accommodation.Said method 800 also comprises provides the said optical surface of maintenance against the aligning power (see 806) of said reference plane to locate said optics.Said optical surface and reference plane can be configured to when said aligning power is provided, and keep said optics by predetermined orientation.In some embodiments, said method 800 also can comprise and removes said optics (seeing 808) and alternatively, and different opticses is inserted said parts spatial accommodation (seeing 810).Said different optics can have identical or different optical property.In other words, said different optics can be the refill-unit with identical optical performance, or said different optics can have different optical properties.

Figure 48 and 49 provides the skeleton view and the side-view of said light source (or exciting light module) 604 respectively.One or more opticses (like lens or strainer) as used herein, that light source module comprises one or more light sources (like laser, Jupiter, photodiode, laser diode) that are fixed to module frame and also comprises and the predetermined position fixing with respect to said one or more light sources that is fixed to said module frame.Said light source module is configurable for removably to be coupled in the imaging system, so that the user can install or change said light source module relatively apace.In concrete embodiment, said light source module 604 constitutes SLS module 604, and said SLS module 604 comprises said first and second SLS 614 and 616.As shown in the figure, said SLS module 604 comprises module frame 660 and module lid 662.A plurality of image-forming blocks can be fixed in the said module frame 660 relative to each other fixed position.For example, said first and second SLS 614 and 616, said exciting light strainer 635 and said lens 624 and 625 can be installed on the said module frame 660.In addition, said SLS module 604 can comprise and is configured to first and second scatterers 664 (Figure 48) and 666 that transmit respectively from the heat energy of said first and second SLS 614 and 616.

Said SLS module 604 can be made and moulding by certain size with said module frame 660, so that the individual can and easily operate to be fit into said imaging system 600 with the said SLS module 660 of its held.Just in this point, said SLS module 604 has the weight that the grownup can support.

Said SLS module 604 is configured to be placed in the said module spatial accommodation 719 (Figure 41) and removably is coupled to said base plate 702 (Figure 41).As shown in the figure, said module frame 660 has a plurality of, and said face comprises mounting face 670 and mating surface 671 (Figure 48).In the embodiment shown, said module frame 660 is rectangle or piece shape substantially, but said module frame 660 can have other shapes in substituting embodiment.Said mounting face 670 is configured to be mounted to the said base plate 702 of said module spatial accommodation 719.Just in this point, at least a portion of said module spatial accommodation 719 can moulding to hold and to support said SLS module 604.Similar with said parts spatial accommodation 713, said module spatial accommodation 719 can be limited on one or more surfaces, and said one or more surfaces provide reached at the area of space that wherein can hold said SLS module 604.Said surface can be the surface of said base plate 702.For example, in the embodiment shown, said module spatial accommodation 719 is pits of said base plate 702.Said mounting face 670 can have supplies said base plate 702 and or rather, the profile of said module spatial accommodation 719 substantially.For example, said mounting face 670 can be planar substantially and comprise from wherein outstanding directing pin 672 (Figure 49), and said directing pin 672 is configured to be inserted in the said base plate 702 in the (not shown) of corresponding hole.Said directing pin 672 can be the fastening piece (like screw) that is configured to said module frame 660 to the said base plate 702 of being convenient to removably to be coupled.In concrete embodiment, said directing pin 672 is inserted into said base plate 702 with nonopiate angle.Shown in figure 49, said scatterer 666 can be coupled to said module frame 660, so that have side-play amount 676 from said mounting face 670 to said scatterer 666.

Said module frame 660 can be included in passage point of crossing 685 first and second optical channels 682 and 684 intersected with each other.Said SLS 614 and 616 can be fixed to said module frame 660 and have fixed position relative to each other.Said SLS 614 and 616 is positioned, so that optical signal is directed passing separately said optical channel 682 and 684 towards said passage point of crossing 685 along light path substantially.Said light path can be directed toward said exciting light strainer 635.In the embodiment shown, said light path is perpendicular to one another, until arriving said exciting light strainer 635.Said exciting light strainer 635 is positioned with at least a portion that reflects the said optical signal that said SLS 616 generates and transmits at least a portion of the said optical signal that said SLS614 generates.As shown in the figure, be directed leaving said SLS module 604 from each said optical signal of said SLS 614 and 616 along the common path and through common module window 674.Said module window 674 extends through said mating surface 671.

Figure 50 is the plat that is installed to the said SLS module 604 on the said base plate 702.In the embodiment shown, said SLS module 604 is configured to and leans against on the said base plate 702, so that said terrestrial gravitation g is convenient to said SLS module 604 supportings above that.Just in this point, said SLS module 604 can provide and be easy to remove or isolating integrated device from said optical module 600.For example, remove the shell (not shown) of said mensuration system or receive get into said optical module after, said SLS module 604 can be grasped and removed or change by the individual.When said SLS module 604 is positioned at 702 last times of said base plate, said mating surface 671 can mesh optics 680.Said optics 680 can be adjacent with said module window 674, so that the said optical signal that said SLS module 604 generates is through said optics 680 transmission.

Though shown embodiment is described to use the SLS module that has first and second SLS, can exciting light be guided on the said sample with other modes.For instance, said SLS module 604 can be included in only SLS and another optics (for example lens or strainer) of the fixed position that has in the module frame relative to each other.Equally, can use plural SLS.In a similar fashion, optical module can comprise only a laser apparatus or two above laser apparatus.

Yet embodiment as herein described is not limited only to have the modularization activating system, like said SLS module 604.For example, said imaging system 600 can be used the light source that is not mounted to module frame.More specifically, laser apparatus can directly be mounted to other parts of said base plate or said imaging system, maybe can be mounted to framework, and said framework is installed in the said imaging system conversely.

Turn back to Figure 38, said imaging system 600 can have image focusing system 840, and said image focusing system 840 comprises said object or sample holder 650, optical system 842 and said imaging detector 610.Said optical system 842 is configured to guiding from the detector surface 844 of the optical signal of said sample holder 650 light emission of the said sample area 608 of said flow cell 606 (for example, from) to said imaging detector 610.Shown in figure 38, said optical system 842 comprises said optics 623,644,631 and 642.Said optical system 842 can comprise other opticses.Shown in configuration in, said optical system 842 has and closes on object that said sample holder 650 is provided with or sample plane 846 and close on the plane of delineation 848 that said detector surface 844 is provided with.Said imaging detector 610 is configured on said detector surface 844 and obtains object or sample image.

In some embodiments, said image focusing system 840 is configured to respect to said detector 610 and moves the said plane of delineation 848 and catch test pattern.More specifically, the said plane of delineation 848 can be moved, so that the said plane of delineation 848 extends with nonparallel mode with respect to said detector surface 844 and intersects with said detector surface 844.Can confirm the position in said point of crossing through analyzing said test pattern.Said then position can be used to confirm the focal power of said imaging system 600.In concrete embodiment, said image focusing system 840 adopts rotatable mirror, and said rotatable mirror operationally is coupled to the actuator that is used for moving said rotatable mirror.But, said image focusing system 840 can move other opticses that said optical signal guided to said detector surface 844, or said image focusing system 840 can move said detector 610.In either case, the said plane of delineation 848 can relatively be moved with respect to said detector surface 844.For example, said image focusing system 840 can mobile lens.

In concrete embodiment, said imaging detector 610 is configured to and utilizes rotatable mirror 642 to obtain test pattern, to confirm the focal power of said imaging system 600.According to determined focal power, said imaging system 600 can move said sample holder 650, so that said object or sample are placed in the said sample plane 846.For example, said sample holder 650 can be configured to move the distance (z representes like Δ) that said sample area 608 is scheduled to the z direction.

Figure 51 is the plat that several parts in the said image focusing system 840 are shown.The installation component 852 that as shown in the figure, said image focusing system 840 comprises the rotatable mirror assembly 850 that comprises said mirror 642, be installed on it said mirror 642 and being configured to said installation component 852 and said mirror 642 around turning axle R ₆The actuator or the rotating mechanism 854 of rotation.Said mirror 642 be configured to the reflection be received from said sample area 608 (Figure 38) optical signal 863 towards said imaging detector 610 and on said detector surface 844.In the embodiment shown, said mirror 642 directly reflects said optical signal 863 (the intervention optics that does not promptly have the said optical signal 863 of reboot) on said detector surface 844.Yet, in substituting embodiment, have the optics that the said optical signal 863 of other influence is propagated.

In the embodiment shown, said image focusing system 840 also comprises being configured to and prevents that 642 rotations of said mirror from surpassing the positive stop 860 and 862 of predetermined rotational positions.Said positive stop 860 and 862 has with respect to said axle R ₆The fixed position.Said installation component 852 is configured to according to whether just obtaining sample image or test pattern, around said axle R ₆Between said positive stop 860 and 862, rotate.Therefore, said mirror 642 can rotate between test position (or orientation) and image space (or orientation).Only for instance, said mirror 642 can be around said axle R ₆Between different position of rotation from about 5 ° to about 12 ° of rotations.In concrete embodiment, said mirror 642 can be around said axle R ₆Rotate about 8 °.

Figure 52 is the skeleton view of said mirror assembly 850.As shown in the figure, said installation component 852 comprises inner frame 864 and support bracket 866.Said inner frame 864 is configured to and is coupled to said mirror 642 and also is coupled to said support bracket 866.Said inner frame 864 can interact with said support bracket 866 each other and with a plurality of holding screws 868, so that the inching to the orientation of said mirror 642 to be provided.Just in this point, said installation component 852 can constitute universal mirror installation component.Still as shown in the figure, said installation component 852 is coupled to said rotating mechanism 854.In the embodiment shown, said rotating mechanism 854 comprises direct drive-motor.Yet, can use various alternate rotating mechanisms, like direct current (DC) motor, electromagnetic coil drive, linear actuators, piezoelectric motor or the like.Still shown in Figure 52, said positive stop 860 can have with respect to said rotating mechanism 854 and said axle R ₆The fixed position.

As discussed above, said rotating mechanism 854 is configured to around said axle R ₆Rotation or rotate said mirror 642.Shown in Figure 52, said mirror 642 has along said axle R ₆The geometric centre C that extends.The said geometric centre C of said mirror 642 is with respect to said axle R ₆Skew.In some embodiments, said rotating mechanism 854 is configured in less than 500 milliseconds said mirror 642 is moved between said test position and image space.In concrete embodiment, said rotating mechanism 854 be configured to less than 250 milliseconds or less than 160 milliseconds in said mirror 642 is moved between said test position and image space.

Figure 53 is the synoptic diagram at the said mirror 642 of said image space.As shown in the figure, from the said optical signal 863 of said sample area 608 (Figure 38) by said mirror 642 reflections and be directed toward the said detector surface 844 of said imaging detector 610.According to the configuration of said optical system 842 and the z-position of said sample holder 610, said sample area 608 can be fully on the focus or not on focus (being out of focus) fully.Figure 53 illustrates two plane of delineation 848A and 848B.Said plane of delineation 848A is overlapping with said detector surface 844 substantially, and just in this point, corresponding sample image has acceptable or enough focal powers.Yet said plane of delineation 848B and said detector surface 844 are spaced apart out.Therefore, the sample image that when said plane of delineation 848B and said detector surface 844 are spaced apart out, is obtained possibly not have enough focal powers.

Figure 54 and Figure 55 illustrate sample image 870 and 872 respectively.When said plane of delineation 848A and said detector surface 844 were overlapping, said sample image 870 was images that said imaging detector 610 detects.When said plane of delineation 848B and said detector surface 844 were not overlapping, said sample image 872 was images that said imaging detector 610 detects.(said sample image 870 and 872 comprises provides DNA bunch of fluorescent emission when being excited by predetermined excitation spectrum.) shown in Figure 54 and 55, said sample image 870 has acceptable focal power, wherein each quilt of said bunch along said sample image 870 limits clearly, and the acceptable focal power that said sample image 872 does not have each quilt of wherein said bunch to limit clearly.

Figure 56 is the synoptic diagram at the said mirror 642 of said focal position.As shown in the figure, at the said mirror 642 of said focal position by around said axle R ₆Rotation θ angle.Equally, reflected and be directed toward the said detector surface 844 of said imaging detector 610 by said mirror 642 from the said optical signal 863 of said sample area 608 (Figure 38).Yet the said optical system 842 among Figure 56 is provided so that the said plane of delineation 848 is moved with respect to said detector surface 844.More specifically, the said plane of delineation 848 can't parallel and said detector surface 844 extend, and on the contrary, intersects at level crossing point PI with said detector surface 844.Though said mirror 642 is in said focal position, said imaging system 600 can obtain the test pattern of said sample area 608.Shown in Figure 56, depend on said sample area 608 focal degree during the imaging stage, said level crossing point PI can betide the different positions on the said detector surface 844.

For example, Figure 57 and Figure 58 illustrate test pattern 874 and 876 respectively.The image that 874 expressions of said test pattern obtain when said sample area 608 is on focus, and said test pattern 876 is represented the image that when said optical system 842 out of focus, obtains.As shown in the figure, said test pattern 874 has focal zone or position FL ₁(distance at itself and said benchmark edge 880 is XD ₁) and said test pattern 876 have focal zone or position FL ₂(distance at itself and said benchmark edge 880 is XD ₂).Said focal position FL ₁And FL ₂Can confirm by image analysis module 656 (Figure 38).

Confirm the said focal position FL in said test pattern 874 and 876 ₁And FL ₂, said image analysis module 656 can be confirmed the position of best focal power in the corresponding test pattern.More specifically, said analysis module 656 can be confirmed along the focusing score of the difference of said test pattern 874 and 876 x-dimension.Said analysis module 656 can calculate the focusing score on each point based on one or more image quality parameters.The example of image quality parameter comprises the square error between picture contrast, spot size, signal noise ratio (snr) of image and the said image interior pixel.For instance, when calculating the focusing score, said analysis module 656 can calculate correlated variation factor in the said image.Variable quantity in the selected part of said correlated variation factor presentation video or image between the pixel intensity.As a further example, when calculating the focusing score, said analysis module 656 can calculate the size of the hot spot that derives from said image.Said hot spot can be expressed as Gauss's hot spot and size can be measured as full width at half maximum (FWHM), and in this case, less spot size is relevant with improved focusing usually.

Confirm described in the said test pattern behind the focal position FL the said distance X D that said analysis module 656 can be measured then or confirm that said focal position FL and said benchmark edge 880 are spaced apart or separate.Said distance X D then can be relevant with respect to the z-position of said sample plane 846 with said sample area 608.For example, said analysis module 656 can be confirmed the said distance X D shown in Figure 58 ₂Corresponding to the said sample area 608 of said sample plane 846 distance, delta z.Just in this point, said sample holder 650 can be moved said distance, delta z then, in said sample plane 846, to move said sample area 608.Therefore, the said focal position FL in test pattern can indicate the position of said sample area 608 with respect to said sample plane 846.As used herein, phrase " is indicated said object (or sample) with respect to said object (or sample) planar position " and is comprised the factor (for example said focal position) of utilizing, so that model or the algorithm that more suitably is used for confirming said distance, delta z to be provided.

Figure 59 is the block diagram of the method 890 of a kind of focus that is used to control optical imaging system of explanation.Said method 890 comprises providing to have rotatable mirror and be configured to the optical system (see 892) of direct light signal on the detector surface.Said detector surface can be similar to said detector surface 844.Said optical system can have the object plane of closing on object, like said sample plane 846.Said optical system also can have the plane of delineation that closes on said detector surface, like the said plane of delineation 848.Said rotatable mirror can be rotatable between image space and focal position.

Said method 890 also comprises the said mirror of rotation to said focal position (seeing 894) and the test pattern (seeing 896) that when said mirror is in said focal position, obtains said object.Said test pattern can have best focal power at focal position.Said focal position can be indicated the position of said object with respect to said object plane.In addition, said method 890 also can comprise based on said focal position said object is moved towards said object plane (seeing 898).

The description that is appreciated that preceding text is in order to explain, and unrestricted.For example, above-mentioned embodiment (and/or its aspect) use that can mutually combine.In addition, can make many modifications adapting to particular case or material to embodiment, and not deviate from scope of the present invention.Though the parameter that concrete parts described herein and process are intended to limit various embodiments, they never are restrictive but exemplary embodiments.After checking the description of preceding text, many other embodiments will be conspicuous to one skilled in the art.Therefore, the four corner of the said scope of the present invention equivalent that should be endowed together with these claims with reference to appended claim is confirmed.In appended claim, term " comprises " and " wherein " is used as the simple and easy English equivalent of " comprising " and " therein " separately.In addition, " first ", " second " and " the 3rd " etc. and and are not intended to its object are forced digital requirement only with marking in the claim hereinafter.In addition; The writing of the claim of hereinafter restriction be not with the form of means-plus-function and can't make explanations for the 6th section based on 35U.S.C. § 112, only and if after said claim restriction clearly uses phrase " to be meant ", connect the invalid statement of function of further structure.

Claims (56)

1. a nucleic acid sequencing system is characterized in that, said nucleic acid sequencing system comprises:

(a) comprise following Stage microscope

(i) be configured to the supporting structure of holding dismountable fluidic hardware, said supporting structure comprises towards along the basal plane of Z-direction and be configured to said dismountable fluidic hardware fixing on it;

(ii) a plurality of towards the reference plane of direction separately along the XY plane; And

(iii) comprise the alignment components that is configured to the movably registration arm that between withdrawal and offset position, moves; Wherein said registration arm is configured to when said registration arm is in said offset position, supports said dismountable fluidic hardware against said reference plane;

(b) comprise following fluid storage system

(i) has the shell in chamber;

(ii) be configured to the temperature-controlling module of regulating the temperature in the said chamber; And

The fluid that (iii) comprises the clamper, hoisting appliance and the suction pipe array that are used for the fluid storage device pipettes assembly,

Wherein said hoisting appliance comprises the drive-motor that is configured to respect to the two-way mobile said suction pipe array of said clamper;

(c) flow system, said flow system be configured to the guiding sequencing reagent from said fluid storage device to the position that is configured to the said supporting structure of holding said dismountable fluidic hardware;

(d) comprise following exciting light module:

(i) have first and second semiconductor light sources (SLS) of fixed position relative to each other, said first and second SLS are configured to the optical excitation signal that provides different; And

(ii) have with respect to the fixed position of said first and second SLS and the optics of pre-determined direction; Said optics allows to pass wherein and reflect the optical signal from said the 2nd SLS from the optical signal transmission of a said SLS, and the optical signal of said reflection and transmission is directed leaving said module along a common path;

(e) detector; And

(f) be configured to the optical system of guiding from exciting light to the position that is configured to the said supporting structure of holding said dismountable fluidic hardware of said exciting light module; Wherein said optical system further is configured to position to the said detector of direct emitted light from being configured to the said supporting structure of holding said dismountable fluidic hardware

Wherein said optical system is included in rotatable mirror between image space and the focal position, and

Wherein said mirror is configured to and reflects the said said detector that emits light into.

2. according to the nucleic acid sequencing system of claim 1, it is characterized in that, further comprise said dismountable fluidic hardware, said dismountable fluidic hardware comprises and comprises following flow cell:

(i) have the substrate of flow passage, wherein said flow passage comprises imaging moiety and non-imaging moiety, and wherein said imaging moiety is connected by jet ground through curved part with non-imaging moiety, and said imaging moiety and non-imaging moiety extend parallel to each other;

The inlet that (ii) extends into said substrate and be communicated with the said imaging moiety fluid of said flow passage; And

The outlet that (iii) extends into said substrate and be communicated with the said non-imaging moiety fluid of said flow passage, wherein said inlet and said outlet are adjoined setting each other at an end of said flow cell.

3. according to the nucleic acid sequencing system of claim 2, it is characterized in that the width of the said imaging moiety of said flow passage is greater than the width of the said non-imaging moiety of said flow passage.

4. according to the nucleic acid sequencing system of claim 3, it is characterized in that the said imaging moiety of said flow passage and non-imaging moiety have the height that equates substantially.

5. according to claim 2,3 or 4 nucleic acid sequencing system, it is characterized in that the surface of the said imaging moiety of said flow passage is configured to place a plurality of DNA bunches above that.

6. according to the nucleic acid sequencing system of claim 5, it is characterized in that a plurality of DNA bunches on the surface of the said imaging moiety of said flow passage.

7. according to claim 2,3 or 4 nucleic acid sequencing system, it is characterized in that the said curved part of said flow passage comprises tapered section and middle portion,

Wherein said tapered section connects said imaging moiety and said middle portion, and

The width dimensions of wherein said tapered section reduces to said middle portion from the said imaging moiety of said flow passage.

8. according to the nucleic acid sequencing system of claim 2, it is characterized in that, further comprise said dismountable fluidic hardware, said dismountable fluidic hardware comprises and comprises following flow cell shell

(i) be configured to the spatial accommodation that holds said flow cell, said spatial accommodation is pressed certain size and is made and moulding, when being positioned at said retracted position with the said registration arm of box lunch, allows said flow cell unsteady with respect to said flow cell shell; And

(ii) be coupled to the packing ring of said flow cell shell; Said packing ring has the entrance and exit passage and comprises compressible material; Said packing ring is with respect to said spatial accommodation setting; When being positioned at said offset position with the said registration arm of box lunch, the said entrance and exit of said flow cell respectively with the said entrance and exit passage rough alignment of said packing ring.

9. according to Claim 8 nucleic acid sequencing system is characterized in that said supporting structure further comprises alignment members, and

Wherein said flow cell shell comprises the said spatial accommodation setting of next-door neighbour and by the recess of the sized of holding said alignment members and moulding; The edge of said flow cell extends in recess separately, so that said alignment members directly meshes the said edge of said flow cell.

10. according to Claim 8 or 9 nucleic acid sequencing system, it is characterized in that, further comprise the identification XMTR in the chamber that is placed in said flow cell shell.

11. the nucleic acid sequencing system according to claim 2 or 8 is characterized in that, further comprises the cap assemblies that is coupled to said supporting structure and is configured to be removably installed in said dismountable fluidic hardware top.

12. nucleic acid sequencing system according to claim 11; It is characterized in that; Said cap assemblies has top surface and the space of watching that is positioned at said top surface; The said space of watching has the degree of depth that records to said dismountable fluidic hardware from said top surface, and the wherein said space of watching makes and moulding by certain size, to hold the imaging len that extends into the said degree of depth in said top surface below.

13. the nucleic acid sequencing system according to claim 12 is characterized in that, said cap assemblies comprises a plurality of compression arms, and said compression arm is configured to presses to said basal plane and relative to each other biasing independently with said flow cell.

14. nucleic acid sequencing system according to claim 11; It is characterized in that; Said cap assemblies comprises the jet port of said flow system, and said jet port is coupled to said cover housing and is configured to the corresponding entrance and exit that when said cap assemblies is installed to said device top, meshes said flow cell.

15. nucleic acid sequencing system according to claim 11; It is characterized in that; Said cap assemblies comprises that identification reader and said flow cell comprise the identification XMTR, and said identification reader is configured to when said cap assemblies is installed to said flow cell top and is set up near said identification XMTR.

16. the nucleic acid sequencing system according to claim 11 is characterized in that, said alignment components operatively is coupled to said cap assemblies; When said cap assemblies is installed to said dismountable fluidic hardware top, said alignment components with said dismountable fluidic hardware with respect to the said spacial alignment of watching.

17. the nucleic acid sequencing system according to claim 11 is characterized in that, said reference plane comprises first reference plane and second reference plane; When said registration arm was positioned at said offset position, said first reference plane was configured to stop said fluidic hardware to move with the direction along said X axle and said second reference plane is configured to stop said fluidic hardware to move with the direction along said Y axle.

18. nucleic acid sequencing system according to claim 17; It is characterized in that; Said registration arm is configured at said cap assemblies and supports said dismountable fluidic hardware before the said basal plane, supports said dismountable fluidic hardware in the fixed position against said reference plane along said XY plane.

19. according to claim 1,2,3 or 4 nucleic acid sequencing system, it is characterized in that said supporting structure further comprises the radiating module with said basal plane, said radiating module is configured to transferring heat energy and passes said basal plane.

20. according to claim 1,2,3 or 4 nucleic acid sequencing system; It is characterized in that, further comprise the fluid storage device, said fluid storage device comprises pallet; And a plurality of compositions hole in the said pallet, said a plurality of single hole has opening at the top in said hole.

21. the nucleic acid sequencing system according to claim 20 is characterized in that, the said clamper that is used for said fluid storage device comprises pair of guide rails.

22. nucleic acid sequencing system according to claim 21; It is characterized in that; Said fluid storage device further comprises the lip that extends along first and second limits of said pallet, and wherein said guide rail is configured to the said lip that clamping is extended along said first and second limits of said pallet.

23. nucleic acid sequencing system according to claim 20; It is characterized in that; Said fluid pipettes device and further comprises position transducer, and wherein said fluid storage device further comprises identification tag, and wherein said position transducer is configured to the label of reception from said identification tag.

24. the nucleic acid sequencing system according to claim 20 is characterized in that, said a plurality of compositions hole comprises [and rectangular opening.

25. nucleic acid sequencing system according to claim 24; It is characterized in that; Said rectangular opening has the degree of depth that storage and the other end from an end of said storage to said storage increase, and the darker end that wherein said hole is configured at said storage holds suction pipe.

26. nucleic acid sequencing system according to claim 20; It is characterized in that said a plurality of compositions hole comprises the hole, the hole that is configured to comprise primer nucleic acid that are configured to comprise polysaccharase, is configured to comprise the hole of nucleic acid denaturation agent and is configured to comprise the hole with reversible terminator part and fluorescently-labeled Nucleotide.

27. nucleic acid sequencing system according to claim 26; It is characterized in that said a plurality of compositions hole comprises the hole, the hole that comprises primer nucleic acid that comprise polysaccharase, comprises the hole of nucleic acid denaturation agent and comprises the hole with reversible terminator part and fluorescently-labeled Nucleotide.

28. the nucleic acid sequencing system according to claim 26 is characterized in that, said a plurality of compositions hole further comprises the hole that is configured to comprise nucleic acid samples to be checked order.

29. the nucleic acid sequencing system according to claim 28 is characterized in that, said a plurality of compositions hole further comprises the hole that comprises nucleic acid samples to be checked order.

30. the nucleic acid sequencing system according to claim 20 is characterized in that, the said opening at the top in said single composition hole comprises from the edge of the outstanding distance of said upper surface of said pallet.

31. the nucleic acid sequencing system according to claim 20 is characterized in that, said fluid storage device comprises further that protective foil and the said suction pipe of the said opening at the top that covers single hole are configured to and pierces through said protective foil.

32., it is characterized in that said hoisting appliance comprises the delivery platform that is configured to the said suction pipe array of supporting according to claim 1,2,3 or 4 nucleic acid sequencing system.

33. the nucleic acid sequencing system according to claim 32 is characterized in that, further comprises having the guide plate that plate opening is wherein passed in said suction pipe slip.

34. the nucleic acid sequencing system according to claim 32 is characterized in that, said delivery platform further comprises the guide pin that is fixed to and extends with the direction that is parallel to said suction pipe from said delivery platform.

35. the nucleic acid sequencing system according to claim 34 is characterized in that, further comprises the fluid storage device, said fluid storage device comprises pallet, and a plurality of compositions hole in the said pallet,

Wherein said fluid storage device further comprises pin hole, and wherein said pin hole is positioned on the upper surface of said pallet and is configured to when said elevator is positioned at fluid and pipettes the position, holds the said guide pin between at least two of said composition hole.

36. the nucleic acid sequencing system according to claim 35 is characterized in that, said guide pin is bigger than the distance that said suction pipe extends, thereby said guide pin was configured to before said suction pipe is inserted into said composition hole, arrived said fluid storage device.

37. according to claim 1,2,3 or 4 nucleic acid sequencing system; It is characterized in that; Further comprise the central controller that is coupled to said first and second light sources and said flow system communicatedly; Said unit is configured to and starts said flow system so that the inflow of said sequencing reagent is configured to the position of the said supporting structure of holding said dismountable fluidic hardware and is configured to after predetermined generated time section, activates said first and second light sources.

38. according to claim 1,2,3 or 4 nucleic acid sequencing system, it is characterized in that said exciting light module comprises module frame,

Wherein said first and second semiconductor light sources (SLS) are fixed to said module frame, and

Wherein said optics is fixed to said module frame.

39. nucleic acid sequencing system according to claim 38; It is characterized in that; Said module frame is included in passage point of crossing first and second optical channels intersected with each other; Said first and second SLS are set at the inside of said first and second optical channels respectively, and said optics is set at said passage point of crossing.

40. the nucleic acid sequencing system according to claim 38 is characterized in that, further comprises being configured to first and second scatterers that transmit respectively from the heat energy of said first and second SLS.

41. the nucleic acid sequencing system according to claim 38 is characterized in that, said optical system further comprises the base plate of the parts spatial accommodation with the said bearing surface of bearing surface and edge, and said parts spatial accommodation is limited reference plane at least in part.

42. nucleic acid sequencing system according to claim 38; It is characterized in that; The mounting face of said module frame is planar substantially, and wherein guide pin is outstanding from the said mounting face of said module frame, and said guide pin is inserted in the interior corresponding hole of parts spatial accommodation of said base plate.

43. according to claim 1,2,3 or 4 nucleic acid sequencing system; It is characterized in that; Further comprise and being configured to when said mirror is in said focal position; Analysis is in the image analysis module of the detected test pattern of said detector surface; Said test pattern has best focal power at the focal position of said test pattern, indicates the position of said object with respect to said object plane at the said focal position of said test pattern, and wherein said Stage microscope is configured to based on said focal position and moves said dismountable fluidic hardware towards said object plane.

44. according to claim 1,2,3 or 4 nucleic acid sequencing system; It is characterized in that; Said mirror has turning axle, and said system further comprises a pair of positive stop that has with respect to the fixed position of said axle, and said positive stop prevents that said mirror rotation from surpassing predetermined rotational positions.

45., it is characterized in that said optical system further comprises according to claim 1,2,3 or 4 nucleic acid sequencing system:

(i) have bearing surface and along the base plate of the parts spatial accommodation of said bearing surface, said parts spatial accommodation is limited reference plane at least in part;

(ii) have and be configured to reflected light or transmit the optics that light passes optical surface wherein; And

(iii) draw together component holder and operationally be coupled to the installing device of the biasing element of said retainer; Said retainer supports said optics, extends beyond said bearing surface entering light path so that the space segment of said optical surface is faced the path part of said reference plane and said optical surface; Said biasing element provides the aligning power of the said optical surface of supporting against said reference plane.

46. the nucleic acid sequencing system according to claim 45 is characterized in that, said retainer comprises towards the outstanding alignment features of said reference plane; When said biasing element provided said aligning power, said alignment features meshed the complementary recess of said base plate.

47. the nucleic acid sequencing system according to claim 46 is characterized in that, said biasing element comprises and being configured to when being compressed, store mechanical can elastic component.

48. the nucleic acid sequencing system according to claim 47 is characterized in that, said elastic component comprises the whisker of the said optics of promotion against said reference plane.

49. the nucleic acid sequencing system according to claim 44 is characterized in that, said optical surface is that planar and said reference plane are planar.

50. the nucleic acid sequencing system according to claim 44 is characterized in that, said optics comprises spectral filter.

51. the nucleic acid sequencing system according to claim 44 is characterized in that, said optics comprises mirror.

52. nucleic acid sequencing system according to claim 44; It is characterized in that; Said parts spatial accommodation is the first parts spatial accommodation and said optical system comprises the second parts spatial accommodation; Said installing device and said optics constitute first optics that is positioned at the said first parts spatial accommodation, and said optical system further comprises second optics that is positioned at the said second parts spatial accommodation.

53. the nucleic acid sequencing system according to claim 44 is characterized in that, said retainer and said biasing element are positioned at said parts spatial accommodation.

54. the nucleic acid sequencing system according to claim 44 is characterized in that, said biasing element promote said optics against said reference plane or the said optics of drawing against said reference plane.

55. the nucleic acid sequencing system according to claim 44 is characterized in that, said parts spatial accommodation is the pit of said base plate.

56., it is characterized in that said fluid storage system further comprises being configured and opens so that the door of the approach that gets into said chamber to be provided according to claim 1,2,3 or 4 nucleic acid sequencing system.

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