Patent Description:
This disclosure relates to a method of measuring at least one time-varying signal emission from the contents of each of a plurality of receptacles while the contents of all receptacles are subject to repeated cycles of temperature variations within a thermal cycling range as set out in the appended set of claims.

Diagnostic assays are widely used in clinical diagnosis and health science research to detect or quantify the presence or amount of biological antigens, cell or genetic abnormalities, disease states, and disease-associated pathogens or genetic mutations in an organism or biological sample. Where a diagnostic assay permits quantification, practitioners may be better able to calculate the extent of infection or disease and to determine the state of a disease over time. Diagnostic assays are frequently focused on the detection of chemicals, proteins or polysaccharides antigens, antibodies, nucleic acids, amino acids, biopolymers, cells, or tissue of interest. A variety of assays may be employed to detect these diagnostic indicators.

Nucleic acid-based assays, in particular, generally include multiple steps leading to the detection or quantification of one or more target nucleic acid sequences in a sample. The targeted nucleic acid sequences are often specific to an identifiable group of proteins, cells, tissues, organisms, or viruses, where the group is defined by at least one shared sequence of nucleic acid that is common to members of the group and is specific to that group in the sample being assayed. A variety of nucleic acid-based detection methods are fully described by <CIT>, and <CIT>.

Detection of a targeted nucleic acid sequence frequently requires the use of a probe comprising a nucleic acid molecule having a nucleotide base sequence that is substantially complementary to at least a portion of the targeted sequence or its complement. Under selective assay conditions, the probe will hybridize to the targeted sequence or its complement in a manner permitting a practitioner to detect the presence of the targeted sequence in a sample. Techniques of effective probe preparation are known in the art. In general, however, effective probes are designed to prevent non-specific hybridization with itself or any nucleic acid molecule that will interfere with detecting the presence of the targeted sequence. Probes may include, for example, a label capable of detection, where the label is, for example, a radiolabel, a fluorophore or fluorescent dye, biotin, an enzyme, a chemiluminescent compound, or another type of detectable signal known in the art.

To detect different nucleic acids of interest in a single assay, different probes configured to hybridize to different nucleic acids, each of which may provide detectibly different signals can be used. For example, different probes configured to hybridize to different targets can be formulated with fluorophores that fluoresce at a predetermined wavelength when exposed to excitation light of a prescribed excitation wavelength. Assays for detecting different target nucleic acids can be performed in parallel by alternately exposing the sample material to different excitation wavelengths and detecting the level of fluorescence at the wavelength of interest corresponding to the probe for each target nucleic acid during the real-time monitoring process. Parallel processing can be performed using different signal detecting devices constructed and arranged to periodically measure signal emissions during the amplification process, and with different signal detecting devices being configured to generate excitation signals of different wavelengths and to measure emission signals of different wavelengths.

Because the probe hybridizes to the targeted sequence or its complement in a manner permitting detection of a signal indicating the presence of the targeted sequence in a sample, the strength of the signal is proportional to the amount of target sequence or its complement that is present. Accordingly, by periodically measuring, during an amplification process, a signal indicative of the presence of amplicon, the growth of amplicon overtime can be detected. Based on the data collected during this "real-time" monitoring of the amplification process, the amount of the target nucleic acid that was originally in the sample can be ascertained. Exemplary systems and methods for real time detection and for processing real time data to ascertain nucleic acid levels are described, for example, in <CIT>, "Signal measuring system for conducting real-time amplification assays.

Challenges may arise, however, when measuring emission signals during an amplification process or other process. The target sequence or its complement, or other emission signal source, may be contained in a receptacle that is held within an incubator or other processing module that is fully or partially enclosed and for which access by a signal detector to the receptacle or other source for measuring the emission signal may not be practical. Moreover, for space utilization efficiencies and/or other efficiencies (such as thermal efficiencies), the receptacles or other emission signal sources may positioned in a spatial arrangement for which it is not efficient or practical to place a signal detector in operative position to measure the emission signals. For example, a plurality of receptacles or emission signal sources may be arranged in a rectangular arrangement whereby the receptacles are closely spaced in multiple rows of two or more receptacles each. In such a spatial arrangement, it may not be practical or efficient to provide a signal detector for each receptacle position or to move a signal detector with respect to the receptacle positions to sequentially measure signal emissions from each of the receptacles.

<CIT> discloses a method of repeated measurement of emitted fluorescence from multiple samples in multiple tubes held in a carousel, in which time-varying signal emissions from the contents of each of the tubes are detected while the contents of the tubes are subject to repeated cycles of temperature variations within a temperature cycler.

Aspects of the disclosure are embodied in an apparatus for detecting a signal emission from each of a plurality of potential signal emission sources. The apparatus comprises a plurality of signal transmission conduits, a conduit reformatter, one or more signal detectors, and a signal detector carrier. The signal transmission conduits correspond in number to the number of signal emission sources. Each signal transmission conduit is associated with at least one of the signal emission sources and is configured to transmit a signal emitted by the associated signal emission source between a first end and a second end thereof. The conduit reformatter is constructed and arranged to secure the first ends of the respective signal transmission conduits in a first spatial arrangement corresponding to a spatial arrangement of the signal emission sources, such that the first end of each signal transmission conduit is positioned to receive an emission signal emitted by an associated signal emission source, and to secure the second ends of the respective signal transmission conduits in a second spatial arrangement different from the first spatial arrangement. The signal detectors are configured to detect a signal emitted by each signal emission source. The signal detector carrier is configured to carry at least a portion of the one or more signal detectors and to move at least a portion of each signal detector in a path that sequentially places the signal detector in signal detecting positions with respect to the second ends of the signal transmission conduits arranged in the second spatial arrangement.

According to further aspects of the disclosure, the signal emission is an optical signal and the signal transmission conduits comprise optical fibers.

According to further aspects of the disclosure, the first spatial arrangement is rectangular and comprises two or more rows, each row including two or more of the first ends of the signal transmission conduits.

According to further aspects of the disclosure, the second spatial arrangement comprises one or more circles, whereby the second ends of a plurality of signal transmission conduits are positioned about the circumference of a circle.

According to further aspects of the disclosure, the second spatial arrangement comprises one or more bundles whereby the second ends of a plurality of signal transmission conduits are collected in a bundle wherein the second ends of the transmission fibers in the bundle are in close proximity to each other.

According to further aspects of the disclosure, the signal detector carrier comprises a carousel configured to move at least a portion of the one or more signal detectors in a path corresponding to the one or more circles of the second spatial arrangement.

According to further aspects of the disclosure, the conduit reformatter comprises a reformatter frame comprising an interface plate configured to secure the first ends of the respective signal transmission conduits in the first spatial arrangement, a base configured to secure the first ends of the respective signal transmission conduits in the second spatial arrangement, and a side structure connecting the interface plate to the base at spaced-apart positions with respect to each other.

According to further aspects of the disclosure, the apparatus further comprises heat dissipating fins extending from the interface plate.

According to further aspects of the disclosure, the apparatus further comprises a signal coupling element operatively disposed with respect to the first end of each signal transmission conduit.

According to further aspects of the disclosure, the signal detector carrier is constructed and arranged to be rotatable about an axis of rotation so as to move each of the one or more signal detectors in a circular path, and the apparatus further comprises a detector carrier drive operatively associated with the signal detector carrier. The detector carrier drive comprises a motor, a drive pulley coupled to or part of the signal detector carrier such that rotation of the drive pulley causes a corresponding rotation of the signal detector carrier, and a belt operatively coupling the motor to the drive pulley.

According to further aspects of the disclosure, the detector carrier drive further comprises a home position detector configured to detect a rotational position of the detector carrier.

According to further aspects of the disclosure, the signal detector carrier is configured to rotate about an axis of rotation, and the apparatus further comprises a rotary connector transmitting power and/or data between the one more signal detectors carried on the signal detector carrier and a non-rotating data processor and/or power source.

According to further aspects of the disclosure, the rotary connector comprises a slip ring connector.

According to further aspects of the disclosure, the each signal emission source comprises a substance that emits light of a predetermined emission wavelength when subjected to an excitation light of a predetermined excitation wavelength, and the signal detector is configured to generate an excitation light of the predetermined excitation wavelength and detect light of the predetermined emission wavelength.

According to further aspects of the disclosure, the apparatus comprises more than one signal detector, each configured to generate an excitation light of a different predetermined excitation wavelength and to detect light of a different predetermined emission wavelength.

According to further aspects of the disclosure, each of the signal emission sources is in optical communication with a single signal transmission conduit.

According to further aspects of the disclosure, each of the plurality of signal transmission conduits transmits both an excitation and an emission signal.

According to further aspects of the disclosure, the each signal detector comprises an excitation source carried on the signal detector carrier and configured to generate an excitation signal, excitation optics components carried on the signal detector carrier and configured to direct an excitation signal from the excitation source to the second end of a signal transmission conduit when the signal detector is in a signal detecting position with respect to the second end of the transmission conduit, emission optics components carried on the signal detector carrier and configured to direct an emission signal transmitted by a signal transmission conduit when the signal detector is in a signal detecting position with respect to the second end of the transmission conduit, and an emission detector configured to detect an emission signal directed by the emission optics components from the second end of the transmission conduit to the emission detector when the signal detector is in a signal detecting position with respect to the second end of the transmission conduit.

According to further aspects of the disclosure, the emission detector is carried on the signal detector carrier.

According to further aspects of the disclosure, the emission detector comprises a photodiode.

According to further aspects of the disclosure, the emission detector is fixed and disposed adjacent to the signal detector carrier.

According to further aspects of the disclosure, the emission detector comprises a camera.

According to further aspects of the disclosure, the emission detector is associated with at least one excitation source and is configured to detect an emission signal transmitted by a single transmission conduit.

According to further aspects of the disclosure, the signal detector carrier is configured to selectively place each set of excitation optics components into operative association with the emission detector, and the emission detector is configured to detect an emission signal transmitted by all single transmission conduits simultaneously.

Further aspects of the disclosure are embodied in an apparatus for transmitting a signal emission from each of a plurality of potential signal emission sources. The apparatus comprises a plurality of signal transmission conduits and a conduit reformatter. Each signal transmission conduit is configured to transmit a signal emitted by one or more of the signal emission sources between a first end and a second end thereof. The conduit reformatter is constructed and arranged to secure the first ends of the respective signal transmission conduits in a first spatial arrangement corresponding to a spatial arrangement of the signal emission sources, such that the first end of each signal transmission conduit is positioned to receive an emission signal emitted by one or more of the signal emission sources, and to secure the second ends of the respective signal transmission conduits in a second spatial arrangement different from the first spatial arrangement.

The present invention concerns a method of measuring at least one time-varying signal emission from the contents of each of a plurality of receptacles while the contents of all receptacles are subject to repeated cycles of temperature variations within a thermal cycling range as set out in the appended set of claims.

Further aspects of the disclosure are embodied in an apparatus for detecting an emission signal from each of a plurality of emission signal sources, wherein each emission signal is excited by an excitation signal. The apparatus comprises one or more excitation sources configured to generate an excitation signal that is directed at an emission signal source, one or more emission detectors, each emission detector being associated with at least one excitation source and being configured to detect an emission signal emitted by an excitation source and excited by the excitation signal generated by the associated excitation signal source, and a carrier configured to move the one or more excitation sources and the one or more emission detectors relative to the emission signal sources to thereby index each emission detector and associated excitation source past each of the emission signal sources.

According to further aspects of the disclosure, the each emission signal source comprises a substance that emits light of a predetermined emission wavelength when subjected to an excitation signal of a predetermined excitation wavelength and each excitation source is configured to generate an excitation light of the predetermined excitation wavelength and each associated emission detector is configured to detect light of the predetermined emission wavelength.

According to further aspects of the disclosure, the apparatus comprises more than one excitation source, each configured to generate an excitation light of a different predetermined excitation wavelength, and more than one associated emission detector, each configured to detect light of a different predetermined emission wavelength.

According to further aspects of the disclosure, the carrier is configured to rotate about an axis of rotation and move each emission detector and associated excitation source in a circular path.

Other features and characteristics of the present disclosure, as well as the methods of operation, functions of related elements of structure and the combination of parts, and economies of manufacture, will become more apparent upon consideration of the following description and the appended claims with reference to the accompanying drawings, all of which form a part of this specification, wherein like reference numerals designate corresponding parts in the various figures.

The accompanying drawings, which are incorporated herein and form part of the specification, illustrate various, non-limiting embodiments of the present disclosure. In the drawings, common reference numbers indicate identical or functionally similar elements.

Unless defined otherwise, all terms of art, notations and other scientific terms or terminology used herein have the same meaning as is commonly understood by one of ordinary skill in the art to which this disclosure belongs. Many of the techniques and procedures described or referenced herein are well understood and commonly employed using conventional methodology by those skilled in the art. As appropriate, procedures involving the use of commercially available kits and reagents are generally carried out in accordance with manufacturer defined protocols and/or parameters unless otherwise noted.

As used herein, "a" or "an" means "at least one" or "one or more.

This description may use relative spatial and/or orientation terms in describing the position and/or orientation of a component, apparatus, location, feature, or a portion thereof. Unless specifically stated, or otherwise dictated by the context of the description, such terms, including, without limitation, top, bottom, above, below, under, on top of, upper, lower, left of, right of, in front of, behind, next to, adjacent, between, horizontal, vertical, diagonal, longitudinal, transverse, etc., are used for convenience in referring to such component, apparatus, location, feature, or a portion thereof in the drawings and are not intended to be limiting.

Aspects of the present disclosure involve apparatus and procedures for transmitting and/or measuring signals emitted by potential emission signal sources and can be used in conjunction with nucleic acid diagnostic assays, including "real-time" amplification assays and "end-point" amplification assays.

There are many established procedures in use for amplifying nucleic acids, including the polymerase chain reaction (PCR), (see, e.g.,<CIT>), transcription-mediated amplification (TMA), (see, e.g., <CIT>), ligase chain reaction (LCR), (see, e.g., <CIT>), strand displacement amplification (SDA), (see, e.g.,<CIT>), and loop-mediated isothermal amplification (see, e.g., <CIT>). A review of several amplification procedures currently in use, including PCR and TMA, is provided in <NPL>).

Real-time amplification assays can be used to determine the presence and amount of a target nucleic acid in a sample which, by way of example, is derived from a pathogenic organism or virus. By determining the quantity of a target nucleic acid in a sample, a practitioner can approximate the amount or load of the organism or virus in the sample. In one application, a real-time amplification assay may be used to screen blood or blood products intended for transfusion for bloodborne pathogens, such as hepatitis C virus (HCV) and human immunodeficiency virus (HIV). In another application, a real-time assay may be used to monitor the efficacy of a therapeutic regimen in a patient infected with a pathogenic organism or virus, or that is afflicted with a disease characterized by aberrant or mutant gene expression. Real-time amplification assays may also be used for diagnostic purposes, as well as in gene expression determinations. Exemplary systems and methods for performing real-time amplification assays are described in <CIT>, entitled "Methods for Performing Multi-Formatted Assays," and in <CIT>, entitled, "System for performing multi-formatted assays.

In addition to implementation of embodiments of the disclosure in conjunction with real-time amplification assays, embodiments of the disclosure may also be implemented in conjunction with end point amplification assays. In end-point amplification assays, the presence of amplification products containing the target sequence or its complement is determined at the conclusion of an amplification procedure. Exemplary systems and methods for end-point detection are described in <CIT>, entitled "Automated Process For Isolating and Amplifying a Target Nucleic Acid Sequence. " In contrast, in "real-time" amplification assays, the amount of amplification products containing the target sequence or its complement is determined during an amplification procedure. In the real-time amplification assay, the concentration of a target nucleic acid can be determined using data acquired by making periodic measurements of signals that are functions of the amount of amplification product in the sample containing the target sequence, or its complement, and calculating the rate at which the target sequence is being amplified from the acquired data.

For real-time amplification assays, the probes are, in certain embodiments, unimolecular, self-hybridizing probes having a pair of interacting labels that interact and thereby emit different signals, depending on whether the probes are in a self-hybridized state or hybridized to the target sequence or its complement. See, e.g., <CIT>; <CIT>; <CIT>; and <CIT>. Other probes are known, including complementary, bimolecular probes, probes labeled with an intercalating dye and the use of intercalating dyes to distinguish between single-stranded and double-stranded nucleic acids. See, e.g., <CIT>; <CIT>; and <CIT>. Examples of interacting labels include enzyme/substrate, enzyme/cofactor, luminescent/quencher, luminescent/adduct, dye dimers and Förrester energy transfer pairs. Methods and materials for joining interacting labels to probes for optimal signal differentiation are described in the above-cited references. A variety of different labeled probes and probing mechanisms are known in the art, including those where the probe does not hybridize to the target sequence. See, e.g., <CIT> and <CIT>. The embodiments of the present disclosure operate regardless of the particular labeling scheme utilized provided the moiety to be detected can be excited by a particular wavelength of light and emits a distinguishable emission spectra.

In an exemplary real-time amplification assay, the interacting labels include a fluorescent moiety, or other emission moiety, and a quencher moiety, such as, for example, <NUM>-(<NUM>-dimethylaminophenylazo) benzoic acid (DABCYL). The fluorescent moiety emits light energy (i.e., fluoresces) at a specific emission wavelength when excited by light energy at an appropriate excitation wavelength. When the fluorescent moiety and the quencher moiety are held in close proximity, light energy emitted by the fluorescent moiety is absorbed by the quencher moiety. But when a probe hybridizes to a nucleic acid present in the sample, the fluorescent and quencher moieties are separated from each other and light energy emitted by the fluorescent moiety can be detected. Fluorescent moieties having different and distinguishable excitation and emission wavelengths are often combined with different probes. The different probes can be added to a sample, and the presence and amount of target nucleic acids associated with each probe can be determined by alternately exposing the sample to light energy at different excitation wavelengths and measuring the light emission from the sample at the different wavelengths corresponding to the different fluorescent moieties. In another embodiment, different fluorescent moieties having the same excitation wavelength, but different and distinguishable emission wavelengths are combined with different probes. The presence and amount of target nucleic acids associated with each probe can be determined by exposing the sample to a specific wavelength light energy and the light emission from the sample at the different wavelengths corresponding to the different fluorescent moieties is measured.

In one example of a multiplex, real-time amplification assay, the following may be added to a sample prior to initiating the amplification reaction: a first probe having a quencher moiety and a first fluorescent dye (having an excitation wavelength λex1 and emission wavelength ) joined to its <NUM>' and <NUM>' ends and having specificity for a nucleic acid sequence derived from HCV; a second probe having a quencher moiety and a second fluorescent dye (having an excitation wavelength λex2 and emission wavelength λem2) joined to its <NUM>' and <NUM>' ends and having specificity for a nucleic acid sequence derived from HIV Type <NUM> (HIV-<NUM>); and a third probe having a quencher moiety and a third fluorescent dye (having an excitation wavelength λex3 and emission wavelength λem3) joined to its <NUM>' and <NUM>' ends and having specificity for a nucleic acid sequence derived from West Nile virus (WNV). After combining the probes in a sample with amplification reagents, the samples can be periodically and alternately exposed to excitation light at wavelengths λex1, λex2, and λex3, and then measured for emission light at wavelengths λem1, λem2, and λem3, to detect the presence (or absence) and amount of all three viruses in the single sample. The components of an amplification reagent will depend on the assay to be performed, but will generally contain at least one amplification oligonucleotide, such as a primer, a promoter-primer, and/or a promoter oligonucleotide, nucleoside triphosphates, and cofactors, such as magnesium ions, in a suitable buffer.

Where an amplification procedure is used to increase the amount of target sequence, or its complement, present in a sample before detection can occur, it is desirable to include a "control" to ensure that amplification has taken place. Such a control can be a known nucleic acid sequence that is unrelated to the sequence(s) of interest. A probe (i.e., a control probe) having specificity for the control sequence and having a unique fluorescent dye (i.e., the control dye) and quencher combination is added to the sample, along with one or more amplification reagents needed to amplify the control sequence, as well as the target sequence(s). After exposing the sample to appropriate amplification conditions, the sample is alternately exposed to light energy at different excitation wavelengths (including the excitation wavelength for the control dye) and emission light is detected. Detection of emission light of a wavelength corresponding to the control dye confirms that the amplification was successful (i.e., the control sequence was indeed amplified), and thus, any failure to detect emission light corresponding to the probe(s) of the target sequence(s) is not likely due to a failed amplification. Conversely, failure to detect emission light from the control dye may be indicative of a failed amplification, thus calling into question the results from that assay. Alternatively, failure to detect emission light may be due to failure or deteriorated mechanical and/or electrical performance of an instrument (described below) for detecting the emission light.

Apparatus and procedures embodying aspects of the disclosure may be used a variety of nucleic acid amplification procedures, including in conjunction with real-time PCR, which requires accurate/rapid thermocycling between denaturation (~<NUM>), annealing (~<NUM>), and synthesis (~<NUM>) temperatures. For this purpose, receptacles containing a reaction mixture that is to be subject to PCR are held in a thermocycler configured to effect temperature cycling between the denaturation, annealing, and synthesis phases. Emission signal monitoring (e.g., of fluorescence) of the contents of the receptacles held in the thermocycler occurs at one or many color wavelengths during each temperature cycle between <NUM>, <NUM>, and synthesis <NUM>. PCR components include; for example, a forward and a reverse amplification oligonucleotides, and a labeled poly or oligonucleotide probe. During one exemplary PCR procedure, nucleic acid amplification oligonucleotides hybridize to opposite strands of a target nucleic acid and are oriented with their <NUM>' ends facing each other so that synthesis by a polymerization enzyme such as a polymerase extends across the segment of nucleic acid between them. While the probe is intact, the proximity of the quencher dye quenches the fluorescence of the reporter dye. During amplification if the target sequence is present, the fluorogenic probe anneals downstream from one of the amplification oligonucleotide sites and is cleaved by the <NUM>' nuclease activity of the polymerization enzyme during amplification oligonucleotide extension. The cleavage of the probe separates the reporter dye from the quencher dye, thus rendering detectable the reporter dye signal and, eventually, removing the probe from the target strand, allowing amplification oligonucleotide extension to continue to the end of the template strand.

One round of PCR synthesis will result in new strands of indeterminate length which, like the parental strands, can hybridize to the amplification oligonucleotides upon denaturation and annealing. These products accumulate arithmetically with each subsequence cycle of denaturation, annealing to amplification oligonucleotides, and synthesis. The second cycle of denaturation, annealing, and synthesis produces two single-stranded products that together compose a discrete double-stranded product which comprises the length between the amplification oligonucleotide ends. Each strand of this discrete product is complementary to one of the two amplification oligonucleotides and can therefore participate as a template in subsequent cycles. The amount of this product doubles with every subsequent cycle of synthesis, denaturation and annealing. This accumulates exponentially so that <NUM> cycles should result in a <NUM><NUM>-fold (<NUM> million-fold) amplification of the discrete product.

Detection, and, optionally, measurement, of emission signals from emission signal sources, such as receptacles containing reaction materials undergoing amplification as described above can be performed in accordance with aspects of the present disclosure with a signal detection module. A signal detection module embodying aspects of the present disclosure is indicated by reference number <NUM> in <FIG>. The signal detection module includes an upright reformatter frame <NUM>. Two signal detector heads <NUM> are attached to a lower end of the reformatter frame <NUM> and an interface plate <NUM> is attached to an upper end of the reformatter frame <NUM>. In general, the reformatter frame includes sides <NUM>, <NUM> which, in the illustrated embodiment, comprise generally vertical columns, and a base <NUM> within which are formed a plurality of fiber-positioning holes <NUM>. Note that the designation of the reformatter frame <NUM> as being upright or the sides <NUM>, <NUM> as being vertical is merely to provide a convenient reference with respect to the orientation of the signal detection module <NUM> as shown in <FIG>, and such terms of orientation are not intended to be limiting. Accordingly, the signal detection module <NUM> could be oriented at any angle, including vertical or horizontal, or any angle therebetween. The reformatter frame has a variety of purposes, including organizing and arranging a plurality of optical transmission fibers <NUM> between an excitation/emission area and a detection area in an optimum optical pathway orientation. In particular embodiments the reformatter also provides for controlled orientation of a plurality of optical transmission fibers <NUM> between the fins of a heat sink to a detection area.

Signal transmission conduits, such as optical transmission fibers <NUM> extend between the interface plate <NUM> and the base <NUM> of the reformatter frame <NUM>. In the present context, an optical transmission fiber, or optical fiber, comprises a flexible, transparent rod made of glass (silica) or plastic that functions as a waveguide, or light pipe, to transmit light between the two ends of the fiber. Optical fibers typically include a transparent core surrounded by an opaque or transparent cladding material having a lower index of refraction than the core material. A light transmission is maintained within the core by total internal reflection. Each optical fiber may comprise a single fiber having a single fiber core, or each fiber may comprise a fiber bundle of two or more fibers. Fiber bundlers may be preferred if a tight bend radius is required for the transmission fiber <NUM>. In certain embodiments it may be preferable to provide an optical fiber cladding that is resistant to the effects of high heat indexes in that the optical transmission properties of the fiber are maintained in the presence of heat indexes well-above room temperature.

In one aspect of the disclosure, the reformatter frame is constructed and arranged to reconfigure the relative spatial arrangements of the fibers <NUM> from their first ends to their second ends so as to rearrange the transmission fibers <NUM> into a spatial arrangement in which they can be more efficiently interrogated by a signal measuring device to measure a signal transmitted therethrough. In the context of this description, the first end of the fiber <NUM> corresponds to the end of the fiber closest to the signal emission source is being measured, and the second end of the fiber corresponds to the end of the fiber closest to the signal detector. This is merely a convenient terminology for distinguishing one end of the transmission fiber <NUM> from another end of the transmission fiber <NUM>. Otherwise, the designation of the ends of the fibers as being a first end or a second end is arbitrary.

The first ends of the transmission fibers <NUM> are attached to the interface plate <NUM>, for example extending into or through openings formed through the interface plate <NUM>. Signal coupling elements <NUM>, e.g., ferrules, may be provided in each of the openings formed in the interface plate <NUM> for securely attaching each optical transmission fiber <NUM> to the interface plate <NUM>. Although not shown in <FIG>, each opening formed in the interface plate <NUM> may be in signal transmission communication with an emission signal source. In one embodiment, a signal emission source may comprise a receptacle containing the contents of a chemical or biological assay. In the case of optical emission signals, the receptacles may be positioned and held so as to optically isolate each receptacle from the surrounding receptacles. In addition, as noted above, the receptacles may be held within an incubator device located in optical communication with the interface plate <NUM>, configured to alter the temperature of receptacles or maintain the receptacles at a specified temperature. In such an application, it may be desirable that the interface plate <NUM> is formed of a suitably heat-conducting material, such as aluminum or copper, and that the interface plate <NUM> further include heat dissipating fins <NUM> formed on one side of the interface plate <NUM> for dissipating heat from the interface plate <NUM> by convection. Also, coupling elements (ferrules) <NUM> may be thermally insulating to insulate the transmission fibers <NUM> from the heat of the receptacles held within the incubator. Suitable insulating materials include Ultem (polyethylene ketone (PEEK)).

In the embodiment illustrated in <FIG>, the transmission fibers <NUM> are attached to the interface plate <NUM> in a rectangular configuration comprising a plurality of rows, each row having one or more transmission fibers <NUM>. As shown in the illustrated embodiment, in an application in which the interface plate <NUM> includes heat dissipating fins <NUM>, the transmission fibers <NUM> may extend between adjacent fins <NUM> into an associated opening formed in the interface plate <NUM>. The illustrated embodiment includes twelve rows of five transmission fibers <NUM> each, for a total of sixty transmission fibers that can be employed for interrogating up to sixty individual emission sources, such as reaction receptacles containing reaction materials therein. Each row of transmission fibers <NUM> may be disposed between a pair of adjacent heat-dissipating fins <NUM>.

The second ends of the transmission fibers <NUM> are connected to the base <NUM> of the reformatter frame <NUM>, for example, by being aligned with or inserted into or through fiber-positioning holes <NUM>. The fiber-positioning holes <NUM> are in a spatial arrangement that is different from the spatial arrangement fiber-receiving holes formed in the interface plate <NUM> and are in a position that can be more efficiently interrogated by one or more signal detectors. In the illustrated embodiment, each of the fiber position holes <NUM> is arranged in a circle, <FIG> exemplifies two such arrangements, each circle accommodating a plurality of the transmission fibers <NUM> extending from the interface plate <NUM>. Other spatial arrangements are contemplated, including, two or more concentric circles, one or more open rectangles, one or more ovals, etc..

The length of the fiber reformatter <NUM> is defined by the distance between the base <NUM> and the interface plate <NUM> and is selected by balancing two, sometimes competing considerations. On the one hand, to make the signal detection module <NUM> as compact as possible, the smallest possible length of the fiber reformatter <NUM> is desired. On the other hand, because the flexibility of the transmission fibers <NUM> may be limited, a longer fiber reformatter <NUM> will make it easier to bend each transmission fiber <NUM> when reformatting the fiber from its position within the fiber arrangement in the interface plate <NUM> to its position in the fiber arrangement in the base <NUM> of the fiber reformatter <NUM>. In one embodiment, using thirty fibers having a diameter of <NUM>, a fiber reformatter having a length of <NUM> - <NUM> was found to be suitable. In other embodiments, plastic fibers having a diameter of <NUM> and a length of <NUM> +/- <NUM> were used.

A somewhat modified embodiment of the signal detection module embodying aspects of the present disclosure is represented by reference number <NUM> in <FIG>, <FIG>, and <FIG>. The signal detection module <NUM> includes a reformatter frame <NUM> that includes sides <NUM>, <NUM> and a base <NUM>. An interface plate <NUM> is attached to one end of the reformatter frame <NUM>, and two signal detector heads <NUM> are attached to the base <NUM> at an opposite end of the reformatter frame <NUM>. As opposed to the embodiment show in <FIG>, in which the base <NUM> of the reformatter frame <NUM> forms a generally orthogonal angle with respect to the sides <NUM>,<NUM> of the reformatter frame <NUM> such that the base <NUM> is generally parallel to the interface plate <NUM>, the reformatter frame <NUM> of signal detection module <NUM> is configured such that the base <NUM> is at an acute angle with respect to the sides <NUM>, <NUM> so that the base <NUM> is not parallel to the interface plate <NUM>.

Transmission fibers <NUM> extend from a first end thereof connected to the interface plate <NUM> in a first spatial arrangement to a second end thereof connected to the base <NUM> in a second spatial arrangement. As with the embodiment shown in <FIG>, the transmission fibers <NUM> are reformatted from a generally rectangular configuration attached to the interface plate <NUM> into two circular arrangements, each accommodating half of the transmission fibers <NUM>, attached to the base <NUM>.

As also shown in <FIG>, a processing module <NUM>, such as an incubator, including a plurality of receptacle holders <NUM>, each configured to hold one or more receptacles <NUM>, is positioned above the interface plate <NUM>. In the illustrated embodiment, the receptacle holders <NUM> are constructed and arranged to hold sixty receptacles <NUM> arranged in twelve rows of five receptacles <NUM> each. In one embodiment, processing module <NUM> may be an incubator, and each receptacle holder <NUM> may be constructed and arranged to impart thermal energy to the receptacles <NUM> held thereby to change and/or maintain the temperature of the contents of each receptacle <NUM>. In one embodiment, processing module <NUM> comprises an incubator as disclosed in Application Serial Number<CIT>, to the extent published in <CIT>, which claims priority therefrom.

For applications in which heat dissipation from the interface plate <NUM> is necessary or desirable, such as when the processing module <NUM> disposed on the interface plate <NUM> comprises an incubator or other heat-generating device, heat dissipating fins <NUM> may be provided on the interface plate <NUM>. To augment heat dissipation via the heat dissipating fins <NUM>, the signal detection module <NUM> may include a fan <NUM> disposed within a fan housing <NUM> mounted to the reformatter frame <NUM>. Fan <NUM> is constructed and arranged to generate air flow over the heat dissipating fins <NUM> to enhance the convective heat dissipation from the fins <NUM>.

<FIG> show front and rear, respectively, perspective views of the fiber reformatter frame <NUM> of the signal detection module <NUM> shown in <FIG>. The signal detector heads <NUM>, the processing module <NUM>, the fan <NUM>, and the fan housing <NUM> are not shown in <FIG>. The reformatter frame <NUM> includes sides <NUM>, <NUM>, a base <NUM> attached to one end of the sides <NUM>, <NUM>, and an interface plate <NUM> attached to an opposite end of the sides <NUM>, <NUM>. Signal coupling elements <NUM> are attached to each of the fiber-receiving openings formed in the interface plate <NUM>. As explained above, coupling elements <NUM>, which may comprise ferrules, are constructed and arranged to couple a signal, e.g., an optic signal, from the corresponding transmission fiber <NUM> to an object to be interrogated, such as the contents of a receptacle, and/or couple an optical emission from the object into the transmission fiber <NUM>.

The base <NUM> includes two openings <NUM>, <NUM>, each configured to accommodate one of the signal detector heads <NUM>. A plurality of fiber-positioning holes <NUM> is provided around each of the openings <NUM>, <NUM>. <FIG> show only a portion of each of the transmission fibers <NUM> extending from the interface plate <NUM>. In the illustrated embodiment, the transmission fibers <NUM> are connected to the interface plate <NUM> in a rectangular configuration, and the fiber-positioning holes <NUM> formed in the base <NUM> are in a circular configuration so as to reformat the transmission fibers <NUM> from the rectangular configuration at the first ends thereof to a circular configuration at the second ends thereof.

<FIG> is a perspective view of an alternative embodiment of a reformatter frame <NUM>. Reformatter frame <NUM> includes sides <NUM>, <NUM> and a base <NUM> having an opening <NUM> formed therein with a plurality of fiber-positioning holes <NUM> positioned around the opening <NUM> in a generally circular configuration. An interface plate <NUM> is attached to the sides <NUM>, <NUM> of the frame <NUM> at an end thereof opposite the base <NUM>. Interface plate <NUM> includes a plurality of coupling elements <NUM>, e.g., ferrules, and may include heat dissipating fins <NUM> disposed on a side of the interface plate <NUM> opposite the coupling elements <NUM>. Each coupling element <NUM> corresponds to a fiber-receiving opening (not shown) formed through the interface plate <NUM>. As can be seen in <FIG>, the coupling elements <NUM> are arranged in a rectangular configuration of six rows of five coupling elements <NUM> each. The number of openings <NUM> formed in the base <NUM> preferably corresponds to the number of coupling elements <NUM> formed in the interface plate <NUM>. Thus, it can be appreciated that the reformatter frame <NUM> shown in <FIG> has half the capacity of the reformatter frame <NUM> shown in <FIG>, and that the reformatter frame <NUM> corresponds essentially to a doubling of the reformatter frame <NUM> with a second opening <NUM> and corresponding fiber-positioning holes <NUM> surrounding the opening and six additional rows of five coupling elements <NUM> attached to the interface plate <NUM>. However, one of skill in the art would appreciate that reformatter frame <NUM> could be configured to have the same capacity, or more or less capacity to that of reformatter frame <NUM> shown in <FIG>.

<FIG> shows an exemplary mapping of the spatial arrangement of fiber positions in the interface plate <NUM> of the reformatter frame <NUM>. As shown in <FIG>, the interface plate <NUM> includes six rows, or banks, of five fiber positions each, designated T1-T5, T6-T10, T11-T15, T16-.

<FIG> shows a mapping of the spatial arrangement of fiber positions of the fiber-positioning holes <NUM> formed in the base <NUM> of the reformatter frame <NUM>. In the illustrated embodiment, <NUM> fiber-positioning holes <NUM> are formed in the base <NUM>, and are designated F1, F2, F3, F4,. F35, starting at the lower (six o'clock) position with respect to the opening <NUM>.

<FIG> is a table showing an exemplary mapping of the rectangularly-arranged interface positions T1-T30 in the interface plate <NUM> to thirty of the circularly-arranged fiber-positioning hole positions F1-F35 in the base <NUM>. This is exemplary only; other mappings between the fiber positions in the interface plate <NUM> and the fiber positions in the base <NUM> are contemplated. In this embodiment, the number of interface positions in the interface plate <NUM> is exceeded by the number of fiber-positioning holes in the base <NUM> (e.g., <NUM> vs. <NUM>). Fluorescent calibration targets can be placed in the additional fiber-positioning holes in the base to test and/or calibrate the signal detectors of the signal detector head <NUM>.

In an alternative embodiment, the number of interface positions in the interface plate <NUM> is equal to the number of fiber-positioning holes in the base <NUM> (e.g., <NUM>). It has been determined that the autofluorescence of the signal transmission fibers can also be used as a fluorescent calibration target. For example, autofluorescence of the signal transmission fibers can be used to determine the rotary positions of the detector carrier <NUM> at which signal measurements should be taken. An exemplary process is as follows.

Starting at a known rotary position, e.g., as determined by a home flag associated with the detector carrier <NUM>, the detector carrier <NUM> can be rotated, counting steps of the motor <NUM>, until the autofluorescence signal detected by each signal detector <NUM> - each of which may be configured to detect a signal of a different wavelength - reaches a peak. Due to manufacturing and assembly tolerances, the number of motor steps at which each signal detector detects a peaks signal may be somewhat different. For example, in a system including five signal detectors <NUM>, one signal detector <NUM> may peak at <NUM> steps from the home flag position, another at <NUM> steps, another at <NUM> steps, another at <NUM> steps, and another at <NUM> steps. The calibrated position at which a measurement is taken may be determined as to be the closest whole number of steps to the average of the five measurements, i.e., <NUM> steps (from an average of <NUM> steps) from the home position. If the tolerances in the placement of the fiber positioning holes <NUM> are sufficiently small, so that the number of motor steps between fibers is known and repeatable, no further calibration is necessary. Subsequent measurements can be taken every known number of steps after the calibrated position of the first measurement. If the tolerances are not sufficiently small, measurement positions for all fibers can be calibrated in a similar manner - i.e., by stepping off the motor for each fiber position and taking an average of the number of steps at which the signal detectors detect peak signals. It may be desirable to perform this calibration procedure at final assembly of the apparatus, at laboratory installation of the apparatus, after any service is performed on the apparatus, or before each time the apparatus is operated. <FIG> shows an alternative embodiment of a thirty-fiber reformatter frame <NUM>, including sides <NUM>, <NUM>, a base <NUM> with an opening <NUM> and fiber-positioning openings <NUM> surrounding opening <NUM>, and an interface plate <NUM> having coupling elements <NUM> and heat dissipating fins <NUM> connected to an end of the frame <NUM> opposite the base <NUM>. Fiber reformatter frame <NUM> is comparable to the frame <NUM> shown in <FIG> and accommodates thirty transmission fibers (not shown in <FIG>) configured at the first ends thereof at the interface plate <NUM> in a rectangular configuration of six rows of five fibers each and configured at the second ends thereof at the base <NUM> in a circular configuration disposed within the fiber-positioning holes <NUM> surrounding the opening <NUM>. The reformatter frame <NUM> shown in <FIG> differs from the reformatter frame <NUM> shown in <FIG> in that the base <NUM>, the opening <NUM>, and fiber-positioning openings <NUM> are substantially centered with respect to the interface plate <NUM>. In the reformatter frame <NUM> shown in <FIG>, on the other hand, the base <NUM>, openings <NUM>, and fiber-positioning openings <NUM> are laterally offset with respect to the center of the interface plate <NUM>.

The signal detector head <NUM> is shown in <FIG>. The signal detector head <NUM> may be attached to a reformatter frame (<NUM>, <NUM>, <NUM>, <NUM>) and is constructed and arranged to index one or more signal detectors into operative positions with respect to each transmission fiber disposed in a fiber-positioning hole of the base of the reformatter frame. Although, signal detector head <NUM> is configured to be coupled to any reformatter frame, including reformatter frames <NUM>, <NUM>, <NUM> and <NUM> described herein, for simplicity of the description, the signal detector head <NUM> will be described in the context of its implementation on reformatter frame <NUM> shown in <FIG>.

In the embodiment shown in <FIG>, the signal detector head <NUM> includes a base plate <NUM> configured to be attached to the base <NUM> of the reformatter frame <NUM> and including a plurality of fiber tunnels <NUM> arranged in a configuration corresponding to the spatial arrangement of fiber-positioning holes <NUM> formed in the base <NUM> of the reformatter frame <NUM> so that each fiber tunnel <NUM> will align with a corresponding one of the fiber-positioning holes <NUM>.

In general, the signal detector head is configured to move one or more signal detectors to sequentially place each signal detector into an operative position with respect to each transmission fiber <NUM> to detect a signal transmitted by the transmission fiber. The signal detector head <NUM> further includes a detector carrier <NUM>, which, in the illustrated embodiment, comprises a carousel that carries a plurality of signal detectors <NUM> in a circular pattern. In the illustrated embodiment, the signal detector head <NUM> includes six individual signal detectors <NUM>, each mounted on a printed circuit board <NUM> and each configured to excite and detect a different emission signal or an emission signal having different characteristics.

As will be described in further detail below, the detector carrier <NUM> is configured so as to be rotatable with respect to the base plate <NUM>. A detector drive system <NUM> constructed and arranged to effect powered movement, e.g., rotation, of the detector carrier <NUM> includes a drive motor <NUM> supported on a motor mount portion <NUM> of the base plate <NUM>. A drive belt <NUM> is disposed on an output shaft wheel <NUM> of the motor <NUM> and around a pulley wheel <NUM> that is attached to or part of the detector carrier <NUM>. As can be appreciated, rotation of the output shaft wheel <NUM> of the motor <NUM> causes a corresponding rotation of the pulley wheel <NUM> and the detector carrier <NUM> via the belt <NUM>.

As would be further appreciated by persons of ordinary skill in the art, the configuration of the detector drive system <NUM> is exemplary, and other mechanisms and arrangements may be employed to effect powered movement of the detector carrier <NUM>. For example, the output shaft wheel <NUM> may comprise an output gear that directly engages gear teeth formed about the outer periphery of the pulley wheel <NUM>, or the pulley wheel <NUM> could be coupled to the output shaft wheel <NUM> indirectly by a gear train comprising one or more intermediate gears between the output shaft wheel (gear) <NUM> and the pulley wheel <NUM>. Alternatively, a drive motor could be configured with its rotating output shaft attached concentrically to the detector carrier <NUM> and its axis of rotation so that rotation of the output shaft by the motor causes a direct corresponding rotation of the detector carrier <NUM>. Other arrangements and configurations for effecting powered movement of the detector carrier <NUM> will be appreciated by persons of ordinary skill in the art. In particularly preferred embodiments, the detector carrier <NUM> and detector drive system <NUM> are configured to provide for rotation of the detector carrier <NUM> in a single direction.

Motor <NUM> is preferably a stepper motor and may include a rotary encoder. The detector carrier <NUM> may include one or more positional or status feedback sensors. For example, the detector carrier <NUM> may include a home flag <NUM> that is detected by an optical detector <NUM> for indicating a rotational "home" position of the carrier <NUM>. Optical sensor <NUM> may comprise a slotted optical sensor comprising an optical transmitter and receiver in which the path between the transmitter and receiver is broken by the passage of the home flag <NUM>. Persons of ordinary skill in the art will recognize, however, that other sensors for indicating a home position may be used. Such sensors may comprise proximity sensors, magnetic sensors, capacitive sensors, etc..

A rotary connector transmits data and/or power signals between the rotating detector carrier <NUM> and the signal detectors <NUM> carried thereon, and a non-rotating reference environment, such as a controller and power source as described in more detail below. In the illustrated embodiment, the base <NUM> of the signal detector head <NUM> includes cylindrical housing <NUM> projecting upwardly from a planar portion of the base <NUM>, and a slip ring connector <NUM> is positioned at an end of the cylindrical housing <NUM>. The slip ring connector <NUM> includes a rotating element disposed inside the cylindrical housing <NUM> and a non-rotating element <NUM>, attached or otherwise coupled to the non-rotating cylindrical housing <NUM> by an intermediate ring <NUM>, to which are attached data/power cables <NUM>. The slip ring connector <NUM> transmits data and/or power signals between the rotating detector carrier <NUM> and the signal detectors <NUM> carried thereon, and a non-rotating reference environment, such as a controller and power source as described in more detail below.

Further details of the signal detector head <NUM> are shown in <FIG>, which is a transverse cross-sectional view of the detector head <NUM> along the line XIII-XIII in <FIG>. Each signal detector <NUM> includes a detector housing <NUM> within which are formed an excitation channel <NUM> and an emission channel <NUM>, which, in the illustrated embodiment, are generally parallel to one another. An excitation source <NUM>, such as an LED, is mounted on the printed circuit board <NUM> at the base of the excitation channel <NUM>. An emission detector <NUM>, such as a photodiode, is coupled to the printed circuit board <NUM> and is disposed within the emission channel <NUM>.

The detector carrier <NUM> further includes, positioned adjacent the signal detector housing <NUM>, a filter plate <NUM> having a central opening <NUM> formed therein and defining an annulus. Within the annulus, an emission filter opening <NUM> and an excitation filter opening <NUM> are formed in alignment with the emission channel <NUM> and the excitation channel <NUM>, respectively, of each signal detector housing <NUM>. An excitation lens <NUM> and an excitation filter <NUM> are disposed in the excitation opening <NUM>. Although a single excitation lens <NUM> and a single excitation filter <NUM> are shown in <FIG>, the signal detector <NUM> may include multiple excitation filters and/or multiple excitation lenses. Similarly, an emission filter <NUM> and an emission lens <NUM> are disposed in the emission opening <NUM>. Although a single emission filter <NUM> and a single emission lens <NUM> are shown in <FIG>, the signal detector <NUM> may include multiple emission lenses and/or multiple emission filters.

The detector carrier <NUM> further includes, adjacent the filter plate <NUM>, a mirror plate <NUM> having a central opening <NUM> and defining an annulus. The annulus of the mirror plate <NUM> has formed therein openings aligned with the emission opening <NUM> and the excitation opening <NUM> formed in the filter plate <NUM> for each signal detector <NUM>. A mirror <NUM> is disposed in the mirror plate <NUM> in general alignment with the excitation channel <NUM>, and a dichroic filter <NUM> is disposed in the mirror plate <NUM> in general alignment with the emission channel <NUM>. Mirror <NUM> is oriented at an angle (e.g. <NUM>°) with respect to the excitation channel <NUM> so as to be configured to redirect a light beam.

The detector carrier <NUM> further includes an objective lens plate <NUM> having a central opening <NUM> formed therein and defining an annulus. A lens opening <NUM> is formed through the annulus of the objective lens plate <NUM> in general alignment with the emission channel <NUM> of each signal detector <NUM>. An objective lens <NUM> is disposed within the lens opening <NUM>.

The base plate <NUM> is disposed adjacent the objective lens plate <NUM> and includes fiber tunnels <NUM> formed about the perimeter thereof. Although base plate <NUM> and objective lens plate <NUM> are depicted as abutting one-another in <FIG>, it is contemplated that there can be a designated distance, forming an air gap, between the base plate <NUM> and the objective lens plate <NUM>. Also, objective lens plate <NUM> and mirror plate <NUM> are depicted as abutting one-another in <FIG>, it is contemplated that there can be a designated distance, forming an air gap, between the objective lens plate <NUM> and the mirror plate <NUM>.

The detector carrier <NUM>, comprising the objective lens plate <NUM>, the mirror plate <NUM>, and the filter plate <NUM>, as well as the signal detectors <NUM> carried thereon, are rotatable with respect to the base plate <NUM> so that each objective lens <NUM> associated with each of the signal detectors <NUM> can be selectively placed into operative alignment with one of the fiber tunnels <NUM> disposed in the base plate <NUM>. Thus, in the illustrated embodiment having six signal detectors <NUM>, at any given time, six of the fiber tunnels <NUM> are in operative, optical alignment with one of the objective lenses <NUM> and its corresponding signal detector <NUM>.

Operation of the signal detector <NUM> in an exemplary embodiment is illustrated schematically in <FIG>. The detector <NUM> shown is a fluorometer that is constructed and arranged to generate an excitation signal of a particular, predetermined wavelength that is directed at the contents of a receptacle to determine if a probe or marker having a corresponding emission signal of a known wavelength is present. When the signal detector head <NUM> includes multiple fluorometers - e.g., six - each fluorometer is configured to excite and detect an emission signal having a different wavelength to detect a different label associated with a different probe hybridized to a different target analyte. When a more frequent interrogation of a sample is desired for a particular emission signal, it may be desirable to incorporate two or more fluorometers configured to excite and detect a single emission signal on the signal detector head <NUM>.

An excitation signal is emitted by the excitation source <NUM>. Excitation source, as noted above, may be an LED and may generate light at a predetermined wavelength, e.g. red, green, or blue light. Light from the source <NUM> passes through and is focused by an excitation lens <NUM> and then passes through the excitation filter <NUM>. As noted, <FIG> is a schematic representation of the signal detector <NUM>, and the focusing functionality provided by the excitation lens <NUM> may be effected by one or more separate lenses disposed before and/or after the filter element <NUM>. Similarly, the filter functionality provided by the filter element <NUM> may be effected by one or more individual filters disposed before and/or after the one or more lenses that provide the focusing functionality. Filter element <NUM> may comprise a low band pass filter and a high band pass filter so as to transmit a narrow wavelength band of light therethrough. Light passing through the excitation lens <NUM> and excitation filter element <NUM> is reflected laterally by the mirror <NUM> toward the dichroic <NUM>. The dichroic <NUM> is constructed and arranged to reflect substantially all of the light that is within the desired excitation wavelength range toward the objective lens <NUM>. From the objective lens <NUM>, light passes into a transmission fiber <NUM> and toward the receptacle at the opposite end thereof. The excitation signal is transmitted by the transmission fiber <NUM> to a receptacle so as to expose the contents of the receptacle to the excitation signal.

A label that is present in the receptacle and is responsive to the excitation signal will emit an emission signal. At least a portion of any emission from the contents of the receptacle enters the transmission fiber <NUM> and passes back through the objective lens <NUM>, from which the emission light is focused toward the dichroic <NUM>. Dichroic <NUM> is configured to transmit light of a particular target emission wavelength range toward the emission filter <NUM> and the emission lens <NUM>. Again, the filtering functionality provided by the emission filter <NUM> may be effected by one or more filter elements and may comprise a high band pass and low band pass filter that together transmit a specified range of emission wavelength that encompasses a target emission wavelength. The emission light is focused by the emission lens <NUM>, which may comprise one or more lenses disposed before and/or after the filter elements represented in <FIG> by emission filter <NUM>. The emission lens <NUM> thereafter focuses the emission light of the target wavelength at the detector <NUM>. In one embodiment, the detector <NUM>, which may comprise a photodiode, will generate a voltage signal corresponding to the intensity of the emission light at the prescribed target wavelength that impinges the detector.

Returning again to <FIG>, a flanged tube <NUM> extends through the central opening <NUM> of the objective lens plate <NUM> and through the cylindrical housing <NUM> of the base plate <NUM>. The flanged tube <NUM> includes a cylindrical tube <NUM> extending through the central opening <NUM> and the cylindrical housing <NUM> and a radial flange <NUM> disposed within the central opening <NUM> of the mirror plate <NUM> and secured by suitable fasteners, such as screws or bolts, to the objective lens plate <NUM>. Longitudinally-spaced bearing races <NUM>, <NUM> are disposed between the interior of the cylindrical housing <NUM> and the exterior of the cylindrical tube <NUM> of the flanged tube <NUM>. Thus, as can be appreciated, the flanged tube <NUM> will rotate, with the detector carrier <NUM>, with respect to the base plate <NUM> and the cylindrical housing <NUM>.

Further details of an exemplary representation of the slip ring <NUM> are also shown in <FIG>. The slip ring connector <NUM> is disposed at the end of the cylindrical tube <NUM> opposite the radial flange <NUM>. As noted above, the cylindrical tube <NUM> rotates with the detector carrier <NUM>, while the cylindrical housing <NUM> remains stationary with the base plate <NUM>. The slip ring connector <NUM>, which may comprise slip rings and brushes as are known, includes stationary components attached or otherwise coupled to the cylindrical housing <NUM> and rotating components attached or otherwise coupled to the rotating cylindrical tube <NUM>. In general, components <NUM>, <NUM> represent non-rotating portion(s) of the slip ring <NUM> in which fixed contact components, such as the brush(es), are located, component <NUM> located inside tube <NUM> represents rotating portion(s) of the slip ring <NUM> that rotate with the tube <NUM> and in which rotating contact elements, such as the ring(s) are located, and cable <NUM> represents a power and/or data conductor(s) connecting component <NUM> with the printed circuit board <NUM> and which rotates with the printed circuit board <NUM> and the signal detector carrier <NUM>.

As the detector carrier <NUM> rotates, each of the signal detectors <NUM> is sequentially placed in an operative position with respect to a second end of a different transmission fiber <NUM> to interrogate (i.e., measure a signal from) an emission signal source located at a first end of the transmission fiber <NUM>. The detector carrier <NUM> pauses momentarily at each transmission fiber <NUM> to permit the signal detector <NUM> to detect an emission signal transmitted through the transmission fiber <NUM>. Where the signal detector <NUM> is a fluorometer, the detector carrier pauses momentarily to permit the signal detector to generate an excitation signal of a specified wavelength that is transmitted by the transmission fiber <NUM> to the emission signal source (receptacle) and to detect fluorescence of a specified wavelength excited by the excitation signal that is emitted by the contents of the receptacle and transmitted by the transmission fiber <NUM> to the fluorometer. Thus, in an embodiment, each transmission fiber <NUM> can be employed to transmit both an excitation signal and the corresponding emission signal, ad each signal detector can be used to scan multiple transmission fibers and associated emission signal sources.

The emission signal source associated with each transmission fiber <NUM> is interrogated once by each signal detector <NUM> for every revolution of the detector carrier <NUM>. Where the signal detector head <NUM> includes multiple signal detectors <NUM> configured to detect different signals, each emission signal source is interrogated once for each different signal for every revolution of the detector carrier. Thus, in the case of a nucleic acid diagnostic assay, which may include PCR amplification, the contents of each receptacle is interrogated for each target analyte corresponding to the different probes employed (as indicated by different colored labels) once for each revolution of the detector carrier <NUM>.

In one embodiment, in which base plate <NUM> of the signal detector head <NUM> includes thirty (<NUM>) fiber tunnels for thirty (<NUM>) transmission fibers <NUM>, the signal detector carrier rotates one revolution every four (<NUM>) seconds, stopping at least ten (<NUM>) milliseconds at each fiber tunnel to measure an emission signal transmitted by the associated transmission fiber. Again, if the signal detector head include multiple signal detectors (e.g., six (<NUM>) fluorometers), the signal detector head will measure an emission for each of the six different wavelengths of interest once every four (<NUM>) seconds. Accordingly, time vs. emission signal intensity data can be generated for each receptacle for each wavelength.

When performing PCR, it is not necessary to synchronize the signal data acquisition with the thermal cycles of the PCR process. That is, it is not necessary that the emission signal of each receptacle be measured at the same temperature point (e.g., <NUM>) in the PCR cycle. By recording data every four seconds during the entire PCR process, a sufficient number of data points will be collected at each temperature of the PCR thermal cycle. The signal emission data is synchronized with specific temperatures by recording a time stamp for each emission signal measurement and a time stamp for each temperature of the thermal cycling range. Thus, for example, to identify all signal measurements occurring at a temperature of <NUM>, the time stamps of the signal measurements are compared to the temperature time stamps corresponding to a temperature of <NUM>° C.

The time duration of a thermal cycle is variable, depending on the assay being performed. The minimum time interval is dictated by how fast the thermocycler can ramp temperatures up and down. For a cycler that can ramp the vial filled with fluid from <NUM>° C to <NUM>° C in about <NUM> seconds, an exemplary cycle would be anneal at <NUM>° C for <NUM> seconds, a <NUM> second from <NUM>° C to <NUM>° C, , denature at <NUM>° C for <NUM> seconds, and <NUM> second ramp back down from <NUM>° C to <NUM>°, and then begin another cycle with a <NUM> second anneal, Thus, this exemplary anneal-denature cycle would be a <NUM> second cycle.

The control and data acquisition system of the signal detector head <NUM> is shown schematically in <FIG>. As shown in <FIG>, the detector carrier <NUM> carries one or more signal detectors <NUM>, each of which may, in one embodiment, include an excitation source <NUM>, an excitation lens <NUM>, a mirror <NUM>, a dichroic <NUM>, an objective lens <NUM>, an emission lens <NUM>, and an emission detector <NUM> as described above. Each receptacle <NUM> carried in, e.g., a processing module <NUM> (see <FIG>), is coupled to a transmission fiber <NUM> that terminates in the base plate <NUM> of the signal detector head <NUM>. Motor <NUM> is mechanically coupled to the detector carrier <NUM> by a motor coupler <NUM> to effect powered movement (e.g., rotation) of the detector carrier <NUM>. A controller <NUM> may be coupled to a controllable power source <NUM> and to the motor <NUM> for providing motor control signals and receiving motor position feedback signals, e.g., from a rotary encoder. Controller <NUM> may also be coupled to other feedback sensors, such as the home sensor <NUM>, for detecting a rotational position of the detector carrier <NUM>. Controller <NUM> also provides controlled power signals, via the slip ring connector <NUM>, to the excitation sources <NUM> rotatably carried on the detector carrier <NUM> and coupled to the printed circuit board <NUM>. The functionality of controller <NUM> may be provided by one controller or multiple controllers in functional communication with each other. Moreover, one or more controllers, or one or more component(s) thereof, may be carried on the rotating portion of the detector head <NUM>, such as on the printed circuit board <NUM>. Voltage signals from the emission detectors <NUM>, coupled to the printed circuit board <NUM>, and other data may be carried from the detector carrier <NUM>, via the slip ring connector <NUM>, to a processor <NUM> for storing and/or analyzing the data. Alternatively, processor <NUM>, or one or more component(s) thereof, may be carried on the rotating portion of the detector head <NUM>, such as on the printed circuit board <NUM>.

An exemplary control configuration of the signal detector head <NUM> is represented by reference number <NUM> in <FIG>. An optics controller <NUM> may be provided for each detector carrier, or rotor, and coupled to the printed circuit board <NUM> to which the excitation sources (LED) <NUM> and emission detectors (PD (photodiode)) <NUM> are attached. Each optics controller <NUM> may include a microcontroller <NUM>, e.g., a PIC18F-series microcontroller available from Microchip Technology Inc. , an analog to digital converter <NUM>, and an integrated amplifier <NUM> (e.g., one for each emission detector (PD) <NUM>). A constant current driver <NUM> (e.g. one for each excitation source <NUM>) is controlled by the microcontroller <NUM> and generates control signals (e.g., controlled power) to the excitation source <NUM>. Controller <NUM> receives power at <NUM> (e.g., <NUM> V) from the slip ring connector <NUM> and includes a serial data link RS-<NUM><NUM> for commutations between the controller <NUM> and the slip ring connector <NUM>.

An exemplary control configuration <NUM> may include a motion controller <NUM> for each detector drive <NUM> (see <FIG>). At <NUM>, motion controller <NUM> receives power, e.g., <NUM> VDC, <NUM> watts from controllable power source <NUM> (see <FIG>), that is transmitted to the optics controller <NUM> via the slip ring <NUM>. Motion controller <NUM> may communicate with an external controller via a serial data link <NUM>. In one embodiment, controller <NUM> communicates with a controller of the thermocycler to synchronize operation of the signal detector head <NUM> with operation of the thermocycler. Controller <NUM> may include a serial data link RS-<NUM><NUM> for communications between the controller <NUM> and the slip ring <NUM>. Controller <NUM> may further include a microcontroller <NUM>, e.g., a PIC18F-series microcontroller available from Microchip Technology Inc. and a PMD chip set <NUM>, which is a motor controller to control the stepper motor. A stepper motor driver <NUM> is controlled by the microcontroller <NUM> and generates motor control signals for the motor <NUM> of the optics rotor (i.e., detector drive). A slotted optical sensor input <NUM> receives signals from the home flag sensor <NUM> and communicates such signals to the microcontroller <NUM>.

An alternative embodiment of a signal detector head embodying aspects of the present disclosure is indicated by reference number <NUM> in Figs. <NUM> and <NUM>. Signal detector head <NUM> includes a filter wheel <NUM> and a camera <NUM> oriented in a radial focal direction with respect to the filter wheel <NUM>. In general, signal detector head <NUM> employs the camera <NUM> to image a plurality of bundled fibers to detect a signal transmitted by each fiber. The filter wheel <NUM> can be indexed to selectively couple each of one or more excitation sources and emission filters with the fiber bundle and the camera <NUM> to direct an excitation signal of a specified characteristic, e.g., wavelength, to the fibers of the fiber bundle and to direct emission signals of a specified characteristic, e.g., wavelength, from the fibers of the fiber bundle to the camera <NUM>.

More particularly, signal detector head <NUM> includes a filter wheel <NUM> that comprises a body <NUM>. Body <NUM> may be a body or assembly of revolution configured to be rotatable about a central axis. A motor <NUM> is coupled to the filter wheel <NUM> by a transmission element <NUM> to effect powered rotation of the filter wheel <NUM>. Transmission element <NUM> may comprise any suitable transmission means for transmitting the rotation of the motor <NUM> to the filter wheel <NUM>. Exemplary transmissions include interengaged gears, belts and pulleys, and an output shaft of the motor <NUM> directly attached to the body <NUM>, etc. Motor <NUM> may be a stepper motor to provide precise motion control and may further include a rotary encoder. The filter wheel <NUM> may further include a home flag for indicating one or more specified rotational positions of the filter wheel <NUM>. Suitable home flags include slotted optical sensors, magnetic sensors, capacitive sensors, etc. A fiber bundle <NUM> includes a plurality of fibers fixed at the first ends thereof with respect to the filter wheel <NUM>, e.g., to a fixed plate <NUM> located adjacent to the filter wheel <NUM>, by a fiber mounting block <NUM>. The second ends of the respective fibers are coupled to each of a plurality of signal sources positioned in a first specified arrangement, and may include receptacles (such as receptacles <NUM>) positioned in a rectangular arrangement.

The filter wheel <NUM> includes one or more optics channels <NUM> and is movable so as to selectively index each optics channel <NUM> into an operative, optical communication with the fiber bundle <NUM> and the camera <NUM>. Each optics channel <NUM> includes an excitation channel <NUM> formed in an axial direction within the body <NUM> of the index wheel <NUM> for transmitting an excitation signal to the fiber bundle <NUM> and an emission channel <NUM> extending radially from the excitation channel <NUM> to a radial opening on the outer periphery of the filter wheel <NUM>.

An excitation source <NUM>, e.g., a bright light LED, is disposed within the excitation channel <NUM>. The excitations sources <NUM> of all the emission channels <NUM> may be connected to a printed circuit board <NUM>. One or more lenses <NUM> and one or more excitation filters <NUM> are positioned within the excitation channel <NUM> to condition light emitted by the source <NUM>. Each optics channel <NUM> may be configured to generate and transmit an excitation signal of a specified wavelength. In such an embodiment, filter(s) <NUM> are configured to transmit light at the desired wavelength.

Each channel <NUM> includes a dichroic <NUM> configured to transmit that portion of the excitation signal that is at or near the prescribed excitation wavelength.

When the optics channel <NUM> is in optical communication with the fiber bundle <NUM> - such as by rotating he filter wheel <NUM> until the optics channel <NUM> is aligned with a fiber tunnel <NUM> within, or adjacent to, which the fiber bundle <NUM> is secured - an objective lens <NUM> transmits the excitation signal from the excitation channel <NUM> into each fiber of the fiber bundle <NUM>. Emissions from the emissions sources at the opposite ends of the fibers are transmitted by each fiber of the fiber bundle <NUM> back through the objective lens <NUM> and into the optic channel <NUM>. Dichroic <NUM> may be configured to reflect light of a specified emission wavelength. Thus, that portion of the emission light transmitted by the fiber bundle <NUM> into the optics channel <NUM> that is at the specified emission wavelength is reflected by the dichroic <NUM> into the emission channel <NUM>.

An emission filter <NUM> is disposed within the emission channel <NUM> and is configured to transmit light having the desired emission wavelength. The emission channel <NUM> terminates at a radial opening formed about the outer periphery of the body <NUM>. In an embodiment, the optics channel <NUM> is oriented with respect to the camera <NUM> such that an optic channel <NUM> that is in optical communication with the fiber bundle <NUM> is also in optical communication with the camera <NUM>.

When the optics channel <NUM> is an operative position with respect to the camera <NUM>, the radial opening of the emission channel <NUM> is aligned with image relay optics <NUM> that transmit emission light from the emission channel <NUM> into the camera <NUM>. Camera <NUM> then images the emission signals transmitted by all fibers in the fiber bundle <NUM> at once. To determine the signal transmitted by each fiber - and thus the signal emitted by the signal emission source associated with the fiber - the pixels of the camera's pixel matrix are mapped to the fiber locations within the fiber bundle to identify the one or more pixels of the pixel array that correspond to each fiber. By interrogating the signal imaged at each pixel or group of pixels associated with a fiber, the signal (e.g. the color (wavelength) and/or intensity) of the mission signal transmitted by that fiber can be determined.

Suitable cameras include CMOS camera such as the IDS UI-5490HE camera or CCD camera such as the Lumenera LW11059 or the Allied GE4900. Preferably, the camera has at least <NUM> megapixels and has a high frame rate.

In an embodiment, the filter wheel <NUM> includes multiple (e.g., <NUM> to <NUM>) optics channels <NUM>, each configured to excite and detect an emission of a different wavelength or other specific, distinguishing characteristic. Thus by rotating the filter wheel to index each optics channel <NUM> with respect to the fiber bundle <NUM> and camera <NUM>, signals of each distinguishing characteristic can be measure from all fibers and associated signal emission sources.

It will be appreciated that the signal detector head may include one or more additional cameras positioned and be coupled to one or more additional fiber bundles to permit simultaneous imaging of the multiple fiber bundles.

Aspects of the disclosure are implemented via control and computing hardware components, user-created software, data input components, and data output components. Hardware components include computing and control modules (e.g., system controller(s)), such as microprocessors and computers, configured to effect computational and/or control steps by receiving one or more input values, executing one or more algorithms stored on non-transitory machine-readable media (e.g., software) that provide instruction for manipulating or otherwise acting on the input values, and output one or more output values. Such outputs may be displayed or otherwise indicated to a user for providing information to the user, for example information as to the status of the instrument or a process being performed thereby, or such outputs may comprise inputs to other processes and/or control algorithms. Data input components comprise elements by which data is input for use by the control and computing hardware components. Such data inputs may comprise positions sensors, motor encoders, as well as manual input elements, such as keyboards, touch screens, microphones, switches, manually-operated scanners, etc. Data output components may comprise hard drives or other storage media, monitors, printers, indicator lights, or audible signal elements (e.g., buzzer, horn, bell, etc.).

Software comprises instructions stored on non-transitory computer-readable media which, when executed by the control and computing hardware, cause the control and computing hardware to perform one or more automated or semi-automated processes.

While the present disclosure has been described and shown in considerable detail with reference to certain illustrative embodiments, including various combinations and sub-combinations of features, those skilled in the art will readily appreciate other embodiments and variations and modifications thereof as encompassed within the scope of the present invention as set out in the appended set of claims.

Claim 1:
A method of measuring at least one time-varying signal emission from the contents of each of a plurality of receptacles (<NUM>) while the contents of all receptacles are subject to repeated cycles of temperature variations within a thermal cycling range, the method comprising:
measuring the signal emission from the contents of each receptacle (<NUM>) at different times separated by repeating intervals of time and recording the signal emission measurement and a time stamp for each receptacle at each interval;
recording a time stamp for each temperature of the thermal cycling range; and
synchronizing the signal emission of each receptacle to a specific temperature within the thermal cycling range by comparing time stamps of the signal emission measurements of each receptacle to a time stamp for each temperature of the thermal cycling range.