Patent Publication Number: US-2009218517-A1

Title: Multiplex fluorescence detection device having removable optical modules

Description:
CROSS REFERENCE TO RELATED APPLICATIONS 
     This application is a division of U.S. patent application Ser. No. 11/174,754, filed Jul. 5, 2005 which application claims the benefit of U.S. Provisional Application No. 60/667,461, filed Apr. 1, 2005, the entire content of which is incorporated herein by reference. 
    
    
     TECHNICAL FIELD 
     The invention relates to assaying systems and, more particularly, techniques for the detection of multiple target species using fluorescent dyes. 
     BACKGROUND 
     Optical disc systems are often used to perform various biological, chemical or bio-chemical assays. In a typical system, a rotatable disc is used as a medium for storing and processing fluid specimens, such as blood, plasma, serum, urine or other fluid. 
     One type of analysis is polymerase chain reaction (PCR), which is often used for nucleic acid sequence analysis. In particular, PCR is often used for DNA sequencing, cloning, genetic mapping, and other forms of nucleic acid sequence analysis. 
     In general, PCR relies on the ability of DNA-copying enzymes to remain stable at high temperatures. There are three major steps in PCR: denaturation, annealing, and extension. During the denaturation, a liquid sample is heated at approximately 94° C. During this process, double DNA strands “melt” open into single stranded DNA and all enzymatic reactions stop. During annealing, the single stranded DNA is cooled to 54° C. At this temperature, primers bind or “anneal” to the ends of the DNA strands. During extension, the sample is heated to 75° C. At this temperature, nucleotides add to the primers and eventually a complementary copy of the DNA template is formed. 
     There are a number of existing PCR instruments designed to determine levels of specific DNA and RNA sequences in the sample during the PCR in real-time. Many of the instruments are based on the use of fluorescent dyes. In particular, many conventional real-time PCR instruments detect a fluorescent signal produced proportionally during amplification of a PCR product. 
     Conventional real-time PCR instruments use different methods for detection of different fluorescent dyes. For example, some conventional PCR instruments incorporate white light sources with filter wheels for spectrally resolving each dye. The white light sources are tungsten halogen bulbs, which have a lifetime maxima of a few thousand hours. The filter wheels are typically complicated electromechanical parts that are susceptible to wear. 
     SUMMARY 
     In general, the invention relates to techniques for the detection of multiple target species in real-time PCR (polymerase chain reaction), referred to herein as multiplex PCR. In particular, a multiplex fluorescence detection device is described that incorporates a plurality of optical modules. Each of the optical modules may be optimized for detection of a respective fluorescent dye at a discrete wavelength band. In other words, the optical modules may be used to interrogate multiple, parallel reactions at different wavelengths. The reaction may, for example, occur within a single process chamber (e.g., well) of a rotating disk. Additionally, each optical module may be removable to quickly change the detection capabilities of the device. 
     The plurality of optical modules may be optically coupled to a single detector by a multi-legged optical fiber bundle. In this manner, multiplexing can be achieved by using a plurality of optical modules and a single detector, e.g., a photomultiplier tube. The optical components in each optical module may be selected to maximize sensitivity and minimize the amount of spectral crosstalk, i.e., signals from one dye on another optical module. 
     In one embodiment, a device comprises a motor to rotate a disk having a plurality of process chambers each holding a respective sample and a plurality of fluorescent dyes, a plurality of optical modules, and a housing having a plurality of locations adapted to receive the optical modules wherein each of the optical modules includes an optical channel having a light source selected for a different one of the dyes and a lens to capture fluorescent light emitted from the disk. 
     In another embodiment, a system comprises a data acquisition device. The system further comprises a detection device coupled to the data acquisition device, wherein the detection device comprises a motor to rotate a disk having a plurality of process chambers each holding a respective sample and a plurality of fluorescent dyes, a plurality of optical modules, and a housing having a plurality of locations adapted to receive the optical modules wherein each of the optical modules includes an optical channel having a light source selected for a different one of the dyes and a lens to capture fluorescent light emitted from the disk. 
     In an additional embodiment, a method comprises rotating a disk having a plurality of process chambers each having a plurality of species that emit fluorescent light at different wavelengths, exciting the disk with a plurality of light beams to produce a plurality of emitted fluorescent light beams, capturing the fluorescent light beams with a plurality of different optical modules, wherein the modules are optically configured for the different wavelengths, containing the plurality of different modules within a housing. 
     The invention may provide one or more advantages. For example, the modular design may allow a technician to quickly and efficiently interchange detection modules depending on the particular reactions being performed. Moreover, the technician may select detection modules that are optically optimized for different reactions. Further, different combinations of detection modules may be installed and utilized within the real-time, multiplex PCR device. 
     While the device may be capable of conducting real-time PCR, the device may be capable of analyzing any type of biological reaction while it occurs. The device may be able to modulate the temperature of each reaction independently or as a selected group, and the device may be able to support multiple stages of reactions by including a valve between two chambers. This valve may be opened during reactions through the use of a laser which delivers a burst of energy to the valve. 
     In some embodiments, the device may be portable and robust to allow operation in remote areas or temporary laboratories. The device may include a data acquisition computer for analyzing the reactions in real-time, or the device may communicate the data to another device through wired or wireless communication interfaces. 
     The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims. 
    
    
     
       BRIEF DESCRIPTION OF DRAWINGS 
         FIG. 1  is a block diagram illustrating an exemplary embodiment of a multiplex fluorescence detection device. 
         FIG. 2  is a schematic diagram illustrating an exemplary detection module, which may correspond to any of a plurality of detection modules of the fluorescence detection device of  FIG. 1 . 
         FIG. 3  is a perspective diagram illustrating a front view of an exemplary set of removable optical modules within the device housing. 
         FIG. 4  is a perspective diagram illustrating the exemplary set of removable optical modules within the device housing. 
         FIG. 5  is a perspective diagram illustrating a front side view of an exemplary set of removable optical modules having one module removed to expose a module connector. 
         FIGS. 6A and 6B  are perspective diagrams illustrating the components within exemplary main removable optical modules. 
         FIGS. 7A and 7B  are perspective diagrams illustrating the components within exemplary supplemental removable optical modules. 
         FIG. 8  is a block diagram illustrating an example embodiment of the multiplex fluorescence detection device in further detail. 
         FIG. 9  is a block diagram of the a single detector coupled to four optical fibers of the optical fiber bundle. 
         FIG. 10  is a flow diagram illustrating exemplary operation of the multiplex fluorescence detection device. 
         FIG. 11  is a flow diagram illustrating an exemplary method if detecting light and sampling data from the disk. 
         FIGS. 12 and 13  show the absorption and emission spectra of commonly used fluorescent dyes that may be utilized for multiplex PCR. 
         FIGS. 14A and 14B  illustrate raw data acquired from two exemplary detection modules with a single detector during a PCR analysis. 
         FIG. 15  is a graph that shows the data once adjusted for a time offset. 
         FIGS. 16A and 16B  show a limit of detection (LOD) for the data received from two exemplary detection modules. 
         FIG. 17  is an exemplary screen shot of a temperature control user interface. 
         FIG. 18  is an exemplary screen shot of an optical control user interface. 
         FIG. 19  is an exemplary screen shot of a real-time PCR user interface. 
     
    
    
     DETAILED DESCRIPTION 
       FIG. 1  is a block diagram illustrating an exemplary embodiment of a multiplex fluorescence detection device  10 . In the illustrated example, device  10  has four optical modules  16  that provide four “channels” for optical detection of four different dyes. In particular, device  10  has four optical modules  16  that excite different regions of rotating disk  13  at any given time, and collect emitted fluorescent light energy at different wavelengths from the dyes. As a result, modules  16  may be used to interrogate multiple, parallel reactions occurring within sample  22 . 
     The multiple reactions may, for example, occur simultaneously within a single chamber of a rotating disk  13 . Each of optical modules  16  interrogates sample  22  and collects fluorescent light energy at different wavelengths as the disk  13  rotates. For example, excitation sources within modules  16  may be sequentially activated for periods sufficient to collect data at the corresponding wavelengths. That is, an optical module  16 A may be activated for a period of time to collect data at a first range of wavelengths selected for a first dye corresponding to a first reaction. The excitation source may then be deactivated, and an excitation source within module  16 B may be activated to interrogate sample  22  at a second range of wavelengths selected for a second dye corresponding to a second reaction. This process continues until data has been captured from all optical modules  16 . In one embodiment, each of the excitation sources within optical modules  16  is activated for an initial period of approximately two seconds to reach steady state followed by an interrogation period which lasts for 10-50 rotations of disk  13 . In other embodiments, the excitation sources may be sequenced for shorter (e.g., 1 or 2 milliseconds) or longer periods. In some embodiments, more than one optical module may be activated simultaneously for concurrent interrogation of sample  22  without stopping the rotation of disk  13 . 
     Although a single sample  22  is illustrated, disk  13  may contain a plurality of chambers holding samples. Optical modules  16  may interrogate some or all of the different chambers at different wavelengths. In one embodiment, disk  13  includes 96 chambers space around a circumference of disk  13 . With a 96 chamber disk and four optical modules  16 , device  10  may be capable of acquiring data from 384 different species. 
     In one embodiment, optical modules  16  include excitation sources that are inexpensive high power light emitting diodes (LEDs), which are commercially available in a variety of wavelengths and have long lifetimes (e.g., 100,000 hours or more). In another embodiment, conventional halogen bulbs or mercury lamps may be used as excitation sources. 
     As illustrated in  FIG. 1 , each of optical modules  16  may be coupled to one leg of a fiber optic bundle  14 . Fiber optic bundle  14  provides a flexible mechanism for collection of fluorescent signals from optical modules  16  without loss of sensitivity. In general, a fiber optic bundle comprises multiple optical fibers laid side by side and bonded together at the ends and encased in a flexible protective jacket. Alternatively, fiber optic bundle  14  may comprise a smaller number of discrete, large diameter multi-mode fibers, either glass or plastic, having a common end. For example, for a four-optical module device, fiber optic bundle  16  may comprise four discrete multimode fibers, each having a 1 mm core diameter. The common end of the bundle contains the four fibers bound together. In this example, the aperture of detector  18  may be 8 mm, which is more than sufficient for coupling to the four fibers. 
     In this example, fiber optic bundle  14  couples optical modules  16  to a single detector  18 . The optical fibers carry the fluorescent light collected by optical modules  16  and effectively deliver the captured light to detector  18 . In one embodiment, detector  18  is a photomultiplier tube. In another embodiment, the detector may include multiple photomultiplier elements, one for each optical fiber, within the single detector. In other embodiments, one or more solid-state detectors may be used. 
     The use of a single detector  18  may be advantageous in that it allows use of a highly sensitive and possibly expensive detector (e.g., a photomultiplier), while maintaining a minimal cost in that only a single detector need be used. A single detector is discussed herein; however, one or more detectors may be included for detecting a greater number of dyes. For example, four additional optical modules  16  and a second detector may be added to the system to allow for the detection of eight different wavelengths emitted from one disk. An exemplary fiber optic bundle coupled to a single detector for use with rotating disk  13  is described in U.S. Patent Application Publication No. 2006-0223172-A1, entitled “MULTIPLEX FLUORESCENCE DETECTION DEVICE HAVING FIBER BUNDLE COUPLING MULTIPLE OPTICAL MODULES TO A COMMON DETECTOR,” filed on Jul. 5, 2005, the entire content of which is hereby incorporated by reference. 
     Optical modules  16  are removable from the device and easily interchangeable with other optical modules that are optimized for interrogation at different wavelengths. For example, optical modules  16  may be physically mounted within locations of a module housing. Each of optical modules  16  may be easily inserted within a respective location of the housing along guides (e.g., recessed grooves) that mate with one or more marking (e.g., guide pins) of the optical module. Each optical module includes an optical output port (shown in  FIGS. 6A and 7A ) for coupling to one leg of fiber optic bundle  14 . The optical output port may have a threaded end coupled to a threaded connector of the leg. Alternatively, a form of “quick-connect” may be used (e.g., a slidable connection having an o-ring and a catch pin) that allows fiber optic bundle  14  to be slidably engaged and disengaged from the optical output port. Moreover, each of optical modules  16  may have one or more electrical contacts for electronically coupling to control unit  23  when fully inserted. 
     The modular architecture of device  10  allows the device to be easily adapted for all of the fluorescent dyes used in a given analysis environment, such as multiplex PCR. Other chemistries that may be used in device  10  include Invader (Third Wave, Madison, Wis.), Transcripted-mediated Amplification (GenProbe, San Diego, Calif.), fluorescence labeled enzyme linked immunosorbent assay (ELISA) or fluorescence in situ hybridization (FISH). The modular architecture of device  10  may provide another advantage in that the sensitivity of each optical module  16  can be optimized by choice of the corresponding excitation source (not shown) and excitation and detection filters for a small specific target range of wavelengths in order to selectively excite and detect a corresponding dye in the multiplex reaction. 
     For purpose of example, device  10  is illustrated in a 4-color multiplex arrangement, but more or less channels can be used with the appropriate fiber optic bundle  14 . This modular design allows a user to easily upgrade device  10  in the field by simply adding another optical module  16  to base  20  and inserting one leg of fiber optic bundle  14  into the new optical module. Optical modules  16  may have integrated electronics that identify the optical modules and download calibration data into an internal control module or other internal electronics (e.g., control unit  23 ) of device  10 . 
     In the example of  FIG. 1 , samples  22  are contained in chambers of disk  13 , which is mounted on a rotating platform under the control of control unit  23 . A slot sensor trigger  27  provides an output signal utilized by control unit  23  and data acquisition device  21  for synchronizing data acquisition with chamber position during disk rotation. Slot sensor trigger  27  may be a mechanical or optical sensor. For example, the sensor may be a laser which sends a beam of light to disk  13  and control unit  23  uses a sensor detecting light passing through a slot in disk  13  to locate the chambers on the disk. In other embodiments, disk  13  may include a tab, protrusion or reflective surface in addition to or in place of the slot. Slot sensor trigger  27  may use any physical structure or mechanism to locate the radial position of disk  13  as it rotates. Optical modules  16  may be physically mounted above rotating platform  25 . As a result, optical modules  16  are overlapped with different chambers at any one time. 
     Detection device  10  also includes a heating element (not shown) for modulating the temperature of the sample  22  on disk  13 . The heating element may comprise a cylindrical halogen bulb contained within a reflective enclosure. The reflective chamber is shaped to focus radiation from the bulb onto a radial section of disk  13 . Generally, the heated area of disk  13  would resemble a ring as disk  13  spins. In this embodiment, the shape of the reflective enclosure may be a combination of elliptical and spherical geometries that allow precise focusing. In other embodiments, the reflective enclosure may be of a different shape or the bulb may broadly irradiate a larger area. In other embodiments, the reflective enclosure may be shaped to focus the radiation from the bulb onto a single area of the disk  13 , such as a single process chamber containing a sample  22 . 
     In some embodiments, the heating element may heat air and force the hot air over one or more samples to modulate the temperature. Additionally, the samples may be heated directly by the disk. In this case, the heating element may be located in platform  25  and thermally couple to disk  13 . Electrical resistance within the heating element may heat a selected region of the disk as controlled by control unit  23 . For example, a region may contain one or more chambers, possibly the entire disk. An exemplary heating element for use with rotating disk  13  is described in U.S. Patent Application Publication No. 2007-0009382-A1, entitled “HEATING ELEMENT FOR A ROTATING MULTIPLEX FLUORESCENCE DETECTION DEVICE,” filed on Jul. 5, 2005, the entire content of which is hereby incorporated by reference. 
     Alternatively, or in addition, device  10  may also includes a cooling component (not shown). A fan is included in device  10  to supply cold air, i.e., room temperature air, to disk  13 . Cooling may be needed to modulate the temperature of the sample appropriately and store samples after an experiment has completed. In other embodiments, the cooling component may include thermal coupling between platform  25  and disk  13 , as platform  25  may reduce its temperature when needed. For example, some biological samples may be stored at 4 degrees Celsius to reduce enzyme activity or protein denaturing. 
     Detection device  10  may also be capable of controlling reaction species contained within a process chamber. For example, it may be beneficial to load some species in a process chamber to generate one reaction and later adding another species to the sample once the first reaction has terminated. A laser homing valve may be added to control a valve position separating an inner holding chamber from the process chamber, thereby controlling the addition of species to the chamber during rotation of disk  13 . This laser device may be located within one of optical modules  16  or separate from the optical modules. Directly below the laser, under disk  13 , may be a laser sensor for positioning the laser relative to disk  13 . 
     In one embodiment, the laser is a near infrared (NIR) laser with at least two power settings. Under a low power setting, the laser positioning sensor may indicate that the laser is in position over the chamber valve by recognizing the NIR light though a slot in disk  13 . Once the laser is in position, control unit  23  directs the laser to output a short burst of high power energy to heat the valve and open it. The open valve may then allow the inner fluid specimen to flow toward from the inside chamber to the outside process chamber and conduct a second reaction. In some embodiments, disk  13  may contain a plurality of valves to generate a plurality of reactions in sequence. More than one set of laser and laser sensor may also be used when utilizing multiple chamber valves. An exemplary laser homing valve control system for use with rotating disk  13  is described in U.S. Patent Application Publication No. 2007-0009383-A1, entitled “VALVE CONTROL SYSTEM FOR A ROTATING MULTIPLEX FLUORESCENCE DETECTION DEVICE,” filed on Jul. 5, 2005, the entire content of which is hereby incorporated by reference. 
     Data acquisition device  21  may collect data from device  10  for each dye either sequentially or in parallel. In one embodiment, data acquisition system  21  collects the data from optical modules  16  in sequence, and corrects the spatial overlap by a trigger delay for each one of the optical modules measured from slot sensor trigger  27 . 
     One application for device  10  is real-time PCR, but the techniques described herein may be extended to other platforms that utilize fluorescence detection at multiple wavelengths. Device  10  may combine rapid thermal cycling, utilizing the heating element, and centrifugally driven microfluidics for isolation, amplification, and detection of nucleic acids. By making use of multiplex fluorescence detection, multiple target species may be detected and analyzed in parallel. 
     For real-time PCR, fluorescence is used to measure the amount of amplification in one of three general techniques. The first technique is the use of a dye, such as Sybr Green (Molecular Probes, Eugene, Oreg.), whose fluorescence increases upon binding to double-stranded DNA. The second technique uses fluorescently labeled probes whose fluorescence changes when bound to the amplified target sequence (hybridization probes, hairpin probes, etc.). This technique is similar to using a double-stranded DNA binding dye, but is more specific because the probe will bind only to a certain section of the target sequence. The third technique is the use of hydrolysis probes (Taqman™, Applied BioSystems, Foster City Calif.), in which the exonuclease activity of the polymerase enzyme cleaves a quencher molecule from the probe during the extension phase of PCR, making it fluorescently active. 
     In each of the approaches, fluorescence is linearly proportional to the amplified target concentration. Data acquisition system  21  measures an output signal from detector  18  (or alternatively optionally sampled and communicated by control unit  23 ) during the PCR reaction to observe the amplification in near real-time. In multiplex PCR, the multiple targets are labeled with different dyes that are measured independently. Generally speaking, each dye will have different absorbance and emission spectra. For this reason, optical modules  16  may have excitation sources, lenses and related filters that are optically selected for interrogation of sample  22  at different wavelengths. 
     Some examples of suitable construction techniques or materials that may be adapted for use in connection with the present invention may be described in, e.g., commonly-assigned U.S. Pat. No. 6,734,401 titled “ENHANCED SAMPLE PROCESSING DEVICES SYSTEMS AND METHODS” (Bedingham et al.) and U.S. Pat. No. 7,026,168 titled “SAMPLE PROCESSING DEVICES.” Other useable device constructions may be found in, e.g., U.S. Provisional Patent Application Ser. No. 60/214,508 filed on Jun. 28, 2000 and entitled “THERMAL PROCESSING DEVICES AND METHODS”; U.S. Provisional Patent Application Ser. No. 60/214,642 filed on Jun. 28, 2000 and entitled “SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS”; U.S. Provisional Patent Application Ser. No. 60/237,072 filed on Oct. 2, 2000 and entitled “SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS”; U.S. Provisional Patent Application Ser. No. 60/260,063 filed on Jan. 6, 2001 and titled “SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS”; U.S. Provisional Patent Application Ser. No. 60/284,637 filed on Apr. 18, 2001 and titled “ENHANCED SAMPLE PROCESSING DEVICES, SYSTEMS AND METHODS”; and U.S. Pat. No. 6,814,935 titled “SAMPLE PROCESSING DEVICES AND CARRIERS.” Other potential device constructions may be found in, e.g., U.S. Pat. No. 6,627,159 titled “CENTRIFUGAL FILLING OF SAMPLE PROCESSING DEVICES” (Bedingham et al.). The entire content of these disclosures are incorporated herein by reference. 
       FIG. 2  is a schematic diagram illustrating an exemplary optical module  16 A, which may correspond to any of optical modules  16  of  FIG. 1 . In this example, optical module  16 A contains a high-power excitation source, LED  30 , a collimating lens  32 , an excitation filter  34 , a dichrotic filter  36 , a focusing lens  38 , a detection filter  40 , and a lens  42  to focus the fluorescence into one leg of fiber optic bundle  14 . 
     Consequently, the excitation light from LED  30  is collimated by collimating lens  32 , filtered by excitation filter  34 , transmitted through dichrotic filter  36 , and focused into the sample  22  by focusing lens  38 . The resulting fluorescence emitted by the sample is collected by the same focusing lens  38 , reflected off of dichrotic filter  36 , and filtered by detection filter  40  before focused into one leg of fiber optic bundle  14 . The optic bundle  14  then transfers the light to detector  18 . 
     LED  30 , collimating lens  32 , excitation filter  34 , dichrotic filter  36 , focusing lens  38 , detection filter  40 , and lens  42  are selected based on the specific absorption and emission bands of the multiplex dye with which optical module  16 A is to be used. In this manner, multiple optical modules  16  may be configured and loaded within device  10  to target different dyes. 
     Table 1 lists exemplary components that may be used in a 4-channel multiplex fluorescence detection device  10  for a variety of fluorescent dyes. FAM, HEX, JOE, VIC, TET, ROX are trademarks of Applera, Norwalk, Calif. Tamra is a trademark of AnaSpec, San Jose, Calif. Texas Red is a trademark of Molecular Probes. Cy 5 is a trademark of Amersham, Buckinghamshire, United Kingdom. 
     
       
         
           
               
               
               
               
               
             
               
                 TABLE 1 
               
               
                   
               
               
                 Optical 
                   
                 Excitation 
                 Detection 
                   
               
               
                 Module 
                 LED 
                 Filter 
                 Filter 
                 Dye 
               
               
                   
               
             
            
               
                 1 
                 blue 
                 475 nm 
                 520 nm 
                 FAM, Sybr Green 
               
               
                 2 
                 green 
                 530 nm 
                 555 nm 
                 HEX, JOE, VIC, TET 
               
               
                 3 
                 orange 
                 580 nm 
                 610 nm 
                 TAMRA, ROX, Texas Red 
               
               
                 4 
                 red 
                 630 nm 
                 670 nm 
                 Cy 5 
               
               
                   
               
            
           
         
       
     
     One advantage of the described modular, multiplex detection architecture is the flexibility in optimizing detection for a wide variety of dyes. Conceivably a user may have a bank of several different optical modules that can be plugged into device  10  as needed, of which N can used at any one time, where N is the maximum number of channels supported by the device. Therefore, device  10  and optical modules  16  may be used with any fluorescent dye and PCR detection method. A larger fiber optic bundle may be used to support a larger number of detection channels. Moreover, multiple fiber optic bundles may be used with multiple detectors. For example, two 4-legged fiber optic bundles may be used with eight optical modules  16  and two detectors  18 . 
       FIG. 3  is a perspective diagram illustrating a front view of an exemplary set of removable optical modules within the device housing. In the example of  FIG. 3 , device  10  includes base arm  44  and module housing  46 . Main optical module  48 , supplemental optical module  52  and supplemental optical module  56  are contained within module housing  46 . Optical modules  48 ,  52  and  56  produce optical output beams  49 ,  53  and  57 , respectively, that sequentially excite different process chambers of disk  13 . In other words, output beams  49 ,  53  and  57  follow the curvature of disk  13  to each excite the same radial position of the disk which contains the process chambers. Slot sensor trigger  27  includes infrared light source  31  which produces light  35  that is detected by detector  33 . 
     Each of optical modules  48 ,  52  and  56  includes a respective release lever  50 ,  54  or  58 , respectively, for engaging module housing  46 . Each release lever may provide an upward bias to engage a respective latch formed within module housing  46 . A technician or other user depresses release levers  50 ,  54  or  58 , respectively, in order to unlatch and remove optical module  48 ,  52  or  56  from module housing  46 . Barcode reader  29  includes laser  62  for identifying disk  13 . 
     Base arm  44  extends from detection device  10  and provides support for module housing  46  and optical modules  48 ,  52  and  56 . Module housing  46  may be securely mounted atop base arm  44 . Module housing  46  may contain a location adapted to receive a respective one of optical modules  48 ,  52  and  56 . Although described for exemplary purposes with respect to module housing  46 , module housing  46  of detection device  10  may have a plurality of locations for receiving optical modules  48 ,  52  and  56 . In other words, a separate housing need not be used for optical modules  48 ,  52  and  56 . 
     Each location of module housing  46  may contain one or more tracks or guides which help to correctly position the associated optical module within the location when a technician or other user inserts the optical module. These guides may be located along the top, bottom, or sides of each locations. Each of optical modules  48 ,  52  and  56  may include guides or tracks that mate with the guides or tracks of the locations of module housing  46 . For example, module housing  46  may have protruding guides which mate with recessed guides in optical modules  48 ,  52  and  56 . 
     In some embodiments, module housing  46  may not completely enclose each of optical modules  48 ,  52  and  56 . For example, module housing  46  may provide mounting points to secure each of optical modules  48 ,  52  and  56  to base arm  44 , but portions or all of each optical module may be exposed. In other embodiments, module housing  46  may completely enclose each of optical modules  48 ,  52  and  56 . For example, module housing  46  may include a single door that closes over optical modules  48 ,  52  and  56 , or a respective door for each of the modules. This embodiment may be appropriate for applications where the modules are seldom removed or detection device  10  is subjected to extreme environmental conditions. 
     A technician may easily remove any of optical modules  48 ,  52  or  56 , and may be completed by using only one hand. For example, the technician may rest his or her forefinger under a molded lip located beneath release lever  54  of optical module  52 . The technician&#39;s thumb may then press down release lever  54  to release optical module  52  from module housing  46 . While grasping optical module  52  between the thumb and forefinger, the technician may pull back on the optical module to remove the optical module from detection device  10 . Other methods may be used to remove any of optical module  48 ,  52  or  56 , including methods utilizing two-handed removal. Inserting any of optical module  48 ,  52  or  56  may be accomplished in a reversed manner with one or two hands. 
     In the example of  FIG. 3 , the components of two optical modules are combined to form main optical module  48 . Main optical module  48  may contain light sources that produce two different wavelengths of light and detectors for detecting each different wavelength of fluorescence from the samples in disk  13 . Therefore, main optical module  48  may connect to two legs of fiber optic bundle  14 . In this manner, main optical module  48  may be viewed as a dual-channeled optical module having two independent optical excitation and collection channels. In some embodiments, main optical module  48  may contain optical components for more than two optical modules. In other cases, module housing  46  contains a plurality (e.g., two or more) of single-channeled optical modules, such as supplemental optical modules  52  and  56 . 
     As illustrated in  FIG. 3 , main optical module  48  may also contain components for a laser valve control system  51  (located within optical module  48 ). Laser valve control system  51  detects disk  13  location by a small slot located near the outer edge of disk  13 . A detector (not shown) detects low power laser light  55  to map the location of disk  13  with respect to the motor which spins the disk. The control unit  23  uses the map to locate valves (not shown) on disk  13 . 
     Laser valve control system  51  focuses laser light  55  on the valves that separate holding chambers towards the center of disk  13  from process chambers near the outer edge of disk  13 . When the contents of the holding chambers are to be moved to the associated process chambers, laser valve control system  51  applies laser light  55  to heat a valve separating the chambers, causing the value open and providing fluid communication between the two chambers. In particular, once the valve is open, the contents from the inner holding chamber may then flow towards the outer process chamber as disk  13  is spinning. Detection device  10  may then monitor the subsequent reaction in the process chamber. Contents within a chamber may include substances in a fluid or solid state. 
     In some embodiments, laser valve control system  51  may be contained within a single-channeled optical module, e.g., supplemental optical module  54  or supplemental optical module  56 . In other embodiments, laser valve control system  51  may be mounted to detection device  10  separately from any of optical modules  48 ,  52  or  56 . In this case, laser valve control system  51  may be removable and adapted to engage a location within module housing  46  or a different housing of detection device  10 . 
     In the example of  FIG. 3 , slot sensor trigger  27  is located near the removable modules, on either side of disk  13 . In one embodiment, slot sensor trigger  27  contains a light source  31  to emit infrared (IR) light  35 . Detector  33  detects IR light  35  when the slot in disk  13  allows the light to pass through the disk to detector  33 . Control unit  23  may use this information to synchronize disk  13  location as it is spinning with data from optical modules  48 ,  54  and  56 . In some embodiments, slot sensor trigger  27  may extend from base arm  44  to reach the outer edge of disk  13  during device  10  operation. In other embodiments, a mechanical detector may be used to detect the position of disk  13 . 
     Barcode reader  29  uses laser  62  to read a barcode located on the side edge of disk  13 . The barcode identifies the type of disk  13  to allow proper operation of device  10 . In some embodiments, the barcode may identify the actual disk to assist a technician in tracking data to specific samples from multiple disks  13 . 
     All surface components of optical modules  48 ,  52  and  56  may be constructed of a polymer, composite, or metal alloy. For example, high molecular weight polyurethane may be used in forming the surface components. In other cases, an aluminum alloy or carbon fiber structure may be created. In any case, the material may be resistant to heat, fatigue, stress, and corrosion. As detection device  10  may come into contract with biological materials, the structures may be sterilizable in the event chamber contents leak out of disk  13 . 
       FIG. 4  is an perspective diagram illustrating the exemplary set of removable optical modules  48 ,  52  and  56  within module housing  46  of detection device  10 . In the example of  FIG. 4 , base arm  44  supports barcode reader  29  as well as the removable optical modules  48 ,  52  and  56  attached within module housing  46 . Disk  13  is located beneath optical modules  48 ,  52  and  56  with the process chambers located under a respective optical path of each of the modules at different moments in time. 
     Within module housing  46 , the fronts of supplementary module  56  and main optical module  48  can be seen. Supplementary module  56  contains molded lip  59  and release lever  58 . As previously described, molded lip  59  may be used to grasp module  56  when removing or inserting the module into module housing  46 . All of optical modules  48 ,  52  and  56  may have a respective molded lip and release lever, or a single release lever may be used to remove all of the optical modules. In some embodiments, optical modules  48 ,  52  and  56  may contain a different component for grasping the module. For example, each of optical modules  48 ,  52  and  56  may contain a handle for removing the respective module in a vertical or horizontal direction from module housing  46 . 
     The location of optical modules  48 ,  52  and  56  within module housing  46  may be fixed in order to separately excite different samples within disk  13  at any particular moment in time. For example, main optical module  48  may be located slightly further toward base arm  44  than supplemental optical modules  52  and  56 , which are offset to a location at either side of the main module. Moreover, optical modules  48 ,  52  and  56  may be offset in a horizontal direction (indicated by the arrow in  FIG. 4 , where X is the distance the outside light beams are offset from the inside light beams) so that the excitation light beams produced by the modules follows the curvature of disk  13 . In this arrangement, the light beams produced by optical modules  48 ,  52  and  56  traverse the same path as disk  13  rotates, thereby exciting and collecting light from process chambers located along the path. In other embodiments, optical modules  48 ,  52  and  56  are aligned such that the excitation light beams traverse different paths around rotating disk  13 . 
     In this example, base arm  44  contains electrical contact board  66  which extends into module housing  46 . Inside module housing  46 , electrical contact board  66  may contain electrical contacts for each of optical modules  48 ,  52  and  56 . Electrical contact board  66  may be electrically coupled to control unit  23 . In some embodiments, each of optical modules  48 ,  52  and  56  may have a separate associated electrical contact board which is connected to control unit  23 . 
     Fiber optic coupler  68  couples one leg of the fiber optic bundle  14  to an optical output port of optical module  56 . Although not shown, each of optical modules  48 ,  52  and  56  include an optical output port adapted to engage a respective fiber optic coupler mounted to module housing  46 . The connection between fiber optic coupler  68  and the leg of fiber optic bundle  14  may be a threaded screw lock, snap closure or friction fit. 
     Barcode reader  29  produces laser light  64  for reading the barcode of disk  13 . The laser light  64  follows a direct path where it interacts with the outer edge of disk  13 . The light  64  may spread out to cover a large area of disk  13  at one time. Barcode reader  29  reads the barcode on disk  13  when the disk is rotating at slow speeds. In other embodiments, barcode reader  29  may read the barcode periodically during operation to make sure a new disk has not been loaded in device  10 . The barcode reader  29  may detect more than one barcode on disk  13  in other embodiments. 
     In some embodiments, base arm  44  may be movable with respect to disk  13 . In this case, base arm  44  could be configurable to detect samples on different sized disks or samples located within an interior of disk  13 . For example, a larger disk containing more process chambers or larger process chambers may be used by moving the base arm  44  further away from the center of disk  13 . Module housing  46  may also have a configurable position for each of optical module  48 ,  52  or  56  so that each module may be movable to one or more circular paths of process chambers around disk  13 . 
       FIG. 5  is perspective diagram illustrating a front side view of an exemplary set of removable optical modules having one module removed to expose a module connector. In particular, module housing  46  is not shown in  FIG. 5 , and optical module  56  has been removed to expose optical modules  52  and  48  along with the connections for removed module  56 . 
     Release lever  58  ( FIG. 3 ) of optical module  56  securely attaches to attachment post  69  mounted to base arm  44 . In this example, attachment post  69  extends into optical module  56  and couples to release lever  58 . In other embodiments, other attachment mechanisms may be used to fix optical module  56  to base arm  44 , such as a screw or snap fixation device. 
     Base arm  44  provides two different operational connections within module housing  46  for receiving and engaging optical module  56 , once inserted. In particular, base arm  44  provides electrical contact board  66 , which includes electrical connections  70  for coupling to the electrical contacts (not shown) contained within optical module  56 . Electrical connections  70  allow control unit  23  to communicate with electrical components within module  56 . For example, module  56  may include electrical circuits, hardware, firmware, or any combination thereof. In one example, the internal electrical components may store and output to control unit  23  unique identification information, such as a serial number. Alternatively, or in addition, the electrical components may provide information describing the specific characteristics of the optical components contained within the removable module  56 . For example, the electrical components may include programmable read-only memory (PROM), flash memory, or other internal or removable storage media. Other embodiments may include a set of resistors, a circuit or an imbedded processor for outputting a unique signature of optical modules  48 ,  52  or  56  to control unit  23 . In another example, optical module  56  may include a laser source and other components that form part of a laser valve control system, i.e. laser valve control system  51 . 
     Electrical contact board  66  may be removed and replaced with another version associated with a different removable optical module. This option may support upgrades in device capability. In other embodiments, connections  70  may contain more or less connection pins. 
     In addition, base arm  44  and module housing  46  provide optical channel  72  within the location for receiving optical module  56 . Optical channel  72  is connected to fiber optic coupler  68  ( FIG. 4 ) that interfaces with a leg of fiber optic bundle  14 . Optical channel  72  inserts into a location within optical module  56 . The light captured by optical module  56  may be directed through optical channel  72 , fiber optic coupler  68  and fiber optic bundle  15  to the detector. Fittings between these connections may be tight to ensure that light does not escape or enter the optical path. 
     In some embodiments, the connections to optical module  56  may be arranged in a different configuration. For example, the connections may be located in another position for accepting optical module  56  from another direction. In other embodiments, electrical connections may be located on one side of optical module  56  while an optical connection is located on a second surface of module  56 . In any case, the electrical and optical connections located within the location of module housing  46  accommodate a removable optical module, i.e., optical module  56  in this example. 
     The optical and electrical connections of module  56  described in  FIG. 5  may be used with any module, including optical modules  48  and  52 . In addition, the connections for each optical module may not be identical. Since connections may be modified for coupling with a desired removable optical module, the connections utilized by any particular optical module inserted within a particular location of module housing  46  may vary at any time. 
       FIG. 6A  is perspective diagram illustrating the components within an exemplary main removable optical module  48 A. In the example of  FIG. 6A , main optical module  48 A includes release lever  50 , pivot pin  51  and latch  74 . Internal housing  78  separates each side of module  48 A and contains electrical contacts pad  80  connected to ribbon  81 . Optical components include LED  82 , collimating lens  84 , excitation filter  86 , dichrotic filter  88 , focusing lens  90 , detection filter  92  and lens  94 . Optical output port  17  couples to a leg of fiber optic bundle  14 . A separate set of optical components for a second optical channel (not shown) are located on the other side of internal housing  78 . In addition, main module  48 A includes connector  96 , laser diode  98  and focusing lens  100  as part of a laser valve control system  51  controlled by control unit  23 . 
     Release lever  50  is attached to optical module  48 A by a pivot pin  61 . Pivot pin  61  allows release lever  50  to rotate about the axis of the pin. When release lever  50  is depressed, arm  63  rotates counter-clockwise to raise latch  74 . Once latch  74  is raised, optical module  48 A may be free for removal from module housing  46 . There may be a spring or other mechanism maintaining a bias force against release lever  50  to maintain latch  74  in a down position. In some embodiments, a spring may be included around pivot pin  61  to provide a moment arm that keeps latch  74  in the down, or latched, position. In other embodiments, other mounting mechanisms may be added to or used in place of the described lever. For example, optical module  48 A may be attached to module housing  46  by one or more screws or pins. 
     Mounting board  76  may be installed within optical module  48 A for attaching communication ribbon  81  and LED  82 . Ribbon  81  is connected to electrical contacts pad  80  and provides a connection between the pad and electrical components within optical module  48 A. Contacts pad  80  and ribbon  81  may carry the information required for both sides of main optical module  48 A, including the laser valve control system  51  and any internal memory or other storage medium. Ribbon  81  may be flexible for weaving within optical module  48 A. Ribbon  81  may contain a plurality of electrically conductive wires to communicate signals between the electrical components and control unit  23  and/or to deliver power to the electrical components. In some embodiments, each electrical component may have a separate cable connecting the component with control unit  23 . A technician may need to disconnect a cable or flex circuit from module housing  46  when removing optical module  48 A from the housing. 
     In some embodiments, optical module  48 A may contain a detector for detecting light from disk  13  and electronics for processing and storing the data. The electronics may contain a telemetry circuit for wirelessly transmitting data representing the detected light to control unit  23 . Wireless communication may be performed by infrared light, radio frequency, Bluetooth, or other telemetry technique. Optical module  48 A may also include a battery to power the electronics, which may be rechargeable by control unit  23 . 
     LED  82  is affixed to mounting board  76  and electrically coupled to ribbon  81 . LED  82  produces excitation light  49  of a predetermined wavelength to excite the sample  22 . After light  49  leaves LED  82 , the light is expanded by collimating lens  84  before the light enters excitation filter  86 . The light  49  of one wavelength band is passed by dichrotic filter  88  and is focused on a sample by focusing lens  90 . The light  49  excites the sample and fluorescence is collected by focusing lens  90  and delivered to detection filter  92  by dichrotic filter  88 . The resulting wavelength band of light is collected by lens  94  and delivered to optical output port  17  where the collected fluorescent light enters a leg of fiber optic bundle  14  for conveyance to detector  18 . 
     Internal housing  78  may support all components included in the excitation of the sample and detection of fluorescent light emitted by the sample for a selected wavelength. On the other side of internal housing  78 , a similar configuration of optical components may be included to produce light of a different wavelength and detect the corresponding different fluorescent wavelength. Separation of each side may eliminate light contamination from one side entering the optical channel of the other side. 
     Housed partially between each side of module  48 A may be the components of the laser valve control system  51 , including connector  96 , laser diode  98  and focusing lens  100 . Internal housing  78  may provide physical support for these components. Ribbon  81  is connected to connector  96  for communicating drive signals and power to the laser source. Laser diode  98  is connected to connector  96  and produces the laser energy  55  used to open valves on disk  13 . Laser diode  98  delivers this near-infrared (NIR) light to focusing lens  100  for directing the laser energy  55  to specific valves on disk  13 . An NIR sensor may be located below disk  13  for locating particular valves that need to be opened. In other embodiments, these components may be housed separately from the optical components. 
     In some embodiments, emission lens  98  and focusing lens  100  of laser valve control system  51  may be contained within a single-channeled optical module, such as supplemental optical module  52  and  56  ( FIG. 3 ). 
       FIG. 6B  is a perspective diagram illustrating the components within a different optical module substantially similar to  FIG. 6A . Optical module  48 B includes many of the same components as optical module  48 A. Differences include nut  85 , flex circuit  87  and flex circuit connector  89 . 
     Optical module  48 B does not require a latch mechanism for attaching to module housing  46 . Alternatively, nut  85  is threaded and is engaged by a matching threaded bolt attached through module housing  46 . Once tightened, optical module  48 B is securely attached to detection device  10 . In other embodiments, a different fastening device may be used. For example, a pin or track may lock optical module  48 B into place. 
     Flex circuit  87  provides the electrical connection between components of optical module  48 B with control unit  23 . Flex circuit  87  is flexible to move between multiple locations. Flex circuit connector  89  is coupled to flex circuit  87  and provides a secure connection between optical module  48 B. Flex circuit connector  89  must be disengaged to completely remove optical module  48 B from module housing  46 . 
       FIG. 7A  is a perspective diagram illustrating the components within an exemplary supplemental optical module that may be easily removed from or inserted into detection device  10 . In the example of  FIG. 7A , optical module  56 A includes release lever  58 , pivot pin  59  and latch  102 , similar to main optical module  48 A. Optical module  56 A also includes electrical contacts pad  106  connected to ribbon  107 . Ribbon  107  may also be connected to mounting board  104 . Similar to main optical module  48 A, optical components include LED  108 , collimating lens  110 , excitation filter  112 , dichrotic filter  114 , focusing lens  116 , detection filter  118  and lens  120 . Optical output port  19  couples to a leg of fiber optic bundle  14 . 
     Release lever  58  is attached to optical module  56 A by a pivot pin  65 . Pivot pin  65  allows the release lever to rotate about the axis of the pin. When release lever  58  is depressed, arm  67  rotates counter-clockwise to raise latch  102 . Once latch  102  is raised, optical module  56 A may be free for removal from module housing  46 . There may be a spring or other mechanism maintaining a bias force against release lever  58  to maintain latch  102  in a down position. Alternatively, a spring may be located above latch  102 . In some embodiments, a spring may be included around pivot pin  65  to provide a moment arm that keeps latch  102  in the down, or latched, position. In other embodiments, other mounting mechanisms may be added to or used in place of the described lever. For example, optical module  56 A may be attached to module housing  46  by one or more screws or pins. 
     Mounting board  104  may be installed within optical module  56 A for attaching communication ribbon  107  and LED  108 . Ribbon  107  is connected to electrical contacts pad  106  and provides a connection between the pad and electrical components within optical module  56 A. Contacts pad  106  and ribbon  107  may carry the information required for operating the optical components. Ribbon  107  may be flexible for weaving within optical module  56 A. Ribbon  107  may contain a plurality of electrically conductive wires to communicate signals between the components and control unit  23  and/or deliver power to the electrical components. In some embodiments, each electrical component may have a separate cable connecting the component with control unit  23 . A technician may need to disconnect a cable or flex circuit from module housing  46  when removing optical module  56 A from the housing. 
     In some embodiments, optical module  56 A may contain a detector for detecting light from disk  13  and electronics for processing and storing the data. The electronics may contain a telemetry circuit for wirelessly transmitting data representing the detected light to control unit  23 . Wireless communication may be performed by infrared light, radio frequency, Bluetooth, or other telemetry technique. Optical module  56 A may also include a battery to power the electronics, which may be rechargeable by control unit  23 . 
     LED  108  is affixed to mounting board  104  and electrically coupled to ribbon  107 . LED  108  produces excitation light  101  of a predetermined wavelength to excite the sample  22 . After light  101  leaves LED  108 , the light is expanded by collimating lens  110  before the light enters excitation filter  112 . The light  101  of one wavelength band is passed by dichrotic filter  114  and is focused on a sample by focusing lens  116 . The light  101  excites the sample and fluorescence is collected by focusing lens  116  and delivered to detection filter  118  by dichrotic filter  114 . The resulting wavelength band of light is collected by lens  120  and delivered to optical output port  19  where the collected fluorescent light enters a leg of fiber optic bundle  14  for conveyance to detector  18 . 
     Supplemental optical module  56 A may also contain the components of the laser valve control system  51 . Laser valve control system  51  may be the only system used within device  10  or one of a plurality of laser valve control systems. The components used for this system may be similar to the components described in optical module  48 A of  FIG. 6A . 
     The components of supplemental optical module  56 A may be similar to any supplemental optical module or any optical module used to emit and detect one wavelength band of light. In some embodiments, the components may be altered in configuration to accommodate different experimental applications. For example, any optical modules may be modified to be inserted from a different direction or to be placed within the device at a different position with respect to disk  13 . In any case, the optical modules may be removable to provide modification flexibility to device  10 . 
       FIG. 7B  is a perspective diagram illustrating the components within a different supplemental optical module substantially similar to  FIG. 7A . Optical module  56 B includes many of the same components as optical module  56 A. Differences include nut  91 , flex circuit  93  and flex circuit connector  95 . 
     Optical module  56 B does not require a latch mechanism for attaching to module housing  46 . Alternatively, nut  91  is threaded and is engaged by a matching threaded bolt attached through module housing  46 . Once tightened, optical module  56 B is securely attached to detection device  10 . In other embodiments, a different fastening device may be used. For example, a pin or track may lock optical module  56 B into place. 
     Flex circuit  93  provides the electrical connection between components of optical module  56 B with control unit  23 . Flex circuit  93  is flexible to move between multiple locations. Flex circuit connector  95  is coupled to flex circuit  93  and provides a secure connection between optical module  56 B. Flex circuit connector  95  must be disengaged to completely remove optical module  56 B from module housing  46 . 
       FIG. 8  is a functional block diagram of the multiplex fluorescence detection device  10 . In particular,  FIG. 8  indicates the electrical connections between device components and the general paths of light through the components. In the example of  FIG. 8 , device  10  includes at least one processor  122  or other control logic, memory  124 , disk motor  126 , light source  30 , excitation filter  34 , lens  38 , detection filter  40 , collecting lens  42 , detector  18 , slot sensor trigger  27 , communication interface  130 , heating element  134 , laser  136  and power source  132 . As shown in  FIG. 3 , lens  38  and collecting lens  42  need not be electrically connected to another component. Further, light source  30 , filters  34  and  40 , lens  38  and collecting lens  42  are representative of one optical module  16 . Although not illustrated in  FIG. 8 , device  10  may contain additional optical modules  16 , as described previously. In that case, each additional optical module may include components arranged substantially similarly as to those shown in  FIG. 8 . 
     Light follows a certain path through several components in  FIG. 8 . Once light is emitted by light source  30 , it enters excitation filter  34  and leaves as light of a discrete wavelength. It then passes through lens  38  where it leaves detection device  10  and excites sample  22  within a process chamber (not shown). Sample  22  responds by fluorescing at a different wavelength, at which time this fluorescent light enters lens  38  and is filtered by detection filter  40 . Filter  40  removes background light of wavelengths outside of the desired fluorescence from sample  22 . The remaining light is sent through collecting lens  42  and enters a leg of fiber optic bundle  14  before being detected by detector  18 . Detector  18  subsequently amplifies the received light signal. 
     Processor  122 , memory  124  and communication interface  130  may be part of control unit  23 . Processor  122  controls disk motor  126  to rotate or spin disk  13  as needed to collect fluorescence information or move fluid through disk  13 . Processor  122  may use disk position information received from slot sensor trigger  27  to identify the location of chambers on disk  13  during rotation and synchronize the acquisition of florescence data received from the disk. 
     Processor  122  may also control when the light source  30  within optical module  16  is powered on and off. In some embodiments, processor  122  controls excitation filter  34  and detection filter  40 . Depending on the sample being illuminated, processor  122  may change the filter to allow a different wavelength of excitation light to reach the sample or a different wavelength of fluorescence to reach collecting lens  42 . In some embodiments, one or both filters may be optimized for the light source  30  of the particular optical module  16  and not changeable by processor  122 . 
     Collecting lens  42  is coupled to one leg of fiber bundle  14  that provides an optical path for the light from the collecting lens to detector  18 . Processor  122  may control the operation of detector  18 . While detector  18  may constantly be detecting all light, some embodiments many utilize other acquisition modes. Processor  122  may determine when detector  18  collects data and may programmatically set other configuration parameters of detector  18 . In one embodiment, detector  18  is a photomultiplier tube that capture fluorescence information from light provided by collecting lens  42 . In response, detector  18  produces an output signal  128  (e.g., an analog output signal) representative of the received light. Although not shown in  FIG. 8 , detector  18  may concurrently receive light from other optical modules  16  of device  10 . In that case, output signal  128  electrically represents a combination of the optical input received by detector  18  from the various optical modules  16 . 
     Processor  122  may also control data flow from device  10 . Data such as sampled fluorescence from detector  18 , temperature of the samples from heating element  134  and related sensors, and disk rotation information may be stored into memory  124  for analysis. Processor  122  may comprise any one or more of a microprocessor, digital signal processor (DSP), application specific integrated circuit (ASIC), field-programmable gate array (FPGA), or other digital logic circuitry. Moreover, processor  122  provides an operating environment for firmware, software, or combinations thereof, stored on a computer-readable medium, such as memory  124 . 
     Memory  124  may include one or more memories for storing a variety of information. For example, one memory may contain specific configuration parameters, executable instructions, and one may contain collected data. Therefore, processor  122  may use data stored in memory  124  for controlling device operation and calibration. Memory  124  may include any one or more of a random access memory (RAM), read-only memory (ROM), electronically-erasable programmable ROM (EEPROM), flash memory, or the like. 
     Processor  122  may additionally control heating element  134 . Based upon the instructions contained within memory  124 , the heating element  134  may be selectively driven to control the temperature of one or more chambers according to desired heating profiles. Generally, heating element heats one radial section of disk  13  as the disk spins. Heating element  134  may comprise a halogen bulb and reflector for focusing heating energy on a specific area of disk  13 . In other embodiments, heating element  134  may heat one or more chambers sequentially. This embodiment would require disk  13  to be stationary while a chamber is heated. In any embodiment, heating element  134  may be capable of turning on and off extremely quickly as needed. 
     Laser  136  is used to control valve opening which allows contents of a holding chamber to flow to another chamber on disk  13 , e.g., a reaction well or process chamber. Processor  122  and supporting hardware drives laser  136  to selectively open specific valves contained with disk  13 . Processor  122  may interact with a laser sensor underneath disk  13  for determining the position of the laser relative to the desired valve. When in position, processor  122  outputs signals to direct laser  136  to produce a burst of energy targeted at the valve. In some cases, the burst may last for approximately 0.5 seconds, while other embodiments may include opening times of shorter or greater duration. A laser energy and pulse duration may be controlled by processor  122  through communication with laser  136 . 
     Processor  122  utilizes communication interface  130  to communicate with data acquisition system  21 . The communication interface  130  may include a single method or combination of methods to transfer data. Some methods may include a universal serial bus (USB) port or IEEE 1394 port for hardwire connectivity with high data transfer rates. In some embodiments, a storage device may be directly attached to one of these ports for data storage for post processing. The data may be pre-processed by processor  122  and ready for viewing, or the raw data may need to be completely processed before analyzing can begin. 
     Communications with detection device  10  may also be accomplished by radio frequency (RF) communication or a local area network (LAN) connection. Moreover, connectivity may be achieved by direct connection or through a network access point, such as a hub or router, which may support wired or wireless communications. For example detection device  10  may transmit data on a certain RF frequency for reception by the target data acquisition device  21 . Data acquisition device  21  may be a general purpose computer, a notebook computer, a handheld computing device, or an application-specific device. Further, multiple data acquisition devices may receive the data simultaneously. In other embodiments, the data acquisition device  21  may be included with detection device  10  as one integrated detection and acquisition system. 
     In addition, detection device  10  may be able to download updated software, firmware, and calibration data from a remote device over a network, such as the internet. Communication interface  130  may also enable processor  122  to monitor inventory report any failures. If operational problems occur, processor  122  may be able to output error information to assist a user in trouble shooting the problems by providing operational data. For example, processor  122  may provide information to help the user diagnose a failing heating element or a synchronization problem. 
     Power source  132  delivers operating power to the components of device  10 . Power source  132  may utilize electricity from a standard 115 Volt electrical outlet or include a battery and a power generation circuit to produce the operating power. In some embodiments, the battery may be rechargeable to allow extended operation. For example, device  10  may be portable to detection of biological samples in an emergency, such as a disaster area. Recharging may be accomplished through the 115 Volt electrical outlet. In other embodiments, traditional batteries may be used. 
       FIG. 9  is a functional block diagram of the single detector  18  coupled to four optical fibers of the optical fiber bundle. In this embodiment, detector  18  is a photomultiplier tube. Each leg of fiber optic bundle  14 , optical fiber  14 A, optical fiber  14 B, optical fiber  14 C and optical fiber  14 D, couples to an optical input interface  138  of detector  18 . In this manner, light carried by any of optical fibers  14  is provided to a single optical input interface  138  of detector  18 . The optical input interface  138  provides the aggregate light to electron multiplier  140 . Anode  142  collects the electrons and produces a corresponding analog signal as output signal. 
     In other words, as shown, the optical fibers  14  fit within the input optical aperture for detector  18 . Consequently, detector  18  may be used to detect light from each leg of optic bundle  14  simultaneously. Optical input interface  138  provides the light to electron multiplier  140 . For a photomultiplier tube, the photons from the optical fibers first hit a photoemissive cathode, which in turn releases photoelectrons. The photoelectrons then cascade by hitting a series of dynodes, more photoelectrons being emitted upon contact with each dynode. The resulting group of electrons have essentially multiplied the small light signals originally transmitted by the optical fibers  14 . The increased number of electrons finally are collected by anode  142 . This current from anode  142  is transferred by a current to voltage amplifier  144  as an analog output signal which is representative of the optical florescent signals from the sample provided by the plurality of optical modules  16 . 
     Control unit  23  includes an analog to digital (A/D) converter  146  converts the analog signal to a stream of sampled digital data, i.e., a digital signal. Processor  122  receives the digital signal and stores the sampled data in memory  124  for communication to data acquisition device  21 , as described in above. In some embodiments, A/D converter  146  may be contained within detector  18  instead of control unit  23 . 
     In this manner, a single detector  18  may be utilized to collect all light from the optic bundle  14  and produce a signal representative thereof. Once the signal is amplified by amplifier  144  and converted to a digital signal, it may be digitally separated into data corresponding to the light collected by each individual optical modules  16 . The entire (i.e., aggregate) signal may be separated by frequency range into each detected signal representative of each fluorescence. These frequencies may be separated by a digital filter applied by data acquisition device  21  or within device  10 . 
     In other embodiments, the amplified signal may be separated by frequency using analog filters and sent to separate channels before A/D converter  146 . Each channel may then be separately digitized and sent to the data acquisition device. In either case, the single detector is able to capture all florescence information from each optical module  16 . Data acquisition device  21  may then plot and analyze the signal acquired from each chamber of disk  13  in real-time without the need for multiple detectors. 
     In some embodiments, detector  18  may not be a photomultiplier tube. In general, detector  18  may be any type of analog or digital detection device capable of capturing light from multiple legs of an optical delivery mechanism, i.e., fiber bundle  14 , and producing a transmittable representation of the captured light. 
       FIG. 10  is a flow diagram illustrating the operation of the multiplex fluorescence detection device  10 . Initially, a user specifies program parameters on the data acquisition device  21  or via an interface with control unit  23  ( 148 ). For example, these parameters may include a velocity and time period for rotating disk  13 , define temperature profiles for the reaction, and sample locations on disk  13 . 
     Next, the user loads disk  13  into the detection device  10  ( 150 ). Upon securing the device  10 , the user starts the program ( 152 ), causing control unit  23  to begin spinning the disk ( 154 ) at the specified rate. After the disk has begun to spin, two concurrent processes may occur. 
     First, the detection device  10  starts to detect fluorescence from the excitation light ( 156 ) produced by one or more reactions within one or more samples. The detector  18  amplifies the fluorescence signals from each sample, which are synchronized to each respective sample and time at which the fluorescence was emitted ( 158 ). During this process, processor  122  saves the captured data to memory  124  and may communicate the data to data acquisition device  10  in real-time to monitor the progress of the run and for additional processing ( 160 ). Alternatively, processor  122  may save the data within device  10  until the program is complete. The processor  122  continues to detect florescence of the samples and save data until the program is complete ( 162 ). Once the run is complete, control unit  23  stops the disk from spinning ( 164 ). 
     During this process, control unit  23  monitors the disk temperature ( 166 ) and modulates the disk, or each sample, temperature to attain the target temperature for that time ( 168 ). The control unit  23  continues to monitor and control the temperatures until the program is complete ( 170 ). Once the run is complete, control unit  23  holds the temperature of the samples to a target storage temperature, usually 4 degrees Celsius ( 172 ). 
     The operation of device  10  may vary from the example of  FIG. 10 . For example, the disk revolutions per minute may be modified throughout the program, and laser  136  may be utilized to open valves between chambers on the disk to allow for multiple reactions. These steps may occur in any order within the operation, depending on the program the user defines. 
       FIG. 11  is a flow diagram illustrating an exemplary method if detecting light and sampling data from the disk. Initially, a user specifies which modules will detect fluorescence from disk  13 , and control unit  23  turns on the LED of a module ( 149 ). Once the LED has warmed to steady state, control unit  23  spins disk  13  one rotation at the rate of approximately 1470 revolutions per minute ( 151 ). During that rotation, the module collects light fluoresced from the process chambers of disk  13  ( 153 ), and control unit  23  places 16 samples from each process chamber in the memory BIN associated with each process chamber ( 155 ). 
     If disk  13  must be spun another rotation ( 157 ), control unit  23  executes another revolution of disk  13  ( 151 ). If 16 revolutions have been sampled, the module has completed detection with the LED. Therefore, each process chamber was sampled a total of 256 times and data acquisition device  21  integrates the samples to create a histogram of each process chamber. Control unit  23  turns the LED off ( 159 ). If another module must to used to continue detection ( 161 ), control unit  23  turns on the next module LED ( 149 ). If no other modules are needed to collect data, control unit  23  discontinues the collection of data from disk  13 . 
     In some embodiments, each process chamber may be sampled more or less times. Control unit  23  may spin disk  13  at a faster rate to provide quicker results or spin disk  13  slower to acquire more samples. In other embodiments, LEDs from two or more modules may be turned on to detect fluorescence simultaneously in multiple wavelengths. 
     Example 
       FIGS. 12 and 13  show the absorption and emission spectra of commonly used fluorescent dyes that may be utilized with device  10  for multiplex PCR. In these examples, the absorption maxima of the dyes vary from 480-620 nm, and the resulting emission maxima vary from 520-670 nm. The signals for each dye in  FIG. 12  are numbered as FAM  174 , Sybr  176 , JOE  178 , TET  180 , HEX  182 , ROX  184 , Tx Red  186 , and Cy5  188 . The signals in  FIG. 13  are FAM  190 , Sybr  192 , TET  194 , JOE  196 , HEX  198 , ROX  200 , Tx Red  202 , and Cy5  204 . FAM, HEX, JOE, VIC, TET, ROX are trademarks of Applera, Norwalk, Calif. Tamra is a trademark of AnaSpec, San Jose, Calif. Texas Red is a trademark of Molecular Probes. Cy 5 is a trademark of Amersham, Buckinghamshire, United Kingdom. 
     In one example, a 96 chamber disk was filled with different concentrations of FAM and ROX dye diluted in standard PCR reaction buffer. Four replicates of each dye were added in a 2× dilution series, starting from 200 nM FAM and 2000 nM ROX. Each sample volume was 10 μL. Chamber  82  had a mixture of 5 μL of 200 nM FAM and 5 μL Of 2000 nM ROX. Device  10  was constructed as a two-channel multiplex PCR detection device having two optical modules  16  for detection of the dyes. 
     The first optical module (the FAM module) contained a blue LED, 475 nm excitation filter and a 520 nm detection filter. The second optical module (the ROX module) contained a green LED with a 560 nm excitation filter and a 610 nm detection filter. Another option would be to incorporate an orange LED and an excitation filter at 580 nm to optimize for ROX detection. 
     A PCR analysis was conducted, and fluorescent signals from the samples were multiplexed into a bifurcated fiber optic bundle. The fiber bundle was interfaced with a single detector, specifically a photomultiplier tube (PMT). Data was collected by a National Instruments data acquisition (DAQ) board interfaced with a Visual Basic data acquisition program executing on a general-purpose computer. Data was acquired while the disk was spinning at 1000 revolutions per minute (nominally). The FAM module and the ROX module were sequentially used to interrogate the samples. Each scan consisted of an average of 50 rotations. The raw data from the two optical modules is shown in  FIGS. 14A and 14B . 
     The graph in  FIG. 14A  was acquired by powering the LED in the FAM module, and the graph in  FIG. 14B  was acquired by powering the LED in the ROX module. 
     During the analysis, the collected data clearly showed that there was a time offset associated with optical modules being physically located over different chambers at any one time. An offset value was calculated by determining the time offset between optical modules  1  and  2  for a particular chamber, i.e., chamber  82  in this case. In other words, the time offset indicates the amount of time delay between data captured by the FAM module and data captured by the ROX module for the same chamber. 
       FIG. 15  is a graph that shows the offset-subtracted integrated data for each chamber. FAM is indicated by dotted line bars, ROX is indicated by solid line bars, and the ROX data is placed over the FAM data. The data showed that there was no signal from the ROX dye on optical module  1  and no signal from the FAM dye on optical module  2 . There was a higher background on optical module  1 , which may be rectified by using an optimized set of filters. The data was analyzed to determine the limit of detection (LOD), described as the signal equivalent to the baseline noise level. The baseline noise level was defined as the average of ten scans of a blank chamber plus 3 times the standard deviation. 
     The LOD was determined by a linear least squares fit of the integrated signal plotted against the concentration of the FAM and ROX standards. The LOD of the FAM and ROX modules were calculated to be 1 and 4 nM, respectively, as shown in  FIGS. 16A and 16B . 
       FIG. 17  is an exemplary screen shot of a temperature control user interface. Temperature control screen  250  is highlighted and shows temperature controls  252 . Temperature graph  254  outputs temperature readings while status indicator  256  displays general information. Message window  258  displays commands when running detection device  10 . 
     The technician may select temperature control screen  250  to view temperature information from device  10 . Temperature control screen  250  is one of several screens which may be selected to display information associated with the operation of control unit  23  or data acquisition device  21 . Screen  250  includes temperature controls  252  which display numerical information to the technician. Temperature graph  254  displays graphical temperature information as a graph of temperature as a function of time. In some embodiments, the technician may manually change the values located within temperature controls  252 . 
     Status indicator  256  is always visible to the technician. Status indicator  256  displays relevant operational times, cycle number, temperature and other important information. Message window  258  displays current commands to control unit  23 . Window  258  includes a scroll bar for locating any command delivered to control unit  23  during device  10  operation. In some embodiments, message window  258  may display error information or other important information to the technician. 
       FIG. 18  is an exemplary screen shot of an optical control user interface. Optical control screen  260  is highlighted and shows signal graph  262 . Histogram  264  shows the integrated signal of each process chamber. Screen  260  also includes message window  266  and offset control  268 . 
     Signal graph  262  displays the raw optical data detected by detection device  10 . The signal displayed on graph  262  is the raw signal from optical modules  48 ,  52  and  56  and includes cycles that correspond to the signal change between process chambers. The technician may change offset control  268  to match the binning of signal into appropriate bins representing each process chamber with the signal waveform. The loss of signal between each peak represents detection of light from disk  13  between each process chamber. The corresponding signal is integrated to produce histogram  264  which displays the detected signal from each of 96 process chambers. Control unit  23  integrates 16 samples from a process chamber in each of 16 rotations of disk  13 . Histogram  264  therefore contains 256 samples of the contents in each samples process chamber. In some embodiments, software may automatically adjust offset control  268  by recognizing elements of the raw signal waveform. Message window  266  displays command information and error messages relating to optical control and light detection. 
       FIG. 19  is an exemplary screen shot of a real-time PCR user interface. Data screen  270  is highlighted and shows histogram  272  and product graph  274 . Screen  270  shows the real-time data being collected from the process chambers of disk  13 . Histogram  272  displays the integrated signal for each process chamber while product graph  274  displays the amount of amplified product as a function of cycle number. In other embodiments, results for the process chambers may vary under different applications. 
     Various embodiments of the invention have been described. These and other embodiments are within the scope of the following claims.